Altered Skeletal Muscle Mitochondrial Proteome As the Basis of Disruption of Mitochondrial Function in Diabetic Mice Piotr Zabie

Home , ABHD11, ACADM, ACADSB, Acid phosphatase, APOBEC2, Archain

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Altered skeletal muscle mitochondrial proteome as the basis of disruption of mitochondrial function in diabetic mice

Piotr Zabielski1,4, Ian R. Lanza1, Srinivas Gopala1,5, Carrie J. Holtz Heppelmann2, H. Robert Bergen III2, Surendra Dasari3, K. Sreekumaran Nair1*. 1Division of Endocrinology and Metabolism 2Division of Biochemistry and Molecular Biology 3Division of Biomedical Statistics and Informatics Mayo Clinic College of Medicine 200 First St SW, Rochester, MN 55905

4Present affiliation: Department of Physiology, Medical University of Bialystok, Poland 5Present affiliation: Department of Biochemistry, Sree Chitra Tirunal Institute for Medical Sciences and Technology, Trivandrum, India

* Corresponding author K. Sreekumaran Nair, M.D., Ph.D. Professor of Medicine Division of Endocrinology and Metabolism Mayo Clinic College of Medicine 200 First St SW Rochester, MN 55905 Tel: 5072552415 Email: [email protected]

Running title: Effects of insulin on mitochondria

Key Words: insulin, type I diabetes, mitochondria, proteomics, skeletal muscle, acylcarnitines, βoxidation

Diabetes Publish Ahead of Print, published online December 30, 2015 Diabetes Page 2 of 165

ABSTRACT

Insulin plays pivotal role in cellular fuel metabolism in skeletal muscle (SM). Despite being the primary site of energy metabolism, the underlying mechanism on how insulin deficiency deranges SM mitochondrial physiology remains to be fully understood. Here we report important link between altered skeletal muscle proteome homeostasis and mitochondrial physiology during insulin deficiency. Deprivation of insulin in treated streptozotocin diabetic mice decreased mitochondrial ATP production, reduced coupling and phosphorylation efficiency and increased oxidant emission in skeletal muscle. Proteomic survey revealed that the mitochondrial derangements during insulin deficiency were related to, increased mitochondrial protein degradation and decreased protein synthesis, resulting in reduced abundance of proteins involved in mitochondrial respiration and βoxidation. However, a paradoxical upregulation of proteins involved in cellular uptake of fatty acids triggered an accumulation of incomplete fatty acid oxidation products in skeletal muscle. These data implicate a mismatch of βoxidation and fatty acid uptake as a mechanism leading to increased oxidative stress in diabetes. This notion was supported by elevated oxidative stress in cultured myotubes exposed to palmitate in the presence of a βoxidation inhibitor. Together, these results indicate that insulin deficiency alters the balance of proteins involved in fatty acid transport and oxidation in skeletal muscle, leading to impaired mitochondrial function and increased oxidative stress.

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INTRODUCTION

Prior studies reported insulin’s key role in regulating mitochondrial biogenesis (13) and fuel

metabolism (4). Insulin deficiency in type 1 diabetic (T1D) humans reduces mitochondrial ATP

production (5) despite elevated whole body oxygen consumption (6;7), suggesting an uncoupled

respiration. However, the molecular link between insulin levels, oxidative stress, and altered

mitochondrial function remains unclear.

Mitochondrial function is determined by its proteome quantity and quality. Here we

hypothesized that insulin deficiency alters mitochondrial proteome homeostasis (proteostasis) as

a mechanistic explanation for altered mitochondrial physiology in diabetes. The rationale for this

hypothesis is that insulin is a key hormone regulating muscle protein turnover (810), which is

critical for maintaining not only protein concentrations but also protein quality and function. The

effect of insulin on muscle protein synthesis varies considerably among different proteins (11).

Insulin has been shown to stimulate muscle mitochondrial protein synthesis in swine (2) and

when coinfused with amino acids in humans (3); yet, it does not affect synthesis of myosin

heavy chain (12). These observations indicate that insulin selectively stimulates synthesis and

expression of specific proteins with potential impact on mitochondrial function. Previous studies

also demonstrated that ceramides and longchain fatty acyl CoAs accumulate in muscle during

insulin deficiency (13) and that oxidation of long chain fatty acids increase ROS production (14).

Moreover, the composition of plasma acylcarnitines are altered in type 1 (15;16) and type 2

diabetes (17;18), likely consequent to defective βoxidation. A critical question is whether

insulin deprivation affects the expression of individual mitochondrial proteins that may explain

altered mitochondrial fuel metabolism. Proteome analyses in heart muscle found either up

regulation (19) or downregulation (20) of β oxidation proteins in different diabetic models. It is

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currently unknown how insulin deficiency affects the mitochondrial proteome in skeletal muscle

and whether changes in its proteome homeostasis could explain the muscle mitochondrial

changes seen in diabetes. Moreover, most of the previous studies involving heart proteome and

mitochondrial studies were performed only in insulindeficient states mostly immediately after

inducing diabetes by streptozotocin (STZ), and lack most clinicallyrelevant insulintreated

group. Moreover, studying insulin deficiency effect in insulin treated STZ mice after a period of

stabilization will allow delineation of STZ effect. Inclusion of insulintreated animals could also

shed light on the possible alternations still present in skeletal muscle of treated by insulin by peripheral route diabetic mice. Such knowledge would provide important mechanistic insight

into insulin deprivation and peripheral insulin treatment on skeletal muscle metabolism in both

insulin treated and deprived type 1 diabetes. We accomplished this goal by induction of diabetes by double high dose injection of streptozotocin (STZ) and subsequent treatment of STZdiabetic mice with subcutaneous insulin implants, which ensure longlasting glycaemic control, hard to achieve in mice with injectable insulin regimen.

Here we comprehensively evaluated skeletal muscle mitochondrial physiology in insulin deprived streptozotocin diabetic mice (STZI) in comparison with nondiabetic (ND) controls and insulin treated STZ diabetic mice (STZ+I). Although exogenous insulin treatment cannot normalize all diabetes complications in humans, we sought to determine if exogenous insulin could normalize mitochondrial function and protein expression in STZ mice. The use of SILAC assisted highthroughput proteomics and lipidomic analyses in skeletal muscle allowed us to gain mechanistic insight into the effects of insulin deprivation and treatment on skeletal muscle oxidative metabolism.

METHODS

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Animals

Male 13 week old C57BL/6J mice (Jackson Laboratory, Bar Harbor, ME) were acclimated for

one week prior to the experiment in standard animal facility conditions. The protocol was

approved by the Mayo Clinic Institutional Animal Care and Use Committee. Diabetes was

induced by double highdose intraperitoneal injection of streptozotocin (STZ) as described

previously (13), which generates animals without residual βcell function. To exclude any

adverseeffects of acute STZ toxicity and other adverse factors such as initial hypoglycaemia and

stress we treated all diabetic animals with insulin implants (subcutaneous LinBit insulin implant

at 0.2 U/24 hr, LinShin Canada, Inc. Toronto, Ontario, Canada). Nondiabetic animals (ND)

received implants without insulin. Initial 3week insulin treatment ensured that animals regained

weight and well past the toxic effect of STZ. After 3 weeks of insulin therapy diabetic insulin

treated animals were randomly divided into diabeticdeprived (STZI) and diabetic treated

(STZ+I) groups. The insulin was discontinued in the STZI group by removing implants, which

resulted in return of diabetic phenotype. Mice were sacrificed 1 week later and quadriceps

muscle was harvested for mitochondrial and proteomic analysis. Prior to sacrifice, body

composition by MRI (EchoMRI, Houston, TX) energy expenditure and physical activity were

measured over 24h by a cage calorimetry system, as described previously (21). Plasma glucose,

ketones, HbA1c and free fatty acids content were measured as described earlier (18).

Mitochondrial respiration

Mitochondrial respiration and coupling efficiency was measured by highresolution respirometry

in isolated quadriceps skeletal muscle mitochondria as described earlier (22). Combinations

included: isolated mitochondria only (respiratory State 1), 10mM glutamate and 2mM malate

(State 2), 2.5mM ADP (State 3, CI), 10mM succinate (State 3 CI and CII), 0.5 µM rotenone

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(State 3, CII), 2µg/ml oligomycin (State 4), 2.5µM FCCP (protonophoric respiration uncoupler)

and 2.5µM antimycin A (electron transport chain inhibitor). Measurements were performed in

duplicate and averaged. Oxygen flux rates were expressed per tissue wet weight and per mg

mitochondrial protein as measured by Pierce 660nm protein assay.

Mitochondrial ATP synthesis

Mitochondrial ATP synthesis rates were measured by bioluminescence using a luciferin– luciferase reaction and Veritas Microplate luminometer (Turner Biosystems, Sunnyvale, CA), as described earlier (1). Substrate combinations included: 10 mM glutamate with 1 mM malate

(GM); 20 mM succinate with 0.1 mM rotenone (SR); 0.05 mM palmitoylLcarnitine with 1 mM malate (PCM) 1 mM pyruvate with 0.05 mM palmitoylLcarnitine, 10 mmol/l αketoglutarate and 1 mmol/l malate (PPKM).

Mitochondrial H2O2 emission

Mitochondrial hydrogen peroxide production was measured by continuous monitoring of

Amplex Red oxidation (Invitrogen Corporation, Carlsbad, CA) using a Fluorolog 3 spectrofluorometer (Horiba Scientific, Kyoto, Japan), as described previously (22). Background fluorescence was measured in deenergized mitochondria (State 1 respiration), followed by stepwise addition of 10mM glutamate + 2mM malate (State 2 CI), 10mM succinate (State 2

CI+II), 2.5mM ADP (State 3 CI+II), 2µg/ml oligomycin (State 4 CI+II), 0.5 µM rotenone (State

4 CII), 2.5µM FCCP (Uncoupled ), and 2.5µM antimycin A (respiration inhibitor).

Highthroughput differential proteomic analysis by SILAC approach

13 Quadriceps muscle tissue from fully labeled mice (SILAC mice, C6LLysine, >98% labeled) was used as a reference standard to compare the relative expression of quadriceps muscle

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proteins in ND, STZI and STZ+I mice (n=6 per group) by mass spectrometry, as described in

supplementary file. We used Mascot protein identification engine and FDR approach to identify

peptides in MS spectra. Relative protein expression between experimental groups was measured

using Rosetta Elucidator Software weighted statistics. Vinculin was used as a loading control and

revealed no significant differences in sample/SILAC mixing and SDSPAGE sample loading

(Table S1). Protein expression supplement contains detailed description of all of the identified

and quantified proteins from ND, STZI and STZ+I groups.

Pathway analysis of proteomics data

Pathway enrichment analysis was performed using Ingenuity Systems IPA software package

(Ingenuity Systems, Inc. Redwood City, CA), as described earlier (22). Multiple data entries of

the same protein were resolved by IPA software by filtering entries by their lowest pvalue.

Only proteins with p<0.05 between groups were taken into consideration. To identify

significantly affected pathways, Fisher's exact test was employed and pvalues were expressed as

their –log10 derivatives (e.g. p<0.05 corresponds to p>1.301 on –log10 scale). Additionally, we

compared resulting proteomic dataset with MitoCarta 2.0 mouse mitochondrial proteins database

(23).

Semitryptic peptides detection and quantification.

We followed a twostep workflow to detect and quantify semitryptic peptides from MS/MS data

of each mice cohort (N=3 per group). The details of this approach have been previously reported

(22).

Mixed muscle protein synthesis rates

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The fractional synthesis rates of mixed muscle proteins were measured in mice quadriceps

13 skeletal muscle using L[ring C6]phenylalanine (Cambridge Isotope Laboratories, Tewksbury,

MA) and mass spectrometry, as described earlier (22;24;25).

Immunoblotting

Tissue was pulverized in LN2 and homogenized by sonication on ice in RIPA buffer (Sigma

Aldrich, St. Louis, MO). After denaturation in loading buffer samples were separated by and blotted to nitrocellulose membranes. Membranes were blocked TBS Odyssey® Blocking Buffer

(LiCor, Lincoln, NE) before incubating overnight with primary rabbit, antimouse antibodies for the proteins of interest. Proteins were detected by infrared fluorescent detection (LiCor

Odyssey, Lincoln, NE) using appropriate antimouse and antirabbit secondary antibodies (Li

Cor, Lincoln, NE).

Tissue acylcarnitine profiling

Skeletal muscle concentration of 30 acylcarnitine species were measured using deuterated internal standards and LC/MS/MS, as described previously (26). Individual carnitine and acyl carnitines were quantified against nearest labeled internal standard and standard curves prepared on synthetic compounds. CPT1 activity index was measured by dividing free Lcarnitine value by the sum of C16 and C18 acylcarnitines (27). Short chain and very long chain acylCoA dehydrogenase indexes were calculated according to Chace et al (26).

Cell culture

Differentiated C2C12 myotubes were prepared as described by Boyle et al (28). To mimic insulinaemia differentiation was done in serumpoor medium without additional insulin. The differentiated myotubes were incubated for 15 h with albumin conjugated palmitic acid in differentiation medium. Control cells were incubated with an equal concentration of BSA and

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ethanol/DMSO. MCPA (short and mediumchain acylCoA dehydrogenase inhibitor) was added

to a medium to a medium at the concentration of 500 µM just before its addition to the cells.

Oxygraph studies in C2C12 cells

Mitochondrial respiration in permeabilized C2C12 cells was measured according to Boyle et al.

(28). Myotubes treated as per the experimental conditions were harvested, resuspended in

mitochondrial respiration buffer, permeabilized with digitonin and immediately transferred to a

respiration chamber (~11.5 × 106 cells/2 mL, Oroboros Oxygraph2K, Oroboros Instruments

Corp, Innsbruck, Austria). Compounds were added sequentially to a final concentration

indicated: State 1 – myotubes, State 2 5µM palmitoyl carnitine, 1mM malate, State 3 (CI) –

2mM ADP, 10M cytochrome C, 2mM glutamate, State 3 (CI+CII) – 3mM succinate, State 4

(CI+CII) – 2.5g/l oligomycin, Uncoupled (CI+CII) – 2.5M carbonyl cyanide p(trifluoro

methoxy) phenylhydrazone, Uncoupled (CI) – 0.5 µM rotenone, AA – 2.5µM antymycin A.

Experiments for control, palmitate, palmitate+ MCPA and MCPA alone were done in triplicate

samples.

ROS production in C2C12 cells

Intracellular conversion of nitro blue tetrazolium (NBT; SigmaAldrich) to formazan by

superoxide anion was used to measure the generation of reactive oxygen species in C2C12

myotubes as described in (29).

Statistical analysis

Statistical significance between groups for all the measurements except differential proteomics

was estimated using ANOVA with Tukey Honest Significant Difference (Tukey HSD) posthoc

test. Significance level was set to p<0.05. Significant differences in individual protein expression

from proteomic dataset were identified using zstatistic, as described earlier (22).

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RESULTS:

Body composition and biochemical parameters. STZI were smaller and leaner than ND

controls or STZ+I (Supplementary Figure S1 A). Although STZI had lower total body water,

their hydration ratio was similar to ND controls, showing that diabetic animals were not

dehydrated (Figure S1 B,C) As expected, plasma glucose, ketones, free fatty acids and HbA1c

were higher in STZI mice than STZ+I and ND mice (Figure S1 D,E,F,G). Respiratory quotient

(RQ) was lower in STZI compared to STZ+I or ND, indicating greater reliance on fat as a fuel

substrate during insulin deprivation (Figure S1 H,I,J). Total energy expenditure (Figure S1 K)

and physical activity (Figure S1 L) were decreased in STZI and STZ+I, but the activity

normalized estimate of resting metabolic rate (RMR) was higher in STZI animals and restored

in STZ+I (Figure S1 M). These data indicate, that insulin deprivation in STZ mice elicits whole body metabolic changes characteristic of T1D (6;30), which were largely reversed with exogenous insulin treatment, similar to previous observations in diabetic dogs (31). Elevated

HbA1c in STZ+I mice (Figure S 1G) is likely due to postprandial hyperglycemia (6:30 am plasma glucose in STZ+I mice was 297±28 mg/dl) that was not evident after 3 hours of fasting prior to experiment (Figure S1 D).

Muscle mitochondrial dysfunction with insulin deprivation.

Mitochondrial O2 consumption and ATP production were measured in mitochondria isolated from quadriceps muscle. Maximal (state 3) and submaximal (state 1,2,4) mitochondrial respiration was similar in all groups of mice (Figure 1A, Figure S2A). In contrast, insulin deprivation decreased the levels of mitochondrial complexes I, II, and V, which, with the

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exception of complex II, were restored by insulin treatment (Figure 1B). Insulin deprivation

lowered mitochondrial coupling efficiency. Decreased respiratory control ratios (RCR) in STZI

demonstrates greater mitochondrial proton leak (Figure 1C) and reduction in phosphorylation

efficiency (Figure 1D). Consistent with the notion of mitochondrial uncoupling, mitochondrial

ATP production rates (MAPR) were lower in STZ (Figure 1E, Figure S2B). Uncoupled

respiration is accompanied by greater mitochondrial reactive oxygen species (ROS) emissions as

insulin deprivation markedly increased H2O2 emissions, which were attenuated, albeit

incompletely by insulin treatment (Figure 1F, Figure S2C) Taken together, the parallel

measurements of O2 consumption and ROS production indicate that a greater percentage of

mitochondrial oxygen consumption was accounted for by ROS production in STZI compared to

ND or STZ+I (Figure 1G). Interestingly, mitochondrial superoxide dismutase (MnSOD) was

decreased (Figure 2H). As an additional marker of compromised cellular energy status, AMP

sensitive adenylate kinase1 (AK1) expression was elevated with insulin deprivation (Figure 2H).

Altogether, these results indicate that insulin deprivation disrupts mitochondrial function in the

form of impaired mitochondrial ATP production, decreased phosphorylation efficiency, and

greater ROS emission.

Insulin deprivation decreases mitochondrial protein expression and shifts the balance of

cellular lipid transport proteins.

A SILACassisted proteomic survey suggested that derangements in mitochondrial physiology

could be explained by altered muscle proteome. A total of 149 proteins involved in energy

metabolism were significantly altered in STZI mice compared with ND (Figure 2A, Table

S2A). Consistent with the measurements of mitochondrial function, mitochondrial proteins of

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ETC, TCA cycle and βoxidation were downregulated in STZI compared to ND. Paradoxically, the proteins involved in myocellular uptake of fatty acids were upregulated. Proteins involved in muscular glycolysis and glycogen breakdown were upregulated, whereas of pyruvate generation and mitochondrial transport were downregulated. Altogether, these proteomics data indicate clear patterns of upregulated glycolysis and glycogen breakdown during insulin deprivation, decreased mitochondrial respiratory chain proteins, and increased muscle uptake of lipids.

A comparison of STZI to STZ+I revealed 275 differentially expressed proteins, including 77 involved in energy metabolism (Figure 2B, Table S2B). Insulin treatment upregulated expression of proteins involved in βoxidation, FA uptake while down regulated glycolysis and glycogen breakdown thus upregulating carbohydrate storage. Thus, we provide proteomic evidence that insulin treatment restored the expression of proteins related to FA transport and glycolysis, but not all proteins involved in mitochondrial respiration were restored. Compared to nondiabetic, STZ+I animals still displayed downregulation of mitochondrial proteins involved in ETC/TCA and βoxidation, with lesser difference in the expression of FA transport and glycolysisrelated one (Figure 2C, Figure S3, Table S2C). Overall, the data indicate that insulin deprivation markedly reduced the abundance of mitochondrial proteins involved in energy metabolism, including lipid oxidation, yet increased abundance of proteins involved in cellular fatty acid uptake. Although insulin treatment did not completely normalize the expression of mitochondrial proteins, there was a clear reversal of the fatty acid transporters and glycolysis/glycogen breakdown proteins.

Proteomic evidence of oxidative stress, decreased protein synthesis, and increased protein degradation with insulin deprivation.

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STZI mice demonstrated increased abundance of proteins involved in skeletal muscle oxidative

stress in comparison with ND mice (Figure 2D, Table S2D). The expression of 5 non

mitochondrial antioxidant enzymes was significantly increased, whereas 3 mitochondriatargeted

proteins were down regulated. A notable exception was observed for Parkinson protein 7

(PARK7/DJ1), a redoxsensitive protein, which regulates mitochondrial autophagy (mitophagy)

(Figure S4). This observation suggests that insulin deprivation triggers a ROSrelated

compensatory mechanism at the level of mitochondria, which may increase mitophagy in STZI.

To address the above possibility, we focused on muscle proteins involved in regulation of protein

degradation and synthesis. A total of 5 ubiquitinproteasome pathway proteins were significantly

upregulated in STZI. Further, we used mass spectrometry to measure the abundance of semi

tryptic peptides related to in vivo cellular protein degradation. Although the overall abundance of

semitryptic peptides was similar in ND, STZI, and STZ+I groups, we observed significantly

more peptides originating from mitochondrial proteins during insulin deprivation (Figure S5)

indicating increased degradation of mitochondrial proteins.

The protein content of ribosomal proteins (18 subunits), 3 aminoacyl tRNA synthases, and 4

translation elongation factors (including mitochondrial TUFM) were significantly down

regulated in STZI as compared to ND group (Figure 2D, Table S2D). Similar patterns were

observed for 4 mitochondriatargeted and 3 cytosolic molecular chaperones. These proteomic

changes suggest inhibition of protein synthesis in STZI animals, which was supported by

decreased fractional synthesis rates of muscle proteins observed during insulin deprivation

(Figure S6). The effects of insulin deprivation on proteins involved in protein ubiquitination and

protein synthesis were reversed by insulin treatment in STZ+I mice (Figure 2E, Table S2E).

The same was noted for mitochondrial PARK7/DJ1 and mitochondrial semitryptic peptides

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content. Compared to ND, STZ+I animals displayed similar expression of proteins involved in protein synthesis and degradation with lower expression of those responsible for antioxidant

defense (Figure 2F, Table S2F). These results provide proteomic evidence consistent with increased oxidative stress on proteins during insulin deprivation that is resolved with insulin treatment.

Pathway enrichment analysis.

Pathway analysis was performed to provide additional insight into the major metabolic networks that were affected by insulin deprivation. Pathways involved in energy metabolism, oxidative damage, and protein synthesis were most affected in STZI (Figure 3A, Table S3A).

Mitochondrial energy metabolism and muscle protein synthesis were downregulated in STZI,

whereas glycolysis, glycogen degradation, and oxidative damagerelated pathways were up

regulated. Insulin treatment partially corrected metabolic alternations by mostly upregulating pathways responsible for oxidative phosphorylation and protein synthesis and substantially downregulating glycolysisrelated and oxidative stress response pathways when compared to

STZI (Figure 3B, Table S3B). Of interest, pathways of fat oxidation and mitochondrial FA import (βoxidation, Lcarnitine shuttle) remained downregulated in STZ+I animals when compared to ND. Compared to nondiabetic, STZ+I animals displayed downregulation of mitochondrial metabolism and TCA cycle pathways and upregulation of glycolysis, albeit to a lesser degree than in STZI mice (Figure 3C, Table S3C). Molecular pathways of protein synthesis, degradation and oxidative damage were normalized in STZ+I animals as compared to

ND.

Products of defective fatty acid βoxidation accumulate in skeletal muscle of insulin deprived diabetic animals.

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Figure 4A shows the expression profiles of 23 mitochondrial proteins that are involved in

cellular FA uptake, mitochondrial FA uptake, AC efflux and mitochondrial βoxidation. To

followup on the proteomic evidence of downregulation of muscle mitochondrial βoxidation in

STZI group, we measured intramyocellular acylcarnitines, which are biomarkers of inherited β

oxidation (FOA) disorders (32). STZI mice accumulated shortchain (C2C5) acylcarnitines in

skeletal muscle (Figure 4 B,C). Analysis of CPT1 and shortchain acylCoA dehydrogenase

(SCAD) activity indices suggest inhibition of CPT1 and SCAD (Figure 4D), which is in

agreement with the proteomics and Western Blot results (Figure 4A,E). Interestingly, insulin

treatment normalized shortestchain (C2 to C3) acylcarnitine content, CPT1 and SCAD activity

indices, yet significantly increased longchain AC content and longchain acylCoA

dehydrogenase (LCAD) index, suggesting inhibition of LCAD (Figure 4A,D). Moreover,

accumulation of 3hydroxy acylcarnitine molecular species (Figure 4D, Total OH) was evident

in STZ+I. Together, these results provide evidence of insufficient fatty acid oxidation in skeletal

muscle in STZI, which could be explained on the basis of the paradoxical increase in fatty acid

transport proteins but decreased fatty acid oxidative capacity.

Disruption of βoxidation in C2C12 myotubes under fatty acid load leads to mitochondrial

dysfunction.

To determine if disrupting βoxidation under conditions of increased lipid load could trigger

mitochondrial dysfunction in skeletal muscle cells we measured mitochondrial oxygen

consumption and ROS content of palmitatetreated C2C12 myotubes under βoxidation

inhibition. Since STZI mice exhibit metabolomic and proteomic signs of SCAD deficiency, we

treated cells with methylenecyclopropyl acetic acid (MCPA, an inhibitor of SCAD and MCAD)

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(33) and exposed cells to increased levels of palmitate. Treatment with MCPA suppressed

respiration and coupling efficiency in the presence of palmitate, but not in the absence of palmitate (Figure 5A,B). Inhibition of βoxidation under lipid load led to significantly higher cellular ROS compared to control and palmitatetreated myotubes, which was visible only in the presence of palmitate and MCPA (Figure 5C). The results indicate that mitochondrial capacity

and coupling are reduced, and ROS production is increased when βoxidation is inhibited under

conditions of high fatty acid availability, thus recapitulating the mitochondrial phenotype of

insulin deprived diabetic mice.

DISCUSSION:

The current study demonstrates pivotal role of insulin in regulating mitochondrial physiology.

During insulin deprivation, the mitochondrial uncoupling and decreased phosphorylation

efficiency occurred in combination with elevated mitochondrial ROS production. We

demonstrate that these mitochondrial derangements induced by insulin deficiency are

accompanied by an imbalance between muscle lipid availability and oxidation which is likely

source of excessive oxygen free radical emission. Insulin deprivation increases mobilization of

fatty acids and we observed upregulation of proteins involved in intracellular FA uptake,

transport, and AcylCoA conversion, yet downregulated proteins that are responsible for FA

storage and de novo synthesis. Despite this apparent shift toward lipid utilization during insulin deprivation, proteins involved in mitochondrial FA–CoA import and βoxidation were down

regulated, demonstrating a mismatch between FA uptake and βoxidative capacity. This

mismatch offers a mechanistic explanation for accumulation of intramyocellular lipid

metabolites and ceramides in STZI animals (13;34). The current study demonstrates that

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oxidative stress is elevated under conditions where lipid availability is high and βoxidation

capacity is decreased. Precedent literature links the oversupply of lipids with mitochondrial ROS

production in muscle cell culture (35), rodent muscle (36) and in humans (37). Studies also

suggest that plasma acylcarnitine accumulation in T1D and T2D results from incomplete β

oxidation (17;18). The current study offers a mechanistic link between these two phenomena.

The proteome measurements in the current study demonstrate that insulin deprivation decreased

abundance of βoxidation proteins, increased markers of CPT1 and SCAD inhibition, causing

incomplete lipid oxidation in the form of short chain acyl carnitines. Moreover, inhibition of β

oxidation in muscle cells induced ROS production and decreased mitochondrial function in the

presence of increased lipid availability. These results indicate that mitochondrial ROS emission

arises from increased FA abundance in combination with a defective βoxidation, leading to

accumulation of incomplete FA oxidation products. In addition, despite increased expression of

proteins involved in glycolysis and glycogenolysis, elevated PDHK4 suggests inhibition of PDH

complex and decreased entry of glucosederived pyruvate into TCA cycle (34).

Excess FA during insulin deprivation is expected to increase FA oxidation. Fatty acids are

natural ligands of skeletal muscle’s PPARα nuclear receptors, which regulate transcription of β

oxidation proteins. Surprisingly, we observed downregulation of PPARαregulated proteins in

muscle of STZI mice despite FA overload. Similar findings were shown in C2C12 myotubes

treated with CPT1 inhibitor etomoxir, where moderate suppression of FA oxidation triggered up

regulation of PPARα signaling whereas increasing inhibition lead to profound downregulation

of PPARα target genes (38). The inhibitory effect on PPARα signaling was dependent on

increased oxidative stress, as antioxidants normalized PPARα signaling despite etomoxir

treatment. In the current study, insulin deprivation triggered oxidative stress, which was

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accompanied by downregulation of majority of PPARαdependent proteins, a finding consistent

with decreased PPARα mRNA in STZ mice (39).

Impact of high ROS emission in STZI skeletal muscle is evident in the form of superoxide

generation, DNA damage, increased protein degradation and NRF2mediated oxidative stress

response. Reduced ROSrelated damage to muscle proteins was found to be responsible for

improved mitochondrial function in calorierestricted older mice (22). Moreover, ROSinduced

damage has been reported to cause decreased ATP production, which was ameliorated by

stimulating mtDNA repair through mitochondriatargeted hOGG1 (35) or catalase (40)

overexpression. These studies are consistent with our contention that decreased mitochondrial

ATP production and coupling efficiency during insulin deprivation results from increased

mitochondrial ROS production consequent to imbalance between cellular FA uptake and

oxidation. Indeed, insulin treatment of STZ mice increased mitochondrial coupling and phosphorylation efficiency, decreased oxidative stress, normalized plasma FFA and skeletal

muscle lipid parameters (13), decreased shortchain FA βoxidation products, shifted wholebody metabolism toward carbohydrate utilization as indicated by higher respiratory quotient.

The reduction in mitochondrial efficiency during insulin deprivation is compounded by decreased abundance of mitochondrial proteins. Proteomic analysis of the current study revealed that the majority of the 51 subunits of mitochondrial respiratory complexes, as well as other molecules involved in ATP metabolism such as adenine nucleotide translocases, mitochondrial solute carrier proteins, and many proteins localized to mitochondria are diminished. Previous reports indicated that STZtreated hypoinsulinemic mice show decreased expression of 5 subunits of respiratory complexes (41). The current study offers substantial support the concept that insulin is a key regulator of mitochondrial biology (1). Specifically, insulin stimulated

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mitochondrial protein synthesis and mRNA expression in skeletal muscle of human and swine

(2), increased mitochondrial oxidative capacity (1), and inhibited muscle protein degradation

(9;42). Conversely, shortterm insulin deprivation in T1D individuals decreases mRNA

expression of several mitochondrial proteins in skeletal muscle (5), highlighting an important

role for insulin in regulating mitochondrial biogenesis Here we advanced these findings by

demonstrating that molecular pathways responsible for both mitochondrial (TUFM) and cellular

(EIF2) regulation of protein synthesis are significantly down regulated in the absence of insulin,

which is confirmed by decreased skeletal muscle protein synthesis rates.

The proteomic survey also revealed that insulin deprivation activated the ubiqitin/proteasomal

pathway of protein degradation, which is responsible for removal of misfolded or damaged

proteins (43). These results are consistent with substantial increase in muscle protein degradation

reported based on isotope based studies in insulindeprived T1D individuals (8). Additionally,

we observed both the downregulation of all major classes of chaperones, and increased

abundance of semitryptic peptides originating from mitochondrial proteins in STZI, supporting

a notion that a selective degradation of mitochondrial proteins occurs in the insulindeprived

state, which was corrected by insulin treatment.

A likely cause of this phenomenon is mitophagy due to mitochondrial oxidative damage, as

recently observed in HeLa cells (44). Recent studies indicate that PARK7/DJ1 protein can

stimulate mitophagy and mitochondrial recycling in neuronal cells under excessive

mitochondrial oxidative damage (45;46). The current results indicate an accelerated

mitochondrial protein degradation in skeletal muscle of STZI, as increased ROS emission by

muscle mitochondria is accompanied by decreased mitochondrial [Mn]SOD expression, up

regulation of PARK7/DJ1, and elevation of semitryptic peptides of mitochondrial origin.

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Increased oxidative damage of mitochondrial proteins has led to defective βoxidation, due to

inactivation of CPT1 protein by oxidative carbonylation (47). Therefore, both reduced protein

synthesis and increased autophagy are likely responsible for the decrease in the content of

mitochondrial proteins leading on to defective βoxidation in STZI mice.

To our best knowledge this is the first study that links SM mitochondrial energetic to proteome

imbalance based largesale protein expression profile in diabetes. The purely proteomic study by

Johnson et al. in spontaneouslydiabetic BBDP rats was able to identify only 9 affected proteins

of which 5 were of blood plasma origin (48). The above study reported upregulation of ATP

synthase and down regulation to enolase. We found some molecular similarities with more

numerous papers on proteome changes in type 2 diabetes. The similar downregulation of

PARK7/DJ1 protein and increase in oxidative stressrelated pathways was reported in myotubes

derived from 2diabetic subjects, although accompanied by upregulation of mitochondrial,

TCA and ETC proteins, which is in clear opposition to our findings (49)The differences are

likely due to the treatment status and studying insulin deficient VS insulin deprived states. More

similarities in skeletal muscle protein expression can be drawn between the current study and the

results of Hwang et al., regarding mitochondrial protein alternations and abundance of proteasomal proteins, albeit the latter study focused on T2D and obese individuals (50). Those

data together indicate that although some molecular similarities exist between T1D and T2D

skeletal muscle proteomes, the overall impact is significantly different, presumably due to the

systemic insulin concentrations and tissue insulin resistance in T2D.

Insulin replacement did not completely restore the loss of mitochondrial protein abundance, β

oxidation enzymes, mitochondrial ROS emissions, or acylcarnitine profile in spite of reversal of

the diabetic phenotype, although protein synthesis and oxidative stressrelated pathways returned

Page 21 of 165 Diabetes

to ND level. Interestingly, as compared to controls STZ+I animals had lower expression of both

the fatty acids uptake and βoxidation proteins, which shows that skeletal muscle lipid

metabolism is still defective, even under insulin treatment. This suggests that some aspects of

mitochondrial dysfunction can prevail in T1D diabetes, when insulin therapy failed to fully

restore HbA1c levels to the same level as nondiabetic mice. Here, STZ mice that received

exogenous insulin exhibited normalized plasma glucose in the fasted state, but postprandial

glucose levels remained elevated, which frequently occurs in T1D individuals (51). The same

can be noted for plasma FFA content, which can show excessive postprandial elevation in T1D

patients as compared to normal subjects (52). Postprandial FFA elevation additionally

excerebrates hyperglycaemia, possibly due to induction of fatrelated insulin resistance (5355).

There are many metabolic abnormalities observed in diabetic dogs receiving insulin via systemic

routes versus portal route (31) that may also explain why not all proteomic/metabolic

abnormalities are fully normalized by systemic insulin administration in STZ mice. Antioxidant

treatment was shown to improve skeletal muscle mass, decrease protein ubiquitination and

autophagy (56), reduce postprandial hyperglycaemia, skeletal muscle oxidative stress mediators,

enhances plasma antioxidant capacity (57) and finally, improves mitochondrial function in STZ

diabetic mice (58).

Substantial body of current research underlines the importance of excessive lipid overabundance

in the induction of metabolic dearagements in all major body tissues. Although the current study

shows that lipiddriven ROS production is the major contributor of mitochondrial dysfunction in

skeletal muscle of STZdiabetic mice, the other components of T1D phenotype can affect

mitochondrial physiology. Hyperketonemia was shown to be associated with increased vascular

and immune cells ROS production (59), but also exerts mitoprotective effects in neuronal cells

Diabetes Page 22 of 165

(6062). Contrary to fatty acids, ketone bodies increase ROS in edothelial cells by unknown

mechanism. Moreover mitochndrial fatty acids metabolism in T1D is hard to dissociate from

ketones generation. Other factors such as hyperglycaemia although associate with mitochndrial

dysfunction, contrary to fatty acids are unable to induce mitochndrial dysfunction in C2C12

myotubes (63). Finally, both hypoinsulinaemia and insulin resistance associates with skeletal

muscle mitochondrial dysfunction, suggesting that our findings are slolely dependent on insulin

action in skeletal muscle. Results by Sleigh (64) and Kristensen (65) had shown that people with

insulin (INSR) receptor mution display mitochondrial dysfunction under normoglycaemia,

although involvement of intramuscular lipid accumulation was not ruled out in tis study. In both

studies INSR mutants show increase in ciurculating FFA under basal or clamp conditions. Both

studies do not exclude possibility, that increased fatty acids overabundance, intramuscular

transport and fatty acidsdriven ROS production are the major factors causing mitochondrial

functional changes. Moreover, the observation by Kristiansen et al that INSR mutants displayed

a trend towards the decreased activity of βHAD (βhydroxyacylCoA dehydrogenase, enzyme

of β oxidation pathway), noticeable only under lipid overload supports our hypothesis, that

mismatch between fatty acids supply and oxidation drives ROSrelated mitochondrial

dysfunction in skeletal muscle.

It is of importance to describe the rationale of the model that we have used. The model that has been extensively used in human type 1 diabetic individuals to study the effect of insulin

deficiency involves transient withdrawal of insulin treatment (6668). We employed similar

approach in our STZdiabetic mice treated with insulinimplant. These animals had no residual

βcell activity and insulin withdrawal allowed us to observe the changes attributed solely to

insulindeficiency, without interference of STZ toxicity, immediate insulinitis, hypoglycemia and

Page 23 of 165 Diabetes

effects of stress such as starvation and inactivity caused by T1D induction protocol. We treated

all STZdiabetic animals with insulin implants until normalization of body composition and

glycaemic control, and then withdrew the insulin for a week. In contrast to other models of

multiplelow dose STZ injection or spontaneouslydiabetic mice such as NOD or Akita mice or

BB rats display variable time of onset and degree of diabetes due to residual βcell function

(69;70). From a translational point of view the model that we have used is the most appropriate

in the study of the molecular effects of insulin deprivation and treatment.

In summary, the current study demonstrates that insulin deprivation in STZ diabetic mice leads

to profound disturbance of energy metabolism and multilevel disruption of mitochondrial

function in skeletal muscle. Specifically, insulin deprivation markedly reduced mitochondrial

ATP synthesis, phosphorylation and coupling efficiency and resulted in high ROS emission.

These changes occur in association with increased expression of intramyocellular FA transport

proteins despite decreased expression of proteins involved in mitochondrial FA–CoA import and

beta oxidation that may explain the marked accumulation of incomplete lipid oxidation products

in skeletal muscle of insulin deprived animals. The current results demonstrate that insulin

deprivation alters the balance of proteins involved in fatty acid transport and oxidation, leading

to impaired mitochondrial function and increased oxidative stress in skeletal muscle.

AUTHOR CONTRIBUTIONS

P.Z. and K.S.N. conceived and designed the study; P.Z. and S.G. performed animal experiments;

P.Z., C.J.H., S.D. and H.R.B. III performed SILACassisted proteomic analysis; P.Z., I.R.L. and

S.G. performed mitochondrial functional experiments; S.G. performed WB analysis and cell

Diabetes Page 24 of 165

culture experiments; P.Z., S.D. and I.R.L analyzed data; P.Z, I.R.L. and K.S.N interpreted results

of experiments; P.Z. and I.R.L. prepared figures and drafted manuscript; P.Z., I.R.L., H.R.B III,

S.D., S.G. and K.S.N. edited and revised manuscript; K.S.N coordinated and directed the project;

P.Z., I.R.L., C.J.H., H.R.B. III, S.D., S.G., and K.S.N approved final version of manuscript.

ACKNOWLEDGMENTS

The authors wish to express deep gratitude for the skillful technical work of Katherine Klaus,

Dawn Morse, Jill Schimke, Daniel Jakaitis, and Bushra Ali. Support for this work was provided by National Institutes of Health grants R01 DK41973, Mayo Clinic Metabolomics Resource

Core (U24DK100469) and CTSA Grant UL1 TR000135, and David Murdock Dole

Professorship (KSN) and Stephenson Fellowship (PZ) and IndoUS Science and Technology

Fellowship (2009) and ICMR International Fellowship (201314) (SG). The authors have no

conflict of interest to disclose.

Page 25 of 165 Diabetes

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FIGURE LEGENDS

Figure 1. Insulin deprivation adversely affects skeletal muscle mitochondrial physiology.

Oxygen consumption (JO2) was not different across groups (A). Expression of respiratory

Complex I and V proteins (B) and mitochondrial coupling efficiency (measured by RCR, (C) and

ADP:O ratio, (D)) was reduced by insulin deprivation and corrected by insulin treatment.

Mitochondrial ATP production rate (MAPR, D) was significantly lower with insulin deprivation

and restored with insulin therapy. Mitochondrial hydrogen peroxide (H2O2) emissions were

elevated with insulin deprivation and partially reduced by insulin replacement across all

respiratory states (F). O2 consumption as a % of ROS was higher in STZI (G). Increase in

mitochondrial ROS production was associated with downregulation of mitochondrial Mn

dependent superoxide dismutase (MnSOD) (H). Increased expression of AMPsensitive

adenylate kinase 1 (AK1) confirms low energy state of skeletal muscle in insulin deprived

animals. Substrate combinations description: GM – glutamate and malate; SR – succinate and

rothenone; PCM – palmitoylcarnitine and malate; PPKM – palmitoylcarnitine, pyruvate, α

ketoglutarate and malate. Data are means ±SEM. N=13 per group for mitochondrial functional

measurements, N=6 for western blot measurements. * denotes p<0.05 vs. nondiabetic, # denotes

p<0.05 vs. STZI group.

Figure 2. The impact of insulin deprivation and treatment on skeletal muscle proteome.

Compared to ND, STZI exhibited reduced expression of mitochondrial proteins, but increased

proteins linked with fatty acid uptake/transport and glycolysis/glycogen breakdown (A). These

directional trends were reversed in STZ+I (B), but were still visible as compared to ND (C).

Diabetes Page 36 of 165

Protein markers of oxidative stress and ubiquitination were higher in STZI mice compared to

ND, and proteins linked with protein synthesis were lower (D). These directional trends were

reversed in STZ+I (E) to the levels comparable with ND mice (F). Only significantly affected proteins are shown on volcano plots (log10 pvalue>1.301). Individual protein names and

expression values are given in Tables S2A to S2F for figure panels A to F, respectively.

Figure 3. Canonical pathways affected by insulin deprivation and treatment. Panel A lists pathways affected in STZI compared to ND animals. Panel B lists pathways affected by insulin treatment (STZ+I) as compared to diabetic insulindeprived (STZI), whereas panel C lists pathways which distinguish between STZ+I and ND mice. The middle column of each graph

lists pathway name and overall pathway score presented as –log10 pvalue. Open bars display pathway log10 pvalue score calculated using only downregulated proteins, whereas solid bars

depict the same variable using only upregulated proteins. Significantly affected pathways

display –log10 pvalue score greater than 1.3 (p<0.05). All significantly affected pathways from

STZI vs. nondiabetic, STZ+I vs. STZI and STZ+I vs ND comparisons are listed in Table S3A

S3B and S3C, respectively.

Figure 4. Both insulin deprivation and treatment leads to accumulation of acylcarnitines

and suggests incomplete fatty acid βoxidation in skeletal muscle of T1D diabetic mice.

Expression of FA intracellular transport and βoxidation proteins is affected in insulindeprived

and not fully corrected by insulin replacement, as revealed by highthroughput proteomic

analysis (A) and western blot (A,E). Insulin deprivation increases skeletal muscle shortchain

acylcarnitine content (B,C) and elevates CPT1 and SCHAD inhibition indexes (D). Insulin

Page 37 of 165 Diabetes

treatment corrects expression of proteins of intracellular FA uptake and shortchain FA β

oxidation (A), reverses SCAC accumulation and CPT1 and SCHAD inhibition indexes (B,C),

but leads to accumulation of mediumchain (MCAC), longchain (LCAC) and 3hydroxy (total

OH) acylcarnitine species (B,C) and increases LCHAD inhibition index (D). SCAC –C2 to C5

acylcarnitines, MCAC –C6 to C12 acyl carnitines, LCAC 14 to 20 acylcarnitines. Data

are means ±SEM. N=6 per group. * denotes p<0.05 vs. nondiabetic, # denotes p<0.05 vs. STZI

group.

Figure 5. Inhibition of βoxidation in palmitatetreated C2C12 cells mimics mitochondrial

disturbances observed in skeletal muscle of diabetic animals. Inhibition of βoxidation by

MCPA ((methylenecyclopropyl)acetic acid, SCHAD and MCHAD inhibitor) significantly

decreases mitochondrial oxygen consumption (A) and mitochondrial coupling efficiency (RCR,

B) and elevates cellular reactive oxygen species (ROS) content (C) in C2C12 cells treated with

palmitate. The adverse effects of βoxidation inhibition were observed only under both palmitate

and MCPA treatment (PA+MCPA) and were not observed in control cells treated with MCPA.

Ccontrol cells; PA – palmitatetreated cells, PA+MCPA – palmitate and MCPA treated cells,

MCPA – control cells treated with MCPA. Data are means ±SEM. N=3 per experiment. *

denotes p<0.05 vs. control, # denotes p<0.05 vs MCPA group, $ denotes p<0.05 vs PA group.

Diabetes Page 38 of 165 600 A ND STZ-I 400 STZ+I O2 J 200 (pmol/s/mg protein)

0 ) ) ) I II II A te 1 te 2 C + C te 4 A a a I a t t 3 ( C 3 ( t S S te 3 ( e S ND a t STZ-I STZ+I t te ta S ta S S CI 2.0 B CII # 1.5 CIII

1.0 # AU CIV * * * 0.5 * CV Vinculin 0.0 CI CII CIII CIV CV

3.0 150 5.0 C # D E # 2.8 # # # 4.0 2.6 * * 100 2.4 3.0 2.2 * * * 2.0 ADP:O 2.0 50 *

1.0 0.4 MAPR (% control) RCR (state 3/state 4) 0.2 0.0 0.0 0 GM SR PCM PPKM

4000 15 0.8 100 F G * * * * 80 3000 * 0.6 O 10 O * 2 2 %ROS %ROS 2 # * 60

O * 2 2000 # 0.4 %ROS

H #

2 * * * 40 * * O 5 1000 0.2 mol/min/mg protein) # * 20 m ( * # * # 0 0 0.0 0 I) I) I) I) I) d State 2 State 4 Uncoupled State 3 Antimycin A C I I I I le ( I+ I+ I+ (C p 2 C C C u ( ( ( 4 o non-phosphorylating phosphorylating te 2 3 4 e c a t n t te te te ta U S ta ta ta S S S S 2.5 ND STZ-I STZ+I H * 2.0 AK1 1.5 Vinculin AU 1.0 * MnSOD 0.5 Vinculin 0.0 AK1 MnSOD STZ-I vs. ND STZ+I vs. STZ-I STZ+I vs. ND Page40 39 of 165 40 Diabetes 40 A Other mitochondrial B ETC/TCA cycle C ETC/TCA cycle ETC/TCA cycle Other mitochondrial Other mitochondrial 30 B-oxidation 30 B-oxidation 30 B-oxidation FA uptake/transport FA uptake/transport FA uptake/transport 20 Glycolysis/glycogen breakdown 20 Glycolysis/glycogen breakdown 20 Glycolysis/glycogen breakdown -log(p-value) -log(p-value) -log(p-value) 10 10 10

0 0 0 -1.0 -0.5 0.0 0.5 1.0 -1.0 -0.5 0.0 0.5 1.0 -1.0 -0.5 0.0 0.5 1.0 log (fold-change) log (fold-change) log (fold-change)

STZ-I vs. ND Other cellular proteins STZ+I vs. STZ-I Other cellular proteins STZ+I vs. ND Other cellular proteins 20 20 20 D Protein synthesis / chaperone E Protein synthesis / chaperone F Protein synthesis / chaperone Protein ubiquitination Protein ubiquitination Protein ubiquitination 15 15 15 Oxidative stress Oxidative stress Oxidative stress

10 10 10 -log(p-value) -log(p-value) 5 5 -log(p-value) 5

0 0 0 -1 0 1 -1 0 1 -1 0 1 log (fold-change) log (fold-change) log (fold-change) A STZ-I vs. Control DiabetesB STZ+I vs. STZ-I Page 40 of 165

Mitochondrial dysfunction Mitochondrial dysfunction 36.0 3.52 TCA cyle TCA cyle 17.60 7.99 Glycolysis Glycolysis 8.44 9.55 Glycogen degradation Glycogen degradation 4.65 3.40 Fatty acid β-oxidation Fatty acid β-oxidation 7.01 5.51 Mitochondrial L-carnitine shuttle Mitochondrial L-carnitine shuttle 2.93 1.26 Protein kinase A signaling Protein kinase A signaling 2.61 2.45 Superoxide radicals generation Superoxide radicals generation 2.74 3.11 DNA damage regulation DNA damage regulation 1.76 2.19 NRF2 oxidative stress response NRF2 oxidative stress response 1.70 1.68 EIF2 signaling EIF2 signaling 2.58 4.98 tRNA charging tRNA charging 1.25 2.43 mTOR signaling mTOR signaling 0.49 1.23 Calcium signaling Calcium signaling 8.29 5.21 Actin cytoskeleton signaling Actin cytoskeleton signaling 5.11 2.73 50 40 20 15 10 5 0 0 5 10 15 20 20 15 10 5 0 0 5 10 15 20 -log (p-value) Overall -log(p-value) -log (p-value) -log (p-value) Overall -log(p-value) -log (p-value) down-regulated upregulated down-regulated upregulated

C STZ+I vs. Control Mitochondrial dysfunction 27 TCA cyle 19.3 Glycolysis 2.8 Glycogen degradation 2.89 Fatty acid β-oxidation 8.01 Mitochondrial L-carnitine shuttle 3.36 Protein kinase A signaling 1.65 Superoxide radicals generation 1.76 DNA damage regulation 0.73 NRF2 oxidative stress response 3.04 EIF2 signaling N.D. tRNA charging 0.83 mTOR signaling N.D. Calcium signaling 9.65 Actin cytoskeleton signaling 3.69 40 30 20 15 10 5 0 0 5 10 15 20 -log (p-value) Overall -log(p-value) -log (p-value) down-regulated upregulated Page 41of165 pmol/mg acyl-carnitine (pmol/mg) SILAC ratio 200 400 100 200 300 400 0.0 0.5 1.0 1.5 2.0 2.5 10 15 20 25 0 5 0 C B A Cellular FA uptake FA Cellular * * # * C2 FATP1 * SC-AC # # * *

C3 CD36 * # * * MC-AC * C4 *

FABP3 * # # STZ+I STZ+I STZ-I STZ-I ND ND * C5:0 * # *

Mitochondrial FA uptake FA Mitochondrial CPT1

LC-AC * # * C6:0 * #

CPT2 * * C8:0 * Total AC # # MCAT *

C8:1 * * #

GOT2 * Fold change # 0 1 2 3 4 *

C10:0 * * D

CRAT * * *

C10:1 AC efflux # *

CPT1 index * *

# ACAA1 # *

C12:0 * * * ACAA2 * SCHAD Index #

C12:1 * SBCAD *

* C14:0

LCHAD index * SCAD #

C14:1 * # *

MCAD * * Total OH * C14:2 # # *

LCAD * #

C16:0 * # Mitochondrial FA FA Mitochondrial Diabetes *

0.0 0.5 AU 1.0 1.5 VLCAD *

C16:1 * # E VLCAD(9) *

C18:0 * * # FATP1 * * #

ECHS1 * β * C18:1 -oxidation # *

ECI1 * C18:2 *

ACADS # # *

M/SCHAD * C20:1 * # * * ACDM * * C20:2 * HADH # ACADM ACADS vinculin FATP1 * * C20:3 HADHA * # * * * C20:4 * HADHB ND STZ-I STZ+I Diabetes Page 42 of 165 60 A Control PA PA+MCPA 40 MCPA **# O2 J * 20 *# (pmol/s/mgprotein)

AA State1 State2 State3 (CI)

State3 (CI+CII) State4 (CI+CII) Uncoupled (CII) Uncoupled (CI+CII) 5 B 0.6 C *#$ 4 0.5 # 0.4 3 * # 0.3 RCR RCR 2 0.2 1 0.1 0 0.0 Coupled Uncoupled Cellular ROS content Page 43 of 165 Diabetes

RefSeq/UniPr Symbol Entrez Gene Name ot/Swiss-Prot Accession AARS alanyl-tRNA synthetase Q3TZ32 ABCB7 ATP-binding cassette, sub-family B (MDR/TAP), member 7 Q61102 ABCC9 ATP-binding cassette, sub-family C (CFTR/MRP), member 9 P70170 ABCE1 ATP-binding cassette, sub-family E (OABP), member 1 P61222 ABHD11 abhydrolase domain containing 11 D3YYK0 ACAA2 acetyl-CoA acyltransferase 2 Q8BWT1 ACAD9 acyl-CoA dehydrogenase family, member 9 Q3ULL9 ACADL acyl-CoA dehydrogenase, long chain P51174 ACADM acyl-CoA dehydrogenase, C-4 to C-12 straight chain Q91WS8 ACADS acyl-CoA dehydrogenase, C-2 to C-3 short chain Q91W85 ACADSB acyl-CoA dehydrogenase, short/branched chain Q7TMY2 ACADVL acyl-CoA dehydrogenase, very long chain B1AR27 ACAT1 acetyl-CoA acetyltransferase 1 Q8QZT1 ACLY ATP citrate lyase A2A4H2 ACO1 aconitase 1, soluble P28271 ACO2 aconitase 2, mitochondrial Q99KI0 ACOT2 acyl-CoA thioesterase 2 Q9QYR9 ACOT9 acyl-CoA thioesterase 9 Q9R0X4 ACOT13 acyl-CoA thioesterase 13 Q4VA32 ACP1 acid phosphatase 1, soluble Q9D358 ACSL1 acyl-CoA synthetase long-chain family member 1 P41216 ACSL3 acyl-CoA synthetase long-chain family member 3 Q8K1J7 ACTA1 actin, alpha 1, skeletal muscle P68134 ACTB actin, beta Q3UBP6 ACTBL2 actin, beta-like 2 Q8BFZ3 ACTC1 actin, alpha, cardiac muscle 1 Q3UIJ3 ACTN1 actinin, alpha 1 Q7TPR4 ACTN2 actinin, alpha 2 Q8K3Q4 ACTN3 actinin, alpha 3 O88990 ACTR3 ARP3 actin-related protein 3 homolog (yeast) Q99JY9 ACTR1A ARP1 actin-related protein 1 homolog A, centractin alpha (yeast) P61164 ACYP1 acylphosphatase 1, erythrocyte (common) type Q4VAF0 ACYP2 acylphosphatase 2, muscle type Q5SPV7 ADAD1 adenosine deaminase domain containing 1 (testis-specific) Q5SUE7 ADCK3 aarF domain containing kinase 3 Q60936 ADCY10 adenylate cyclase 10 (soluble) Q8C0T9 ADH5 alcohol dehydrogenase 5 (class III), chi polypeptide Q6P5I3 ADH1C alcohol dehydrogenase 1C (class I), gamma polypeptide Q3UKA4 ADIPOQ adiponectin, C1Q and collagen domain containing Q60994 ADK adenosine kinase P55264-2 ADPRH ADP-ribosylarginine hydrolase Q3U5N4 ADSL adenylosuccinate lyase Q8VCD4 ADSSL1 adenylosuccinate synthase like 1 Q3UBP0 AFG3L2 AFG3 ATPase family gene 3-like 2 (S. cerevisiae) Q8JZQ2 AGL amylo-alpha-1, 6-glucosidase, 4-alpha-glucanotransferase Q8CE68 AGPAT3 1-acylglycerol-3-phosphate O-acyltransferase 3 C4B4E7 AHCY adenosylhomocysteinase Q3TF14 AHNAK AHNAK nucleoprotein Q6UL10 AHSG alpha-2-HS-glycoprotein P29699 AIFM1 apoptosis-inducing factor, mitochondrion-associated, 1 Q9Z0X1 AIMP2 aminoacyl tRNA synthetase complex-interacting multifunctional proteinQ8R3V2 2 Diabetes Page 44 of 165

AK1 adenylate kinase 1 Q9R0Y5 AK3 adenylate kinase 3 Q9D8W6 AKR1A1 aldo-keto reductase family 1, member A1 (aldehyde reductase) Q9JII6 AKR1B1 aldo-keto reductase family 1, member B1 (aldose reductase) Q3UDY1 Akr1b10 aldo-keto reductase family 1, member B10 (aldose reductase) Q8CI22 AKR7A2 aldo-keto reductase family 7, member A2 (aflatoxin aldehyde reductase)Q8CG76 ALAD aminolevulinate dehydratase Q9DD05 ALB albumin Q546G4 ALDH2 aldehyde dehydrogenase 2 family (mitochondrial) P47738 ALDH1A1 aldehyde dehydrogenase 1 family, member A1 P24549 ALDH6A1 aldehyde dehydrogenase 6 family, member A1 Q8K0L1 ALDH7A1 aldehyde dehydrogenase 7 family, member A1 Q9DBF1-2 ALDOA aldolase A, fructose-bisphosphate Q5FWB7 ALDOB aldolase B, fructose-bisphosphate Q91Y97 AMD1 adenosylmethionine decarboxylase 1 D3Z6H8 AMPD1 adenosine monophosphate deaminase 1 Q3V1D3 ANK1 ankyrin 1, erythrocytic Q02357-7 ANKRD2 ankyrin repeat domain 2 (stretch responsive muscle) B2RS77 ANKRD27 ankyrin repeat domain 27 (VPS9 domain) C4TGC3 ANXA1 annexin A1 P10107 ANXA2 annexin A2 Q542G9 ANXA4 annexin A4 P97429 ANXA5 annexin A5 P48036 ANXA6 annexin A6 Q8BSS4 ANXA7 annexin A7 Q3TJ49 ANXA11 annexin A11 Q921F1 AOC3 amine oxidase, copper containing 3 (vascular adhesion protein 1) O70423 APEH N-acylaminoacyl-peptide hydrolase Q8R146 APOA1 apolipoprotein A-I Q8BPD5 APOA4 apolipoprotein A-IV P06728 APOA1BP apolipoprotein A-I binding protein Q8K4Z3 APOBEC2 apolipoprotein B mRNA editing enzyme, catalytic polypeptide-like 2 Q9WV35 APOO apolipoprotein O Q9DCZ4 APRT adenine phosphoribosyltransferase Q6PK77 AQP1 aquaporin 1 (Colton blood group) Q3TLW5 ARCN1 archain 1 Q5XJY5 Arf1 ADP-ribosylation factor 1 P84078 ARF4 ADP-ribosylation factor 4 Q14BR4 ARF5 ADP-ribosylation factor 5 P84084 ARHGDIA Rho GDP dissociation inhibitor (GDI) alpha Q99PT1 ARL1 ADP-ribosylation factor-like 1 P61211 ARL3 ADP-ribosylation factor-like 3 Q543P7 ARL6IP5 ADP-ribosylation-like factor 6 interacting protein 5 Q8R5J9 ARL8B ADP-ribosylation factor-like 8B Q9CQW2 ARPC3 actin related protein 2/3 complex, subunit 3, 21kDa O15145 ARPC4 actin related protein 2/3 complex, subunit 4, 20kDa P59999 ART3 ADP-ribosyltransferase 3 B7ZNM3 ASPH aspartate beta-hydroxylase A2AL76 ASPN asporin Q99MQ4 ASRGL1 asparaginase like 1 Q8C0M9 ATAD1 ATPase family, AAA domain containing 1 Q9D5T0 ATIC 5-aminoimidazole-4-carboxamide ribonucleotide formyltransferase/IMPQ9CWJ9 cyclohydrolase ATL2 atlastin GTPase 2 Q6PA06 ATP8 ATP synthase F0 subunit 8 P03930 ATP1A1 ATPase, Na+/K+ transporting, alpha 1 polypeptide Q8VDN2 Page 45 of 165 Diabetes

ATP1A2 ATPase, Na+/K+ transporting, alpha 2 polypeptide Q6PIE5 ATP1B1 ATPase, Na+/K+ transporting, beta 1 polypeptide P14094 ATP1B2 ATPase, Na+/K+ transporting, beta 2 polypeptide Q3UR55 ATP2A1 ATPase, Ca++ transporting, cardiac muscle, fast twitch 1 Q8R429 ATP2A2 ATPase, Ca++ transporting, cardiac muscle, slow twitch 2 O55143 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunitD3Z6F5 1, cardiac muscle ATP5B ATP synthase, H+ transporting, mitochondrial F1 complex, beta polypeptideP56480 ATP5C1 ATP synthase, H+ transporting, mitochondrial F1 complex, gamma polypeptideA2AKU9 1 ATP5D ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunitQ9D3D9 ATP5F1 ATP synthase, H+ transporting, mitochondrial Fo complex, subunit B1 Q5I0W0 Atp5h ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d Q9DCX2 ATP5I ATP synthase, H+ transporting, mitochondrial Fo complex, subunit E Q5EBI8 ATP5J ATP synthase, H+ transporting, mitochondrial Fo complex, subunit F6 P97450 ATP5L ATP synthase, H+ transporting, mitochondrial Fo complex, subunit G Q9CPQ8 ATP5O ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit Q9DB20 ATP6V1B2 ATPase, H+ transporting, lysosomal 56/58kDa, V1 subunit B2 P62814 BAG3 BCL2-associated athanogene 3 A6H663 BAI3 brain-specific angiogenesis inhibitor 3 Q80ZF8 BANF1 barrier to autointegration factor 1 O54962 BCAP31 B-cell receptor-associated protein 31 A2ALM8 BDH1 3-hydroxybutyrate dehydrogenase, type 1 Q3UL45 BGN biglycan P28653 BIN1 bridging integrator 1 Q6P1B9 BLMH bleomycin hydrolase Q8R016 BLVRA biliverdin reductase A Q9CY64 BLVRB biliverdin reductase B (flavin reductase (NADPH)) Q3U6G1 BPGM 2,3-bisphosphoglycerate mutase Q3TAQ8 BPNT1 3'(2'), 5'-bisphosphate nucleotidase 1 Q3UBN8 BSG basigin (Ok blood group) P18572 BTF3 basic transcription factor 3 Q64152 BZW2 basic leucine zipper and W2 domains 2 Q3V199 C3 complement component 3 Q80XP1 C11orf67 chromosome 11 open reading frame 67 Q8R0P4 C12orf5 chromosome 12 open reading frame 5 Q8BZA9 C19orf70 chromosome 19 open reading frame 70 Q8R404 C1orf123 chromosome 1 open reading frame 123 A2A8E2 C1QBP complement component 1, q subcomponent binding protein Q8R5L1 C21orf33 chromosome 21 open reading frame 33 Q9D172 C22orf28 chromosome 22 open reading frame 28 Q3TJ01 C9orf41 chromosome 9 open reading frame 41 Q80UY1 CA1 carbonic anhydrase I Q3TS19 CA2 carbonic anhydrase II P00920 CA3 carbonic anhydrase III, muscle specific P16015 CAB39 calcium binding protein 39 Q8VDZ8 CACNA1S calcium channel, voltage-dependent, L type, alpha 1S subunit Q02789 CACNA2D1 calcium channel, voltage-dependent, alpha 2/delta subunit 1 O08532-2 CACNB1 calcium channel, voltage-dependent, beta 1 subunit A2A542 CACNG1 calcium channel, voltage-dependent, gamma subunit 1 O70578 Calm1 (includes others)calmodulin 1 Q3UKW2 CALR calreticulin B2MWM9 CALU calumenin O35887 CAMK2A calcium/calmodulin-dependent protein kinase II alpha P11798 Camk2b calcium/calmodulin-dependent protein kinase II, beta Q5SVJ0 CAMK2D calcium/calmodulin-dependent protein kinase II delta Q6PHZ2 CAMK2G calcium/calmodulin-dependent protein kinase II gamma Q923T9 Diabetes Page 46 of 165

CAND1 cullin-associated and neddylation-dissociated 1 Q3UMI9 CAND2 cullin-associated and neddylation-dissociated 2 (putative) Q6ZQ73 CANX calnexin P35564 CAP1 CAP, adenylate cyclase-associated protein 1 (yeast) P40124 CAP2 CAP, adenylate cyclase-associated protein, 2 (yeast) Q9CYT6 CAPN1 calpain 1, (mu/I) large subunit O35350 CAPN2 calpain 2, (m/II) large subunit Q3U8S5 CAPN3 calpain 3, (p94) A2AVV2 CAPN5 calpain 5 O08688 CAPNS1 calpain, small subunit 1 D3YW48 CAPZA2 capping protein (actin filament) muscle Z-line, alpha 2 Q5DQJ3 CAPZB capping protein (actin filament) muscle Z-line, beta P47757 CARS cysteinyl-tRNA synthetase Q3U716 CASQ1 calsequestrin 1 (fast-twitch, skeletal muscle) Q6P3C3 CASQ2 calsequestrin 2 (cardiac muscle) Q56A03 CAT catalase P24270 CAV1 caveolin 1, caveolae protein, 22kDa P49817 CAV3 caveolin 3 P51637 CBR1 carbonyl reductase 1 P48758 Cbr2 carbonyl reductase 2 Q542P5 CCBL1 cysteine conjugate-beta lyase, cytoplasmic A2AQY8 CCDC18 coiled-coil domain containing 18 Q640L5 CCT2 chaperonin containing TCP1, subunit 2 (beta) P80314 CCT3 chaperonin containing TCP1, subunit 3 (gamma) Q3U4U6 CCT4 chaperonin containing TCP1, subunit 4 (delta) Q3TII0 CCT5 chaperonin containing TCP1, subunit 5 (epsilon) P80316 CCT7 chaperonin containing TCP1, subunit 7 (eta) Q3TJN2 CCT8 chaperonin containing TCP1, subunit 8 (theta) Q3UL22 CCT6A chaperonin containing TCP1, subunit 6A (zeta 1) Q3TI05 CD9 CD9 molecule P40240 CD36 CD36 molecule (thrombospondin receptor) Q08857 CDC42 cell division cycle 42 (GTP binding protein, 25kDa) P60766 CDH13 cadherin 13, H-cadherin (heart) Q8BG11 CDNF cerebral dopamine neurotrophic factor Q8CC36 Ces1b/Ces1ccarboxylesterase 1C D3Z5G7 Ces1d carboxylesterase 1D Q8VCT4 CFL1 cofilin 1 (non-muscle) Q544Y7 CFL2 cofilin 2 (muscle) Q3UHW9 CHAD chondroadherin Q3TYW1 CHCHD3 coiled-coil-helix-coiled-coil-helix domain containing 3 Q9CRB9 CISD1 CDGSH iron sulfur domain 1 Q91WS0 CKB creatine kinase, brain Q04447 CKM creatine kinase, muscle P07310 CKMT2 creatine kinase, mitochondrial 2 (sarcomeric) Q6P8J7 CLEC3B C-type lectin domain family 3, member B P43025 CLIP1 CAP-GLY domain containing linker protein 1 Q922J3 CLTC clathrin, heavy chain (Hc) Q68FD5 CLYBL citrate lyase beta like Q8R4N0 CMBL carboxymethylenebutenolidase homolog (Pseudomonas) Q8R1G2 CMPK1 cytidine monophosphate (UMP-CMP) kinase 1, cytosolic Q9DBP5 CMYA5 cardiomyopathy associated 5 Q70KF4 CNDP2 CNDP dipeptidase 2 (metallopeptidase M20 family) Q9D1A2 CNP 2',3'-cyclic nucleotide 3' phosphodiesterase P16330 COL12A1 collagen, type XII, alpha 1 Q60847 COL1A1 collagen, type I, alpha 1 P11087-2 Page 47 of 165 Diabetes

COL1A2 collagen, type I, alpha 2 Q01149 COL6A1 collagen, type VI, alpha 1 Q04857 COL6A2 collagen, type VI, alpha 2 Q02788 COL6A3 collagen, type VI, alpha 3 O88493 COMP cartilage oligomeric matrix protein A1A557 COMT catechol-O-methyltransferase Q91XH4 COPG1 coatomer protein complex, subunit gamma 1 Q8BP96 COPS2 COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)A2AQE3 COPS3 COP9 constitutive photomorphogenic homolog subunit 3 (Arabidopsis)Q3UQL2 COPS4 COP9 constitutive photomorphogenic homolog subunit 4 (Arabidopsis)O88544 COPS5 COP9 constitutive photomorphogenic homolog subunit 5 (Arabidopsis)O35864 COPS6 COP9 constitutive photomorphogenic homolog subunit 6 (Arabidopsis)O88545 COPS7A COP9 constitutive photomorphogenic homolog subunit 7A (Arabidopsis)Q9CZ04 COQ3 coenzyme Q3 homolog, methyltransferase (S. cerevisiae) A2AJT6 COQ5 coenzyme Q5 homolog, methyltransferase (S. cerevisiae) Q9CXI0 COQ6 coenzyme Q6 homolog, monooxygenase (S. cerevisiae) Q8R1S0 COQ7 coenzyme Q7 homolog, ubiquinone (yeast) Q3TYT1 COQ9 coenzyme Q9 homolog (S. cerevisiae) Q8K1Z0 CORO6 coronin 6 Q920M5-4 COX1 cytochrome c oxidase subunit I Q9MD68 COX2 cytochrome c oxidase subunit II P00405 COX3 cytochrome c oxidase III Q7JCX7 COX4I1 cytochrome c oxidase subunit IV isoform 1 P19783 COX5A cytochrome c oxidase subunit Va P12787 COX5B cytochrome c oxidase subunit Vb P19536 COX6B1 cytochrome c oxidase subunit VIb polypeptide 1 (ubiquitous) P56391 COX6C cytochrome c oxidase subunit VIc Q9CPQ1 COX7A1 cytochrome c oxidase subunit VIIa polypeptide 1 (muscle) Q792A4 COX7A2L cytochrome c oxidase subunit VIIa polypeptide 2 like Q61387 CPT2 carnitine palmitoyltransferase 2 P52825 CPT1B carnitine palmitoyltransferase 1B (muscle) Q3UIM5 CRAT carnitine O-acetyltransferase Q3V1Y3 CRK v-crk sarcoma virus CT10 oncogene homolog (avian) Q64010 CROT carnitine O-octanoyltransferase Q9DC50 CRYAB crystallin, alpha B Q52L78 CRYZ crystallin, zeta (quinone reductase) Q3UYY0 CS citrate synthase Q9CZU6 CSDA cold shock domain protein A Q9JKB3-2 CSE1L CSE1 chromosome segregation 1-like (yeast) Q9ERK4 CSNK2A1 casein kinase 2, alpha 1 polypeptide Q60737 CSRP3 cysteine and glycine-rich protein 3 (cardiac LIM protein) Q545C7 CST3 cystatin C A2APX2 CST7 cystatin F (leukocystatin) O89098 CTSD cathepsin D P18242 CUL3 cullin 3 Q6ZQ84 CUL5 cullin 5 Q2M4H5 CYB5R1 cytochrome b5 reductase 1 Q9DB73 CYB5R3 cytochrome b5 reductase 3 Q9DCN2 CYC1 cytochrome c-1 Q9D0M3 CYCS cytochrome c, somatic Q56A15 DARS aspartyl-tRNA synthetase Q3TF87 DBI diazepam binding inhibitor (GABA receptor modulator, acyl-CoA bindingP31786 protein) DBT dihydrolipoamide branched chain transacylase E2 Q7TND9 DCN decorin P28654 DCTN1 dynactin 1 D3YX34 Diabetes Page 48 of 165

DCTN2 dynactin 2 (p50) Q3TPZ5 DDB1 damage-specific DNA binding protein 1, 127kDa Q91YC8 DDOST dolichyl-diphosphooligosaccharide--protein glycosyltransferase O54734 DDX1 DEAD (Asp-Glu-Ala-Asp) box helicase 1 Q91VR5 DDX39B DEAD (Asp-Glu-Ala-Asp) box polypeptide 39B Q9Z1N5 DDX3X DEAD (Asp-Glu-Ala-Asp) box polypeptide 3, X-linked B7ZWF1 DECR1 2,4-dienoyl CoA reductase 1, mitochondrial Q4FJK0 DES desmin P31001 DHDH dihydrodiol dehydrogenase (dimeric) Q8K0E9 DHRS4 dehydrogenase/reductase (SDR family) member 4 Q99LB2 DHRS7C dehydrogenase/reductase (SDR family) member 7C Q8CHS7 DHX15 DEAH (Asp-Glu-Ala-His) box polypeptide 15 O35286 DLAT dihydrolipoamide S-acetyltransferase Q8BMF4 DLD dihydrolipoamide dehydrogenase O08749 DLST dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarateQ9D2G2 complex) DMD dystrophin P11531 DNAJA2 DnaJ (Hsp40) homolog, subfamily A, member 2 Q9QYJ0 DNAJA3 DnaJ (Hsp40) homolog, subfamily A, member 3 Q99M87 DNAJA4 DnaJ (Hsp40) homolog, subfamily A, member 4 Q8R1X2 DNAJC24 DnaJ (Hsp40) homolog, subfamily C, member 24 Q91ZF0-2 DNM1L dynamin 1-like Q8K1M6 DNPEP aspartyl aminopeptidase Q9Z2W0 DOCK6 dedicator of cytokinesis 6 Q6ZPS1 DPP3 dipeptidyl-peptidase 3 Q99KK7 DPYSL2 dihydropyrimidinase-like 2 O08553 DSTN destrin (actin depolymerizing factor) Q4FK36 DTNA dystrobrevin, alpha Q9D2N4-2 DUPD1 dual specificity phosphatase and pro isomerase domain containing 1 Q8BK84 DUSP3 dual specificity phosphatase 3 B1AQF3 DYNC1H1 dynein, cytoplasmic 1, heavy chain 1 Q9JHU4 DYNC1I2 dynein, cytoplasmic 1, intermediate chain 2 A2BFF5 DYNLL2 dynein, light chain, LC8-type 2 Q9D0M5 DYSF dysferlin, limb girdle muscular dystrophy 2B (autosomal recessive) Q9ESD7 ECH1 enoyl CoA hydratase 1, peroxisomal O35459 ECHS1 enoyl CoA hydratase, short chain, 1, mitochondrial Q8BH95 ECI1 enoyl-CoA delta isomerase 1 Q8QZV3 Eef1a1 eukaryotic translation elongation factor 1 alpha 1 P10126 EEF1A2 eukaryotic translation elongation factor 1 alpha 2 P62631 EEF1B2 eukaryotic translation elongation factor 1 beta 2 O70251 EEF1D eukaryotic translation elongation factor 1 delta (guanine nucleotide exchangeP57776 protein) EEF1G eukaryotic translation elongation factor 1 gamma Q4FZK2 EHD1 EH-domain containing 1 Q9WVK4 EHD2 EH-domain containing 2 Q8BH64 EHD4 EH-domain containing 4 Q9EQP2 EIF5 eukaryotic translation initiation factor 5 P59325 EIF2C2 eukaryotic translation initiation factor 2C, 2 Q8CJG0 EIF2S3 eukaryotic translation initiation factor 2, subunit 3 gamma, 52kDa Q9Z0N1 EIF3J eukaryotic translation initiation factor 3, subunit J Q2YDW1 EIF3L eukaryotic translation initiation factor 3, subunit L Q8QZY1 EIF4A1 eukaryotic translation initiation factor 4A1 P60843 EIF4A2 eukaryotic translation initiation factor 4A2 P10630 EIF4E eukaryotic translation initiation factor 4E Q3TK95 EIF4G1 eukaryotic translation initiation factor 4 gamma, 1 A0PJB5 Eif5a eukaryotic translation initiation factor 5A P63242 EMB embigin P21995 Page 49 of 165 Diabetes

EMC1 ER membrane protein complex subunit 1 A1L2Z3 EML1 echinoderm microtubule associated protein like 1 B9EKL9 ENO1 enolase 1, (alpha) P17182 ENO2 enolase 2 (gamma, neuronal) P17183 ENO3 enolase 3 (beta, muscle) P21550 EPDR1 ependymin related protein 1 (zebrafish) Q99M71 EPHX2 epoxide hydrolase 2, cytoplasmic Q3UQ71 EPRS glutamyl-prolyl-tRNA synthetase Q8CGC7 ERBB4 v-erb-a erythroblastic leukemia viral oncogene homolog 4 (avian) B2KGF5 ERC1 ELKS/RAB6-interacting/CAST family member 1 Q99MI1 ESD esterase D Q9R0P3 ETFA electron-transfer-flavoprotein, alpha polypeptide Q99LC5 ETFB electron-transfer-flavoprotein, beta polypeptide Q9DCW4 ETFDH electron-transferring-flavoprotein dehydrogenase Q921G7 F13A1 coagulation factor XIII, A1 polypeptide Q3V3W7 FABP1 fatty acid binding protein 1, liver Q3V2F7 FABP3 fatty acid binding protein 3, muscle and heart (mammary-derived growthQ5EBJ0 inhibitor) FABP4 fatty acid binding protein 4, adipocyte Q542H7 FAHD1 fumarylacetoacetate hydrolase domain containing 1 Q3UQY4 FAM154B family with sequence similarity 154, member B Q8BQB6 FAM210A family with sequence similarity 210, member A Q8BGY7 FAM213A family with sequence similarity 213, member A Q9CYH2 FAM213B family with sequence similarity 213, member B Q9DB60 FAM75A3 (includes others)family with sequence similarity 75, member A2 Q5MAT5 FAM82B family with sequence similarity 82, member B Q9DCV4 FARSB phenylalanyl-tRNA synthetase, beta subunit Q3TG12 FASN fatty acid synthase P19096 FBP2 fructose-1,6-bisphosphatase 2 Q3TKP4 FECH ferrochelatase P22315 FGB fibrinogen beta chain Q3TGR2 FGG fibrinogen gamma chain Q8VCM7 FH fumarate hydratase Q3UIA9 FHL1 four and a half LIM domains 1 A2AEX6 FHL3 four and a half LIM domains 3 A6H6N4 FIS1 fission 1 (mitochondrial outer membrane) homolog (S. cerevisiae) Q9CQ92 FITM1 fat storage-inducing transmembrane protein 1 Q91V79 FKBP3 FK506 binding protein 3, 25kDa Q3UBU9 FLNC filamin C, gamma D3YW87 FMOD fibromodulin Q543D2 FNDC3B fibronectin type III domain containing 3B Q6NWW9 FTH1 ferritin, heavy polypeptide 1 P09528 FUNDC2 FUN14 domain containing 2 Q9D6K8 FXR1 fragile X mental retardation, autosomal homolog 1 Q61584 Gapdh/LOC100042025glyceraldehyde-3-phosphate dehydrogenase P16858 GAPDHS glyceraldehyde-3-phosphate dehydrogenase, spermatogenic Q3V2I5 GARS glycyl-tRNA synthetase Q9CZD3 GART phosphoribosylglycinamide formyltransferase, phosphoribosylglycinamideQ3UJP8 synthetase, phosphoribosylaminoimidazole synthetase GBAS glioblastoma amplified sequence O55126 GBE1 glucan (1,4-alpha-), branching enzyme 1 Q9D6Y9 GC group-specific component (vitamin D binding protein) P21614 GDI1 GDP dissociation inhibitor 1 P50396 GDI2 GDP dissociation inhibitor 2 Q61598 GFM1 G elongation factor, mitochondrial 1 Q8K0D5 GLO1 glyoxalase I Q9CPU0 GLOD4 glyoxalase domain containing 4 Q9CPV4 Diabetes Page 50 of 165

GLRX3 glutaredoxin 3 Q9CQM9 GLRX glutaredoxin (thioltransferase) Q3U6L3 GLUD1 glutamate dehydrogenase 1 P26443 GLUL glutamate-ammonia ligase P15105 Gm10349/Nutf2nuclear transport factor 2 Q3U8H8 Gm3837/Pdcd5programmed cell death 5 P56812 GMPR guanosine monophosphate reductase Q9DCZ1 GNAI2 guanine nucleotide binding protein (G protein), alpha inhibiting activity Q3TXK7polypeptide 2 Gnas GNAS (guanine nucleotide binding protein, alpha stimulating) complexQ6R0H7 locus GNB2 guanine nucleotide binding protein (G protein), beta polypeptide 2 Q3U9V4 GNB2L1 guanine nucleotide binding protein (G protein), beta polypeptide 2-like 1P68040 GOT1 glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferaseQ3UJH8 1) GOT2 glutamic-oxaloacetic transaminase 2, mitochondrial (aspartate aminotransferaseP05202 2) GPCPD1 glycerophosphocholine phosphodiesterase GDE1 homolog (S. cerevisiae)A2AMD4 GPD1 glycerol-3-phosphate dehydrogenase 1 (soluble) P13707 GPD2 glycerol-3-phosphate dehydrogenase 2 (mitochondrial) Q64521 GPD1L glycerol-3-phosphate dehydrogenase 1-like B2RSR7 GPI glucose-6-phosphate isomerase P06745 GPS1 G protein pathway suppressor 1 Q3MIA8 GPT glutamic-pyruvate transaminase (alanine aminotransferase) Q566C3 GPX3 glutathione peroxidase 3 (plasma) P46412 GPX4 glutathione peroxidase 4 O70325 GRB2 growth factor receptor-bound protein 2 B1AT92 GRHPR glyoxylate reductase/hydroxypyruvate reductase Q3T9Z2 GRPEL1 GrpE-like 1, mitochondrial (E. coli) Q3UTB8 GSK3A glycogen synthase kinase 3 alpha Q2NL51 GSN gelsolin A2AL35 GSR glutathione reductase P47791 Gsta4 glutathione S-transferase, alpha 4 P24472 GSTM1 glutathione S-transferase mu 1 P15626 GSTM3 glutathione S-transferase mu 3 (brain) P48774 GSTM4 glutathione S-transferase mu 4 Q8R5I6 GSTM5 glutathione S-transferase mu 5 P10649 GSTO1 glutathione S-transferase omega 1 O09131 GSTP1 glutathione S-transferase pi 1 P19157 GSTZ1 glutathione S-transferase zeta 1 Q9WVL0 GYS1 glycogen synthase 1 (muscle) Q9Z1E4 H1F0 H1 histone family, member 0 P10922 H2afv H2A histone family, member V B2RVP5 HADH hydroxyacyl-CoA dehydrogenase Q61425 HADHA hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydrataseQ8BMS1 (trifunctional protein), alpha subunit HADHB hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydrataseQ99JY0 (trifunctional protein), beta subunit HAGH hydroxyacylglutathione hydrolase Q99KB8 HARS histidyl-tRNA synthetase Q3TKU3 HBA1/HBA2 hemoglobin, alpha 1 Q9CWS5 HBB hemoglobin, beta P02088 HBD hemoglobin, delta P02089 HDHD2 haloacid dehalogenase-like hydrolase domain containing 2 Q3UGR5 HELZ helicase with zinc finger A2AAU3 HHATL hedgehog acyltransferase-like Q9D1G3 HIBADH 3-hydroxyisobutyrate dehydrogenase Q99L13 HIBCH 3-hydroxyisobutyryl-CoA hydrolase Q8QZS1 Higd1a HIG1 domain family, member 1A Q9JLR9 HINT1 histidine triad nucleotide binding protein 1 P70349 HINT2 histidine triad nucleotide binding protein 2 Q5M9J2 Page 51 of 165 Diabetes

HIST1H1C histone cluster 1, H1c P15864 HIST1H1E histone cluster 1, H1e P43274 HIST1H2AD histone cluster 1, H2ad A0AUV1 HIST1H2BL histone cluster 1, H2bl A0JLV3 Hist2h2aa1/Hist2h2aa2histone cluster 2, H2aa1 NP_038577 HIST2H3C (includes histoneothers) cluster 2, H3c A1L0U3 Hist2h4 (includes others)histone cluster 2, H4 NP_835499 HK2 hexokinase 2 O08528 HNRNPA3 heterogeneous nuclear ribonucleoprotein A3 Q8BG05 HNRNPA2B1heterogeneous nuclear ribonucleoprotein A2/B1 B7ZP22 HNRNPAB heterogeneous nuclear ribonucleoprotein A/B Q20BD0 HNRNPF heterogeneous nuclear ribonucleoprotein F Q9Z2X1-2 HNRNPH1 heterogeneous nuclear ribonucleoprotein H1 (H) O35737 HNRNPK heterogeneous nuclear ribonucleoprotein K B2M1R6 HNRNPM heterogeneous nuclear ribonucleoprotein M B8JK30 HNRPDL heterogeneous nuclear ribonucleoprotein D-like D3YTQ3 HOMER1 homer homolog 1 (Drosophila) Q9Z2Y3 HOOK3 hook homolog 3 (Drosophila) Q5BKS5 HPX hemopexin Q3UKP2 HRAS v-Ha-ras Harvey rat sarcoma viral oncogene homolog C0H5X4 HRC histidine rich calcium binding protein B9EIW1 HSD17B4 hydroxysteroid (17-beta) dehydrogenase 4 P51660 HSD17B8 hydroxysteroid (17-beta) dehydrogenase 8 P50171-2 HSD17B10 hydroxysteroid (17-beta) dehydrogenase 10 Q99N15 HSP90AA1 heat shock protein 90kDa alpha (cytosolic), class A member 1 P07901 HSP90AB1 heat shock protein 90kDa alpha (cytosolic), class B member 1 Q71LX8 HSP90B1 heat shock protein 90kDa beta (Grp94), member 1 P08113 HSPA4 heat shock 70kDa protein 4 Q61316 HSPA5 heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) A2AUF6 HSPA9 heat shock 70kDa protein 9 (mortalin) P38647 HSPA1A/HSPA1Bheat shock 70kDa protein 1A Q61696 HSPA1L heat shock 70kDa protein 1-like A1L347 HSPB1 heat shock 27kDa protein 1 P14602 HSPB6 heat shock protein, alpha-crystallin-related, B6 Q5EBG6 HSPB7 heat shock 27kDa protein family, member 7 (cardiovascular) Q5FW72 HSPD1 heat shock 60kDa protein 1 (chaperonin) P63038 HSPE1 heat shock 10kDa protein 1 (chaperonin 10) Q4KL76 HSPG2 heparan sulfate proteoglycan 2 Q05793 IARS2 isoleucyl-tRNA synthetase 2, mitochondrial Q810V2 IARS isoleucyl-tRNA synthetase Q6NXK4 IDH1 isocitrate dehydrogenase 1 (NADP+), soluble Q3TJ51 IDH2 isocitrate dehydrogenase 2 (NADP+), mitochondrial P54071 IDH3A isocitrate dehydrogenase 3 (NAD+) alpha Q9D6R2 IDH3B isocitrate dehydrogenase 3 (NAD+) beta Q91VA7 IDH3G isocitrate dehydrogenase 3 (NAD+) gamma P70404 IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) Q99LC4 IGKC immunoglobulin kappa constant P01837 IMMT inner membrane protein, mitochondrial Q3TEY5 IMPA1 inositol(myo)-1(or 4)-monophosphatase 1 O55023 Impdh2 inosine 5'-phosphate dehydrogenase 2 P24547 INMT indolethylamine N-methyltransferase P40936 IPO5 importin 5 Q8BKC5-2 IPO7 importin 7 Q9EPL8 ISOC1 isochorismatase domain containing 1 Q9D096 ISOC2 isochorismatase domain containing 2 P85094 Diabetes Page 52 of 165

ITPA inosine triphosphatase (nucleoside triphosphate pyrophosphatase) Q60I30 IVD isovaleryl-CoA dehydrogenase Q9JHI5 JPH1 junctophilin 1 Q9ET80 JPH2 junctophilin 2 Q3U077 JSRP1 junctional sarcoplasmic reticulum protein 1 Q3MI48 KBTBD5 kelch repeat and BTB (POZ) domain containing 5 Q9D783 KBTBD10 kelch repeat and BTB (POZ) domain containing 10 A2AUC9 KERA keratocan O35367 KLHL31 kelch-like 31 (Drosophila) Q8BWA5 KNG1 kininogen 1 O08677-2 KPNA3 karyopherin alpha 3 (importin alpha 4) Q543M7 KPNA4 karyopherin alpha 4 (importin alpha 3) O35343 KPNB1 karyopherin (importin) beta 1 P70168 KRT10 keratin 10 A2A513 KRT17 keratin 17 Q9QWL7 KRT73 keratin 73 Q6NXH9 KRT79 keratin 79 Q8VED5 LAMA2 laminin, alpha 2 Q60675 LAMB2 laminin, beta 2 (laminin S) Q8R0Y0 LAMC1 laminin, gamma 1 (formerly LAMB2) P02468 LAMP2 lysosomal-associated membrane protein 2 A2A430 LANCL2 LanC lantibiotic synthetase component C-like 2 (bacterial) Q9JJK2 LAP3 leucine aminopeptidase 3 Q9CPY7 LDB3 LIM domain binding 3 Q9JKS4-4 LDHA lactate dehydrogenase A Q3THB4 Ldhb lactate dehydrogenase B P16125 LETM1 leucine zipper-EF-hand containing transmembrane protein 1 Q9Z2I0 LGALS1 lectin, galactoside-binding, soluble, 1 P16045 LMCD1 LIM and cysteine-rich domains 1 Q3TVW6 LMNA lamin A/C B3RH24 LMNB1 lamin B1 P14733 LONP1 lon peptidase 1, mitochondrial Q3V2D0 LRPPRC leucine-rich pentatricopeptide repeat containing Q6PB66 LRRC20 leucine rich repeat containing 20 Q8CI70 LRRC59 leucine rich repeat containing 59 Q3TF84 LTA4H leukotriene A4 hydrolase Q3UY71 LUM lumican P51885 LYPLA1 lysophospholipase I P97823-2 MACROD1 MACRO domain containing 1 Q922B1 MAGED1 melanoma antigen family D, 1 B1ASQ5 MAP1LC3A microtubule-associated protein 1 light chain 3 alpha Q91VR7 MAP2K1 mitogen-activated protein kinase kinase 1 P31938 MAP2K2 mitogen-activated protein kinase kinase 2 Q63932 MAP2K4 mitogen-activated protein kinase kinase 4 P47809 MAP2K6 mitogen-activated protein kinase kinase 6 P70236 MAPK12 mitogen-activated protein kinase 12 O08911 MARC2 mitochondrial amidoxime reducing component 2 Q922Q1 MARCKS myristoylated alanine-rich protein kinase C substrate Q05BL6 MARS methionyl-tRNA synthetase Q68FL6 MAT2A methionine adenosyltransferase II, alpha Q3THS6 MB myoglobin Q3UVB1 MBP myelin basic protein P04370-7 MCCC1 methylcrotonoyl-CoA carboxylase 1 (alpha) Q99MR8 MCCC2 methylcrotonoyl-CoA carboxylase 2 (beta) Q3ULD5 MDH1 malate dehydrogenase 1, NAD (soluble) P14152 Page 53 of 165 Diabetes

MDH2 malate dehydrogenase 2, NAD (mitochondrial) P08249 MDP1 magnesium-dependent phosphatase 1 Q9D967 ME1 malic enzyme 1, NADP(+)-dependent, cytosolic Q9DBF9 MGST3 microsomal glutathione S-transferase 3 Q9CPU4 MLEC malectin Q6ZQI3 MLH1 mutL homolog 1, colon cancer, nonpolyposis type 2 (E. coli) Q9JK91 MPC1 mitochondrial pyruvate carrier 1 P63030 MPC2 mitochondrial pyruvate carrier 2 Q9D023 MPI mannose phosphate isomerase Q924M7 MPST mercaptopyruvate sulfurtransferase Q3UW66 MPZ myelin protein zero P27573 MSN moesin P26041 MTCH2 mitochondrial carrier 2 A2AFW7 MTHFD1 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 1, methenyltetrahydrofolateQ922D8 cyclohydrolase, formyltetrahydrofolate synthetase MTM1 myotubularin 1 B1AW21 Mug1/Mug2 murinoglobulin 1 P28665 Mup1 (includes others)major urinary protein 1 A2AKN9 MURC muscle-related coiled-coil protein A2AMM0 MUT methylmalonyl CoA mutase P16332 MYBPC1 myosin binding protein C, slow type Q6P6L5 MYBPC2 myosin binding protein C, fast type Q5XKE0 MYBPH myosin binding protein H Q148P3 MYH1 myosin, heavy chain 1, skeletal muscle, adult Q5SX40 MYH2 myosin, heavy chain 2, skeletal muscle, adult Q5SX41 MYH3 myosin, heavy chain 3, skeletal muscle, embryonic P13541 MYH4 myosin, heavy chain 4, skeletal muscle Q5SX39 MYH7 myosin, heavy chain 7, cardiac muscle, beta B2RXX9 MYH8 myosin, heavy chain 8, skeletal muscle, perinatal P13542 MYH11 myosin, heavy chain 11, smooth muscle O08638 MYH13 myosin, heavy chain 13, skeletal muscle B1AR69 MYH14 myosin, heavy chain 14, non-muscle B3F3T1 MYH7B myosin, heavy chain 7B, cardiac muscle, beta A2AQP0 MYL1 myosin, light chain 1, alkali; skeletal, fast P05977-2 MYL2 myosin, light chain 2, regulatory, cardiac, slow P51667 MYL3 myosin, light chain 3, alkali; ventricular, skeletal, slow P09542 MYL4 myosin, light chain 4, alkali; atrial, embryonic A2A6Q8 MYL6 myosin, light chain 6, alkali, smooth muscle and non-muscle Q60605 MYL6B myosin, light chain 6B, alkali, smooth muscle and non-muscle Q8CI43 MYLK2 myosin light chain kinase 2 B2RXZ9 MYLPF myosin light chain, phosphorylatable, fast skeletal muscle P97457 MYO1C myosin IC Q9WTI7 MYOG myogenin (myogenic factor 4) P12979 MYOM1 myomesin 1, 185kDa Q62234-2 MYOM2 myomesin (M-protein) 2, 165kDa Q14BI5 MYOM3 myomesin family, member 3 A2ABU4 MYOT myotilin Q9JIF9 MYOZ1 myozenin 1 Q9JK37 MYOZ2 myozenin 2 Q9JJW5 MYOZ3 myozenin 3 Q8R4E4 Naca nascent polypeptide-associated complex alpha polypeptide P70670 NAMPT nicotinamide phosphoribosyltransferase Q3TLX1 NAP1L4 nucleosome assembly protein 1-like 4 A2RSB1 NARS asparaginyl-tRNA synthetase Q8BP47 NCEH1 neutral cholesterol ester hydrolase 1 Q8BLF1 NCL nucleolin P09405 Diabetes Page 54 of 165

ND4 NADH dehydrogenase, subunit 4 (complex I) P03911 ND5 NADH dehydrogenase, subunit 5 (complex I) Q9MD82 NDRG2 NDRG family member 2 Q9QYG0 NDUFA2 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2, 8kDa Q9CQ75 NDUFA4 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4, 9kDa Q62425 NDUFA5 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa Q9CPP6 NDUFA6 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 6, 14kDa Q9CQZ5 NDUFA12 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 Q7TMF3 NDUFA8 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8, 19kDa Q9DCJ5 NDUFA9 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 9, 39kDa Q6GTD3 NDUFA10 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 10, 42kDa Q99LC3 NDUFA11 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 11, 14.7kDaQ9D8B4 NDUFA7 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7, 14.5kDa Q9Z1P6 NDUFA13 NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 13 Q9ERS2 NDUFAF4 NADH dehydrogenase (ubiquinone) complex I, assembly factor 4 Q9D1H6 NDUFB3 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 3, 12kDa Q9D6H6 NDUFB11 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11, 17.3kDa B1AV40 NDUFB5 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5, 16kDa Q8BU20 NDUFB4 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 4, 15kDa Q4VAE8 NDUFB7 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7, 18kDa Q9CR61 NDUFB9 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9, 22kDa Q9CQJ8 NDUFB10 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 10, 22kDa Q9DCS9 NDUFB8 NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 8, 19kDa Q9D6J5 NDUFC2 NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2, 14.5kDaQ9CQ54 NDUFS1 NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzymeQ91VD9 Q reductase) NDUFS2 NADH dehydrogenase (ubiquinone) Fe-S protein 2, 49kDa (NADH-coenzymeQ91WD5 Q reductase) NDUFS3 NADH dehydrogenase (ubiquinone) Fe-S protein 3, 30kDa (NADH-coenzymeQ9DCT2 Q reductase) NDUFS4 NADH dehydrogenase (ubiquinone) Fe-S protein 4, 18kDa (NADH-coenzymeQ923F9 Q reductase) NDUFS5 NADH dehydrogenase (ubiquinone) Fe-S protein 5, 15kDa (NADH-coenzymeQ99LY9 Q reductase) NDUFS6 NADH dehydrogenase (ubiquinone) Fe-S protein 6, 13kDa (NADH-coenzymeP52503 Q reductase) NDUFS7 NADH dehydrogenase (ubiquinone) Fe-S protein 7, 20kDa (NADH-coenzymeQ9DC70 Q reductase) NDUFS8 NADH dehydrogenase (ubiquinone) Fe-S protein 8, 23kDa (NADH-coenzymeQ8K3J1 Q reductase) NDUFV1 NADH dehydrogenase (ubiquinone) flavoprotein 1, 51kDa Q91YT0 NDUFV2 NADH dehydrogenase (ubiquinone) flavoprotein 2, 24kDa Q9D6J6 NDUFV3 NADH dehydrogenase (ubiquinone) flavoprotein 3, 10kDa Q8BK30 Neb nebulin A2AQB2 NEFL neurofilament, light polypeptide Q05DD2 NEK7 NIMA (never in mitosis gene a)-related kinase 7 Q9ES74 NEXN nexilin (F actin binding protein) Q7TPW1 NID1 nidogen 1 Q3TKX9 NIN ninein (GSK3B interacting protein) Q674R4 NIT2 nitrilase family, member 2 Q9JHW2 NME1 NME/NM23 nucleoside diphosphate kinase 1 Q5NC81 NME2 NME/NM23 nucleoside diphosphate kinase 2 Q5NC82 NNT nicotinamide nucleotide transhydrogenase Q61941 NOL3 nucleolar protein 3 (apoptosis repressor with CARD domain) Q9D1X0 NOMO1 (includes others)NODAL modulator 1 Q6GQT9 NPEPPS aminopeptidase puromycin sensitive Q11011 NPLOC4 nuclear protein localization 4 homolog (S. cerevisiae) P60670 NPM1 nucleophosmin (nucleolar phosphoprotein B23, numatrin) Q61937 NQO2 NAD(P)H dehydrogenase, quinone 2 Q9JI75 NRAS neuroblastoma RAS viral (v-ras) oncogene homolog Q3TMF4 NRBP1 nuclear receptor binding protein 1 D3YUV1 NT5C3 5'-nucleotidase, cytosolic III Q9D020-1 NT5DC3 5'-nucleotidase domain containing 3 Q3UHB1 Page 55 of 165 Diabetes

NUDT2 nudix (nucleoside diphosphate linked moiety X)-type motif 2 P56380 OAT ornithine aminotransferase P29758 OBSCN obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF A2AAJ9 OCIAD2 OCIA domain containing 2 Q9D8W7 OGDH oxoglutarate (alpha-ketoglutarate) dehydrogenase (lipoamide) Q60597 OGN osteoglycin Q543C5 OLA1 Obg-like ATPase 1 Q3TJF2 OSBP oxysterol binding protein Q3B7Z2 OTUB1 OTU domain, ubiquitin aldehyde binding 1 Q7TQI3 OXCT1 3-oxoacid CoA transferase 1 Q9D0K2 OXSR1 oxidative-stress responsive 1 Q6ZPX7 P4HB prolyl 4-hydroxylase, beta polypeptide P09103 PA2G4 proliferation-associated 2G4, 38kDa D3YVH7 PABPC4 poly(A) binding protein, cytoplasmic 4 (inducible form) Q91YZ8 PACSIN3 protein kinase C and casein kinase substrate in neurons 3 Q543N7 PADI2 peptidyl arginine deiminase, type II Q08642 PAFAH1B1 platelet-activating factor acetylhydrolase 1b, regulatory subunit 1 (45kDa)P63005 PAICS phosphoribosylaminoimidazole carboxylase, phosphoribosylaminoimidazoleQ9CQ38 succinocarboxamide synthetase PANK4 pantothenate kinase 4 Q80YV4-2 PARK7 parkinson protein 7 Q99LX0 PBXIP1 pre-B-cell leukemia homeobox interacting protein 1 Q3TVI8 PC pyruvate carboxylase Q05920 PCBP1 poly(rC) binding protein 1 P60335 PCBP2 poly(rC) binding protein 2 B2M1R7 PCCA propionyl CoA carboxylase, alpha polypeptide Q3UGC8 PCCB propionyl CoA carboxylase, beta polypeptide A0PJE6 PCMT1 protein-L-isoaspartate (D-aspartate) O-methyltransferase P23506 PDHA1 pyruvate dehydrogenase (lipoamide) alpha 1 Q3UFJ3 PDHB pyruvate dehydrogenase (lipoamide) beta Q9D051 PDHX pyruvate dehydrogenase complex, component X Q8BKZ9 PDIA3 protein disulfide isomerase family A, member 3 P27773 PDK2 pyruvate dehydrogenase kinase, isozyme 2 Q8VC63 PDK4 pyruvate dehydrogenase kinase, isozyme 4 Q544J2 Pdlim3 PDZ and LIM domain 3 O70209 PDLIM5 PDZ and LIM domain 5 Q8CI51-2 PDLIM7 PDZ and LIM domain 7 (enigma) B8JJB5 PDP1 pyruvate dehyrogenase phosphatase catalytic subunit 1 A2AJP9 PDPR pyruvate dehydrogenase phosphatase regulatory subunit Q7TSQ8 PEA15 phosphoprotein enriched in astrocytes 15 Q62048 PEBP1 phosphatidylethanolamine binding protein 1 P70296 PFKFB1 6-phosphofructo-2-kinase/fructose-2,6-biphosphatase 1 A2AFM9 PFKM phosphofructokinase, muscle P47857 PFN1 profilin 1 P62962 Pfn2 profilin 2 Q9JJV2 PGAM1 phosphoglycerate mutase 1 (brain) Q9DBJ1 PGAM2 phosphoglycerate mutase 2 (muscle) Q5NCI4 PGD phosphogluconate dehydrogenase Q9DCD0 PGK1 phosphoglycerate kinase 1 P09411 PGLS 6-phosphogluconolactonase Q9CQ60 PGM1 phosphoglucomutase 1 Q3UGE3 PGP phosphoglycolate phosphatase Q8CHP8 PHB2 prohibitin 2 Q3V235 PHB prohibitin P67778 PHKA1 phosphorylase kinase, alpha 1 (muscle) A2AI87 PHKB phosphorylase kinase, beta Q7TSH2 Diabetes Page 56 of 165

PHKG1 phosphorylase kinase, gamma 1 (muscle) P07934 PHPT1 phosphohistidine phosphatase 1 Q9DAK9 PICALM phosphatidylinositol binding clathrin assembly protein Q7M6Y3 PITPNA phosphatidylinositol transfer protein, alpha P53810 Pkm pyruvate kinase, muscle P52480 PLAA phospholipase A2-activating protein P27612 PLCD4 phospholipase C, delta 4 Q8K3R3-2 PLEC plectin Q9QXS1 PLIN3 perilipin 3 Q9DBG5 PLIN4 perilipin 4 O88492-2 PLXNA4 plexin A4 Q80UG2 PMP2 peripheral myelin protein 2 P24526 PON3 paraoxonase 3 Q4FZK0 POSTN periostin, osteoblast specific factor Q62009 PPA1 pyrophosphatase (inorganic) 1 Q4FK49 PPFIA3 protein tyrosine phosphatase, receptor type, f polypeptide (PTPRF), interactingB8QI35 protein (liprin), alpha 3 PPIA peptidylprolyl isomerase A (cyclophilin A) P17742 PPIB peptidylprolyl isomerase B (cyclophilin B) Q9DCY1 PPIC peptidylprolyl isomerase C (cyclophilin C) Q3UC73 PPID peptidylprolyl isomerase D Q3UB60 PPP1CA protein phosphatase 1, catalytic subunit, alpha isozyme P62137 PPP1CB protein phosphatase 1, catalytic subunit, beta isozyme P62141 PPP2CA protein phosphatase 2, catalytic subunit, alpha isozyme P63330 PPP2R1A protein phosphatase 2, regulatory subunit A, alpha Q76MZ3 PPP2R2A protein phosphatase 2, regulatory subunit B, alpha Q6P1F6 PPP3CA protein phosphatase 3, catalytic subunit, alpha isozyme B2RRX2 PPP3R1 protein phosphatase 3, regulatory subunit B, alpha Q63810-2 PRDM16 PR domain containing 16 A2A930 PRDX1 peroxiredoxin 1 P35700 PRDX2 peroxiredoxin 2 Q61171 PRDX3 peroxiredoxin 3 P20108 PRDX5 peroxiredoxin 5 P99029 PRDX6 peroxiredoxin 6 O08709 PRELP proline/arginine-rich end leucine-rich repeat protein Q9JK53 PREP prolyl endopeptidase Q9QUR6 PRKAB2 protein kinase, AMP-activated, beta 2 non-catalytic subunit Q6PAM0 PRKACA protein kinase, cAMP-dependent, catalytic, alpha P05132-2 PRKACB protein kinase, cAMP-dependent, catalytic, beta P68181 PRKAG1 protein kinase, AMP-activated, gamma 1 non-catalytic subunit Q3TWR3 PRKAG3 protein kinase, AMP-activated, gamma 3 non-catalytic subunit Q8BGM7-2 PRKAR2A protein kinase, cAMP-dependent, regulatory, type II, alpha Q8K1M3 PRKCA protein kinase C, alpha Q4VA93 PRKDC protein kinase, DNA-activated, catalytic polypeptide P97313 PROSC proline synthetase co-transcribed homolog (bacterial) Q9Z2Y8 PRPH peripherin P15331-3 PRPS1 phosphoribosyl pyrophosphate synthetase 1 Q3TI27 PRUNE prune homolog (Drosophila) Q8BIW1 PRX periaxin O55103 PSMA1 proteasome (prosome, macropain) subunit, alpha type, 1 Q9R1P4 PSMA2 proteasome (prosome, macropain) subunit, alpha type, 2 P49722 PSMA3 proteasome (prosome, macropain) subunit, alpha type, 3 O70435 PSMA4 proteasome (prosome, macropain) subunit, alpha type, 4 Q9R1P0 PSMA5 proteasome (prosome, macropain) subunit, alpha type, 5 Q9Z2U1 PSMA6 proteasome (prosome, macropain) subunit, alpha type, 6 Q9QUM9 PSMA7 proteasome (prosome, macropain) subunit, alpha type, 7 Q9Z2U0 Page 57 of 165 Diabetes

PSMB1 proteasome (prosome, macropain) subunit, beta type, 1 Q6RI64 PSMB2 proteasome (prosome, macropain) subunit, beta type, 2 A2A882 PSMB3 proteasome (prosome, macropain) subunit, beta type, 3 Q545G0 PSMB4 proteasome (prosome, macropain) subunit, beta type, 4 P99026 PSMB5 proteasome (prosome, macropain) subunit, beta type, 5 O55234 PSMB6 proteasome (prosome, macropain) subunit, beta type, 6 Q60692 PSMB7 proteasome (prosome, macropain) subunit, beta type, 7 A2AQL6 PSMC1 proteasome (prosome, macropain) 26S subunit, ATPase, 1 Q542I9 PSMC2 proteasome (prosome, macropain) 26S subunit, ATPase, 2 Q3UIH5 PSMC3 proteasome (prosome, macropain) 26S subunit, ATPase, 3 A2AGN7 PSMC4 proteasome (prosome, macropain) 26S subunit, ATPase, 4 Q3TFA5 PSMC5 proteasome (prosome, macropain) 26S subunit, ATPase, 5 B1ARK2 PSMC6 proteasome (prosome, macropain) 26S subunit, ATPase, 6 Q14AQ1 PSMD1 proteasome (prosome, macropain) 26S subunit, non-ATPase, 1 Q3TXS7 PSMD2 proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 Q8VDM4 PSMD3 proteasome (prosome, macropain) 26S subunit, non-ATPase, 3 P14685 PSMD4 proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 O35226 PSMD6 proteasome (prosome, macropain) 26S subunit, non-ATPase, 6 Q99JI4 PSMD7 proteasome (prosome, macropain) 26S subunit, non-ATPase, 7 P26516 PSMD8 proteasome (prosome, macropain) 26S subunit, non-ATPase, 8 Q9CX56 PSMD11 proteasome (prosome, macropain) 26S subunit, non-ATPase, 11 Q8BG32 PSMD12 proteasome (prosome, macropain) 26S subunit, non-ATPase, 12 Q3TRH2 PSMD13 proteasome (prosome, macropain) 26S subunit, non-ATPase, 13 Q9WVJ2 PSMD14 proteasome (prosome, macropain) 26S subunit, non-ATPase, 14 A2AR77 PSME1 proteasome (prosome, macropain) activator subunit 1 (PA28 alpha) Q5HZK3 PTMS parathymosin Q66JR8 PTRF polymerase I and transcript release factor O54724 PTRH2 peptidyl-tRNA hydrolase 2 Q5SXR0 PVALB parvalbumin Q545M7 PYGB phosphorylase, glycogen; brain Q3UGT5 PYGM phosphorylase, glycogen, muscle Q9WUB3 Pzp pregnancy zone protein D3YW52 QDPR quinoid dihydropteridine reductase Q8BVI4 RAB10 RAB10, member RAS oncogene family P61027 RAB12 RAB12, member RAS oncogene family P35283 RAB14 RAB14, member RAS oncogene family A2AL34 RAB18 RAB18, member RAS oncogene family P35293 RAB21 RAB21, member RAS oncogene family Q0PD35 RAB35 RAB35, member RAS oncogene family Q6PHN9 RAB11A RAB11A, member RAS oncogene family Q0PD45 RAB11B RAB11B, member RAS oncogene family P46638 RAB1A RAB1A, member RAS oncogene family Q0PD67 RAB1B RAB1B, member RAS oncogene family Q9D1G1 RAB2A RAB2A, member RAS oncogene family P53994 RAB5A RAB5A, member RAS oncogene family Q3UCX7 Rab5b RAB5B, member RAS oncogene family B2RPS1 RAB6A RAB6A, member RAS oncogene family P35279 RAB7A RAB7A, member RAS oncogene family P51150 RAB8A RAB8A, member RAS oncogene family Q0PD50 RAC1 ras-related C3 botulinum toxin substrate 1 (rho family, small GTP bindingQ3TLP8 protein Rac1) RAD23A RAD23 homolog A (S. cerevisiae) B7ZNQ1 RALA v-ral simian leukemia viral oncogene homolog A (ras related) P63321 RAN RAN, member RAS oncogene family P62827 RAP1A RAP1A, member of RAS oncogene family C5H0E8 RARS arginyl-tRNA synthetase Q9D0I9 Diabetes Page 58 of 165

RBM3 RNA binding motif (RNP1, RRM) protein 3 Q545K5 RCN1 reticulocalbin 1, EF-hand calcium binding domain Q05186 RDX radixin Q3TH46 REEP5 receptor accessory protein 5 Q5QGU0 RHOA ras homolog family member A Q3TN61 RNH1 ribonuclease/angiogenin inhibitor 1 Q91VI7 RNPEP arginyl aminopeptidase (aminopeptidase B) Q8VCT3 RPL6 ribosomal protein L6 Q3UCH0 RPL8 ribosomal protein L8 P62918 RPL10A ribosomal protein L10a P53026 RPL11 ribosomal protein L11 A2BH07 RPL12 ribosomal protein L12 Q5BLK0 RPL13 ribosomal protein L13 P47963 RPL22 ribosomal protein L22 P67984 RPL23 ribosomal protein L23 P62830 RPL24 ribosomal protein L24 Q8BP67 RPL27 ribosomal protein L27 P61358 RPL30 ribosomal protein L30 Q497D7 RPL31 ribosomal protein L31 P62900 RPL38 ribosomal protein L38 Q9JJI8 RPL35A ribosomal protein L35a O55142 RPL13A ribosomal protein L13a Q3TDS9 RPL18A ribosomal protein L18a P62717 RPL9 ribosomal protein L9 P51410 RPL3L ribosomal protein L3-like Q9CQ09 RPL7A ribosomal protein L7a P12970 RPLP0 ribosomal protein, large, P0 Q5M8R8 RPLP1 ribosomal protein, large, P1 P47955 RPLP2 ribosomal protein, large, P2 P99027 RPN1 ribophorin I Q5RKP4 RPN2 ribophorin II A2ACG7 RPS10 ribosomal protein S10 Q3U9P0 RPS11 ribosomal protein S11 Q3UC02 RPS5 ribosomal protein S5 Q91V55 Rps17 ribosomal protein S17 Q3TK12 RPS8 ribosomal protein S8 P62242 Rps9 ribosomal protein S9 Q6ZWN5 RPS18 ribosomal protein S18 P62270 RPS19 ribosomal protein S19 Q9CZX8 RPS13 ribosomal protein S13 Q5BLJ7 RPS14 ribosomal protein S14 O70569 RPS16 ribosomal protein S16 A4FUS1 RPS2 ribosomal protein S2 P25444 Rps20 ribosomal protein S20 P60867 RPS3 ribosomal protein S3 Q5YLW3 RPS4Y1 ribosomal protein S4, Y-linked 1 P62702 RPS23 ribosomal protein S23 Q497E1 RPS26 ribosomal protein S26 P62855 RPS15A ribosomal protein S15a P62245 RPS3A ribosomal protein S3A P97351 RPS7 ribosomal protein S7 P62082 RPSA ribosomal protein SA B2CY77 RRAS2 related RAS viral (r-ras) oncogene homolog 2 P62071 RSU1 Ras suppressor protein 1 A2AUR7 RTN2 reticulon 2 O70622-2 Page 59 of 165 Diabetes

RTN4 reticulon 4 Q99P72-1 RYR1 ryanodine receptor 1 (skeletal) Q80X16 S100A1 S100 calcium binding protein A1 Q91V77 SAMM50 sorting and assembly machinery component 50 homolog (S. cerevisiae)Q8BGH2 SAR1A SAR1 homolog A (S. cerevisiae) Q99JZ4 SAR1B SAR1 homolog B (S. cerevisiae) Q0VGU0 SARS seryl-tRNA synthetase Q3U6F6 SCP2 sterol carrier protein 2 P32020-2 SCRN3 secernin 3 Q3TMH2 SDHA succinate dehydrogenase complex, subunit A, flavoprotein (Fp) Q8K2B3 SDHB succinate dehydrogenase complex, subunit B, iron sulfur (Ip) A2AA77 SDHC succinate dehydrogenase complex, subunit C, integral membrane protein,Q5XK33 15kDa SDPR serum deprivation response Q63918 SEC22B SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)O08547 SEC23A Sec23 homolog A (S. cerevisiae) Q01405 SEC61B Sec61 beta subunit Q9CQS8 SELENBP1 selenium binding protein 1 P17563 SEPSECS Sep (O-phosphoserine) tRNA:Sec (selenocysteine) tRNA synthase Q6P6M7 SEPT7 septin 7 Q3UNN1 SERBP1 SERPINE1 mRNA binding protein 1 Q9CY58 SERPINA1 serpin peptidase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin),Q00898 member 1 Serpina3k (includes others)serine (or cysteine) peptidase inhibitor, clade A, member 3K P07759 SERPINB6 serpin peptidase inhibitor, clade B (ovalbumin), member 6 Q60854 SERPINC1 serpin peptidase inhibitor, clade C (antithrombin), member 1 Q543J5 SERPINF1 serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epitheliumQ5ND38 derived factor), member 1 SERPINF2 serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epitheliumQ61247 derived factor), member 2 SERPINH1 serpin peptidase inhibitor, clade H (heat shock protein 47), member 1, Q3TJK3(collagen binding protein 1) SFPQ splicing factor proline/glutamine-rich Q8VIJ6 SGCD sarcoglycan, delta (35kDa dystrophin-associated glycoprotein) A2ACH6 SGCG sarcoglycan, gamma (35kDa dystrophin-associated glycoprotein) P82348 SH3BGR SH3 domain binding glutamic acid-rich protein Q9WUZ7 SLC16A3 solute carrier family 16, member 3 (monocarboxylic acid transporter 4) P57787 SLC25A3 solute carrier family 25 (mitochondrial carrier; phosphate carrier), memberQ3THU8 3 SLC25A4 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator),Q8BVI9 member 4 SLC25A5 solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator),P51881 member 5 SLC25A11 solute carrier family 25 (mitochondrial carrier; oxoglutarate carrier), memberQ5SX53 11 SLC25A12 solute carrier family 25 (aspartate/glutamate carrier), member 12 Q8BH59 SLC25A20 solute carrier family 25 (carnitine/acylcarnitine translocase), member 20Q7TPW6 SLC25A42 solute carrier family 25, member 42 Q8R0Y8 SLC27A1 solute carrier family 27 (fatty acid transporter), member 1 Q3TP13 SLC37A4 solute carrier family 37 (glucose-6-phosphate transporter), member 4 Q9Z295 SLC44A2 solute carrier family 44, member 2 Q8BY89 SLC4A1 solute carrier family 4, anion exchanger, member 1 (erythrocyte membraneP04919 protein band 3, Diego blood group) SMS spermine synthase P97355 SMYD1 SET and MYND domain containing 1 Q6DFW7 SMYD2 SET and MYND domain containing 2 Q8R5A0 SNRPD3 small nuclear ribonucleoprotein D3 polypeptide 18kDa P62320 SNTA1 syntrophin, alpha 1 Q3UVD6 SNX3 sorting nexin 3 Q78ZM0 SOD1 superoxide dismutase 1, soluble P08228 SOD2 superoxide dismutase 2, mitochondrial P09671 SPEG SPEG complex locus Q62407 SPOCK2 sparc/osteonectin, cwcv and kazal-like domains proteoglycan (testican)Q9ER58 2 SPR sepiapterin reductase (7,8-dihydrobiopterin:NADP+ oxidoreductase) Q64105 SPRYD4 SPRY domain containing 4 Q91WK1 Diabetes Page 60 of 165

SPTAN1 spectrin, alpha, non-erythrocytic 1 A3KGU5 SRL sarcalumenin Q7TQ48 SRPR signal recognition particle receptor (docking protein) Q9DBG7 SRPRB signal recognition particle receptor, B subunit P47758 SSBP1 single-stranded DNA binding protein 1, mitochondrial Q8R2K3 SSR4 signal sequence receptor, delta Q3TVJ8 ST13 suppression of tumorigenicity 13 (colon carcinoma) (Hsp70 interacting Q99L47protein) STAC3 SH3 and cysteine rich domain 3 Q8BZ71 STAT5B signal transducer and activator of transcription 5B P42232 STIM1 stromal interaction molecule 1 P70302 STIP1 stress-induced-phosphoprotein 1 Q60864 STK4 serine/threonine kinase 4 A2A5L8 STRAP serine/threonine kinase receptor associated protein Q9Z1Z2 SUCLA2 succinate-CoA ligase, ADP-forming, beta subunit Q3U6C7 SUCLG1 succinate-CoA ligase, alpha subunit Q9WUM5 Sumo2 SMT3 suppressor of mif two 3 homolog 2 (yeast) P61957 SYNCRIP synaptotagmin binding, cytoplasmic RNA interacting protein Q7TMK9 SYNM synemin, intermediate filament protein Q70IV5-2 SYNPO2 synaptopodin 2 B2RY03 SYNPO2L synaptopodin 2-like B2RQK7 SYPL1 synaptophysin-like 1 Q3TVX7 SYPL2 synaptophysin-like 2 A2AE45 TAGLN2 transgelin 2 Q9WVA4 TAGLN transgelin P37804 TALDO1 transaldolase 1 Q93092 TARS threonyl-tRNA synthetase Q3U630 TARSL2 threonyl-tRNA synthetase-like 2 Q8BLY2 TCAP titin-cap (telethonin) O70549 TCEB1 transcription elongation factor B (SIII), polypeptide 1 (15kDa, elongin C)P83940 TCP1 t-complex 1 P11983 TEC tec protein tyrosine kinase P24604-2 TECR trans-2,3-enoyl-CoA reductase Q52L67 TF transferrin Q921I1 TFAM transcription factor A, mitochondrial D3Z0F3 TFRC transferrin receptor (p90, CD71) Q62351 TGFBI transforming growth factor, beta-induced, 68kDa A1L353 TGM2 transglutaminase 2 (C polypeptide, protein-glutamine-gamma-glutamyltransferase)P21981 THBS4 thrombospondin 4 Q9Z1T2 THOP1 thimet oligopeptidase 1 Q8C1A5 TIMM44 translocase of inner mitochondrial membrane 44 homolog (yeast) Q2NLC5 TIMM50 translocase of inner mitochondrial membrane 50 homolog (S. cerevisiae)Q9D880 TKT transketolase P40142 TMED5 transmembrane emp24 protein transport domain containing 5 A2RS96 TMED9 transmembrane emp24 protein transport domain containing 9 Q3TFU8 TMED10 transmembrane emp24-like trafficking protein 10 (yeast) Q9D1D4 TMEM43 transmembrane protein 43 Q9DBS1 TMEM109 transmembrane protein 109 Q3UBX0 TMEM233 transmembrane protein 233 D3Z1U7 TMEM14C transmembrane protein 14C Q9CQN6 TMEM38A transmembrane protein 38A Q3TMP8 TMOD1 tropomodulin 1 Q3KP84 TMOD4 tropomodulin 4 (muscle) Q9JLH8 TNNC1 troponin C type 1 (slow) P19123 TNNC2 troponin C type 2 (fast) P20801 TNNI1 troponin I type 1 (skeletal, slow) Q9WUZ5 Page 61 of 165 Diabetes

TNNI2 troponin I type 2 (skeletal, fast) P13412 TNNT1 troponin T type 1 (skeletal, slow) B7ZNV4 TNNT3 troponin T type 3 (skeletal, fast) Q9QZ47-11 TNPO1 transportin 1 Q3TKD0 TNXB tenascin XB O35452 TPI1 triosephosphate isomerase 1 P17751 Tpm1 tropomyosin 1, alpha B7ZNL3 TPM2 tropomyosin 2 (beta) Q9D1R6 TPM3 tropomyosin 3 P21107 TPPP3 tubulin polymerization-promoting protein family member 3 Q9CRB6 TPT1 tumor protein, translationally-controlled 1 P63028 TRAP1 TNF receptor-associated protein 1 Q3TK29 TRDN triadin Q8VIN8 TRIM63 tripartite motif containing 63, E3 ubiquitin protein ligase Q38HM4 TRIM72 tripartite motif containing 72 Q1XH17 TRIP10 thyroid hormone receptor interactor 10 Q8CJ53 TST thiosulfate sulfurtransferase (rhodanese) D3YYT7 TTN titin A2ASS6 TTR transthyretin P07309 TUBA8 tubulin, alpha 8 Q9JJZ2 TUBA1A tubulin, alpha 1a P68369 TUBA3E tubulin, alpha 3e NP_033472 TUBA4A tubulin, alpha 4a P68368 TUBB3 tubulin, beta 3 class III Q9ERD7 TUBB tubulin, beta class I P99024 TUBB2A tubulin, beta 2A class IIa Q7TMM9 TUBB4B tubulin, beta 4B class IVb P68372 TUFM Tu translation elongation factor, mitochondrial Q8BFR5 TWF2 twinfilin, actin-binding protein, homolog 2 (Drosophila) Q9Z0P5 TXN thioredoxin P10639 TXNDC17 thioredoxin domain containing 17 Q9CQM5 TXNL1 thioredoxin-like 1 Q3U8R9 UACA uveal autoantigen with coiled-coil domains and ankyrin repeats Q8CIA8 UBA1 ubiquitin-like modifier activating enzyme 1 Q02053 UBAC1 UBA domain containing 1 A2AHB3 UBC ubiquitin C A5JUZ1 UBE2K ubiquitin-conjugating enzyme E2K P61087 UBE2L3 ubiquitin-conjugating enzyme E2L 3 P68037 UBE2M ubiquitin-conjugating enzyme E2M P61082 Ube2n ubiquitin-conjugating enzyme E2N P61089 UBE2V1 ubiquitin-conjugating enzyme E2 variant 1 B7ZBY7 UBE2V2 ubiquitin-conjugating enzyme E2 variant 2 Q4VBX4 UCHL3 ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) Q9JKB1 UGGT1 UDP-glucose glycoprotein glucosyltransferase 1 Q6P5E4 UGP2 UDP-glucose pyrophosphorylase 2 Q91ZJ5 UNC45B unc-45 homolog B (C. elegans) Q8CGY6-2 UQCR10 ubiquinol-cytochrome c reductase, complex III subunit X Q8R1I1 UQCRB ubiquinol-cytochrome c reductase binding protein Q9D855 UQCRC1 ubiquinol-cytochrome c reductase core protein I Q3TIC8 UQCRC2 ubiquinol-cytochrome c reductase core protein II Q9DB77 UQCRFS1 ubiquinol-cytochrome c reductase, Rieske iron-sulfur polypeptide 1 Q9CR68 UQCRQ ubiquinol-cytochrome c reductase, complex III subunit VII, 9.5kDa Q9CQ69 USMG5 up-regulated during skeletal muscle growth 5 homolog (mouse) Q78IK2 USP5 ubiquitin specific peptidase 5 (isopeptidase T) P56399 USP14 ubiquitin specific peptidase 14 (tRNA-guanine transglycosylase) Q9JMA1 Diabetes Page 62 of 165

USP35 ubiquitin specific peptidase 35 NP_001170883 VAMP3 vesicle-associated membrane protein 3 (cellubrevin) A2A895 VAPA VAMP (vesicle-associated membrane protein)-associated protein A, 33kDaQ9WV55 VAPB VAMP (vesicle-associated membrane protein)-associated protein B andQ9QY76 C VAT1 vesicle amine transport protein 1 homolog (T. californica) Q3TXD3 VCL vinculin Q64727 VCP valosin containing protein Q01853 VDAC1 voltage-dependent anion channel 1 Q60932-2 VDAC2 voltage-dependent anion channel 2 Q60930 VDAC3 voltage-dependent anion channel 3 Q5EBQ0 VIM vimentin Q3TWV0 VKORC1L1 vitamin K epoxide reductase complex, subunit 1-like 1 Q6TEK5 VMP1 vacuole membrane protein 1 Q99KU0 VPS35 vacuolar protein sorting 35 homolog (S. cerevisiae) Q3TJ43 VWA5A von Willebrand factor A domain containing 5A Q99KC8 WARS tryptophanyl-tRNA synthetase Q3U6U7 WDR1 WD repeat domain 1 Q3TE06 WFS1 Wolfram syndrome 1 (wolframin) Q3TDI2 XPNPEP1 X-prolyl aminopeptidase (aminopeptidase P) 1, soluble Q3TL27 YARS tyrosyl-tRNA synthetase Q91WQ3 YBX1 Y box binding protein 1 Q3UBT1 YWHAB tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,Q9CQV8 beta polypeptide YWHAE tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,Q5SS40 epsilon polypeptide YWHAG tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,A8IP69 gamma polypeptide YWHAH tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,P68510 eta polypeptide YWHAQ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,P68254 theta polypeptide YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein,P63101 zeta polypeptide ZBTB38 zinc finger and BTB domain containing 38 Q3LR78 ZFYVE16 zinc finger, FYVE domain containing 16 Q80U44 ZNF251 zinc finger protein 251 Q3USU9 Page 63 of 165 Diabetes

Log Ratio(STZ-I/ND) p-value(STZ-I/ND) Log Ratio(STZ+I/ND) p-value(STZ+I/ND)

-0.366 3.92E-01 -0.322 4.81E-01 -0.410 4.55E-01 -0.178 7.54E-01 0.216 8.25E-01 0.149 8.70E-01 -0.228 7.11E-01 -0.419 5.49E-01 -0.499 2.15E-01 -0.279 4.87E-01 -0.672 1.83E-42 -0.523 1.13E-27 -0.418 2.34E-02 -0.327 1.26E-01 -0.461 4.68E-19 -0.51 3.68E-23 -0.512 8.01E-13 -0.454 1.33E-13 -0.344 4.27E-01 0.091 8.47E-01 -0.243 7.92E-01 -0.206 8.15E-01 -0.246 2.22E-16 -0.301 4.44E-16 -0.440 7.89E-25 -0.295 1.12E-12 -2.660 1.46E-01 -2.175 2.16E-01 0.262 1.30E-01 0.078 6.45E-01 0.073 3.80E-08 0.05 1.44E-04 0.767 4.98E-01 -0.465 4.65E-02 -0.055 9.06E-01 0.374 5.03E-01 -0.450 5.05E-02 -0.258 1.49E-01 0.170 4.60E-01 -0.104 6.78E-01 -0.235 5.81E-19 -0.318 1.87E-42 -0.185 8.87E-01 -0.698 6.12E-01 0.241 1.82E-06 0.452 2.77E-30 0.089 8.17E-02 0.099 1.00E-01 0.348 7.32E-05 0.495 3.70E-13 0.409 2.13E-03 0.558 7.48E-06 -0.839 5.72E-06 -0.287 7.30E-02 -0.977 5.95E-27 -0.242 9.78E-03 -0.069 2.70E-03 0.244 7.01E-07 0.038 9.07E-01 -0.06 8.87E-01 -0.105 4.77E-01 -0.03 8.95E-01 0.045 7.97E-01 -0.071 7.42E-01 0.102 6.35E-01 -0.098 6.60E-01 0.051 8.38E-01 0.094 7.25E-01 0.285 3.60E-03 -0.288 3.22E-02 0.018 9.44E-01 -0.05 8.30E-01 0.131 9.71E-02 -0.068 3.55E-01 0.487 7.23E-02 0.468 1.10E-01 0.269 6.87E-02 -0.102 5.19E-01 -0.476 6.29E-02 -0.237 3.76E-01 0.552 4.40E-01 0.524 4.61E-01 0.123 4.01E-02 0.061 2.90E-01 0.235 1.24E-20 0.094 3.25E-03 -0.438 5.60E-01 -0.382 6.28E-01 -0.125 4.52E-02 -0.127 1.59E-01 -0.100 8.63E-01 -0.628 2.80E-01 0.075 2.28E-01 -0.106 1.46E-01 0.183 3.93E-01 0.04 8.35E-01 0.914 1.55E-06 0.495 1.67E-04 -0.320 4.91E-03 -0.191 8.47E-02 -0.477 7.14E-03 -0.061 7.37E-01 Diabetes Page 64 of 165

0.193 1.08E-09 0.016 5.81E-01 -0.387 6.04E-01 -0.107 9.03E-01 0.086 8.45E-01 0.073 8.70E-01 0.164 5.73E-07 -0.06 5.85E-02 -0.296 4.81E-02 -0.218 3.15E-01 -0.057 8.13E-01 -0.066 7.31E-01 -0.253 3.62E-01 -0.379 2.07E-01 -0.672 4.23E-18 -0.61 2.15E-35 -0.156 9.13E-03 -0.453 2.35E-13 0.211 6.22E-01 0.389 5.07E-01 0.364 2.88E-03 -0.113 9.73E-02 -0.016 9.63E-01 0.041 9.20E-01 0.187 4.16E-06 0.1 2.75E-04 0.212 2.09E-01 0.097 4.76E-01 -0.758 2.40E-01 -0.268 5.79E-01 0.070 4.65E-04 0.101 5.73E-07 0.139 5.83E-01 0.202 3.67E-01 -0.387 4.94E-01 -0.191 6.87E-01 0.224 4.28E-01 0.036 8.42E-01 0.170 6.59E-01 0.085 8.99E-01 0.279 3.61E-07 0.107 7.95E-02 0.161 4.84E-01 0.492 4.51E-01 0.266 9.90E-03 -0.056 5.07E-01 0.212 6.53E-27 0.192 4.75E-19 -0.075 7.37E-01 -0.284 4.55E-02 0.281 3.15E-02 0.407 1.09E-03 0.766 2.12E-07 -0.226 1.27E-01 -0.037 9.20E-01 -0.101 7.79E-01 0.401 1.98E-03 0.337 9.96E-03 0.368 1.04E-01 0.793 1.77E-01 0.310 2.03E-01 -0.13 5.55E-01 0.502 6.13E-11 0.346 3.36E-04 -0.419 7.02E-02 -0.294 1.71E-01 0.235 3.99E-01 0.258 3.49E-01 0.379 3.93E-01 -0.372 2.46E-01 -0.369 6.97E-01 0.238 7.63E-01 0.049 3.45E-01 0.54 2.47E-01 -0.271 5.27E-01 0.086 8.71E-01 0.036 6.33E-01 0.018 7.70E-01 0.167 1.42E-01 -0.018 8.89E-01 0.291 4.85E-01 -0.14 7.46E-01 -0.199 6.16E-01 -0.003 1.00E+00 0.404 4.25E-01 0.275 5.66E-01 -0.256 5.09E-01 -0.045 9.23E-01 -0.317 5.86E-01 -0.546 3.57E-01 -0.128 6.13E-01 -0.096 7.17E-01 0.074 8.10E-01 0.004 9.93E-01 0.119 2.90E-01 -0.188 1.60E-01 0.525 3.30E-05 0.353 6.05E-02 0.141 1.54E-01 0.106 3.36E-01 -0.096 8.96E-01 0.033 9.59E-01 0.153 1.51E-01 -0.078 3.58E-01 -0.013 9.28E-01 -0.131 4.67E-01 -0.447 7.51E-01 -0.103 9.43E-01 0.164 3.91E-01 -0.141 2.94E-01 Page 65 of 165 Diabetes

0.283 5.51E-09 -0.137 9.61E-05 -0.698 2.28E-03 -0.397 2.35E-02 0.546 6.78E-02 0.334 2.01E-01 0.217 1.24E-23 0.105 3.48E-10 0.238 3.77E-06 0.101 2.64E-02 -0.185 9.97E-08 -0.118 7.02E-05 -0.202 4.44E-16 -0.127 4.29E-07 -0.150 5.18E-05 -0.144 2.40E-06 -0.206 2.47E-01 -0.206 2.24E-01 -0.238 6.74E-08 -0.2 2.52E-06 -0.300 5.10E-12 -0.25 4.04E-11 -0.211 2.94E-04 -0.177 1.38E-03 -0.499 1.82E-01 -0.207 5.79E-01 -0.286 1.33E-04 -0.261 2.72E-05 -0.201 2.86E-05 -0.161 8.97E-05 0.040 9.08E-01 -0.11 7.97E-01 -0.289 5.33E-01 -0.036 9.41E-01 -0.053 9.46E-01 0.012 9.88E-01 0.248 6.33E-01 0.394 5.03E-01 0.160 4.25E-01 -0.203 3.65E-01 -0.218 7.83E-01 -0.567 4.10E-01 0.680 2.51E-03 0.625 7.38E-04 -0.239 9.24E-10 -0.178 1.16E-07 -0.068 6.62E-01 -0.101 5.23E-01 0.606 4.82E-01 -0.12 9.00E-01 -0.380 5.73E-01 -0.09 8.81E-01 0.286 2.08E-01 -0.064 7.88E-01 -0.217 6.72E-01 -0.097 8.70E-01 -0.425 1.14E-01 -0.451 1.13E-01 -0.263 3.55E-01 0.1 7.27E-01 0.499 2.45E-01 0.268 4.77E-01 0.178 5.49E-01 0.266 3.63E-01 -0.462 3.95E-01 -0.67 2.35E-01 -0.014 9.37E-01 -0.32 1.07E-01 -0.353 2.75E-02 -0.121 4.32E-01 0.033 8.43E-01 -0.098 5.91E-01 -0.233 2.43E-01 -0.276 2.83E-01 -0.177 4.07E-02 0.131 3.51E-02 -0.056 8.76E-01 0.042 9.23E-01 0.609 4.91E-01 -0.216 7.89E-01 -0.001 1.00E+00 -0.341 6.55E-01 -0.271 1.20E-01 -0.356 4.81E-02 0.536 1.06E-41 0.189 3.35E-13 0.127 5.81E-01 0.028 9.10E-01 0.060 2.62E-01 -0.085 1.41E-01 0.145 4.30E-05 -0.083 1.74E-02 0.120 2.75E-03 0.031 3.54E-01 0.084 7.07E-01 -0.092 6.80E-01 0.083 2.99E-01 0.065 7.12E-01 -0.097 1.83E-01 -0.046 5.84E-01 -0.050 9.33E-01 -0.155 7.94E-01 0.171 6.37E-02 0.018 8.53E-01 -0.109 2.62E-01 -0.144 1.18E-01 -0.069 7.24E-01 -0.149 5.50E-01 0.044 5.78E-01 0.107 3.29E-01 Diabetes Page 66 of 165

-0.071 9.04E-01 0.494 6.85E-01 -0.628 5.29E-02 -0.322 3.23E-01 0.110 5.00E-01 0.02 9.04E-01 0.366 3.04E-01 0.003 9.93E-01 -0.130 5.72E-02 -0.051 4.97E-01 -0.086 1.34E-02 -0.146 1.67E-03 0.060 7.85E-01 -0.088 7.01E-01 -0.106 8.79E-01 0.115 8.80E-01 0.282 5.61E-02 0.393 4.57E-02 -0.170 5.45E-01 -0.229 4.55E-01 0.707 5.61E-22 0.763 4.24E-23 0.615 2.00E-08 0.835 5.66E-12 -0.247 3.23E-01 -0.421 1.23E-01 0.446 1.94E-04 -0.086 7.21E-01 -0.284 2.19E-05 -0.244 7.45E-04 1.398 1.52E-09 0.163 2.86E-01 0.372 1.98E-02 -0.191 4.41E-01 0.371 9.37E-03 -0.109 4.32E-01 0.221 6.09E-01 -0.644 1.64E-01 -0.648 1.43E-01 -0.892 3.33E-02 -0.274 5.20E-01 -0.175 6.51E-01 0.102 8.08E-01 0.127 7.39E-01 -0.163 6.12E-02 0.109 6.36E-01 -0.245 4.39E-01 0.159 6.45E-01 -0.127 4.44E-01 -0.067 6.93E-01 -0.053 7.07E-01 -0.129 3.35E-01 -0.198 1.77E-01 0.135 5.69E-01 -0.182 5.46E-02 -0.184 8.03E-02 -0.112 1.25E-01 0.208 4.01E-01 -0.151 6.86E-01 -0.448 2.96E-01 0.729 3.20E-14 -0.261 1.87E-03 0.219 6.36E-01 0.015 9.26E-01 -0.208 6.58E-01 -0.301 7.26E-01 -0.108 8.30E-01 -0.329 5.59E-01 -0.347 3.91E-01 0.505 2.68E-01 0.374 2.66E-02 -0.252 2.43E-01 0.093 7.52E-01 -0.093 5.03E-01 -0.127 2.42E-05 -0.05 6.28E-02 -0.869 2.18E-01 0.71 2.87E-01 -0.315 2.00E-04 -0.231 2.99E-02 -0.130 2.64E-02 -0.145 3.75E-03 0.239 7.99E-02 0.027 7.96E-01 0.086 9.33E-09 0.069 7.28E-02 -0.646 4.50E-88 -0.379 2.59E-54 0.262 8.49E-01 0.803 5.38E-01 -0.141 8.32E-01 -0.111 8.90E-01 -0.120 3.54E-01 -0.218 1.44E-01 -0.406 3.54E-01 -0.573 2.29E-01 0.078 2.71E-01 -0.155 7.62E-02 0.069 9.06E-01 -0.09 8.62E-01 -0.570 3.57E-02 -0.553 2.03E-02 0.039 8.40E-01 -0.18 4.90E-01 -0.120 7.48E-01 -0.97 5.91E-03 -0.213 8.93E-02 0.527 1.19E-07 1.020 1.84E-03 1.612 1.46E-06 Page 67 of 165 Diabetes

1.632 1.14E-05 1.02 2.01E-04 0.275 3.24E-04 0.037 5.34E-01 0.287 1.66E-01 0.047 6.80E-01 0.278 2.22E-16 0.103 1.00E-02 0.496 6.50E-01 0.568 7.02E-02 0.122 8.76E-01 -0.329 6.81E-01 -0.048 8.18E-01 0.098 8.22E-01 -0.217 4.65E-01 -0.209 5.81E-01 0.120 9.05E-01 0.108 9.14E-01 0.034 9.81E-01 -0.053 9.66E-01 -0.148 4.94E-01 -0.261 2.39E-01 -0.221 5.64E-01 -0.163 7.01E-01 -0.217 3.53E-01 -0.323 1.43E-01 -0.437 1.22E-01 -0.258 3.95E-01 -0.609 2.70E-01 -0.696 1.92E-01 -0.284 4.02E-01 0.213 4.71E-01 0.253 6.36E-01 0.019 9.71E-01 -0.337 2.54E-09 -0.245 2.00E-05 0.049 9.53E-01 -0.042 9.56E-01 -0.392 2.58E-09 -0.269 1.75E-04 -0.331 1.62E-05 -0.213 3.32E-04 -0.029 9.46E-01 -0.175 7.07E-01 -0.321 2.58E-04 -0.211 4.70E-03 -0.386 1.33E-02 -0.267 4.68E-03 -0.374 1.50E-04 -0.256 4.37E-03 -0.344 5.00E-02 -0.239 1.81E-01 -0.398 3.26E-02 -0.317 7.32E-02 -0.777 1.93E-01 -0.412 4.64E-01 -0.793 3.15E-01 0.058 9.27E-01 -0.345 9.99E-05 -0.324 3.80E-04 -0.226 1.44E-10 -0.246 3.02E-12 -0.268 1.24E-10 -0.253 1.06E-06 0.241 7.77E-01 0.014 9.87E-01 0.111 5.01E-01 0.009 9.51E-01 -0.561 8.85E-13 -0.312 4.54E-12 -0.230 2.96E-01 -0.257 2.77E-01 -0.211 2.98E-10 -0.123 2.16E-04 0.149 4.83E-01 -0.181 4.30E-01 -0.137 1.31E-01 -0.208 5.61E-02 0.044 8.99E-01 -0.13 7.35E-01 0.243 7.00E-01 -0.421 9.95E-02 0.280 3.37E-01 0.104 8.38E-01 0.131 1.54E-01 0.033 7.47E-01 0.189 4.22E-01 0.108 5.10E-01 -0.125 8.10E-01 -0.11 8.29E-01 -0.425 4.67E-01 -0.339 5.68E-01 -0.253 8.82E-03 -0.241 4.85E-02 -0.173 7.26E-01 -0.204 7.03E-01 -0.365 1.25E-05 -0.266 1.88E-03 -0.259 7.75E-09 -0.229 5.12E-06 -0.419 3.91E-06 -0.17 9.78E-02 0.063 7.42E-01 -0.182 4.57E-01 -0.077 5.90E-01 -0.051 7.07E-01 0.513 2.11E-02 0.48 1.06E-02 -0.179 8.15E-01 -0.317 6.99E-01 Diabetes Page 68 of 165

-0.241 6.90E-01 -0.191 7.43E-01 0.061 8.95E-01 0.217 6.32E-01 -0.123 7.17E-01 -0.199 5.97E-01 0.393 4.69E-01 -0.081 5.41E-01 -0.088 5.25E-01 0.188 3.83E-01 0.115 4.84E-01 -0.139 5.54E-01 -0.296 2.26E-07 -0.327 3.11E-10 -0.602 1.26E-18 -0.092 2.30E-03 0.103 6.31E-01 -0.233 3.69E-01 -0.201 7.57E-01 -0.108 8.58E-01 0.160 4.57E-02 0.204 7.05E-03 0.409 5.24E-01 -0.218 7.08E-01 -0.251 3.64E-19 -0.257 6.76E-20 -0.114 1.58E-04 -0.127 8.09E-06 -0.318 1.05E-05 -0.295 2.81E-04 -0.205 3.26E-01 -0.39 4.19E-02 -0.068 3.41E-01 -0.23 3.37E-02 -0.235 7.78E-01 -0.901 3.28E-01 -0.272 6.51E-01 -0.248 7.01E-01 0.125 6.06E-01 0.143 5.80E-01 -0.397 3.45E-01 -0.413 2.98E-01 0.097 6.37E-01 -0.162 5.12E-01 0.267 4.49E-01 0.676 1.00E-01 0.243 7.19E-01 0.192 7.80E-01 0.037 8.64E-01 -0.078 7.66E-01 0.563 3.80E-01 -0.03 9.51E-01 -0.255 4.63E-01 -0.263 5.00E-01 -0.969 2.18E-01 -0.954 2.46E-01 0.092 5.03E-01 -0.162 9.79E-02 -0.178 4.60E-01 -0.364 1.09E-01 -0.087 8.89E-01 -0.243 7.13E-01 -0.210 4.10E-01 -0.123 5.87E-01 0.254 5.48E-01 -0.141 8.18E-01 0.291 1.79E-01 -0.613 6.59E-02 -0.310 7.98E-03 -0.292 1.21E-02 -0.289 6.83E-08 -0.268 2.37E-08 -0.125 4.14E-01 0.047 2.24E-01 -0.028 2.20E-01 0.022 3.17E-01 -0.353 4.73E-01 0.099 8.28E-01 -0.514 2.30E-02 -0.308 2.09E-01 -0.651 2.64E-14 -0.146 1.37E-02 -0.070 8.77E-01 -0.255 5.55E-01 0.317 7.83E-04 -0.356 1.17E-03 0.437 3.94E-02 0.102 6.41E-01 0.365 4.81E-01 -0.176 7.13E-01 0.056 8.54E-01 -0.015 9.57E-01 -0.005 9.67E-01 -0.028 7.75E-01 -0.095 4.25E-01 -0.135 2.80E-01 -0.313 6.52E-01 -0.129 8.60E-01 0.139 8.67E-02 -0.003 9.58E-01 0.051 4.49E-01 0.079 2.04E-01 -0.077 7.71E-01 -0.209 5.17E-01 -0.294 4.43E-01 -0.127 6.82E-01 0.035 5.46E-01 -0.103 9.39E-02 0.429 3.21E-01 0.772 1.22E-01 Page 69 of 165 Diabetes

-0.189 7.82E-01 0.254 7.21E-01 -0.249 9.63E-02 -0.367 4.75E-02 0.167 1.78E-08 -0.062 1.15E-02 0.121 3.18E-04 -0.265 6.22E-04 0.113 5.78E-13 -0.309 5.16E-25 -0.276 5.86E-01 0.227 6.87E-01 0.675 1.13E-01 -0.216 2.98E-01 -0.363 3.59E-05 -0.101 2.52E-01 0.349 5.04E-01 0.368 5.26E-01 -0.045 4.11E-01 -0.035 4.11E-01 -0.021 7.55E-01 -0.227 5.93E-02 -0.286 3.79E-10 -0.272 6.41E-30 -0.373 3.57E-14 -0.315 5.06E-18 -0.422 3.78E-08 -0.386 2.69E-07 -0.217 5.53E-01 -0.502 1.01E-01 0.524 6.91E-01 1.353 2.44E-01 0.290 1.56E-06 -0.398 1.48E-33 0.530 3.88E-26 -0.343 5.04E-18 -0.235 2.18E-01 -0.329 1.23E-01 0.219 3.62E-01 0.215 4.09E-01 0.075 8.92E-01 0.033 9.45E-01 0.161 7.11E-01 -0.729 3.64E-01 -0.252 4.73E-02 -0.199 1.32E-01 0.141 6.87E-01 0.161 6.89E-01 -0.437 1.28E-02 -0.366 3.45E-02 -0.228 4.72E-01 0.232 3.43E-01 -2.136 1.95E-07 -1.986 3.27E-06 0.431 1.80E-07 0.158 5.59E-02 -0.401 5.76E-01 -0.113 8.76E-01 -0.058 8.61E-01 -0.169 5.37E-01 -0.427 6.58E-02 -0.323 1.88E-01 -0.237 3.18E-04 0.097 2.30E-03 -0.226 9.59E-08 -0.255 2.50E-04 0.238 1.78E-01 0.05 7.22E-01 -0.115 5.46E-01 -0.111 5.49E-01 -0.019 9.49E-01 -0.163 5.13E-01 0.153 7.19E-01 0.1 8.33E-01 -0.050 1.41E-02 -0.087 2.36E-04 0.924 3.59E-05 0.876 4.06E-19 -0.125 4.33E-01 -0.053 7.15E-01 0.567 1.54E-04 -0.29 1.72E-02 -0.131 8.49E-02 0.192 3.91E-03 -0.577 2.51E-02 -0.049 6.60E-01 0.102 1.28E-14 0.073 2.24E-13 -0.274 4.02E-01 -0.371 2.43E-01 -0.083 2.09E-01 -0.203 5.61E-03 -0.128 5.73E-01 0.03 9.67E-01 -0.304 1.18E-04 -0.176 5.19E-02 -0.341 4.25E-01 -0.274 4.74E-01 -0.312 8.93E-02 0.161 3.99E-01 0.166 8.39E-02 0.111 4.49E-01 0.024 5.43E-01 -0.078 5.53E-02 -1.023 1.08E-01 -0.19 7.75E-01 0.082 1.22E-01 -0.087 1.15E-01 0.096 5.24E-01 -0.187 2.19E-01 Diabetes Page 70 of 165

-0.164 3.03E-01 -0.109 5.94E-01 -0.009 9.76E-01 -0.214 5.28E-01 0.206 2.44E-02 0.172 1.18E-01 1.434 2.30E-01 0.264 8.00E-01 0.024 8.25E-01 -0.24 4.31E-01 -0.377 6.90E-01 -0.236 7.11E-01 0.259 1.67E-02 0.24 1.67E-02 -0.247 3.40E-01 -0.317 2.21E-01 0.427 3.10E-01 0.094 8.27E-01 -0.035 8.42E-01 -0.268 2.34E-01 -0.293 2.60E-02 -0.23 5.31E-01 -0.316 1.05E-23 -0.217 6.27E-10 -0.377 1.09E-19 -0.251 9.69E-13 -0.242 5.11E-01 -0.391 3.85E-01 0.136 1.07E-13 0.094 3.82E-07 0.110 1.80E-02 0.225 3.45E-07 0.147 2.43E-01 -0.003 9.84E-01 0.145 4.28E-14 0.009 6.45E-01 0.122 7.21E-01 -0.27 5.45E-01 -0.187 6.73E-01 -0.009 9.83E-01 0.474 7.96E-02 -0.112 6.46E-01 0.278 2.69E-01 -0.141 7.10E-01 -0.195 7.56E-01 -0.136 7.63E-01 0.206 3.86E-01 0.157 4.68E-01 -0.395 3.11E-01 -0.062 8.67E-01 -0.084 8.95E-01 -0.115 8.84E-01 0.573 1.56E-02 0.592 2.39E-02 0.437 6.10E-01 -0.233 3.60E-01 -0.246 2.88E-01 -0.285 3.22E-01 0.521 4.71E-05 0.27 4.04E-02 0.071 7.82E-01 -0.16 5.11E-01 0.415 1.04E-03 0.201 1.32E-01 0.303 3.20E-07 0.149 1.24E-02 0.553 5.57E-02 -0.171 4.62E-01 0.269 3.99E-06 0.084 2.89E-01 0.335 3.70E-01 -0.164 4.78E-01 -0.047 6.54E-01 -0.099 3.57E-01 0.682 4.80E-03 0.058 8.23E-01 0.231 3.51E-01 0.066 7.76E-01 -0.334 8.71E-05 -0.361 2.42E-06 -0.213 1.58E-12 -0.255 6.85E-25 -0.162 2.05E-13 -0.235 8.49E-27 0.089 7.19E-01 -0.067 8.40E-01 -0.042 8.26E-01 -0.065 7.90E-01 0.177 2.99E-01 -0.444 8.65E-03 0.168 3.89E-06 -0.523 1.46E-14 0.431 7.41E-01 -3.605 1.55E-02 0.128 7.33E-01 -0.46 2.94E-01 0.668 1.66E-02 0.279 2.20E-01 0.085 3.46E-01 -0.034 7.47E-01 -0.380 4.83E-03 -0.445 9.23E-04 -0.255 1.71E-03 -0.179 4.16E-02 -0.634 1.68E-01 -0.452 2.95E-01 0.181 2.40E-01 0.018 8.68E-01 -0.187 6.24E-01 0.118 7.20E-01 Page 71 of 165 Diabetes

0.492 2.42E-01 -0.214 4.62E-01 0.375 1.47E-01 0.007 9.73E-01 0.212 1.39E-02 0.227 1.06E-02 0.247 4.86E-04 0.181 7.20E-02 0.312 1.24E-05 0.179 7.22E-03 0.217 8.25E-02 0.3 6.92E-02 0.226 2.34E-07 0.318 2.04E-08 -0.285 9.87E-02 0.082 3.91E-01 0.137 4.40E-01 -0.075 6.99E-01 0.215 5.25E-01 -0.086 7.44E-01 -0.067 7.70E-01 -0.231 2.78E-01 0.095 8.55E-01 0.363 5.48E-01 0.138 5.70E-01 0.115 6.41E-01 -0.087 2.81E-01 0.088 3.02E-01 -0.456 5.51E-01 -0.11 8.92E-01 -0.332 5.24E-01 -0.242 7.05E-01 -0.107 7.73E-01 0.359 7.63E-01 0.187 4.27E-01 0.296 2.46E-01 0.276 3.52E-03 0.343 1.66E-02 -0.119 7.55E-01 -0.037 9.36E-01 -0.233 8.26E-01 -0.087 9.05E-01 0.043 9.38E-01 -0.218 7.19E-01 -0.223 3.74E-01 -0.198 4.86E-01 -0.162 3.32E-03 -0.137 3.13E-02 -0.025 7.49E-01 -0.035 5.86E-01 -0.291 1.40E-13 -0.11 4.08E-04 -0.267 5.71E-02 -0.022 8.60E-01 -0.182 6.53E-02 -0.254 1.33E-02 0.015 7.84E-01 -0.033 6.42E-01 -0.423 9.34E-20 -0.265 8.48E-10 -0.249 4.13E-01 -0.088 5.40E-01 -0.001 9.60E-01 0.007 9.22E-01 -0.514 9.08E-13 -0.27 4.51E-04 -0.827 3.03E-12 -0.227 8.35E-02 -0.351 6.81E-01 -0.317 7.48E-01 -0.248 3.10E-18 -0.216 5.11E-13 -0.348 7.82E-04 -0.238 4.08E-02 -0.244 1.44E-01 -0.089 4.67E-01 -0.221 3.87E-01 -0.112 6.85E-01 -0.297 5.10E-01 -0.199 6.86E-01 0.187 6.81E-01 -0.272 5.58E-01 0.472 3.90E-19 -0.242 2.88E-13 -0.303 4.22E-15 -0.181 7.40E-09 -0.319 3.49E-24 -0.212 1.73E-11 -0.392 2.05E-10 -0.235 1.06E-03 -2.043 4.89E-03 -1.155 1.89E-01 -1.148 3.95E-05 -0.835 8.02E-03 -0.321 3.71E-39 -0.287 1.47E-31 0.014 9.69E-01 -0.168 6.80E-01 0.421 4.10E-01 0.164 8.01E-01 0.640 6.91E-01 -0.392 8.19E-01 -0.102 5.50E-01 -0.022 9.07E-01 0.027 9.59E-01 0.081 8.85E-01 0.210 4.04E-01 -0.21 3.84E-01 -0.254 5.25E-01 -0.217 6.12E-01 Diabetes Page 72 of 165

0.114 7.02E-01 -0.094 8.30E-01 -0.343 3.30E-03 0.173 3.40E-01 0.092 3.54E-01 -0.097 3.49E-01 -0.008 9.41E-01 0.13 2.01E-01 -0.352 5.33E-01 -0.269 6.41E-01 0.084 4.05E-01 0.062 6.51E-01 -0.207 1.47E-14 -0.1 2.99E-03 0.867 2.86E-13 0.794 6.45E-17 -0.916 1.79E-01 0.194 8.32E-01 0.558 4.86E-01 0.37 6.49E-01 -0.479 5.17E-03 -0.188 3.74E-01 -0.190 2.42E-01 -0.069 7.52E-01 0.082 4.21E-01 -0.107 9.39E-02 1.229 4.88E-01 1.373 2.52E-01 0.467 4.83E-01 0.362 5.77E-01 0.974 2.02E-01 -0.264 7.24E-01 -1.207 8.37E-02 0.328 6.31E-01 -0.193 9.96E-03 0.147 4.45E-01 -0.151 8.42E-01 -0.261 6.89E-01 -0.095 6.39E-01 0.422 6.30E-01 0.484 5.49E-01 0.084 9.29E-01 -0.363 6.90E-01 -0.196 7.89E-01 -0.140 2.99E-01 -0.1 5.93E-01 0.106 3.77E-03 -0.081 5.70E-01 0.097 6.79E-05 -0.047 1.12E-02 -0.919 6.83E-75 -0.51 1.41E-24 -0.500 9.38E-05 -0.402 1.28E-03 -0.085 2.24E-01 -0.251 1.32E-03 -0.386 2.20E-01 -0.304 3.25E-01 0.383 1.16E-10 0.176 2.47E-03 0.432 5.12E-01 -0.175 8.30E-01 -0.261 1.53E-01 -0.198 2.57E-01 -0.711 4.58E-04 -0.439 3.38E-02 -0.243 2.00E-01 -0.282 1.98E-01 -0.029 9.61E-01 0.06 9.29E-01 0.232 1.77E-04 -0.221 1.63E-04 0.632 5.16E-19 0.193 1.71E-02 0.159 1.95E-01 -0.18 2.56E-02 0.241 7.92E-02 0.078 5.84E-01 0.101 7.24E-01 0.125 6.88E-01 -0.032 9.49E-01 -0.384 5.05E-01 0.429 3.65E-01 -0.145 7.84E-01 0.084 8.27E-01 0.04 9.00E-01 0.016 9.57E-01 -0.155 6.14E-01 -0.322 7.25E-03 -0.273 6.74E-02 0.182 4.16E-01 -0.07 7.27E-01 -0.434 4.87E-01 -0.212 7.18E-01 -0.221 6.14E-01 0.036 9.41E-01 0.325 3.32E-01 0.163 6.58E-01 -1.234 6.44E-03 -0.165 6.54E-01 -0.922 9.27E-80 -0.329 2.58E-23 -0.663 5.39E-12 -1.263 2.82E-30 -0.201 6.86E-01 -0.089 8.49E-01 0.184 7.91E-01 0.095 9.13E-01 0.155 6.91E-03 -0.141 1.14E-02 Page 73 of 165 Diabetes

-0.198 9.90E-14 -0.152 4.98E-11 -0.082 8.94E-01 -0.184 7.79E-01 -0.095 1.67E-01 -0.347 3.94E-07 0.119 3.48E-01 -0.313 1.75E-02 0.012 9.85E-01 0.129 8.23E-01 0.349 1.67E-02 0.294 1.50E-01 -0.456 1.84E-02 -0.299 7.54E-02 -0.514 3.36E-06 -0.262 9.60E-03 0.088 3.38E-01 -0.213 9.32E-02 -0.185 7.14E-02 -0.169 2.22E-01 -0.338 1.65E-04 -0.109 1.66E-01 0.089 2.99E-01 0.086 3.27E-01 -0.107 8.01E-01 -0.244 5.86E-01 0.083 8.15E-01 0.028 9.50E-01 -0.010 9.90E-01 -0.632 4.63E-01 -0.423 2.78E-01 -0.189 6.64E-01 -5.141 1.62E-12 -2.066 2.16E-12 0.184 2.79E-02 0.175 2.24E-02 -0.328 6.09E-01 -0.442 4.31E-01 0.263 9.96E-17 0.192 2.22E-16 0.144 1.77E-06 -0.071 1.08E-05 0.256 1.44E-08 0.185 2.89E-05 0.378 1.01E-31 0.226 7.36E-11 0.329 1.26E-12 0.262 2.23E-08 0.349 5.73E-07 0.307 3.41E-06 0.408 2.72E-145 0.381 1.07E-98 0.459 4.22E-02 0.144 3.37E-01 0.352 6.62E-14 0.35 8.52E-19 0.491 1.37E-01 0.147 6.14E-01 0.391 1.21E-22 0.341 3.38E-14 0.343 5.65E-01 -0.083 8.76E-01 0.419 8.33E-03 0.321 6.20E-02 0.260 6.19E-18 0.254 1.65E-17 -0.897 2.20E-19 -0.511 3.80E-08 0.155 5.00E-01 -0.067 7.09E-01 0.243 2.76E-02 0.231 4.69E-02 0.272 3.90E-04 0.235 2.94E-02 0.693 1.36E-01 0.619 4.27E-01 0.324 7.11E-15 -0.078 1.13E-01 -0.055 1.74E-04 0.11 2.78E-02 0.567 5.34E-01 0.048 8.93E-01 -0.212 1.81E-02 -0.131 8.32E-02 0.077 1.59E-06 -0.064 3.56E-03 0.075 1.26E-04 -0.044 9.32E-03 -0.735 3.95E-02 -0.587 1.57E-02 -0.291 1.32E-09 -0.147 1.35E-03 0.053 4.55E-02 0.139 2.26E-04 0.505 3.18E-03 -0.494 8.23E-03 0.329 7.83E-02 0.167 3.17E-01 -0.260 9.81E-05 -0.136 3.09E-02 0.089 5.54E-01 -0.214 9.36E-03 -0.316 3.36E-03 -0.182 1.39E-01 0.111 4.37E-01 -0.117 5.09E-01 -0.727 1.05E-01 -0.496 2.03E-01 0.488 9.45E-02 0.363 2.22E-01 Diabetes Page 74 of 165

-0.331 1.02E-01 -0.187 2.76E-01 -0.447 2.08E-03 -0.216 1.69E-01 -0.367 3.45E-04 -0.056 6.39E-01 -0.485 8.38E-04 -0.281 2.05E-02 -0.214 6.85E-02 -0.172 1.24E-01 -0.414 2.97E-08 -0.296 1.82E-05 -0.371 5.98E-12 -0.319 4.36E-07 -0.375 1.74E-02 -0.15 3.58E-01 -0.363 1.32E-05 -0.256 1.12E-03 -0.435 1.64E-07 -0.317 3.91E-06 -0.334 4.89E-09 -0.226 2.08E-03 -0.645 7.03E-02 -0.317 2.12E-01 -0.432 4.73E-02 -0.285 2.06E-01 -0.367 3.18E-05 -0.213 2.33E-03 -0.484 3.76E-01 -0.549 3.43E-01 -0.432 1.75E-03 -0.311 2.01E-02 -0.521 3.94E-02 -0.275 2.69E-01 -0.332 4.44E-10 -0.25 1.84E-05 -0.395 1.37E-02 -0.315 5.56E-02 -0.581 1.63E-02 -0.418 1.29E-01 -0.479 2.63E-01 -0.312 4.85E-01 -0.244 1.75E-01 -0.203 3.14E-01 -0.301 3.92E-02 -0.218 1.03E-01 -0.267 4.83E-02 -0.187 2.20E-01 -0.333 2.00E-15 -0.221 1.84E-10 -0.327 2.91E-09 -0.248 5.88E-05 -0.399 2.91E-02 -0.277 7.72E-02 -0.312 2.96E-05 -0.201 3.51E-03 -0.415 2.75E-03 -0.319 1.54E-02 -0.418 1.41E-02 -0.327 5.90E-02 -0.635 9.01E-02 -0.433 2.40E-01 -0.311 2.05E-01 -0.234 3.05E-01 -0.325 9.28E-14 -0.206 9.99E-06 -0.410 1.81E-02 -0.231 1.81E-01 -0.353 6.39E-01 -0.138 8.70E-01 -0.144 4.89E-10 -0.125 2.40E-10 -0.798 1.43E-11 -1.239 5.50E-24 0.097 8.55E-01 0.189 6.48E-01 -0.502 7.02E-01 -0.462 8.19E-01 0.437 1.19E-01 0.25 4.39E-01 0.132 7.60E-01 -0.037 9.26E-01 0.049 8.40E-01 -0.288 3.66E-01 -0.323 1.72E-01 -0.382 9.61E-02 0.109 1.32E-04 0.053 4.30E-02 0.376 3.83E-04 0.096 3.49E-01 -0.160 6.84E-01 -0.3 5.06E-01 -0.300 6.38E-01 -0.266 6.91E-01 -0.089 2.62E-01 -0.199 5.33E-02 -0.228 2.02E-01 -0.308 1.35E-01 -0.033 9.42E-01 -0.431 3.54E-01 -0.169 3.82E-01 -0.159 5.30E-01 0.066 9.05E-01 -0.118 8.01E-01 -0.424 5.48E-01 -0.171 8.39E-01 0.208 5.91E-02 -0.33 9.88E-03 -0.432 3.66E-01 -0.478 3.45E-01 Page 75 of 165 Diabetes

-0.138 9.19E-01 -0.537 6.74E-01 -0.034 7.28E-01 0.125 4.43E-01 -0.257 1.30E-02 -0.122 3.09E-01 -0.414 3.74E-01 -0.29 5.30E-01 -0.215 6.74E-08 -0.212 1.04E-08 0.490 8.60E-04 0.435 6.39E-06 0.108 3.94E-01 -0.089 3.76E-01 -0.453 6.61E-02 0.088 5.46E-01 -0.196 2.92E-01 -0.189 3.75E-01 -0.520 1.88E-21 -0.212 2.46E-06 -0.048 6.67E-01 -0.182 6.74E-02 -0.015 7.49E-01 0.016 8.15E-01 0.177 6.80E-01 0.11 7.81E-01 -0.561 1.84E-01 -0.227 5.80E-01 0.167 6.77E-01 0.151 7.05E-01 0.268 8.94E-04 0.197 3.92E-02 0.150 6.98E-01 -0.128 4.81E-01 -0.166 3.27E-01 -0.158 2.12E-01 -0.385 4.70E-01 -0.521 3.31E-01 0.218 2.08E-05 0.016 6.19E-01 0.064 5.53E-01 -0.105 3.42E-01 -0.287 1.16E-01 -0.503 2.18E-02 0.137 7.65E-01 -0.096 7.13E-01 0.040 9.11E-01 -0.021 9.52E-01 -0.337 3.82E-01 -0.274 4.76E-01 -0.252 7.34E-02 -0.113 4.89E-01 0.268 2.30E-01 -0.108 2.79E-01 -0.392 3.49E-04 -0.347 2.23E-03 -0.233 2.71E-06 -0.189 2.45E-05 -0.304 4.41E-09 -0.26 4.91E-07 -0.122 2.55E-01 0.048 5.86E-01 -0.138 7.10E-01 -0.146 5.98E-01 3.148 9.76E-05 -0.75 1.62E-01 0.221 4.67E-01 -0.114 3.86E-01 0.048 2.69E-01 -0.123 4.39E-05 0.221 2.08E-05 0.02 6.89E-01 -0.139 7.55E-01 0.244 5.85E-01 -0.412 2.06E-10 -0.283 2.42E-06 -0.094 9.33E-01 -0.216 8.33E-01 0.139 4.10E-02 -0.057 3.96E-01 -0.394 1.98E-01 0.119 6.67E-01 0.072 2.46E-04 0.175 5.47E-14 0.207 1.52E-07 -0.036 5.10E-01 0.156 9.00E-02 -0.097 2.86E-01 0.089 7.79E-01 -0.228 5.79E-01 0.085 2.50E-06 -0.041 1.85E-01 0.254 3.74E-01 -0.277 2.84E-01 0.242 2.44E-15 0.088 1.15E-04 0.352 1.37E-01 -0.183 1.89E-01 0.205 9.24E-09 -0.098 3.43E-05 0.152 2.21E-01 -0.113 2.96E-01 -0.326 2.32E-01 -0.183 5.18E-01 -0.248 1.21E-04 -0.217 2.68E-04 0.084 1.77E-01 0.146 7.13E-04 -0.053 3.65E-01 -0.084 1.67E-01 Diabetes Page 76 of 165

-0.083 2.76E-01 -0.111 1.01E-01 0.187 3.33E-01 -0.164 6.79E-01 -0.033 9.60E-01 -0.235 7.32E-01 0.145 5.49E-01 0.167 4.79E-01 0.097 6.79E-05 0.022 2.50E-01 0.134 3.36E-01 -0.059 6.68E-01 0.249 3.69E-01 0.073 8.83E-01 -0.327 1.00E-08 -0.275 1.77E-05 -0.280 6.81E-01 -0.357 6.75E-01 0.357 1.18E-01 0.426 8.89E-02 0.546 9.94E-03 0.227 4.10E-01 -1.433 2.77E-01 -0.851 5.65E-01 -0.213 7.35E-01 -0.282 6.41E-01 -0.115 6.87E-01 -0.053 8.62E-01 -0.384 1.72E-01 -0.252 5.47E-01 0.364 9.92E-02 0.141 5.73E-01 0.226 6.77E-03 -0.058 2.64E-01 -0.194 3.87E-01 -0.079 7.18E-01 -0.303 3.03E-01 0.036 8.91E-01 -0.316 7.24E-01 0.146 8.74E-01 -0.124 1.96E-01 0.065 4.42E-01 -0.191 1.38E-02 -0.203 9.38E-02 -0.158 6.95E-01 -0.239 5.59E-01 -0.073 1.20E-01 -0.142 7.20E-03 0.046 4.57E-01 -0.126 7.19E-02 0.199 2.45E-01 0.062 7.72E-01 0.001 9.93E-01 -0.013 9.78E-01 -0.021 7.53E-01 0.041 6.20E-01 0.136 8.47E-03 -0.15 6.46E-06 0.085 8.59E-03 -0.104 5.79E-03 -0.108 8.28E-02 -0.127 4.56E-02 -0.299 4.84E-08 -0.258 5.10E-06 -0.164 6.30E-01 -0.246 4.53E-01 0.557 5.77E-14 0.288 2.59E-06 -0.075 6.66E-01 -0.141 4.61E-01 -0.362 1.99E-01 -0.036 8.99E-01 0.282 3.75E-01 -0.098 3.98E-01 0.292 2.33E-01 0.066 7.32E-01 0.247 9.29E-02 0.091 5.45E-01 -0.539 4.16E-01 0.042 9.46E-01 0.186 6.19E-02 -0.153 2.02E-02 0.045 9.39E-01 -0.065 9.11E-01 0.020 8.82E-01 0.038 7.88E-01 -0.328 2.98E-02 -0.227 1.72E-01 -0.598 6.17E-01 0.053 9.60E-01 0.325 1.92E-01 0.31 2.18E-01 0.142 3.18E-01 -0.223 1.92E-01 -0.595 1.18E-01 -0.746 1.03E-01 0.222 5.05E-01 0.052 8.86E-01 0.192 8.01E-02 0.107 3.26E-01 0.309 8.66E-01 -0.047 8.97E-01 0.178 2.35E-01 -0.395 1.51E-01 0.342 1.05E-06 -0.16 2.37E-02 -0.071 5.46E-01 -0.171 2.02E-01 0.195 2.72E-01 -0.103 3.06E-01 Page 77 of 165 Diabetes

0.046 8.37E-01 -0.156 4.46E-01 -0.039 8.76E-01 -0.185 5.35E-01 -0.115 3.11E-01 -0.296 4.59E-03 0.047 8.91E-01 -0.18 2.61E-01 -0.111 4.10E-01 -0.248 1.27E-01 0.260 6.05E-01 0.316 5.12E-01 0.150 4.98E-01 -0.295 6.65E-02 0.073 7.87E-01 -0.057 8.47E-01 0.054 6.90E-01 0.206 6.91E-01 0.138 5.70E-01 -0.161 2.67E-01 0.077 3.90E-01 -0.127 7.16E-02 0.228 5.51E-01 -0.12 4.91E-01 0.105 5.53E-01 0.07 7.48E-01 0.210 4.52E-01 0.047 8.93E-01 0.113 1.57E-01 -0.266 1.37E-01 0.087 5.01E-01 -0.094 5.44E-01 0.217 6.31E-01 0.206 7.20E-01 0.177 8.30E-01 0.061 9.40E-01 -0.094 8.99E-01 -0.099 9.11E-01 0.192 2.85E-01 -0.195 3.38E-01 0.198 1.65E-01 -0.151 1.47E-01 -0.049 6.84E-01 -0.172 2.44E-01 -0.087 6.76E-01 -0.127 5.11E-01 0.032 9.37E-01 -0.223 5.46E-01 -0.145 7.93E-01 -0.178 7.51E-01 0.053 9.29E-01 0.062 9.18E-01 0.247 1.31E-01 0.066 8.32E-01 0.127 6.20E-01 0.152 7.83E-01 0.215 1.21E-20 0.058 5.76E-03 0.285 8.46E-07 0.005 8.82E-01 0.256 1.11E-15 0.04 6.89E-04 -0.447 2.14E-09 -0.131 1.74E-01 0.118 6.34E-01 -0.208 4.51E-01 -0.212 9.05E-02 -0.167 2.17E-01 -0.239 8.47E-01 -0.357 7.70E-01 0.043 9.05E-01 -0.408 3.21E-01 -0.056 7.14E-01 0.273 1.73E-01 -0.013 9.84E-01 0.33 6.33E-01 0.431 4.91E-01 0.652 3.59E-01 0.174 5.99E-01 0.104 7.17E-01 0.050 5.16E-01 -0.124 2.03E-01 -0.213 1.58E-01 -0.137 4.17E-01 -0.105 8.31E-01 0.147 7.14E-01 0.124 2.10E-01 0.091 5.25E-01 0.133 4.50E-01 0.025 9.26E-01 -0.007 9.78E-01 -0.014 9.75E-01 0.183 4.39E-01 -0.368 4.41E-01 -0.031 7.89E-01 0.207 1.40E-01 -0.148 6.28E-01 -0.238 5.31E-01 0.292 2.35E-01 -0.231 3.65E-01 0.217 6.51E-01 0.201 5.97E-01 0.100 8.09E-01 -0.121 7.79E-01 0.111 5.08E-01 0.067 6.34E-01 0.216 1.41E-01 -0.178 2.41E-01 -0.274 2.80E-01 0.047 7.42E-01 Diabetes Page 78 of 165

-0.139 8.01E-01 -0.051 9.24E-01 0.286 1.11E-01 0.183 3.71E-01 0.126 3.42E-01 0.208 1.31E-01 0.158 1.34E-01 -0.123 2.76E-01 -0.140 4.02E-01 -0.152 4.53E-01 -0.036 6.49E-01 -0.109 1.82E-01 0.510 4.30E-01 -0.354 3.70E-01 -1.064 1.18E-01 -0.257 7.49E-01 -0.360 4.19E-01 -0.351 4.41E-01 -0.694 1.90E-05 0.067 7.84E-01 -0.643 1.04E-05 -0.083 4.46E-01 -0.573 1.15E-03 0.055 6.71E-01 0.570 1.36E-02 0.416 1.07E-01 -0.507 7.57E-02 0.095 7.69E-01 -0.382 9.80E-03 0.124 2.91E-01 -0.553 2.51E-01 -0.34 5.06E-01 -0.678 9.54E-02 0.122 6.91E-01 -0.320 7.37E-01 0.336 6.38E-01 -0.614 1.51E-01 0.083 8.10E-01 -0.062 7.50E-01 0.054 7.88E-01 -0.701 3.40E-03 0.084 7.62E-01 -0.614 2.65E-01 -0.112 8.49E-01 -0.295 5.99E-01 -0.053 9.24E-01 -0.719 5.54E-04 0.094 5.84E-01 -0.136 6.26E-01 -0.084 7.99E-01 -0.381 4.79E-01 -0.491 3.22E-01 -0.674 5.75E-10 -0.118 6.08E-02 -0.273 5.80E-01 -0.45 6.61E-01 -0.234 1.26E-03 0.255 4.48E-01 -0.041 5.61E-01 -0.078 2.45E-01 -0.048 7.06E-01 0.08 6.76E-01 -0.492 3.50E-02 0.084 6.83E-01 -0.461 2.23E-02 0.262 1.78E-01 -0.482 1.59E-01 0.194 3.15E-01 -0.623 7.57E-03 -0.005 9.68E-01 -0.470 4.40E-01 -0.146 8.24E-01 -0.905 2.29E-01 -0.635 4.43E-01 -0.328 1.12E-02 0.058 7.56E-01 -0.514 9.85E-04 0.058 6.93E-01 -0.437 1.32E-01 0.155 5.07E-01 -0.511 3.31E-01 -0.043 9.37E-01 -0.558 6.44E-02 0.101 6.50E-01 -0.583 5.30E-04 -0.252 1.02E-01 -0.530 1.54E-02 0.067 8.33E-01 -0.544 3.76E-04 0.256 1.13E-01 -0.607 5.27E-03 0.356 1.49E-01 -0.708 2.38E-01 0.145 8.03E-01 -0.739 2.35E-01 -0.146 6.97E-01 -0.373 8.03E-02 0.132 4.98E-01 -0.804 1.03E-01 -0.126 7.60E-01 -0.197 2.90E-02 -0.022 8.36E-01 -0.605 1.65E-05 -0.112 4.52E-01 0.291 4.98E-01 -0.235 4.81E-01 0.049 7.79E-01 -0.101 7.59E-01 0.229 5.55E-05 0.068 9.95E-02 Page 79 of 165 Diabetes

0.210 1.17E-08 0.031 3.60E-01 0.157 3.12E-04 -0.092 6.04E-03 -0.210 3.29E-01 -0.213 3.10E-01 -0.229 3.70E-03 -0.129 4.73E-02 -0.042 7.47E-01 -0.148 3.71E-01 0.050 4.43E-01 0.157 1.14E-01 -0.514 9.93E-02 -0.324 4.25E-01 0.847 2.30E-01 0.189 7.54E-01 0.162 1.15E-01 -0.109 3.61E-01 -0.298 6.15E-21 -0.197 4.23E-12 -0.302 1.42E-09 -0.167 3.55E-04 -0.522 3.18E-03 -0.378 2.13E-02 0.331 9.38E-02 -0.299 9.65E-02 -0.184 6.37E-01 -0.223 5.93E-01 0.069 9.24E-01 0.079 9.12E-01 -0.182 5.67E-01 -0.077 8.37E-01 0.150 3.23E-01 0.271 5.37E-02 -0.111 3.95E-01 -0.096 4.28E-01 -0.376 6.34E-01 -0.263 7.67E-01 -0.494 5.91E-03 -0.21 2.34E-01 -0.585 1.22E-17 -0.593 9.63E-12 -1.350 1.45E-01 -0.564 5.27E-01 0.008 8.37E-01 -0.283 5.51E-09 -0.419 1.92E-01 -0.793 2.67E-02 -0.143 1.35E-01 0.791 8.71E-17 0.050 9.55E-01 0.327 7.24E-01 -1.634 2.72E-04 0.527 2.84E-01 -0.070 7.88E-01 -0.05 8.49E-01 0.005 9.83E-01 -0.101 7.64E-01 0.471 4.38E-01 -0.498 3.64E-01 0.113 3.52E-01 -0.021 8.52E-01 0.226 1.27E-01 0.43 2.71E-03 -0.348 8.56E-17 -0.248 3.02E-12 -0.233 1.03E-04 -0.138 4.31E-03 -0.209 4.86E-05 -0.149 6.23E-04 -0.388 7.78E-10 -0.22 2.46E-04 -0.176 8.52E-19 -0.126 5.96E-12 -0.326 7.03E-01 -0.382 7.27E-01 -0.288 4.87E-01 -0.47 4.88E-01 0.413 2.03E-03 -0.387 1.24E-02 0.137 6.79E-01 -0.102 7.79E-01 0.033 9.04E-01 -0.232 3.42E-01 -0.307 7.37E-01 -0.351 7.40E-01 0.118 3.09E-01 -0.208 2.04E-01 0.079 3.85E-02 0.012 7.94E-01 -0.067 9.08E-01 -0.14 8.12E-01 -0.083 8.71E-01 -0.134 7.99E-01 0.055 7.59E-01 -0.123 3.67E-01 0.082 9.05E-01 -0.142 8.47E-01 0.213 9.17E-07 -0.118 1.99E-02 -0.305 8.30E-07 -0.173 6.32E-04 -0.019 9.42E-01 -0.105 7.38E-01 0.263 3.59E-01 0.386 2.22E-01 0.193 2.00E-01 -0.113 4.65E-01 -0.329 1.63E-01 -0.236 3.35E-01 Diabetes Page 80 of 165

-0.276 1.90E-01 -0.395 1.60E-01 0.237 1.18E-22 0.023 2.50E-01 0.254 8.12E-01 -0.143 6.73E-01 0.722 5.37E-01 0.726 4.53E-01 0.057 9.29E-01 0.11 8.66E-01 -0.117 7.65E-01 0.197 6.31E-01 -0.150 4.40E-01 -0.321 9.31E-02 0.092 5.14E-01 0.162 2.87E-01 0.112 4.68E-01 -0.09 6.16E-01 -0.195 4.82E-01 -0.082 8.13E-01 -0.186 5.17E-03 -0.184 1.72E-02 -0.023 9.17E-01 0.006 9.75E-01 -0.189 6.14E-01 -0.251 4.90E-01 -0.240 3.22E-11 -0.186 6.31E-10 -0.246 2.09E-11 -0.214 1.43E-07 0.213 7.45E-01 -0.03 9.66E-01 -0.134 3.64E-01 -0.078 6.56E-01 -0.333 1.26E-01 -0.133 5.33E-01 -0.305 2.28E-02 0.147 1.42E-01 -0.193 5.24E-01 -0.19 5.26E-01 -0.014 8.92E-01 -0.268 1.21E-01 0.335 8.71E-05 0.089 3.19E-01 -0.257 6.17E-01 -0.299 6.02E-01 0.397 3.40E-02 -0.266 2.93E-04 0.049 5.23E-01 -0.091 3.62E-01 0.077 9.31E-01 0.406 6.43E-01 -0.415 3.66E-06 -0.167 4.62E-02 0.056 7.47E-01 -0.24 2.41E-01 0.064 8.35E-01 0.086 7.00E-01 -0.181 1.59E-01 -0.127 3.08E-01 0.181 1.50E-01 0.12 2.23E-01 0.158 3.75E-01 -0.095 5.76E-01 -0.111 3.41E-02 -0.123 2.50E-02 0.009 9.90E-01 -0.047 9.55E-01 -2.132 2.23E-03 -0.024 9.45E-01 0.333 2.10E-05 0.275 1.64E-04 0.378 2.34E-01 -0.05 7.59E-01 1.041 2.59E-01 0.689 8.09E-03 -0.066 5.57E-01 -0.143 1.79E-01 -1.050 6.01E-01 -0.658 7.25E-01 -0.409 3.39E-01 -0.183 6.66E-01 -0.651 1.13E-05 -0.807 5.21E-08 -0.018 9.77E-01 0.035 9.62E-01 0.346 5.74E-01 0.061 9.27E-01 0.139 4.12E-01 0.11 5.62E-01 0.410 7.02E-01 0.23 8.50E-01 0.034 8.70E-01 0.076 5.81E-01 0.320 5.74E-01 0.007 9.91E-01 -0.194 5.41E-01 -0.08 8.15E-01 0.191 4.83E-02 -0.067 2.32E-01 -0.256 3.02E-01 0.794 6.51E-02 0.349 2.60E-04 0.468 1.19E-06 -0.616 2.12E-06 -0.702 5.26E-10 0.263 9.55E-15 0.391 1.53E-31 -0.605 2.25E-01 -0.434 3.56E-01 Page 81 of 165 Diabetes

0.210 8.44E-15 0.409 1.28E-48 0.983 2.28E-05 0.463 3.78E-02 0.290 2.78E-21 0.488 2.31E-59 -0.039 8.74E-01 -0.088 7.27E-01 0.121 8.65E-01 -0.009 9.90E-01 0.172 3.86E-18 0.018 1.34E-01 0.356 1.55E-07 0.595 2.00E-15 0.450 1.55E-04 0.673 2.73E-14 0.570 1.63E-02 0.648 1.82E-02 -0.329 1.37E-01 -0.162 4.28E-01 -0.188 8.33E-03 -0.104 1.12E-01 -0.462 4.45E-02 -0.235 3.38E-01 0.389 2.21E-01 0.226 3.73E-01 -0.287 7.50E-01 0.158 8.52E-01 0.172 4.82E-02 0.207 4.18E-03 0.049 9.83E-01 0.15 9.52E-01 0.019 9.77E-01 -0.187 7.28E-01 -0.090 5.99E-17 -0.061 1.91E-13 -0.489 1.05E-05 0.192 2.12E-01 -0.375 1.04E-01 -0.052 8.72E-01 0.026 8.26E-01 -0.187 1.19E-01 -0.184 3.92E-03 -0.051 3.96E-01 -0.216 7.99E-03 -0.096 4.55E-02 -0.640 4.19E-01 -1.489 1.02E-01 -0.183 4.81E-03 -0.082 1.88E-01 -0.292 4.73E-01 -0.266 5.64E-01 0.076 2.18E-01 -0.073 1.97E-01 -0.179 1.58E-05 0.107 7.87E-03 0.145 8.05E-01 0.076 9.04E-01 0.196 1.30E-01 0.104 3.94E-01 0.510 3.21E-01 -0.097 8.54E-01 0.488 2.34E-01 -0.255 2.19E-01 0.470 4.13E-01 0.404 5.33E-01 0.160 5.43E-03 0.112 8.13E-02 -0.255 3.32E-01 -0.207 5.67E-01 0.351 1.33E-15 0.107 1.50E-02 -0.119 4.39E-01 -0.269 7.89E-02 0.160 3.85E-02 -0.152 8.53E-02 0.239 8.46E-01 0.144 9.34E-01 0.174 2.65E-01 -0.055 7.14E-01 0.067 7.69E-01 0.142 5.91E-01 0.220 1.41E-01 -0.057 7.44E-01 -0.150 8.17E-01 -0.252 7.69E-01 -0.217 3.85E-01 0.186 7.84E-01 0.313 2.28E-16 0.081 4.07E-04 -0.386 4.86E-03 -0.128 3.42E-01 -0.902 1.50E-01 -0.413 5.34E-01 -0.399 2.07E-09 -0.336 2.25E-07 -0.230 8.28E-07 -0.169 9.17E-05 -0.254 1.22E-19 -0.165 1.54E-12 -0.331 5.30E-31 -0.211 1.42E-10 -0.240 2.42E-01 -0.211 2.48E-01 -0.379 1.62E-01 -0.305 2.52E-01 -0.090 8.49E-01 -0.203 3.34E-01 0.192 3.42E-01 0.25 2.10E-01 Diabetes Page 82 of 165

0.721 2.83E-03 0.211 4.32E-01 -0.235 4.57E-01 -0.316 3.57E-01 -0.075 3.28E-01 -0.116 1.80E-01 -0.075 4.98E-01 -0.217 1.64E-02 -0.234 4.16E-01 -0.438 1.89E-01 -0.112 2.00E-01 -0.151 1.01E-01 0.030 1.39E-01 -0.14 1.97E-09 -0.159 2.09E-05 -0.112 5.96E-03 -0.165 3.55E-04 -0.119 1.01E-02 -0.099 8.22E-02 0.127 9.63E-04 -0.314 9.33E-02 0.052 8.27E-01 -0.065 9.16E-01 -0.234 7.44E-01 -0.661 5.55E-01 0.125 9.00E-01 0.134 7.33E-01 -0.264 2.42E-01 0.118 6.33E-01 -0.35 5.37E-01 -0.267 4.89E-01 0.235 6.38E-01 -0.017 8.68E-01 -0.12 8.86E-01 -0.857 4.29E-01 -0.438 6.75E-01 0.246 4.66E-01 0.058 8.87E-01 -0.085 2.90E-01 -0.159 6.49E-02 0.028 8.29E-01 -0.143 2.22E-01 0.514 1.34E-03 -0.16 8.19E-02 0.132 2.93E-04 -0.038 3.68E-01 0.136 7.19E-06 -0.095 4.14E-02 -0.515 4.39E-01 -0.229 4.65E-01 -0.207 5.67E-01 -0.27 5.21E-01 0.139 4.31E-03 -0.146 7.91E-03 0.196 6.51E-01 0.179 6.66E-01 0.016 9.19E-01 0.088 5.41E-01 -0.149 3.17E-01 -0.235 1.27E-01 Page 83 of 165 Diabetes

MitoCarta Log Ratio(STZ+I/STZ-I) p-value(STZ+I/STZ-I) 2.0

0.044 9.21E-01 0.232 6.80E-01 -0.067 9.45E-01 -0.191 7.80E-01 0.22 6.04E-01 ABHD11 0.149 3.71E-03 ACAA2 0.187 5.89E-01 ACAD9 -0.196 2.90E-04 ACADL -0.083 1.30E-01 ACADM 0.435 3.10E-01 ACADS 0.037 9.61E-01 ACADSB -0.11 3.10E-02 ACADVL 0.145 4.36E-04 ACAT1 0.172 6.39E-01 ACLY -0.184 3.26E-01 ACO1 -0.023 8.94E-02 ACO2 -0.531 1.65E-02 ACOT2 0.427 4.57E-01 ACOT9 0.192 4.14E-01 -0.183 4.35E-01 -0.221 3.42E-10 ACSL1 -0.514 7.27E-01 0.212 3.81E-05 0.01 8.72E-01 0.147 9.17E-02 0.149 2.56E-01 0.552 2.30E-03 0.735 9.43E-29 0.355 1.71E-17 -0.098 8.17E-01 0.093 4.38E-01 -0.115 5.94E-01 -0.2 3.05E-01 ACYP2 0.042 8.66E-01 -0.27 1.99E-02 -0.068 7.83E-01 -0.139 3.85E-02 -0.416 2.29E-01 -0.371 1.87E-02 0.239 2.69E-01 -0.028 9.67E-01 -0.062 2.92E-01 ADSL -0.173 1.01E-09 -0.091 8.64E-01 AFG3L2 -0.107 1.94E-01 -0.528 4.12E-01 -0.181 5.42E-03 -0.143 4.41E-01 -0.419 3.25E-02 0.129 2.79E-01 AIFM1 0.416 1.16E-02 Diabetes Page 84 of 165

-0.177 4.83E-10 0.344 6.61E-01 AK3 -0.012 9.77E-01 -0.224 8.80E-13 0.078 6.93E-01 -0.025 9.01E-01 AKR7A2 -0.222 6.80E-01 -0.243 1.13E-06 -0.297 5.05E-06 ALDH2 0.178 7.76E-01 -0.264 1.70E-02 ALDH6A1 0.057 8.91E-01 ALDH7A1 -0.161 5.63E-05 -0.115 4.66E-01 0.49 4.91E-01 -0.058 9.12E-03 0.181 4.39E-01 0.195 6.37E-01 -0.188 5.39E-01 -0.147 6.75E-01 -0.221 2.16E-04 -0.147 5.18E-01 -0.205 4.21E-02 -0.099 1.82E-05 -0.209 3.34E-01 0.126 2.72E-01 -0.992 8.03E-11 -0.064 8.65E-01 -0.096 3.00E-01 -0.463 5.21E-02 -0.183 4.27E-01 APOA1BP -0.156 4.18E-02 0.125 5.90E-01 0.024 9.23E-01 -0.284 4.59E-01 0.607 5.23E-01 -0.107 1.70E-01 0.357 4.55E-01 -0.018 8.17E-01 -0.185 2.00E-01 -0.431 2.50E-01 0.197 6.34E-01 -0.129 7.67E-01 0.211 6.55E-01 -0.228 6.64E-01 0.032 9.08E-01 -0.069 8.31E-01 -0.223 4.89E-02 -0.418 1.35E-03 -0.182 7.32E-02 0.129 8.50E-01 ATAD1 -0.161 5.51E-02 ATIC -0.117 5.39E-01 0.344 6.41E-01 ATP8 -0.241 1.38E-01 Page 85 of 165 Diabetes

-0.127 9.14E-03 0.302 1.79E-01 -0.212 4.65E-01 -0.111 7.10E-09 -0.138 5.51E-03 0.067 3.76E-02 ATP5A1 0.075 1.02E-03 ATP5B 0.022 4.11E-01 ATP5C1 -0.095 6.25E-01 ATP5D 0.037 2.95E-01 ATP5F1 0.05 2.66E-01 ATP5H 0.033 5.63E-01 ATP5I 0.293 5.00E-01 ATP5J 0.025 7.18E-01 ATP5L 0.041 3.96E-01 ATP5O -0.149 7.26E-01 0.253 5.40E-01 0.065 9.32E-01 0.146 7.82E-01 -0.363 1.24E-01 -0.349 6.85E-01 BDH1 0.334 9.51E-02 -0.108 7.63E-03 -0.086 7.92E-01 -0.726 4.65E-01 0.29 6.34E-01 -0.35 1.18E-01 0.12 8.39E-01 0.218 6.99E-01 0.363 1.33E-01 -0.231 5.47E-01 0.088 7.33E-01 -0.208 6.56E-01 -0.306 7.34E-02 0.232 1.87E-01 -0.131 4.59E-01 -0.043 8.68E-01 C1QBP 0.042 5.95E-01 C21orf33 0.098 8.13E-01 -0.824 3.82E-01 -0.34 6.81E-01 -0.324 1.67E-01 -0.284 8.43E-12 -0.099 6.14E-01 -0.145 1.78E-02 -0.228 1.05E-11 -0.089 6.40E-02 -0.193 4.64E-01 -0.092 2.24E-01 0.052 5.08E-01 -0.105 8.33E-01 -0.153 9.44E-02 -0.035 7.60E-01 -0.079 7.49E-01 0.075 4.87E-01 Diabetes Page 86 of 165

0.591 6.36E-01 0.306 2.57E-01 -0.09 5.30E-01 -0.363 4.29E-01 0.446 1.13E-01 -0.06 1.73E-01 -0.148 5.42E-01 0.222 7.86E-01 0.11 5.79E-01 -0.072 8.51E-01 0.056 3.33E-01 0.22 2.92E-02 -0.173 4.41E-01 -0.427 2.99E-04 -0.356 1.06E-01 -1.341 8.67E-09 -0.36 9.96E-04 -0.309 2.43E-02 -0.865 5.10E-02 -0.244 6.09E-01 0.099 8.27E-01 0.025 9.45E-01 0.123 2.12E-01 0.404 2.26E-01 0.125 4.40E-01 -0.076 5.77E-01 0.159 4.06E-01 CCT7 0.213 2.40E-01 0.222 3.62E-01 -0.297 3.28E-01 -0.615 5.98E-17 -0.265 5.73E-01 -0.503 5.25E-01 -0.221 6.40E-01 -0.09 6.79E-01 -0.626 4.57E-03 -0.135 3.99E-01 -0.15 4.62E-05 1.58 2.80E-03 0.084 4.30E-01 CHCHD3 0.062 2.65E-01 -0.247 4.56E-02 -0.099 1.97E-09 0.267 2.22E-16 CKMT2 0.541 6.34E-01 0.03 9.69E-01 -0.098 4.34E-01 0.196 7.07E-01 CLYBL -0.233 5.46E-04 -0.067 8.99E-01 0.017 9.50E-01 -0.219 3.82E-01 -0.85 1.79E-02 0.741 6.24E-11 2.422 1.08E-12 Page 87 of 165 Diabetes

2.591 5.03E-04 -0.319 3.21E-05 -0.335 1.18E-01 -0.291 2.05E-11 0.59 5.23E-02 -0.45 5.67E-01 COMT 0.082 6.78E-01 0.066 8.70E-01 -0.21 8.17E-01 -0.087 9.37E-01 -0.113 5.65E-01 0.085 8.69E-01 -0.106 6.18E-01 0.18 4.98E-01 COQ3 -0.086 8.83E-01 COQ5 0.262 5.08E-01 COQ6 -0.235 6.58E-01 COQ7 0.092 1.27E-01 COQ9 -0.09 9.04E-01 0.122 1.32E-01 COX1 0.118 1.05E-01 COX2 -0.146 7.63E-01 COX3 0.109 1.75E-01 COX4I1 0.12 4.17E-01 COX5A 0.117 2.21E-01 COX5B 0.105 5.26E-01 COX6B1 0.08 6.18E-01 COX6C 0.365 3.60E-01 COX7A1 0.851 2.60E-01 COX7A2L -0.099 4.01E-01 CPT2 -0.053 3.08E-01 CPT1B 0.014 7.27E-01 CRAT -0.228 7.82E-01 -0.102 5.47E-01 CROT 0.041 4.74E-01 -0.026 9.12E-01 0.088 9.32E-03 CS -0.33 1.70E-01 0.264 1.06E-01 -0.175 6.12E-01 -0.382 2.20E-01 -0.257 4.50E-01 -0.098 3.03E-01 -0.256 3.94E-01 0.015 9.62E-01 0.085 8.68E-01 0.26 6.41E-01 CYB5R1 -0.03 9.56E-01 0.103 1.31E-01 CYC1 0.039 3.82E-01 CYCS 0.733 3.59E-05 -0.245 3.38E-01 0.026 8.59E-01 DBT 0.249 1.58E-01 -0.138 8.61E-01 Diabetes Page 88 of 165

0.05 9.27E-01 0.156 7.23E-01 0.143 5.69E-01 -0.294 5.72E-01 0.138 4.60E-01 -0.172 4.82E-01 -0.135 2.47E-02 DECR1 0.51 9.57E-17 -0.336 1.93E-01 0.098 8.95E-01 DHRS4 -0.204 4.54E-02 -0.626 3.75E-01 -0.01 7.86E-01 DLAT -0.013 6.39E-01 DLD 0.023 7.41E-01 DLST -0.185 3.56E-01 -0.146 1.82E-01 -0.666 4.91E-01 DNAJA3 0.024 9.65E-01 0.065 8.70E-01 -0.008 9.57E-01 -0.258 3.04E-01 0.408 1.98E-01 0.095 8.06E-01 -0.115 6.69E-01 -0.593 2.74E-01 -0.008 9.85E-01 -0.186 7.17E-01 -0.178 1.06E-01 -0.186 4.48E-01 -0.156 8.07E-01 0.087 7.42E-01 -0.395 5.25E-01 -0.427 3.47E-02 ECH1 0.0186 8.93E-01 ECHS1 -0.151 3.22E-04 0.013 7.94E-01 0.049 3.18E-02 0.453 3.03E-01 0.541 2.46E-02 0.584 4.53E-09 -0.185 7.02E-01 -0.302 5.19E-03 -0.335 1.12E-01 -0.303 5.38E-01 -0.07 8.26E-01 -0.023 7.70E-01 -0.04 7.25E-01 0.184 7.88E-01 -0.142 7.94E-02 -0.11 3.10E-01 -0.132 6.93E-01 0.252 5.01E-01 -0.138 1.66E-02 0.344 3.38E-01 Page 89 of 165 Diabetes

0.443 5.26E-01 -0.118 5.01E-01 -0.201 3.57E-13 -0.365 1.08E-05 -0.417 8.22E-34 0.503 3.16E-01 -0.374 3.89E-01 0.262 1.26E-03 0.019 9.72E-01 0.01 8.50E-01 -0.206 7.18E-02 -0.117 1.14E-03 ETFA -0.119 3.41E-04 ETFB -0.103 1.03E-01 ETFDH -0.285 3.53E-01 0.83 4.78E-01 -0.318 1.15E-07 -0.873 6.65E-81 0.132 5.83E-01 FAHD1 -0.004 9.86E-01 -0.042 9.35E-01 -0.391 4.47E-01 0.394 3.33E-01 0.02 9.42E-01 0.071 6.95E-01 FAM82B 0.46 1.07E-01 0.15 7.19E-01 FASN -0.378 2.79E-06 0.288 6.54E-01 FECH -0.111 7.12E-01 0.104 6.32E-01 0.057 5.89E-02 FH -0.181 9.09E-04 -0.187 2.87E-01 0.198 4.99E-01 FIS1 -0.144 5.36E-01 -0.179 7.02E-01 0.084 1.72E-01 0.706 2.66E-13 0.072 6.90E-01 -0.702 9.95E-10 FTH1 0.177 1.85E-02 FUNDC2 0.559 9.74E-03 -0.105 9.64E-08 -0.174 6.20E-01 -0.182 4.01E-02 GARS 0.13 6.51E-01 0.128 1.20E-01 GBAS -0.196 2.39E-01 0.474 6.04E-03 -0.162 2.38E-01 -0.073 6.68E-02 0.832 1.93E-01 GFM1 -0.169 1.06E-04 -0.283 1.02E-01 Diabetes Page 90 of 165

0.183 3.19E-01 -0.205 4.86E-01 GLRX 0.048 5.94E-01 GLUD1 -1.624 1.64E-01 -0.083 4.91E-01 0.493 6.10E-01 -0.069 6.42E-01 -0.154 5.85E-01 -0.333 4.15E-01 -0.233 2.24E-01 0.214 1.24E-01 0.099 2.83E-03 0.126 1.35E-03 GOT2 -0.149 7.39E-01 -0.169 3.88E-07 GPD1 0.115 3.40E-02 GPD2 -0.15 3.25E-01 -0.143 6.71E-14 -0.392 3.76E-01 0.178 7.11E-01 -0.586 1.15E-02 -0.231 3.47E-01 GPX4 -0.131 7.75E-01 -0.093 5.22E-01 0.333 4.13E-01 GRPEL1 -0.031 9.67E-01 0.287 2.18E-02 -0.153 5.44E-01 GSR -0.039 8.85E-01 -0.25 4.00E-02 -0.231 3.56E-01 -0.244 2.72E-02 -0.255 1.86E-03 -0.465 1.43E-01 -0.274 2.82E-06 -0.561 1.20E-01 -0.052 5.75E-01 -0.625 2.71E-02 -0.164 4.72E-01 -0.169 3.09E-02 HADH -0.134 4.39E-13 HADHA -0.15 1.86E-08 HADHB -0.157 6.70E-01 HAGH -0.023 9.19E-01 -0.621 4.18E-04 -0.691 1.88E-17 -4.036 7.56E-03 -0.441 2.58E-01 -0.389 1.41E-01 -0.119 2.10E-01 0.496 4.94E-01 HIBADH 0.076 3.59E-01 HIBCH 0.182 7.39E-01 HIGD1A -0.191 2.01E-01 0.304 4.13E-01 HINT2 Page 91 of 165 Diabetes

-0.397 1.42E-01 -0.367 1.40E-01 0.014 8.48E-01 -0.135 1.88E-02 -0.133 4.08E-02 0.057 7.06E-01 0.092 7.13E-02 0.238 2.03E-02 HK2 -0.211 2.52E-01 -0.207 5.47E-01 -0.165 4.59E-01 0.268 6.64E-01 0.209 4.01E-01 0.176 1.03E-02 0.346 6.33E-01 0.09 8.84E-01 0.753 6.62E-01 0.109 6.65E-01 -0.056 5.58E-01 0.082 8.57E-01 0.146 8.89E-01 -0.26 6.74E-01 HSD17B4 0.223 6.30E-01 HSD17B8 -0.128 8.37E-02 HSD17B10 -0.01 9.12E-01 0.257 3.88E-13 0.246 8.41E-02 -0.072 4.20E-01 -0.048 4.26E-01 0.158 3.12E-04 HSPA9 -0.144 3.70E-01 0.009 8.89E-01 0.244 4.22E-04 0.6 5.99E-05 0.034 9.71E-01 HSPB7 0.063 4.66E-02 HSPD1 0.111 3.72E-01 HSPE1 0.155 3.35E-01 0.109 6.95E-01 IARS2 0.098 8.42E-01 -0.459 2.89E-01 IDH1 -0.333 3.53E-18 IDH2 0.141 9.74E-04 IDH3A 0.13 7.04E-04 IDH3B 0.157 3.40E-02 IDH3G 0.888 1.50E-01 0.313 2.87E-01 0.034 2.11E-01 IMMT -0.181 6.28E-01 -0.257 6.98E-01 -1.032 3.55E-01 0.08 6.58E-01 0.054 9.21E-01 -0.141 5.49E-01 0.037 9.34E-01 ISOC2 Diabetes Page 92 of 165

-0.219 5.25E-01 0.282 3.69E-03 IVD -0.184 7.24E-02 0.138 1.19E-01 0.083 8.94E-01 0.061 7.11E-01 0.114 8.18E-05 0.628 1.28E-18 1.11 2.27E-01 -0.188 8.03E-01 0.444 1.15E-02 0.121 5.71E-01 -0.09 1.99E-01 0.144 9.25E-01 -0.105 8.83E-01 -1.238 5.71E-02 1.535 3.96E-02 0.158 2.89E-02 -0.11 8.78E-01 0.734 3.64E-01 -0.399 6.29E-01 0.166 8.58E-01 0.04 8.46E-01 LAP3 -0.085 8.68E-02 -0.144 1.89E-08 LDHA 0.409 1.41E-12 LDHB 0.098 4.64E-01 LETM1 -0.202 1.08E-03 0.082 8.03E-01 -0.208 3.20E-04 -0.363 6.15E-01 0.062 7.28E-01 LONP1 0.271 2.16E-01 LRPPRC -0.038 8.29E-01 0.089 8.84E-01 -0.282 1.39E-05 -0.61 3.65E-19 -0.141 1.79E-01 -0.201 2.01E-01 0.024 9.33E-01 -0.352 5.02E-01 -0.426 2.96E-01 -0.043 9.22E-01 -0.171 5.43E-01 0.049 7.23E-01 -0.252 1.76E-01 0.222 7.08E-01 0.257 6.46E-01 -0.161 6.66E-01 MARS 1.069 1.14E-02 0.593 2.28E-32 -0.6 2.27E-11 0.112 8.27E-01 MCCC1 -0.09 9.11E-01 MCCC2 -0.104 5.45E-02 MDH1 Page 93 of 165 Diabetes

0.081 1.59E-06 MDH2 -0.102 8.89E-01 -0.221 2.25E-05 ME1 -0.212 1.19E-01 0.118 8.42E-01 -0.054 7.22E-01 0.157 3.93E-01 0.251 1.95E-02 -0.091 5.33E-01 0.146 6.68E-01 MPST 0.23 6.85E-04 -0.045 8.15E-01 -0.137 7.87E-01 MTCH2 -0.055 8.93E-01 MTHFD1 -0.622 3.95E-01 0.234 5.08E-01 3.076 5.53E-05 -0.117 3.55E-02 0.259 7.38E-01 MUT -0.071 2.98E-03 -0.116 6.52E-05 0.139 1.26E-05 -0.152 2.36E-04 -0.067 2.17E-01 -0.042 5.49E-01 -0.027 2.20E-01 -0.424 3.52E-09 0.011 8.24E-01 -0.515 2.94E-01 -0.05 3.03E-01 -0.426 3.83E-01 -0.098 4.14E-01 -0.056 1.43E-01 -0.516 3.11E-15 -0.221 4.19E-01 -0.013 9.16E-01 -0.037 6.77E-01 -0.565 1.88E-01 -0.402 2.77E-20 0.049 2.70E-03 -0.584 5.70E-01 0.081 3.43E-01 -0.091 3.98E-07 -0.079 2.52E-06 -0.251 5.16E-01 0.144 1.46E-03 0.086 2.23E-02 -0.343 5.96E-02 -0.162 3.76E-01 0.682 1.73E-05 -0.264 4.93E-02 0.134 1.98E-01 -0.228 1.30E-01 NARS 0.231 6.16E-01 -0.428 3.66E-01 Diabetes Page 94 of 165

0.144 4.08E-01 ND4 0.231 1.79E-01 ND5 0.311 2.94E-04 0.204 1.01E-01 NDUFA2 0.042 6.94E-01 NDUFA4 0.118 1.21E-01 NDUFA5 0.052 3.26E-01 NDUFA6 0.225 1.52E-01 NDUFA12 0.107 1.56E-01 NDUFA8 0.118 1.11E-01 NDUFA9 0.108 9.30E-02 NDUFA10 0.328 3.10E-01 NDUFA11 0.147 5.02E-01 NDUFA7 0.155 8.70E-02 NDUFA13 -0.102 8.57E-01 0.121 3.73E-01 NDUFB3 0.246 3.84E-01 NDUFB11 0.082 1.31E-01 NDUFB5 0.08 5.90E-01 NDUFB4 0.162 5.07E-01 NDUFB7 0.168 6.84E-01 NDUFB9 0.041 7.45E-01 NDUFB10 0.083 5.86E-01 NDUFB8 0.08 5.76E-01 NDUFC2 0.112 6.68E-03 NDUFS1 0.089 1.54E-01 NDUFS2 0.122 3.38E-01 NDUFS3 0.111 1.07E-01 NDUFS4 0.149 2.53E-01 NDUFS5 0.412 5.86E-01 NDUFS6 0.202 6.02E-01 NDUFS7 0.077 6.93E-01 NDUFS8 0.119 2.79E-03 NDUFV1 0.146 2.03E-01 NDUFV2 0.215 7.89E-01 NDUFV3 0.097 1.12E-01 -0.441 5.57E-04 0.092 8.59E-01 0.04 9.85E-01 0.242 1.02E-01 -0.169 6.37E-01 -0.336 2.82E-01 0.057 6.90E-01 NME1 -0.075 2.98E-04 NME2 -0.281 1.24E-03 NNT 0.254 6.09E-01 0.24 7.99E-01 -0.189 1.74E-01 -0.08 6.69E-01 -0.398 3.62E-01 -0.071 8.63E-01 -0.184 7.23E-01 0.254 7.53E-01 -0.229 3.14E-02 NT5C3 -0.046 9.34E-01 Page 95 of 165 Diabetes

-0.399 7.60E-01 NUDT2 0.107 4.88E-01 OAT 0.136 2.71E-01 0.186 6.78E-01 0.053 2.18E-01 OGDH 0.407 7.84E-05 -0.107 3.64E-01 0.331 1.45E-01 -0.155 4.17E-01 0.308 1.20E-09 OXCT1 -0.134 1.80E-01 0.021 6.44E-01 -0.067 8.87E-01 0.334 4.27E-01 -0.016 9.63E-01 0.128 2.50E-01 -0.081 6.74E-01 0.17 1.60E-01 -0.136 7.66E-01 -0.238 6.96E-07 PARK7 -0.169 1.57E-01 -0.216 2.94E-01 PC -0.269 5.26E-01 -0.061 8.70E-01 -0.208 6.61E-01 PCCA 0.139 2.79E-01 PCCB -0.104 2.47E-01 0.044 6.81E-01 PDHA1 0.044 3.69E-01 PDHB 0.044 4.17E-01 PDHX 0.169 9.20E-02 -0.008 9.87E-01 PDK2 -2.468 4.65E-07 PDK4 -0.145 2.26E-01 -0.16 2.56E-05 -0.2 1.09E-04 0.383 3.26E-01 0.301 2.30E-02 PDPR -0.122 9.23E-01 -0.179 1.61E-03 0.514 1.08E-01 0.104 1.99E-08 -0.197 8.77E-05 -0.253 1.27E-02 -0.318 4.43E-01 -0.139 2.93E-04 -0.318 7.34E-02 -0.105 5.65E-10 -0.286 3.24E-02 -0.207 9.24E-09 -0.102 4.72E-01 0.142 6.17E-01 PHB2 0.031 6.08E-01 PHB 0.215 3.47E-05 0.124 1.70E-02 Diabetes Page 96 of 165

-0.028 7.45E-01 -0.126 4.16E-01 -0.203 7.79E-01 -0.084 3.90E-01 -0.11 1.60E-05 -0.194 2.24E-01 -0.176 7.41E-01 0.052 2.77E-01 -0.077 9.32E-01 -0.512 1.85E-02 -0.319 2.47E-01 0.581 7.16E-01 -0.069 8.94E-01 0.063 8.46E-01 0.131 7.30E-01 -0.223 1.53E-01 -0.292 6.78E-04 0.171 4.57E-01 0.339 2.43E-01 0.398 6.72E-01 0.189 4.63E-02 -0.196 6.25E-01 -0.081 8.40E-01 -0.069 1.38E-01 -0.172 2.89E-03 -0.138 5.13E-01 -0.014 9.72E-01 0.062 4.25E-01 -0.211 1.60E-09 PRDX1 -0.152 4.22E-06 PRDX2 -0.028 7.12E-01 PRDX3 -0.08 7.72E-02 PRDX5 -0.207 3.88E-01 PRDX6 -0.269 3.75E-04 -0.066 7.34E-01 0.326 2.33E-01 -0.139 2.52E-01 -0.225 3.18E-01 -0.155 3.12E-01 0.581 4.05E-01 -0.148 4.10E-02 -0.11 8.63E-01 0.018 8.92E-01 -0.255 2.44E-01 PROSC 0.651 5.45E-01 0.08 7.85E-01 -0.365 3.81E-02 0.175 6.04E-01 -0.17 6.60E-01 -0.192 1.83E-01 -0.084 8.03E-01 -0.206 4.49E-01 -0.215 2.67E-03 -0.1 3.33E-01 -0.14 1.57E-01 Page 97 of 165 Diabetes

-0.203 3.05E-01 -0.146 4.42E-01 -0.181 5.46E-02 -0.179 2.45E-01 -0.138 3.35E-01 -0.128 6.64E-01 -0.268 9.15E-02 -0.089 7.63E-01 -0.107 5.82E-01 -0.14 3.67E-01 -0.204 1.51E-02 -0.126 4.98E-01 -0.361 5.51E-01 -0.164 5.48E-01 -0.116 9.54E-02 -0.182 2.70E-01 -0.011 9.85E-01 -0.116 8.71E-01 -0.005 9.94E-01 -0.257 1.92E-01 -0.107 4.72E-01 -0.123 3.51E-01 -0.04 8.18E-01 -0.255 5.39E-01 0.07 9.24E-01 0.009 9.91E-01 -0.235 1.81E-01 -0.132 6.88E-01 PTRH2 -0.158 5.62E-13 -0.28 2.52E-06 -0.271 3.35E-17 0.315 7.74E-04 -0.292 3.23E-01 QDPR 0.268 1.53E-02 -0.118 9.31E-01 -0.452 3.16E-01 0.242 3.02E-01 0.344 6.59E-01 0.221 6.59E-01 RAB35 -0.069 8.23E-01 RAB11A -0.174 6.07E-02 RAB11B 0.075 5.88E-01 0.252 5.58E-01 RAB1B -0.146 1.77E-01 -0.126 5.73E-01 -0.006 9.93E-01 -0.346 4.78E-01 -0.141 2.15E-01 0.147 6.05E-01 -0.307 2.62E-01 -0.016 9.71E-01 -0.22 5.56E-01 -0.044 7.87E-01 -0.201 1.37E-01 0.342 1.56E-01 RARS Diabetes Page 98 of 165

0.088 8.93E-01 -0.103 5.77E-01 0.082 5.58E-01 -0.094 4.03E-01 -0.233 3.78E-01 RHOA -0.243 3.79E-01 -0.353 6.23E-01 0.807 3.57E-01 0.009 9.83E-01 0.693 1.16E-04 RPL10A 0.626 1.70E-07 0.628 7.69E-05 -0.154 4.20E-01 0.544 4.92E-02 0.505 7.93E-04 0.213 6.23E-01 0.8 3.47E-02 0.655 4.32E-01 0.698 9.23E-02 0.116 5.32E-01 0.665 1.28E-03 RPL35A 0.502 3.70E-01 0.242 6.68E-01 0.813 1.17E-05 0.052 8.93E-01 -0.111 8.30E-01 0.71 3.42E-11 0.187 7.13E-01 0.24 1.75E-03 0.097 6.05E-01 0.072 5.24E-01 0.575 9.40E-03 0.723 8.02E-04 0.676 5.54E-02 0.626 1.40E-02 0.324 5.65E-01 0.27 7.42E-01 0.318 2.24E-02 0.571 1.41E-04 0.592 1.88E-02 0.539 2.72E-01 RPS14 0.659 2.10E-02 0.331 2.72E-02 0.554 5.07E-03 0.8 2.58E-08 0.963 4.43E-05 0.853 1.25E-01 0.852 9.51E-02 0.505 1.30E-02 RPS15A 0.818 1.27E-01 0.174 5.90E-02 0.656 9.67E-06 -0.184 5.49E-01 -0.15 6.28E-01 -0.161 1.57E-03 Page 99 of 165 Diabetes

-0.18 3.94E-10 -0.182 6.92E-08 -0.003 9.87E-01 0.1 2.44E-01 SAMM50 -0.105 4.88E-01 0.142 1.50E-01 0.19 6.57E-01 SARS -0.659 2.91E-01 SCP2 -0.087 3.74E-01 0.101 9.23E-04 SDHA 0.135 6.39E-03 SDHB 0.144 3.46E-01 SDHC -0.37 5.78E-02 -0.039 9.26E-01 0.01 9.89E-01 0.106 7.76E-01 0.121 4.12E-01 0.016 9.22E-01 0.113 9.02E-01 0.284 1.72E-01 0.771 3.40E-03 0.786 3.89E-01 -0.292 1.29E-11 -0.374 3.32E-01 0.934 2.70E-35 0.277 7.80E-01 1.83 7.57E-05 0.02 9.43E-01 -0.106 7.43E-01 -0.478 3.56E-01 -0.133 2.37E-01 0.203 1.61E-01 0.1 7.29E-03 SLC25A3 0.082 2.06E-03 SLC25A4 0.067 1.48E-01 SLC25A5 0.168 7.35E-03 SLC25A11 0.049 6.61E-03 SLC25A12 -0.071 9.22E-01 SLC25A20 -0.182 7.82E-01 SLC25A42 -0.8 2.65E-07 -0.239 5.24E-01 -0.223 3.78E-01 -0.045 9.71E-01 -0.248 4.64E-02 -0.075 3.73E-02 -0.073 8.82E-01 0.063 9.27E-01 -0.09 5.31E-01 -0.224 7.24E-01 -0.284 2.43E-10 SOD1 0.132 3.26E-02 SOD2 -0.086 7.93E-01 0.123 6.79E-01 -0.305 4.10E-02 SPR 0.093 7.07E-01 SPRYD4 Diabetes Page 100 of 165

-0.119 6.38E-01 -0.214 2.00E-15 -0.178 5.83E-01 -0.167 4.43E-01 0.053 9.21E-01 SSBP1 0.313 4.26E-01 0.152 3.58E-01 -0.094 3.89E-01 -0.202 3.39E-01 0.113 7.49E-01 0.121 2.23E-01 0.029 8.89E-01 -0.062 8.32E-01 0.079 7.66E-03 SUCLA2 0.032 4.43E-01 SUCLG1 -0.243 7.13E-01 0.057 7.29E-01 0.2 2.28E-01 0.324 1.89E-03 0.003 9.91E-01 -0.289 1.03E-01 -0.246 1.67E-03 -0.043 9.36E-01 -0.647 2.54E-04 -0.099 2.21E-01 0.328 6.97E-01 0.247 2.79E-03 -0.297 1.77E-01 0.022 9.34E-01 0.211 2.71E-02 -0.061 6.20E-01 -0.253 1.98E-01 0.022 7.39E-01 -0.055 9.44E-01 TFAM 2.107 2.37E-03 -0.189 1.46E-01 -0.258 5.07E-01 0.776 1.31E-02 -0.077 4.87E-01 0.333 7.29E-01 TIMM44 0.225 6.09E-01 TIMM50 -0.28 4.05E-02 0.053 9.40E-01 -0.285 6.57E-01 -0.095 5.18E-01 -0.18 8.60E-01 0.041 8.35E-01 -0.313 5.70E-01 0.114 7.64E-01 TMEM14C -0.092 3.42E-01 0.497 1.16E-01 0.119 1.28E-01 -0.664 8.31E-02 0.129 1.09E-06 -0.13 6.38E-01 Page 101 of 165 Diabetes

0.199 2.66E-20 -0.52 1.20E-02 0.198 3.16E-17 -0.049 8.04E-01 -0.13 8.61E-01 -0.152 4.44E-16 0.223 1.70E-06 0.223 5.26E-02 -0.29 1.91E-01 -1.196 1.76E-01 0.14 1.06E-01 0.227 3.74E-01 TRAP1 -0.134 5.47E-01 0.182 8.04E-01 -0.058 5.59E-01 0.101 9.56E-01 -0.205 7.09E-01 TST 0.04 1.97E-09 0.384 4.50E-04 0.341 1.25E-01 -0.213 3.59E-02 0.133 5.71E-02 0.119 1.76E-01 -0.85 2.11E-01 0.101 1.24E-01 0.026 9.41E-01 -0.149 1.31E-03 0.059 1.21E-01 TUFM -0.069 9.17E-01 -0.207 1.07E-01 TXN -0.595 3.31E-01 -0.26 2.15E-01 -0.066 9.08E-01 -0.115 2.90E-02 0.048 8.83E-01 -0.244 1.13E-06 -0.15 3.01E-01 -0.1 2.62E-01 -0.095 9.50E-01 -0.23 1.18E-01 0.076 7.40E-01 -0.277 7.51E-02 -0.102 8.96E-01 0.217 3.62E-01 -0.232 5.99E-15 0.258 9.71E-02 0.49 3.29E-01 0.063 3.54E-01 UQCRB 0.049 1.00E-01 UQCRC1 0.089 4.15E-04 UQCRC2 0.119 1.12E-03 UQCRFS1 0.029 8.62E-01 UQCRQ 0.074 6.97E-01 USMG5 -0.179 3.95E-01 -0.095 5.65E-01 Diabetes Page 102 of 165

-0.51 8.85E-02 -0.081 8.05E-01 -0.129 1.35E-01 -0.142 2.00E-01 -0.204 4.98E-01 -0.095 3.03E-01 -0.123 1.38E-08 0.047 2.05E-01 VDAC1 0.072 1.96E-02 VDAC2 0.064 5.71E-02 VDAC3 0.504 9.67E-02 -0.169 8.15E-01 0.536 5.93E-01 -0.268 2.56E-01 -0.19 4.34E-01 0.096 8.56E-01 -0.247 7.41E-01 0.418 7.32E-01 -0.188 6.34E-01 -0.074 3.30E-01 -0.171 1.38E-01 -0.439 4.19E-03 -0.171 2.36E-04 -0.174 4.90E-11 -0.246 4.36E-01 -0.196 7.58E-01 -0.229 1.98E-06 -0.017 9.68E-01 0.072 5.69E-01 -0.086 5.76E-01 Page 103 of 165 Diabetes

Protein expression by SILAC mouse

We used a previously described a SILAC method (Lanza IR, Zabielski P, Klaus KA, Morse DM, Heppelmann CJ, Bergen HR 3rd, Dasari S, Walrand S, Short KR, Johnson ML, Robinson MM, Schimke JM, Jakaitis DR, Asmann YW, Sun Z, Nair KS. Chronic caloric restriction preserves mitochondrial function in senescence without increasing mitochondrial biogenesis. Cell Metab.2012 Dec 5;16(6):777-88) for comparing the relative expression of quadriceps muscle tissue proteins between ND, STZ-I and STZ+I mice (n=6 per group). The reference labeled mice were generated by feeding female DBA2H strain 13 mice (F0 parental generation) an in-house designed diet containing [ C6]-lysine stable isotope labeled amino acid (Cambridge Isotope Laboratories, Cambridge, MA) as the only source of biologically available lysine. When the plasma free lysine enrichment approached the value of that of the chow enrichment (by GC-MS/MS), all animals were bred to obtain 13 fully labeled pups (F1 generation). Mice from F1 generation were put on [ C6]-lysine diet until sacrificed at 14 weeks. We observed >98% labeling of lysine in muscle tissue, measured at peptide level.

Quadriceps muscle samples from ND, STZ-I and STZ+I mice and fully labeled reference mice were pulverized into fine powder in liquid nitrogen. Muscle powder was suspended in RIPA buffer containing 5mM TCEP and protease and phosphatase inhibitors (Complete Mini protease inhibitors and PhosphoSTOP phosphatase inhibitors, ROCHE Applied Science, Indianapolis, IN) and sonicated on ice (Model 100 Sonic Dismembrator, Fisher Scientific, Waltham, MA). After incubation at 4°C for 30 minutes, samples were centrifuged at 15000g to remove cell debris. Protein content in the resulting supernatant was measured using Pierce 660nM Protein Assay Kit.

Samples were prepared for SDS-PAGE in NuPAGE LDS Sample Buffer with 5mM TCEP at a final protein concentration of 1µg/µl. After heating at 70°C for 10 minutes, samples from experimental animals were mixed in 1:1 (protein/protein) ratio with a reference sample obtained from a labeled animal. 15µg of each combined protein sample was resolved on NuPAGE Novex Bis-Tris Midi precast gels. ANOVA analysis of Vinculin reference protein expression data obtained by LC-MS/MS revealed no significant difference between the amounts of samples loaded in the lanes (Table S1). Gel lanes were cut into 8 sections and the excised gel fractions were incubated in 200 mM Tris for 30 minutes prior to destaining with 50 mM Tris/50% acetronitrile (ACN) for 2 hours. Fractions were then dehydrated with 100% ACN until gel pieces appeared opaque. Proteins were reduced with 20 mM DTT in 50 mM Tris for 60mins at 60°C, followed by dehydration with 100% ACN and alkylation with 40 mM iodoacetamide in 50 mM Tris for 60mins at room temperature. Proteins in the samples were digested overnight at 37°C using 0.2 ug of trysin (Promega, Madison, WI) in 20 mM Tris and 0.0002% zwittergent 3-16. Peptides were extracted using 2% trifluoroacetic acid (TFA) for 30 minutes followed by two ACN extractions, each for another 30 minutes. The peptide-containing fractions were dried to completeness under vacuum and stored at -20°C until further analysis.

LC-MS/MS

Samples were brought up in 0.15% formic acid (FA)/0.05% TFA/ 0.002% zwittergent 3-16. Peptides were loaded onto an OptiPak 0.25 uL cartridge (Optimize Technologies, Oregon City, OR), custom-packed with Michrom Magic C8 (5 um, 200 A), using a 15µL/min flow of 0.15% FA and 0.05 % TFA. After loading and washing, the column was placed in line with a 180mmX0.075mm spray tip packed with Magic C18 (5u, 200A, Michrom BioResources, Auburn, CA). After an initial hold for 5 minutes at 5% B, a gradient to 40%B in 60 minutes was performed, followed by a second gradient to 90% B before re- equilibrating at initial conditions. Mobile phase A was water/ACN/FA (98/2/0.1 by volume). Mobile phase B was ACN/isopropanol/water/FA (80/10/10/0.1 by volume). Survey scans were acquired in the Orbitrap (Thermo Scientific Velos) at 60,000 resolving power using a target ion population of 1e6 charges. Data-dependent MS/MS was conducted on the top 5 doubly- or triply-charged precursors using an isolation width setting of 2.0, normalized collision energy of 35%, and a linear ion trap target ion population of 1e4 charges. Precursor masses selected for tandem MS experiments were placed on an exclusion list for 45 seconds. Diabetes Page 104 of 165

Elucidator analysis

Data files were imported into the Rosetta Elucidator software (Seattle, WA) and the multidimensional labeled-pair pipeline was used for analysis. Peptide peaks were detected from MS1 data and detected peaks were aligned across the sample runs of the same gel section. Peptide peaks with peak time score > 0.8, peak m/z score > 0.9, peak confidence score > 0.6, and charge state < 5 and > 1 were selected for identification. MS/MS spectra present in these peptide peaks were identified using Mascot database search engine (Matrix Science, London, UK) configured to use mouse SwissProt database appended with common contaminants and a reverse decoy database. Mascot was configured to use a peptide precursor tolerance of 10 ppm, fragment tolerance of 0.6 Da and a maximum of 2 missed cleavages. The software was instructed to use the following variable modifications during the search: carbamidomethylation of cysteine, oxidation of methionine, 13 and SILAC labeled [ C6]-lysine. Peptide peaks were annotation using the PeptideProphet algorithm in Elucidator configured 13 to use 5% FDR. SILAC labeled pairs were detected using up to three [ C6]-lysine labels with a 20 ppm m/z tolerance and 0.2 minute retention time tolerance. Light/heavy ratios were calculated for each labeled pair and the peptide rations were merged into protein ratios for each mouse group using Elucidator’s weighted statistics.

In the labeled-pair pipeline, Elucidator was designed to report differences between a pair of labeled and unlabeled groups. In our study, we used the SILAC labeled animal as an internal standard to normalize the data and compare the normalized ratios across the experimental conditions. To compare ND, STZ-I and STZ+I groups, a z-statistic was calculated from the difference between two log-ratios divided by the pooled error, and used to calculate a p-value as a measure of significance for the difference between any two groups. Peptide pairs with the highest detector signal had highest impact on the estimation of L/H protein ratio. Only the proteins present in all experimental animals with at least one “light” (unlabeled) 13 and “heavy” ([ C6]-lysine labeled) peptide pair were used in the analysis. The L/H protein ratio value was calculated for each animal, and used to calculate the intragroup ratio estimation error (σ) of a given protein.

Where:

– ratio estimation error for the protein x, log10 scale.

- “light” (sample) to “heavy” (reference) ratio of the protein x, log10 scale.

– mean detector intensity of “light” (sample) version of protein x.

– mean detector intensity of “heavy” (reference) version of protein x.

– error value for “light” (sample) version of protein x.

– error value for “heavy” (reference) version of protein x.

The group ratio estimation error (σ) of a given protein, together with intragroup ratio values were used to calculate individual protein p-value according to the equations:

Page 105 of 165 Diabetes

Where:

sp (A,B) – sample standard deviation between groups A and B, calculated from pooled variance.

– Ratio estimation error for the protein x in group A

– Ratio estimation error for the protein x in group B

n – total number of animals in both groups

– mean sample (light) to reference (heavy) ratio of the protein X in group A

The difference in the protein expression between the groups was calculated as a “ratio of the ratios” giving the relative change in the expression of the given protein between the experimental groups:

where “L/H protein x ratio A” is mean, weighted, L/H ratio of protein x in group A and “L/H protein x ratio B” is mean, weighted, L/H ratio of protein x in group B.

Diabetes Page 106 of 165

Table S1–Results of MS/MS analysis of Vinculin (VINC) loading control/housekeeping protein expression in experimental animals. The even mixing of experimental samples (light, L) with SILAC reference sample (heavy, H), is confirmed by the lack of statistical difference in Light/Heavy ratio value between animals (based on 5 L/H peptide pairs for each animal). The even loading of samples was proven by the analysis of light only (experimental) peptides ( value based on mean signal intensity of 15 VINC light peptides per animal), which shows no statistical difference. N=6 per group.

VINC light (experimental) VINC L (experimental)/H (reference) peptide ratio peptides intensity Group Mean SD Mean SD ND 0.966 0.063 2.26E+05 2.54E+04 STZ-I 0.958 0.061 2.27E+05 3.31E+04 STZ+I 0.992 0.066 2.21E+05 3.70E+04

SS df MS F p SS df MS F p ANOVA 0 2 0 0.477 0.629 1.04E+8 2 5.22E+7 0.050 0.951 Effect 5.98E-02 15 3.99E-03 1.56E+10 15 1.04E+9 Error

Page 107 of 165 Diabetes

Table S2A – Individual protein differential expression data from figure 2A volcano plot (STZ-I vs. ND comparison) of 149 significantly affected proteins implicated in skeletal muscle energy metabolism. Table lists protein symbols, names and accession numbers as given by UniProt database, together with their expression ratio (in log2 scale), p-value (base and in – log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in the alphabetical order by their respective symbols.

-log10 Log2 p-value p-value Symbol Entrez Gene Name Accession # (STZ-I vs (STZ-I vs Group (STZ-I vs ND) ND) ND)

ACAA2 acetyl-CoA acyltransferase 2 Q8BWT1 -0.672 1.8E-42 41.738 FA metabolism

acyl-CoA dehydrogenase family, ACAD9 Q3ULL9 -0.418 2.3E-02 1.631 FA metabolism member 9

acyl-CoA dehydrogenase, long ACADL P51174 -0.461 4.7E-19 18.330 FA metabolism chain

acyl-CoA dehydrogenase, C-4 to ACADM Q91WS8 -0.512 8.0E-13 12.096 FA metabolism C-12 straight chain

acyl-CoA dehydrogenase, very ACADVL B1AR27 -0.246 2.2E-16 15.654 FA metabolism long chain

ACAT1 acetyl-CoA acetyltransferase 1 Q8QZT1 -0.44 7.9E-25 24.103 FA metabolism

Respiratory chain/TCA ACO2 aconitase 2, mitochondrial Q99KI0 0.073 3.8E-08 7.420 cycle

acyl-CoA synthetase long-chain ACSL1 P41216 -0.235 5.8E-19 18.236 FA metabolism family member 1

ADCK3 aarF domain containing kinase 3 Q60936 0.285 3.6E-03 2.444

amylo-alpha-1, 6-glucosidase, 4- Glycolysis/Glycogen AGL Q8CE68 -0.125 4.5E-02 1.345 alpha-glucanotransferase degradation

apoptosis-inducing factor, AIFM1 Q9Z0X1 -0.32 4.9E-03 2.309 mitochondrion-associated, 1

aldehyde dehydrogenase 2 family ALDH2 P47738 -0.156 9.1E-03 2.040 FA metabolism (mitochondrial)

ALDOA aldolase A, fructose-bisphosphate Q5FWB7 0.187 4.2E-06 5.381 Glycolysis/Glycogen Diabetes Page 108 of 165

degradation

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5A1 mitochondrial F1 complex, alpha Q03265 -0.185 1.0E-07 7.001 cycle subunit 1, cardiac muscle

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5B mitochondrial F1 complex, beta P56480 -0.202 4.4E-16 15.353 cycle polypeptide

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5C1 mitochondrial F1 complex, A2AKV3 -0.15 5.2E-05 4.286 cycle gamma polypeptide 1

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5F1 mitochondrial Fo complex, Q80W36 -0.238 6.7E-08 7.171 cycle subunit B1

ATP synthase, H+ transporting, Respiratory chain/TCA Atp5h mitochondrial F0 complex, Q9DCX2 -0.3 5.1E-12 11.292 cycle subunit d

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5I mitochondrial Fo complex, Q06185 -0.211 2.9E-04 3.532 cycle subunit E

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5L mitochondrial Fo complex, Q9CQY3 -0.286 1.3E-04 3.876 cycle subunit G

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5O mitochondrial F1 complex, O Q9DB20 -0.201 2.9E-05 4.544 cycle subunit

capping protein (actin filament) CAPZA2 P47754 0.707 5.6E-22 21.251 muscle Z-line, alpha 2

calsequestrin 1 (fast-twitch, CASQ1 O09165 0.446 1.9E-04 3.712 skeletal muscle)

CAT catalase P24270 1.398 1.5E-09 8.818

CD36 molecule (thrombospondin CD36 Q08857 0.729 3.2E-14 13.495 FA transport and uptake receptor) Page 109 of 165 Diabetes

coiled-coil-helix-coiled-coil-helix CHCHD3 Q9D9P1 -0.315 2.0E-04 3.699 domain containing 3

CISD1 CDGSH iron sulfur domain 1 Q91WS0 -0.13 2.6E-02 1.578

creatine kinase, mitochondrial 2 CKMT2 Q6P8J7 -0.646 4.5E-88 87.347 (sarcomeric)

coenzyme Q9 homolog (S. Respiratory chain/TCA COQ9 Q8K1Z0 -0.337 2.5E-09 8.595 cerevisiae) cycle

Respiratory chain/TCA COX1 cytochrome c oxidase subunit I Q9MD68 -0.392 2.6E-09 8.588 cycle

Respiratory chain/TCA COX2 cytochrome c oxidase subunit II P00405 -0.331 1.6E-05 4.790 cycle

cytochrome c oxidase subunit IV Respiratory chain/TCA COX4I1 P19783 -0.321 2.6E-04 3.588 isoform 1 cycle

Respiratory chain/TCA COX5A cytochrome c oxidase subunit Va P12787 -0.386 1.3E-02 1.876 cycle

Respiratory chain/TCA COX5B cytochrome c oxidase subunit Vb P19536 -0.374 1.5E-04 3.824 cycle

Respiratory chain/TCA COX6C cytochrome c oxidase subunit VIc Q9CPQ1 -0.398 3.3E-02 1.487 cycle

carnitine palmitoyltransferase 1B CPT1B Q3UIM5 -0.226 1.4E-10 9.842 FA metabolism (muscle)

CPT2 carnitine palmitoyltransferase 2 P52825 -0.345 1.0E-04 4.000 FA metabolism

CRAT carnitine O-acetyltransferase P47934 -0.268 1.2E-10 9.907

Respiratory chain/TCA CS citrate synthase Q9CZU6 -0.211 3.0E-10 9.526 cycle

Respiratory chain/TCA CYC1 cytochrome c-1 Q9D0M3 -0.365 1.3E-05 4.903 cycle

Respiratory chain/TCA CYCS cytochrome c, somatic P62897 -0.259 7.8E-09 8.111 cycle Diabetes Page 110 of 165

2,4-dienoyl CoA reductase 1, DECR1 Q9CQ62 -0.296 2.3E-07 6.646 mitochondrial

dihydrolipoamide S- DLAT Q8BMF4 -0.251 3.6E-19 18.439 acetyltransferase

Respiratory chain/TCA DLD dihydrolipoamide dehydrogenase O08749 -0.114 1.6E-04 3.801 cycle

dihydrolipoamide S- succinyltransferase (E2 Respiratory chain/TCA DLST Q9D2G2 -0.318 1.1E-05 4.979 component of 2-oxo-glutarate cycle complex)

enoyl CoA hydratase, short chain, ECHS1 Q8BH95 -0,310 7,98E-03 2,098 FA metabolism 1, mitochondrial

ECI1 enoyl-CoA delta isomerase 1 Q8QZV3 -0.289 6.8E-08 7.166 FA metabolism

Glycolysis/Glycogen ENO1 enolase 1, (alpha) P17182 0.167 1.8E-08 7.750 degradation

Glycolysis/Glycogen ENO2 enolase 2 (gamma, neuronal) P17183 0.121 3.2E-04 3.498 degradation

Glycolysis/Glycogen ENO3 enolase 3 (beta, muscle) P21550 0.113 5.8E-13 12.238 degradation

electron-transfer-flavoprotein, Respiratory chain/TCA ETFA Q99LC5 -0.286 3.8E-10 9.421 alpha polypeptide cycle

electron-transfer-flavoprotein, Respiratory chain/TCA ETFB Q9DCW4 -0.373 3.6E-14 13.447 beta polypeptide cycle

fatty acid binding protein 3, FABP3 muscle and heart (mammary- Q5EBJ0 0.29 1.6E-06 5.807 FA transport and uptake derived growth inhibitor)

fatty acid binding protein 4, FABP4 Q542H7 0.53 3.9E-26 25.411 FA transport and uptake adipocyte

Glycolysis/Glycogen FBP2 fructose-1,6-bisphosphatase 2 Q3TKP4 0.431 1.8E-07 6.745 degradation

FH fumarate hydratase Q3UIA9 -0.237 3.2E-04 3.498 Respiratory chain/TCA Page 111 of 165 Diabetes

cycle

Gapdh/LOC1 glyceraldehyde-3-phosphate Glycolysis/Glycogen P16858 0.102 1.3E-14 13.893 00042025 dehydrogenase degradation

GBAS glioblastoma amplified sequence Q3TD78 -0.304 1.2E-04 3.928

GLUD1 glutamate dehydrogenase 1 P26443 0.206 2.4E-02 1.613

glutamic-oxaloacetic GOT2 transaminase 2, mitochondrial P05202 -0.377 1.1E-19 18.963 FA transport and uptake (FABPpm) (aspartate aminotransferase 2)

glycerol-3-phosphate Glycolysis/Glycogen GPD1 P13707 0.136 1.1E-13 12.971 dehydrogenase 1 (soluble) degradation

glycerol-3-phosphate Glycolysis/Glycogen GPD2 Q64521 0.11 1.8E-02 1.745 dehydrogenase 2 (mitochondrial) degradation

Glycolysis/Glycogen GPI glucose-6-phosphate isomerase P06745 0.145 4.3E-14 13.369 degradation

GSTM5 glutathione S-transferase mu 5 P10649 0.303 3.2E-07 6.495

HADH hydroxyacyl-CoA dehydrogenase Q61425 -0.334 8.7E-05 4.060 FA metabolism

hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA HADHA thiolase/enoyl-CoA hydratase Q8BMS1 -0,213 1,58E-12 11,802 FA metabolism (trifunctional protein), alpha subunit

hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA HADHB thiolase/enoyl-CoA hydratase Q99JY0 -0.162 2.1E-13 12.688 FA metabolism (trifunctional protein), beta subunit

3-hydroxyisobutyrate HIBADH Q99L13 -0.38 4.8E-03 2.316 dehydrogenase

3-hydroxyisobutyryl-CoA HIBCH Q8QZS1 -0.255 1.7E-03 2.767 hydrolase

hydroxysteroid (17-beta) HSD17B10/ Q99N15 -0.162 3.3E-03 2.479 FA metabolism dehydrogenase 10 / short chain L- Diabetes Page 112 of 165

M/SCHAD 3-hydroxyacyl-CoA dehydrogenase

heat shock protein 90kDa alpha HSP90AB1 Q71LX8 -0.291 1.4E-13 12.854 (cytosolic), class B member 1

heat shock 70kDa protein 9 HSPA9 P38647 -0.423 9.3E-20 19.030 (mortalin)

heat shock 60kDa protein 1 HSPD1 P63038 -0.248 3.1E-18 17.509 (chaperonin)

heat shock 10kDa protein 1 HSPE1 Q64433 -0.348 7.8E-04 3.107 (chaperonin 10)

isocitrate dehydrogenase 2 IDH2 P54071 0.472 3.9E-19 18.409 (NADP+), mitochondrial

isocitrate dehydrogenase 3 Respiratory chain/TCA IDH3A Q9D6R2 -0.303 4.2E-15 14.375 (NAD+) alpha cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA IDH3B Q91VA7 -0.319 3.5E-24 23.457 (NAD+) beta cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA IDH3G P70404 -0.392 2.1E-10 9.688 (NAD+) gamma cycle

inner membrane protein, IMMT Q3TVZ5 -0.321 3.7E-39 38.431 mitochondrial

IVD isovaleryl-CoA dehydrogenase Q9JHI5 -0.343 3.3E-03 2.481 FA metabolism

leucine zipper-EF-hand containing LETM1 Q9Z2I0 -0.5 9.4E-05 4.028 transmembrane protein 1

leucine-rich pentatricopeptide LRPPRC Q99KF9 -0.711 4.6E-04 3.339 repeat containing

malate dehydrogenase 1, NAD Glycolysis/Glycogen MDH1 P14152 0.155 6.9E-03 2.161 (soluble) degradation/TCA Cycle

malate dehydrogenase 2, NAD Respiratory chain/TCA MDH2 P08249 -0.198 9.9E-14 13.004 (mitochondrial) cycle

MPC2 mitochondrial pyruvate carrier 2 Q9D023 -0.514 3.4E-06 5.474 Page 113 of 165 Diabetes

NADH dehydrogenase, subunit 5 Respiratory chain/TCA ND5 Q9MD82 -0.447 2.1E-03 2.682 (complex I) cycle

NADH dehydrogenase Respiratory chain/TCA NDUFA10 (ubiquinone) 1 alpha subcomplex, Q99LC3 -0.334 4.9E-09 8.311 cycle 10, 42kDa

NADH dehydrogenase Respiratory chain/TCA NDUFA12 (ubiquinone) 1 alpha subcomplex, Q5M9K5 -0.375 1.7E-02 1.759 cycle 12

NADH dehydrogenase Respiratory chain/TCA NDUFA13 (ubiquinone) 1 alpha subcomplex, Q9ERS2 -0.367 3.2E-05 4.498 cycle 13

NADH dehydrogenase Respiratory chain/TCA NDUFA2 (ubiquinone) 1 alpha subcomplex, Q9CQ75 -0.485 8.4E-04 3.077 cycle 2, 8kDa

NADH dehydrogenase Respiratory chain/TCA NDUFA5 (ubiquinone) 1 alpha subcomplex, Q9CPP6 -0.414 3.0E-08 7.527 cycle 5, 13kDa

NADH dehydrogenase Respiratory chain/TCA NDUFA6 (ubiquinone) 1 alpha subcomplex, Q9CQZ5 -0.371 6.0E-12 11.223 cycle 6, 14kDa

NADH dehydrogenase Respiratory chain/TCA NDUFA7 (ubiquinone) 1 alpha subcomplex, Q9Z1P6 -0.432 4.7E-02 1.325 cycle 7, 14.5kDa

NADH dehydrogenase Respiratory chain/TCA NDUFA8 (ubiquinone) 1 alpha subcomplex, Q9DCJ5 -0.363 1.3E-05 4.879 cycle 8, 19kDa

NADH dehydrogenase Respiratory chain/TCA NDUFA9 (ubiquinone) 1 alpha subcomplex, Q9DC69 -0.435 1.6E-07 6.785 cycle 9, 39kDa

NADH dehydrogenase Respiratory chain/TCA NDUFB11 (ubiquinone) 1 beta subcomplex, B1AV40 -0.521 3.9E-02 1.405 cycle 11, 17.3kDa

NADH dehydrogenase Respiratory chain/TCA NDUFB3 (ubiquinone) 1 beta subcomplex, Q9CQZ6 -0.432 1.8E-03 2.757 cycle 3, 12kDa Diabetes Page 114 of 165

NADH dehydrogenase Respiratory chain/TCA NDUFB4 (ubiquinone) 1 beta subcomplex, Q9DBH2 -0.395 1.4E-02 1.863 cycle 4, 15kDa

NADH dehydrogenase Respiratory chain/TCA NDUFB5 (ubiquinone) 1 beta subcomplex, Q9CQH3 -0.332 4.4E-10 9.353 cycle 5, 16kDa

NADH dehydrogenase Respiratory chain/TCA NDUFB7 (ubiquinone) 1 beta subcomplex, Q9CR61 -0.581 1.6E-02 1.788 cycle 7, 18kDa

NADH dehydrogenase Respiratory chain/TCA NDUFB8 (ubiquinone) 1 beta subcomplex, Q9D6J5 -0.301 3.9E-02 1.407 cycle 8, 19kDa

NADH dehydrogenase Respiratory chain/TCA NDUFC2 (ubiquinone) 1, subcomplex Q9D846 -0.267 4.8E-02 1.316 cycle unknown, 2, 14.5kDa

NADH dehydrogenase (ubiquinone) Fe-S protein 1, Respiratory chain/TCA NDUFS1 Q91VD9 -0.333 2.0E-15 14.699 75kDa (NADH-coenzyme Q cycle reductase)

NADH dehydrogenase (ubiquinone) Fe-S protein 2, Respiratory chain/TCA NDUFS2 Q91WD5 -0.327 2.9E-09 8.536 49kDa (NADH-coenzyme Q cycle reductase)

NADH dehydrogenase (ubiquinone) Fe-S protein 3, Respiratory chain/TCA NDUFS3 Q9DCT2 -0.399 2.9E-02 1.536 30kDa (NADH-coenzyme Q cycle reductase)

NADH dehydrogenase (ubiquinone) Fe-S protein 4, Respiratory chain/TCA NDUFS4 Q9CXZ1 -0.312 3.0E-05 4.529 18kDa (NADH-coenzyme Q cycle reductase)

NADH dehydrogenase (ubiquinone) Fe-S protein 5, Respiratory chain/TCA NDUFS5 Q99LY9 -0.415 2.8E-03 2.561 15kDa (NADH-coenzyme Q cycle reductase)

NADH dehydrogenase NDUFS6 P52503 -0.418 1.4E-02 1.851 Respiratory chain/TCA (ubiquinone) Fe-S protein 6, Page 115 of 165 Diabetes

13kDa (NADH-coenzyme Q cycle reductase)

NADH dehydrogenase Respiratory chain/TCA NDUFV1 (ubiquinone) flavoprotein 1, Q91YT0 -0.325 9.3E-14 13.032 cycle 51kDa

NADH dehydrogenase Respiratory chain/TCA NDUFV2 (ubiquinone) flavoprotein 2, Q9D6J6 -0.41 1.8E-02 1.742 cycle 24kDa

oxoglutarate (alpha- Respiratory chain/TCA OGDH ketoglutarate) dehydrogenase Q60597 -0.215 6.7E-08 7.171 cycle (lipoamide)

OXCT1 3-oxoacid CoA transferase 1 Q9D0K2 -0.52 1.9E-21 20.726

PARK7 parkinson protein 7 Q99LX0 0.218 2.1E-05 4.682

pyruvate dehydrogenase Respiratory chain/TCA PDHA1 Q3UFJ3 -0.392 3.5E-04 3.457 (lipoamide) alpha 1 cycle

pyruvate dehydrogenase kinase, PDK4 O70571 3.148 9.8E-05 4.011 isozyme 4

pyruvate dehydrogenase PDPR Q7TSQ8 -0.412 2.1E-10 9.686 phosphatase regulatory subunit

Glycolysis/Glycogen PFKM phosphofructokinase, muscle P47857 0.072 2.5E-04 3.609 degradation

phosphoglycerate mutase 2 Glycolysis/Glycogen PGAM2 Q5NCI4 0.085 2.5E-06 5.602 (muscle) degradation

Glycolysis/Glycogen PGK1 phosphoglycerate kinase 1 P09411 0.242 2.4E-15 14.613 degradation

Glycolysis/Glycogen PGM1 phosphoglucomutase 1 Q3UGE3 0.205 9.2E-09 8.034 degradation

PHB prohibitin Q5SQG5 -0.248 1.2E-04 3.917

Glycolysis/Glycogen Pkm pyruvate kinase, muscle P52480 0.097 6.8E-05 4.168 degradation Diabetes Page 116 of 165

PRDX5 peroxiredoxin 5 Q9D6X2 -0.299 4.8E-08 7.315

Glycolysis/Glycogen PYGB phosphorylase, glycogen; brain Q3UGT5 0.285 8.5E-07 6.073 degradation

Glycolysis/Glycogen PYGM phosphorylase, glycogen, muscle Q9WUB3 0.256 1.1E-15 14.955 degradation

succinate dehydrogenase Respiratory chain/TCA SDHA complex, subunit A, flavoprotein Q8K2B3 -0.298 6.2E-21 20.211 cycle (Fp)

succinate dehydrogenase Respiratory chain/TCA SDHB complex, subunit B, iron sulfur A2AA77 -0.302 1.4E-09 8.848 cycle (Ip)

succinate dehydrogenase Respiratory chain/TCA SDHC complex, subunit C, integral Q5XK33 -0.522 3.2E-03 2.498 cycle membrane protein, 15kDa

solute carrier family 25 SLC25A11 (mitochondrial carrier; Q5SX48 -0.388 7.8E-10 9.109 oxoglutarate carrier), member 11

solute carrier family 25 SLC25A12 (aspartate/glutamate carrier), Q8BH59 -0.176 8.5E-19 18.070 member 12

solute carrier family 25 SLC25A3 (mitochondrial carrier; phosphate Q8VEM8 -0.348 8.6E-17 16.068 carrier), member 3

solute carrier family 25 (mitochondrial carrier; adenine SLC25A4 P48962 -0.233 1.0E-04 3.987 nucleotide translocator), member 4

solute carrier family 25 (mitochondrial carrier; adenine SLC25A5 P51881 -0.209 4.9E-05 4.313 nucleotide translocator), member 5

SLC27A1 solute carrier family 27 (fatty acid Q3TP13 0.413 2.0E-03 2.693 FA transport and uptake (FATP1) transporter), member 1

SOD1 superoxide dismutase 1, soluble Q8C355 0.213 9.2E-07 6.038 Page 117 of 165 Diabetes

superoxide dismutase 2, Respiratory chain/TCA SOD2 P09671 -0.305 8.3E-07 6.081 mitochondrial cycle

succinate-CoA ligase, ADP- Respiratory chain/TCA SUCLA2 Q3U6C7 -0.24 3.2E-11 10.492 forming, beta subunit cycle

succinate-CoA ligase, alpha Respiratory chain/TCA SUCLG1 Q9WUM5 -0.246 2.1E-11 10.680 subunit cycle

Glycolysis/Glycogen TPI1 triosephosphate isomerase 1 P17751 0.172 3.9E-18 17.413 degradation

TRAP1 TNF receptor-associated protein 1 Q9CQN1 -0.462 4.5E-02 1.352

Tu translation elongation factor, TUFM Q8BFR5 -0.179 1.6E-05 4.801 mitochondrial

ubiquinol-cytochrome c reductase Respiratory chain/TCA UQCRB Q9D855 -0.399 2.1E-09 8.684 binding protein cycle

ubiquinol-cytochrome c reductase Respiratory chain/TCA UQCRC1 Q3THM1 -0.23 8.3E-07 6.082 core protein I cycle

ubiquinol-cytochrome c reductase Respiratory chain/TCA UQCRC2 Q9DB77 -0.254 1.2E-19 18.914 core protein II cycle

ubiquinol-cytochrome c Respiratory chain/TCA UQCRFS1 reductase, Rieske iron-sulfur Q9CR68 -0.331 5.3E-31 30.276 cycle polypeptide 1

voltage-dependent anion channel VDAC1 Q60932 -0.159 2.1E-05 4.680 1

voltage-dependent anion channel VDAC2 Q60930 -0.165 3.6E-04 3.450 2

tyrosine 3- monooxygenase/tryptophan 5- YWHAE A2ACM8 0.132 2.9E-04 3.533 monooxygenase activation protein, epsilon polypeptide

tyrosine 3- monooxygenase/tryptophan 5- YWHAZ Q8BWN0 0.139 4.3E-03 2.366 monooxygenase activation protein, zeta polypeptide Diabetes Page 118 of 165

Page 119 of 165 Diabetes

Table S2B – Individual protein differential expression data from figure 2B volcano plot (STZ+I vs. STZ-I comparison) of 77 significantly affected proteins implicated in skeletal muscle energy metabolism. Table lists protein symbols, names and accession numbers as given by UniProt database, together with their expression ratio (in log2 scale), p-value (base and in – log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in the alphabetical order by their respective symbols.

-log10 Log2 p-value Accession p-value Symbol Entrez Gene Name (STZ+I vs (STZ+I vs Group # (STZ+I vs STZ-I) STZ-I) STZ-I)

ACAA2 acetyl-CoA acyltransferase 2 Q8BWT1 0.149 3.7E-03 2.431 FA metabolism

acyl-CoA dehydrogenase, long P51174 -0.196 2.9E-04 3.538 FA metabolism ACADL chain

acyl-CoA dehydrogenase, very B1AR27 -0.110 3.1E-02 1.509 FA metabolism ACADVL long chain

ACAT1 acetyl-CoA acetyltransferase 1 Q8QZT1 0.145 4.4E-04 3.361 FA metabolism

acyl-CoA synthetase long-chain P41216 -0.221 3.4E-10 9.466 FA metabolism ACSL1 family member 1

ADCK3 aarF domain containing kinase 3 Q60936 -0.270 2.0E-02 1.701

alcohol dehydrogenase 5 (class Q6P5I3 -0.139 3.9E-02 1.415 FA metabolism ADH5 III), chi polypeptide

aldehyde dehydrogenase 2 family P47738 -0.297 5.1E-06 5.297 FA metabolism ALDH2 (mitochondrial)

Glycolysis/Glycogen aldolase A, fructose-bisphosphate Q5FWB7 -0.161 5.6E-05 4.249 ALDOA degradation

ATP synthase, H+ transporting, Respiratory chain/TCA mitochondrial F1 complex, alpha D3Z6F5 0.067 3.8E-02 1.425 cycle ATP5A1 subunit 1, cardiac muscle

ATP synthase, H+ transporting, Respiratory chain/TCA mitochondrial F1 complex, beta P56480 0.075 1.0E-03 2.991 cycle ATP5B polypeptide

calsequestrin 1 (fast-twitch, O09165 -0.427 3.0E-04 3.524 CASQ1 skeletal muscle)

CAT catalase P24270 -1.341 8.7E-09 8.062

CD36 molecule (thrombospondin Q08857 -0.615 6.0E-17 16.223 FA uptake and transport CD36 receptor)

creatine kinase, mitochondrial 2 Q6P8J7 0.267 2.2E-16 15.654 CKMT2 (sarcomeric)

Respiratory chain/TCA citrate synthase Q9CZU6 0.088 9.3E-03 2.031 CS cycle

DECR1 2,4-dienoyl CoA reductase 1, Q9CQ62 -0.135 2.5E-02 1.607 Diabetes Page 120 of 165

mitochondrial

enoyl CoA hydratase 1, O35459 -0.427 3.5E-02 1.460 FA metabolism ECH1 peroxisomal

ECI1 enoyl-CoA delta isomerase 1 Q8QZV3 -0.151 3.2E-04 3.492 FA metabolism

Glycolysis/Glycogen enolase 1, (alpha) P17182 -0.201 3.6E-13 12.447 ENO1 degradation

Glycolysis/Glycogen enolase 2 (gamma, neuronal) P17183 -0.365 1.1E-05 4.967 ENO2 degradation

Glycolysis/Glycogen enolase 3 (beta, muscle) P21550 -0.417 8.2E-34 33.085 ENO3 degradation

electron-transfer-flavoprotein, Respiratory chain/TCA Q99LC5 -0.117 1.1E-03 2.943 ETFA alpha polypeptide cycle

electron-transfer-flavoprotein, Respiratory chain/TCA Q9DCW4 -0.119 3.4E-04 3.467 ETFB beta polypeptide cycle

fatty acid binding protein 3, muscle and heart (mammary- Q5EBJ0 -0.318 1.2E-07 6.939 FA uptake and transport FABP3 derived growth inhibitor)

fatty acid binding protein 4, Q542H7 -0.873 6.7E-81 80.177 FA uptake and transport FABP4 adipocyte

Glycolysis/Glycogen fructose-1,6-bisphosphatase 2 Q3TKP4 -0.378 2.8E-06 5.554 FBP2 degradation

Gapdh/LOC1 glyceraldehyde-3-phosphate Glycolysis/Glycogen P16858 -0.105 9.6E-08 7.016 00042025 dehydrogenase degradation

GARS glycyl-tRNA synthetase Q9CZD3 -0.182 4.0E-02 1.397

glutamic-oxaloacetic transaminase 2, mitochondrial P05202 0.126 1.4E-03 2.870 FA uptake and transport GOT2 (aspartate aminotransferase 2)

glycerol-3-phosphate Glycolysis/Glycogen P13707 -0.169 3.9E-07 6.411 GPD1 dehydrogenase 1 (soluble) degradation

glycerol-3-phosphate Respiratory chain/TCA Q64521 0.115 3.4E-02 1.469 GPD2 dehydrogenase 2 (mitochondrial) cycle

Glycolysis/Glycogen glucose-6-phosphate isomerase P06745 -0.143 6.7E-14 13.173 GPI degradation

GSTM5 glutathione S-transferase mu 5 P10649 -0.255 1.9E-03 2.730

HADH hydroxyacyl-CoA dehydrogenase Q61425 -0.169 3.1E-02 1.510 FA metabolism

hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA thiolase/enoyl-CoA hydratase Q8BMS1 -0.134 4.4E-13 12.358 FA metabolism (trifunctional protein), alpha HADHA subunit

hydroxyacyl-CoA dehydrogenase/3-ketoacyl-CoA Q99JY0 -0.150 1.9E-08 7.730 FA metabolism thiolase/enoyl-CoA hydratase HADHB (trifunctional protein), beta Page 121 of 165 Diabetes

subunit

HK2 hexokinase 2 O08528 0.238 2.0E-02 1.693

heat shock protein 90kDa alpha Q71LX8 0.257 3.9E-13 12.411 HSP90AB1 (cytosolic), class B member 1

heat shock 70kDa protein 9 P38647 0.158 3.1E-04 3.506 HSPA9 (mortalin)

heat shock 60kDa protein 1 P63038 0.063 4.7E-02 1.332 HSPD1 (chaperonin)

isocitrate dehydrogenase 2 P54071 -0.333 3.5E-18 17.452 IDH2 (NADP+), mitochondrial

isocitrate dehydrogenase 3 Respiratory chain/TCA Q9D6R2 0.141 9.7E-04 3.011 IDH3A (NAD+) alpha cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA Q91VA7 0.130 7.0E-04 3.152 IDH3B (NAD+) beta cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA P70404 0.157 3.4E-02 1.469 IDH3G (NAD+) gamma cycle

IVD isovaleryl-CoA dehydrogenase Q9JHI5 0.282 3.7E-03 2.433 FA metabolism

malate dehydrogenase 2, NAD Respiratory chain/TCA P08249 0.081 1.6E-06 5.799 MDH2 (mitochondrial) cycle

malic enzyme 1, NADP(+)- Glycolysis/Glycogen Q921S3 -0.221 2.3E-05 4.648 ME1 dependent, cytosolic degradation

MPC2 mitochondrial pyruvate carrier 2 Q9D023 0.251 2.0E-02 1.710

NADH dehydrogenase (ubiquinone) Fe-S protein 1, Respiratory chain/TCA Q91VD9 0.112 6.7E-03 2.175 75kDa (NADH-coenzyme Q cycle NDUFS1 reductase)

NADH dehydrogenase Respiratory chain/TCA (ubiquinone) flavoprotein 1, Q91YT0 0.119 2.8E-03 2.554 cycle NDUFV1 51kDa

OXCT1 3-oxoacid CoA transferase 1 Q9D0K2 0.308 1.2E-09 8.921

PARK7 parkinson protein 7 Q99LX0 -0.238 7.0E-07 6.157

pyruvate dehydrogenase kinase, O70571 -2.468 4.7E-07 6.333 PDK4 isozyme 4

pyruvate dehydrogenase Q7TSQ8 0.301 2.3E-02 1.638 PDPR phosphatase regulatory subunit

Glycolysis/Glycogen phosphofructokinase, muscle P47857 0.104 2.0E-08 7.701 PFKM degradation

phosphoglycerate mutase 2 Glycolysis/Glycogen Q5NCI4 -0.139 2.9E-04 3.533 PGAM2 (muscle) degradation

Glycolysis/Glycogen phosphoglucomutase 1 Q3UGE3 -0.207 9.2E-09 8.034 PGM1 degradation

Pkm pyruvate kinase, muscle P52480 -0.110 1.6E-05 4.796 Glycolysis/Glycogen Diabetes Page 122 of 165

degradation

Glycolysis/Glycogen phosphorylase, glycogen; brain Q3UGT5 -0.280 2.5E-06 5.599 PYGB degradation

Glycolysis/Glycogen phosphorylase, glycogen, muscle Q9WUB3 -0.271 3.4E-17 16.475 PYGM degradation

succinate dehydrogenase Respiratory chain/TCA complex, subunit A, flavoprotein Q8K2B3 0.101 9.2E-04 3.035 cycle SDHA (Fp)

succinate dehydrogenase Respiratory chain/TCA A2AA77 0.135 6.4E-03 2.194 SDHB complex, subunit B, iron sulfur (Ip) cycle

solute carrier family 25 (mitochondrial carrier; Q5SX48 0.168 7.4E-03 2.134 SLC25A11 oxoglutarate carrier), member 11

solute carrier family 25 (aspartate/glutamate carrier), Q8BH59 0.049 6.6E-03 2.180 SLC25A12 member 12

solute carrier family 25 (mitochondrial carrier; phosphate Q8VEM8 0.100 7.3E-03 2.137 SLC25A3 carrier), member 3

solute carrier family 25 (mitochondrial carrier; adenine P48962 0.082 2.1E-03 2.686 nucleotide translocator), member SLC25A4 4

SLC27A1 solute carrier family 27 (fatty acid Q3TP13 -0.800 2.7E-07 6.577 FA uptake and transport (FATP1) transporter), member 1

SOD1 superoxide dismutase 1, soluble Q8C355 -0.284 2.4E-10 9.614

superoxide dismutase 2, P09671 0.132 3.3E-02 1.487 SOD2 mitochondrial

succinate-CoA ligase, ADP- Respiratory chain/TCA Q3U6C7 0.079 7.7E-03 2.116 SUCLA2 forming, beta subunit cycle

Glycolysis/Glycogen triosephosphate isomerase 1 P17751 -0.152 4.4E-16 15.353 TPI1 degradation

ubiquinol-cytochrome c reductase Respiratory chain/TCA Q9DB77 0.089 4.2E-04 3.382 UQCRC2 core protein II cycle

ubiquinol-cytochrome c Respiratory chain/TCA reductase, Rieske iron-sulfur Q9CR68 0.119 1.1E-03 2.951 cycle UQCRFS1 polypeptide 1

voltage-dependent anion channel Q60930 0.072 2.0E-02 1.708 VDAC2 2

tyrosine 3- monooxygenase/tryptophan 5- A2ACM8 -0.171 2.4E-04 3.627 monooxygenase activation YWHAE protein, epsilon polypeptide

tyrosine 3- Q8BWN0 -0.229 2.0E-06 5.703 YWHAZ monooxygenase/tryptophan 5- Page 123 of 165 Diabetes

monooxygenase activation protein, zeta polypeptide

Diabetes Page 124 of 165

Table S2E – Individual protein differential expression data from Figure 2C volcano plot (STZ+I vs. ND comparison) of 104 significantly affected proteins implicated in skeletal muscle energy metabolism. Table lists protein symbols, names and accession numbers as given by UniProt database, together with their expression ratio (in log2 scale), p-value (base and in – log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in the alphabetical order by their respective symbols.

-log10 Log2 p-value p-value Symbol Entrez Gene Name Accesion # (STZ+I vs (STZ+I vs Group (STZ+I vs ND) ND) ND)

ACAA2 acetyl-CoA acyltransferase 2 Q8BWT1 -0.523 1.1E-27 26.947 FA metabolism

acyl-CoA dehydrogenase, long ACADL P51174 -0.510 3.7E-23 22.434 FA metabolism chain

acyl-CoA dehydrogenase, C-4 ACADM Q91WS8 -0.454 1.3E-13 12.876 FA metabolism to C-12 straight chain

acyl-CoA dehydrogenase, very ACADVL P50544 -0.301 4.4E-16 15.353 FA metabolism long chain

Respiratory chain/TCA ACO2 aconitase 2, mitochondrial Q99KI0 0.050 1.4E-04 3.842 cycle

acyl-CoA synthetase long- ACSL1 P41216 -0.318 1.9E-42 41.728 FA metabolism chain family member 1

aldehyde dehydrogenase 2 ALDH2 P47738 -0.453 2.4E-13 12.629 FA metabolism family (mitochondrial)

aldolase A, fructose- Glycolysis/Glycogen ALDOA Q5FWB7 0.100 2.8E-04 3.561 bisphosphate degradation

ATP synthase, H+ transporting, mitochondrial F1 complex, Respiratory chain/TCA ATP5A1 D3Z6F5 -0.118 7.0E-05 4.154 alpha subunit 1, cardiac cycle muscle

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5B mitochondrial F1 complex, P56480 -0.127 4.3E-07 6.368 cycle beta polypeptide

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5C1 mitochondrial F1 complex, A2AKU9 -0.144 2.4E-06 5.620 cycle gamma polypeptide 1 Page 125 of 165 Diabetes

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5F1 mitochondrial Fo complex, Q5I0W0 -0.200 2.5E-06 5.599 cycle subunit B1

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5H mitochondrial Fo complex, Q9DCX2 -0.250 4.0E-11 10.394 cycle subunit d

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5L mitochondrial Fo complex, Q9CPQ8 -0.261 2.7E-05 4.565 cycle subunit G

ATP synthase, H+ transporting, Respiratory chain/TCA ATP5O mitochondrial F1 complex, O Q9DB20 -0.161 9.0E-05 4.047 cycle subunit

enoyl CoA hydratase, short ECHS1 Q8BH95 -0,292 1,21E-02 1.918 FA metabolism chain, 1, mitochondrial

CD36 molecule CD36 Q08857 -0.261 1.9E-03 2.728 FA uptake and transport (thrombospondin receptor)

coiled-coil-helix-coiled-coil- CHCHD3 Q9D9P1 -0.231 3.0E-02 1.524 Mitochondrial protein helix domain containing 3

CISD1 CDGSH iron sulfur domain 1 Q91WS0 -0.145 3.8E-03 2.426 Mitochondrial protein

cytochrome c oxidase subunit Respiratory chain/TCA COX1 Q9MD68 -0.269 1.8E-04 3.757 I cycle

cytochrome c oxidase subunit Respiratory chain/TCA COX2 P00405 -0.213 3.3E-04 3.479 II cycle

cytochrome c oxidase subunit Respiratory chain/TCA COX4I1 P19783 -0.211 4.7E-03 2.328 IV isoform 1 cycle

cytochrome c oxidase subunit Respiratory chain/TCA COX5A P12787 -0.267 4.7E-03 2.330 Va cycle

cytochrome c oxidase subunit Respiratory chain/TCA COX5B P19536 -0.256 4.4E-03 2.360 Vb cycle

carnitine palmitoyltransferase CPT1B Q3UIM5 -0.246 3.0E-12 11.520 FA metabolism 1B (muscle) Diabetes Page 126 of 165

carnitine palmitoyltransferase CPT2 P52825 -0.324 3.8E-04 3.420 FA metabolism 2

CRAT carnitine O-acetyltransferase P47934 -0.253 1.1E-06 5.975 Mitochondrial protein

Respiratory chain/TCA CS citrate synthase Q9CZU6 -0.123 2.2E-04 3.666 cycle

Respiratory chain/TCA CYC1 cytochrome c-1 Q9D0M3 -0.266 1.9E-03 2.726 cycle

Respiratory chain/TCA CYCS cytochrome c, somatic Q56A15 -0.229 5.1E-06 5.291 cycle

2,4-dienoyl CoA reductase 1, DECR1 Q9CQ62 -0.327 3.1E-10 9.507 Mitochondrial protein mitochondrial

dihydrolipoamide S- Glycolysis/Glycogen DLAT Q8BMF4 -0.257 6.8E-20 19.170 acetyltransferase degradation

dihydrolipoamide Respiratory chain/TCA DLD O08749 -0.127 8.1E-06 5.092 dehydrogenase cycle

dihydrolipoamide S- succinyltransferase (E2 Respiratory chain/TCA DLST Q9D2G2 -0.295 2.8E-04 3.551 component of 2-oxo-glutarate cycle complex)

ECI1 enoyl-CoA delta isomerase 1 Q8QZV3 -0.268 2.4E-08 7.625 FA metabolism

Glycolysis/Glycogen ENO3 enolase 3 (beta, muscle) P21550 -0.309 5.2E-25 24.287 degradation

electron-transfer-flavoprotein, Respiratory chain/TCA ETFA Q99LC5 -0.272 6.4E-30 29.193 alpha polypeptide cycle

electron-transfer-flavoprotein, Respiratory chain/TCA ETFB Q9DCW4 -0.315 5.1E-18 17.296 beta polypeptide cycle

fatty acid binding protein 3, FABP3 muscle and heart (mammary- Q5EBJ0 -0.398 1.5E-33 32.830 FA uptake and transport derived growth inhibitor)

fatty acid binding protein 4, FABP4 Q542H7 -0.343 5.0E-18 17.298 FA uptake and transport adipocyte Page 127 of 165 Diabetes

Respiratory chain/TCA FH fumarate hydratase Q3UIA9 0.097 2.3E-03 2.638 cycle

glyceraldehyde-3-phosphate Glycolysis/Glycogen GAPDH P16858 0.073 2.2E-13 12.650 dehydrogenase degradation

glutamic-oxaloacetic transaminase 2, mitochondrial GOT2 P05202 -0.251 9.7E-13 12.014 FA uptake and transport (aspartate aminotransferase 2)

glycerol-3-phosphate Glycolysis/Glycogen GPD1 P13707 0.094 3.8E-07 6.418 dehydrogenase 1 (soluble) degradation

glycerol-3-phosphate Glycolysis/Glycogen GPD2 dehydrogenase 2 Q64521 0.225 3.5E-07 6.462 degradation (mitochondrial)

hydroxyacyl-CoA HADH Q61425 -0.361 2.4E-06 5.616 FA metabolism dehydrogenase

hydroxyacyl-CoA dehydrogenase/3-ketoacyl- HADHA CoA thiolase/enoyl-CoA Q8BMS1 -0.255 6.9E-25 24.164 FA metabolism hydratase (trifunctional protein), alpha subunit

hydroxyacyl-CoA dehydrogenase/3-ketoacyl- HADHB CoA thiolase/enoyl-CoA Q99JY0 -0.235 8.5E-27 26.071 FA metabolism hydratase (trifunctional protein), beta subunit

3-hydroxyisobutyrate HIBADH Q99L13 -0.445 9.2E-04 3.035 Mitochondrial protein dehydrogenase

hydroxysteroid (17-beta) HSD17B10 Q99N15 -0.137 3.1E-02 1.504 FA metabolism dehydrogenase 10

heat shock 70kDa protein 9 HSPA9 P38647 -0.265 8.5E-10 9.072 Mitochondrial protein (mortalin)

heat shock 60kDa protein 1 HSPD1 P63038 -0.216 5.1E-13 12.292 Mitochondrial protein (chaperonin)

HSPE1 heat shock 10kDa protein 1 Q64433 -0.238 4.1E-02 1.389 Mitochondrial protein Diabetes Page 128 of 165

(chaperonin 10)

isocitrate dehydrogenase 2 Respiratory chain/TCA IDH2 P54071 -0.242 2.9E-13 12.541 (NADP+), mitochondrial cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA IDH3A Q9D6R2 -0.181 7.4E-09 8.131 (NAD+) alpha cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA IDH3B Q91VA7 -0.212 1.7E-11 10.762 (NAD+) beta cycle

isocitrate dehydrogenase 3 Respiratory chain/TCA IDH3G P70404 -0.235 1.1E-03 2.975 (NAD+) gamma cycle

leucine zipper-EF-hand Mitochondrial solute LETM1 containing transmembrane Q9Z2I0 -0.402 1.3E-03 2.893 transport protein 1

leucine-rich pentatricopeptide LRPPRC Q99KF9 -0.439 3.4E-02 1.471 Mitochondrial protein repeat containing

malate dehydrogenase 2, NAD Respiratory chain/TCA MDH2 P08249 -0.152 5.0E-11 10.303 (mitochondrial) cycle

malic enzyme 1, NADP(+)- Glycolysis/Glycogen ME1 Q9DBF9 -0.347 3.9E-07 6.405 dependent, cytosolic degradation

Page 129 of 165 Diabetes

Table S2D – Individual differential expression from Figure 2D (STZ-I vs. ND comparison) of 60 significantly affected proteins implicated in protein synthesis, protein degradation and oxidative stress response. Table lists protein symbols, names and accession numbers as given by UniProt database database, together with their expression ratio (in log2 scale), p-value (base and in –log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in the alphabetical order by their respective symbols.

-log10 Log2 p-value p-value Symbol Entrez Gene Name Accesion # (STZ-I vs (STZ-I Group (STZ-I vs ND) vs ND) ND)

Oxidative stress and P68134 0.241 1.8E-06 5.740 ACTA1 actin, alpha 1, skeletal muscle cellular damage

Oxidative stress and P24270 1.398 1.5E-09 8.818 CAT catalase cellular damage

Protein synthesis and Q52L78 -0.561 8.9E-13 12.053 CRYAB crystallin, alpha B chaperones

Protein synthesis and Q3TF87 -0.419 3.9E-06 5.408 DARS aspartyl-tRNA synthetase chaperones

eukaryotic translation elongation Protein synthesis and P57776 -0.514 2.3E-02 1.638 EEF1D factor 1 delta (guanine nucleotide chaperones exchange protein)

Protein synthesis and eukaryotic translation elongation Q4FZK2 -0.651 2.6E-14 13.578 EEF1G factor 1 gamma chaperones

Protein synthesis and Q8CGC7 -0.363 3.6E-05 4.445 EPRS glutamyl-prolyl-tRNA synthetase chaperones

Oxidative stress and P09528 0.567 1.5E-04 3.812 FTH1 ferritin, heavy polypeptide 1 cellular damage

Oxidative stress and P15626 0.521 4.7E-05 4.327 GSTM1 glutathione S-transferase mu 1 cellular damage

Oxidative stress and Q8R5I6 0.415 1.0E-03 2.983 GSTM4 glutathione S-transferase mu 4 cellular damage

Oxidative stress and P10649 0.303 3.2E-07 6.495 GSTM5 glutathione S-transferase mu 5 cellular damage

Oxidative stress and P19157 0.269 4.0E-06 5.399 GSTP1 glutathione S-transferase pi 1 cellular damage Diabetes Page 130 of 165

Protein synthesis and heat shock protein 90kDa alpha Q71LX8 -0.291 1.4E-13 12.854 HSP90AB1 (cytosolic), class B member 1 chaperones

Oxidative stress and heat shock protein 90kDa alpha Q71LX8 -0.291 1.4E-13 12.854 HSP90AB1 (cytosolic), class B member 1 cellular damage

Protein synthesis and heat shock protein 90kDa beta P08113 -0.267 5.7E-02 1.243 HSP90B1 (Grp94), member 1 chaperones

Protein synthesis and Q61316 -0.182 6.5E-02 1.185 HSPA4 heat shock 70kDa protein 4 chaperones

Protein synthesis and heat shock 70kDa protein 9 P38647 -0.423 9.3E-20 19.030 HSPA9 (mortalin) chaperones

Protein synthesis and P14602 -0.514 9.1E-13 12.042 HSPB1 heat shock 27kDa protein 1 chaperones

Protein synthesis and heat shock protein, alpha- Q5EBG6 -0.827 3.0E-12 11.519 HSPB6 crystallin-related, B6 chaperones

Protein synthesis and heat shock 60kDa protein 1 P63038 -0.248 3.1E-18 17.509 HSPD1 (chaperonin) chaperones

Protein synthesis and heat shock 10kDa protein 1 Q4KL76 -0.348 7.8E-04 3.107 HSPE1 (chaperonin 10) chaperones

Oxidative stress and mitogen-activated protein kinase P70236 -0.322 7.3E-03 2.140 MAP2K6 kinase 6 cellular damage

Protein synthesis and protein phosphatase 1, catalytic P62141 -0.191 1.4E-02 1.860 PPP1CB subunit, beta isozyme chaperones

Oxidative stress and P35700 0.136 8.5E-03 2.072 PRDX1 peroxiredoxin 1 cellular damage

Oxidative stress and Q61171 0.085 8.6E-03 2.066 PRDX2 peroxiredoxin 2 cellular damage

Oxidative stress and P99029 -0.299 4.8E-08 7.315 PRDX5 peroxiredoxin 5 cellular damage

Protein ubiquitination- proteasome (prosome, Q9Z2U1 0.342 1.1E-06 5.979 PSMA5 macropain) subunit, alpha type, 5 related Page 131 of 165 Diabetes

Protein synthesis and P53026 -0.694 1.9E-05 4.721 RPL10A ribosomal protein L10a chaperones

Protein synthesis and A2BH07 -0.643 1.0E-05 4.983 RPL11 ribosomal protein L11 chaperones

Protein synthesis and Q5BLK0 -0.573 1.2E-03 2.939 RPL12 ribosomal protein L12 chaperones

Protein synthesis and P47963 0.57 1.4E-02 1.866 RPL13 ribosomal protein L13 chaperones

Protein synthesis and P62830 -0.382 9.8E-03 2.009 RPL23 ribosomal protein L23 chaperones

Protein synthesis and O55142 -0.701 3.4E-03 2.469 RPL35A ribosomal protein L35a chaperones

Protein synthesis and P51410 -0.719 5.5E-04 3.256 RPL9 ribosomal protein L9 chaperones

Protein synthesis and Q5M8R8 -0.674 5.8E-10 9.240 RPLP0 ribosomal protein, large, P0 chaperones

Protein synthesis and P99027 -0.234 1.3E-03 2.900 RPLP2 ribosomal protein, large, P2 chaperones

Protein synthesis and Q3U9P0 -0.492 3.5E-02 1.456 RPS10 ribosomal protein S10 chaperones

Protein synthesis and Q3UC02 -0.461 2.2E-02 1.652 RPS11 ribosomal protein S11 chaperones

Protein synthesis and P62270 -0.328 1.1E-02 1.951 RPS18 ribosomal protein S18 chaperones

Protein synthesis and Q9CZX8 -0.514 9.9E-04 3.007 RPS19 ribosomal protein S19 chaperones

Protein synthesis and P25444 -0.583 5.3E-04 3.276 RPS2 ribosomal protein S2 chaperones

Protein synthesis and Q5YLW3 -0.544 3.8E-04 3.425 RPS3 ribosomal protein S3 chaperones Diabetes Page 132 of 165

Protein synthesis and P62702 -0.607 5.3E-03 2.278 RPS4Y1 ribosomal protein S4, Y-linked 1 chaperones

Protein synthesis and P62082 -0.197 2.9E-02 1.538 RPS7 ribosomal protein S7 chaperones

Protein synthesis and B2CY77 -0.605 1.7E-05 4.783 RPSA ribosomal protein SA chaperones

Oxidative stress and P08228 0.213 9.2E-07 6.038 SOD1 superoxide dismutase 1, soluble cellular damage

Oxidative stress and superoxide dismutase 2, P09671 -0.305 8.3E-07 6.081 SOD2 mitochondrial cellular damage

Oxidative stress and Q60864 -0.186 5.2E-03 2.287 STIP1 stress-induced-phosphoprotein 1 cellular damage

Protein synthesis and Q8BLY2 -0.415 3.7E-06 5.437 TARSL2 threonyl-tRNA synthetase-like 2 chaperones

Protein synthesis and tumor protein, translationally- P63028 -0.188 8.3E-03 2.079 TPT1 controlled 1 chaperones

Protein synthesis and Tu translation elongation factor, Q8BFR5 -0.179 1.6E-05 4.801 TUFM mitochondrial chaperones

Protein ubiquitination- ubiquitin-like modifier activating Q02053 0.16 5.4E-03 2.265 UBA1 enzyme 1 related

Protein ubiquitination- A5JUZ1 0.351 1.3E-15 14.876 UBC ubiquitin C related

Protein ubiquitination- ubiquitin-conjugating enzyme E2L P68037 0.16 3.9E-02 1.415 UBE2L3 3 related

Protein ubiquitination- NP_001170883 0.721 2.8E-03 2.548 USP35 ubiquitin specific peptidase 35 related

tyrosine 3- Oxidative stress and monooxygenase/tryptophan 5- Q9CQV8 0.514 1.3E-03 2.873 YWHAB monooxygenase activation cellular damage protein, beta polypeptide

tyrosine 3- Oxidative stress and Q5SS40 0.132 2.9E-04 3.533 YWHAE monooxygenase/tryptophan 5- cellular damage monooxygenase activation Page 133 of 165 Diabetes

protein, epsilon polypeptide

tyrosine 3- Oxidative stress and monooxygenase/tryptophan 5- A8IP69 0.136 7.2E-06 5.143 YWHAG monooxygenase activation cellular damage protein, gamma polypeptide

tyrosine 3- Oxidative stress and monooxygenase/tryptophan 5- P63101 0.139 4.3E-03 2.366 YWHAZ monooxygenase activation cellular damage protein, zeta polypeptide

Diabetes Page 134 of 165

Table S2E – Individual differential expression from Figure 3D (STZ+I vs. STZ-I comparison) of 60 significantly affected proteins implicated in protein synthesis, protein degradation and oxidative stress response. Table lists protein symbols, names and accession numbers as given by UniProt database, together with their expression ratio (in log2 scale), p-value (base and in –log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in the alphabetical order by their respective symbols.

-log10 Log2 p-value p-value Symbol Entrez Gene Name Accesion # (STZ+I vs (STZ+I vs Group (STZ+I vs STZ-I) STZ-I) STZ-I)

Oxidative stress and ACTA1 actin, alpha 1, skeletal muscle P68134 0.212 3.8E-05 4.419 cellular damage

Oxidative stress and CAT catalase P24270 -1.341 8.7E-09 8.062 cellular damage

Protein synthesis and DARS aspartyl-tRNA synthetase Q3TF87 0.733 3.6E-05 4.445 chaperones

eukaryotic translation Protein synthesis and EEF1A2 P62631 0.049 3.2E-02 1.498 elongation factor 1 alpha 2 chaperones

eukaryotic translation elongation factor 1 delta Protein synthesis and EEF1D P57776 0.541 2.5E-02 1.609 (guanine nucleotide exchange chaperones protein)

eukaryotic translation Protein synthesis and EEF1G Q4FZK2 0.584 4.5E-09 8.344 elongation factor 1 gamma chaperones

eukaryotic translation Protein synthesis and Eif5a P63242 -0.138 1.7E-02 1.780 initiation factor 5A chaperones

glutamyl-prolyl-tRNA Protein synthesis and EPRS Q8CGC7 0.262 1.3E-03 2.900 synthetase chaperones

Oxidative stress and FTH1 ferritin, heavy polypeptide 1 P09528 -0.702 1.0E-09 9.002 cellular damage

Protein synthesis and GARS glycyl-tRNA synthetase Q9CZD3 -0.182 4.0E-02 1.397 chaperones

glutathione peroxidase 3 Oxidative stress and GPX3 P46412 -0.586 1.2E-02 1.939 (plasma) cellular damage

Oxidative stress and GSTM1 glutathione S-transferase mu 1 P15626 -0.250 4.0E-02 1.398 cellular damage

Oxidative stress and GSTM4 glutathione S-transferase mu 4 Q8R5I6 -0.244 2.7E-02 1.565 cellular damage

Oxidative stress and GSTM5 glutathione S-transferase mu 5 P10649 -0.255 1.9E-03 2.730 cellular damage

Oxidative stress and GSTP1 glutathione S-transferase pi 1 P19157 -0.274 2.8E-06 5.550 cellular damage

heat shock protein 90kDa Oxidative stress and HSP90AB1 Q71LX8 0.257 3.9E-13 12.411 alpha (cytosolic), class B cellular damage Page 135 of 165 Diabetes

member 1

heat shock protein 90kDa Protein synthesis and HSP90AB1 alpha (cytosolic), class B Q71LX8 0.257 3.9E-13 12.411 chaperones member 1

heat shock 70kDa protein 9 Protein synthesis and HSPA9 P38647 0.158 3.1E-04 3.506 (mortalin) chaperones

Protein synthesis and HSPB1 heat shock 27kDa protein 1 P14602 0.244 4.2E-04 3.375 chaperones

heat shock protein, alpha- Protein synthesis and HSPB6 Q5EBG6 0.600 6.0E-05 4.223 crystallin-related, B6 chaperones

heat shock 60kDa protein 1 Protein synthesis and HSPD1 P63038 0.063 4.7E-02 1.332 (chaperonin) chaperones

malic enzyme 1, NADP(+)- Oxidative stress and ME1 Q921S3 -0.221 2.3E-05 4.648 dependent, cytosolic cellular damage

protein phosphatase 1, Protein synthesis and PPP1CA catalytic subunit, alpha P62137 0.189 4.6E-02 1.334 chaperones isozyme

protein phosphatase 2, Protein synthesis and PPP2R2A Q6P1F6 -0.172 2.9E-03 2.539 regulatory subunit B, alpha chaperones

Oxidative stress and PRDX1 peroxiredoxin 1 B1AXW5 -0.211 1.6E-09 8.796 cellular damage

Oxidative stress and PRDX2 peroxiredoxin 2 Q61171 -0.152 4.2E-06 5.375 cellular damage

proteasome (prosome, Protein ubiquitination- PSMA5 macropain) subunit, alpha Q9Z2U1 -0.215 2.7E-03 2.573 related type, 5

proteasome (prosome, Protein ubiquitination- PSMC4 macropain) 26S subunit, Q3TFA5 -0.204 1.5E-02 1.821 related ATPase, 4

Protein synthesis and RPL10A ribosomal protein L10a P53026 0.693 1.2E-04 3.936 chaperones

Protein synthesis and RPL11 ribosomal protein L11 A2BH07 0.626 1.7E-07 6.770 chaperones

Protein synthesis and RPL12 ribosomal protein L12 Q5BLK0 0.628 7.7E-05 4.114 chaperones

Protein synthesis and RPL22 ribosomal protein L22 P67984 0.544 4.9E-02 1.308 chaperones

Protein synthesis and RPL23 ribosomal protein L23 P62830 0.505 7.9E-04 3.101 chaperones

Protein synthesis and RPL27 ribosomal protein L27 P61358 0.800 3.5E-02 1.460 chaperones

Protein synthesis and RPL35A ribosomal protein L35a O55142 0.665 1.3E-03 2.893 chaperones

RPL9 ribosomal protein L9 P51410 0.813 1.2E-05 4.932 Protein synthesis and Diabetes Page 136 of 165

chaperones

Protein synthesis and RPLP0 ribosomal protein, large, P0 Q5M8R8 0.710 3.4E-11 10.466 chaperones

Protein synthesis and RPLP2 ribosomal protein, large, P2 P99027 0.240 1.8E-03 2.757 chaperones

Protein synthesis and RPS10 ribosomal protein S10 Q3U9P0 0.575 9.4E-03 2.027 chaperones

Protein synthesis and RPS11 ribosomal protein S11 Q3UC02 0.723 8.0E-04 3.096 chaperones

Protein synthesis and RPS13 ribosomal protein S13 Q5BLJ7 0.592 1.9E-02 1.726 chaperones

Protein synthesis and RPS15A ribosomal protein S15a P62245 0.505 1.3E-02 1.886 chaperones

Protein synthesis and RPS16 ribosomal protein S16 A4FUS1 0.659 2.1E-02 1.678 chaperones

Protein synthesis and RPS18 ribosomal protein S18 P62270 0.318 2.2E-02 1.650 chaperones

Protein synthesis and RPS19 ribosomal protein S19 Q9CZX8 0.571 1.4E-04 3.851 chaperones

Protein synthesis and RPS2 ribosomal protein S2 P25444 0.331 2.7E-02 1.565 chaperones

Protein synthesis and RPS3 ribosomal protein S3 Q5YLW3 0.800 2.6E-08 7.588 chaperones

ribosomal protein S4, Y-linked Protein synthesis and RPS4Y1 P62702 0.963 4.4E-05 4.354 1 chaperones

Protein synthesis and RPSA ribosomal protein SA B2CY77 0.656 9.7E-06 5.015 chaperones

superoxide dismutase 1, Oxidative stress and SOD1 P08228 -0.284 2.4E-10 9.614 soluble cellular damage

superoxide dismutase 2, Oxidative stress and SOD2 P09671 0.132 3.3E-02 1.487 mitochondrial cellular damage

threonyl-tRNA synthetase-like Protein synthesis and TARSL2 Q8BLY2 0.247 2.8E-03 2.554 2 chaperones

Oxidative stress and TKT transketolase P40142 -0.280 4.1E-02 1.393 cellular damage

ubiquitin-like modifier Protein ubiquitination- UBA1 Q02053 -0.115 2.9E-02 1.538 activating enzyme 1 related

Protein ubiquitination- UBC ubiquitin C A5JUZ1 -0.244 1.1E-06 5.947 related

Oxidative stress and VCP valosin containing protein Q01853 -0.123 1.4E-08 7.860 cellular damage

tyrosine 3- Oxidative stress and YWHAB Q9CQV8 -0.439 4.2E-03 2.378 monooxygenase/tryptophan cellular damage Page 137 of 165 Diabetes

5-monooxygenase activation protein, beta polypeptide

tyrosine 3- monooxygenase/tryptophan Oxidative stress and YWHAE Q5SS40 -0.171 2.4E-04 3.627 5-monooxygenase activation cellular damage protein, epsilon polypeptide

tyrosine 3- monooxygenase/tryptophan Oxidative stress and YWHAG A8IP69 -0.174 4.9E-11 10.310 5-monooxygenase activation cellular damage protein, gamma polypeptide

tyrosine 3- monooxygenase/tryptophan Oxidative stress and YWHAZ P63101 -0.229 2.0E-06 5.703 5-monooxygenase activation cellular damage protein, zeta polypeptide

Diabetes Page 138 of 165

Table S2F – Individual differential expression from Figure S2F (STZ+I vs. ND comparison) of 32 significantly affected proteins implicated in protein synthesis, protein degradation and oxidative stress response. Table lists protein symbols, names and accession numbers as given by UniProt database, together with their expression ratio (in log2 scale), p-value (base and in –log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in the alphabetical order by their respective symbols.

-log10 Log2 p-value p-value Symbol Entrez Gene Name Accesion # (STZ+I vs (STZ+I vs Group (STZ+I vs ND) ND) ND)

Oxidative stress and ACTA1 actin, alpha 1, skeletal muscle P68134 0.452 2.8E-30 29.558 cellular damage

Oxidative stress and ACTC1 actin, alpha, cardiac muscle 1 Q3UIJ3 0.558 7.5E-06 5.126 cellular damage

Protein ubiquitination- CRYAB crystallin, alpha B Q52L78 -0.312 4.5E-12 11.343 related

DnaJ (Hsp40) homolog, Oxidative stress and DNAJA2 subfamily A, member 2 Q9QYJ0 -0.230 3.4E-02 1.472 cellular damage

eukaryotic translation Protein synthesis and EEF1G elongation factor 1 gamma Q4FZK2 -0.146 1.4E-02 1.863 chaperones

Oxidative stress and FTH1 ferritin, heavy polypeptide 1 P09528 -0.290 1.7E-02 1.764 cellular damage

Protein synthesis and GARS glycyl-tRNA synthetase Q9CZD3 -0.203 5.6E-03 2.251 chaperones

Oxidative stress and GSTM1 glutathione S-transferase mu 1 P15626 0.270 4.0E-02 1.394 cellular damage

Oxidative stress and GSTM5 glutathione S-transferase mu 5 P10649 0.149 1.2E-02 1.907 cellular damage

heat shock protein 90kDa alpha (cytosolic), class B Protein synthesis and HSP90AB1 member 1 Q71LX8 -0.110 4.1E-04 3.389 chaperones

Protein synthesis and HSPA4 heat shock 70kDa protein 4 Q61316 -0.254 1.3E-02 1.876 chaperones

HSPA9 P38647 -0.265 8.5E-10 9.072 heat shock 70kDa protein 9 Protein synthesis and Page 139 of 165 Diabetes

(mortalin) chaperones

Protein synthesis and HSPB1 heat shock 27kDa protein 1 P14602 -0.270 4.5E-04 3.346 chaperones

heat shock 60kDa protein 1 Protein synthesis and HSPD1 (chaperonin) P63038 -0.216 5.1E-13 12.292 chaperones

heat shock 10kDa protein 1 Protein synthesis and HSPE1 (chaperonin 10) Q4KL76 -0.238 4.1E-02 1.389 chaperones

malic enzyme 1, NADP(+)- Oxidative stress and ME1 dependent, cytosolic Q9DBF9 -0.347 3.9E-07 6.405 cellular damage

microsomal glutathione S- Oxidative stress and MGST3 transferase 3 Q9CPU4 -0.313 1.8E-02 1.757 cellular damage

Oxidative stress and PRDX1 peroxiredoxin 1 P35700 -0.150 6.5E-06 5.190 cellular damage

Oxidative stress and PRDX2 peroxiredoxin 2 Q61171 -0.104 5.8E-03 2.237 cellular damage

Oxidative stress and PRDX3 peroxiredoxin 3 P20108 -0.127 4.6E-02 1.341 cellular damage

Oxidative stress and PRDX5 peroxiredoxin 5 P99029 -0.258 5.1E-06 5.292 cellular damage

proteasome (prosome, macropain) subunit, alpha Protein ubiquitination- PSMA5 type, 5 Q9Z2U1 -0.160 2.4E-02 1.625 related

proteasome (prosome, macropain) subunit, beta type, Protein ubiquitination- PSMB3 3 Q545G0 -0.296 4.6E-03 2.338 related

superoxide dismutase 1, Oxidative stress and SOD1 soluble P08228 -0.118 2.0E-02 1.701 cellular damage

superoxide dismutase 2, Oxidative stress and SOD2 mitochondrial P09671 -0.173 6.3E-04 3.199 cellular damage

stress-induced Oxidative stress and STIP1 phosphoprotein 1 Q60864 -0.184 1.7E-02 1.764 cellular damage Diabetes Page 140 of 165

threonyl-tRNA synthetase-like Protein synthesis and TARSL2 2 Q8BLY2 -0.167 4.6E-02 1.335 chaperones

Tu translation elongation Protein synthesis and TUFM factor, mitochondrial Q8BFR5 0.107 7.9E-03 2.104 chaperones

Protein ubiquitination- UBC ubiquitin C A5JUZ1 0.107 1.5E-02 1.824 related

Oxidative stress and VCP valosin containing protein Q01853 -0.140 2.0E-09 8.706 cellular damage

tyrosine 3- monooxygenase/tryptophan 5-monooxygenase activation Oxidative stress and YWHAG protein, gamma polypeptide A8IP69 -0.095 4.1E-02 1.383 cellular damage

tyrosine 3- monooxygenase/tryptophan 5-monooxygenase activation Oxidative stress and YWHAZ protein, zeta polypeptide P63101 -0.146 7.9E-03 2.102 cellular damage

Page 141 of 165 Diabetes

Table S3A – Canonical pathways significantly affected by insulin deprivation (STZ-I vs. ND comparison). Table lists pathway names as given by Ingenuity Pathway Analysis software, pathway p-value (score, as –Log10 p-value derivative) and significantly affected molecular members of a given pathway.

Pathway Name Score Significantly affected proteins

HSD17B10,SDHB,NDUFA9,NDUFA10,PRDX5,CPT1B,NDUFB5,NDUFB4,COX2,NDUFA2,PDH A1,NDUFA5,NDUFS1,SOD2,PARK7,GPD2,NDUFS6,UQCRFS1,NDUFS2,OGDH,COX4I1,NDU Mitochondrial Dysfunction 36 FS4,AIFM1,NDUFA8,SDHA,COX1,NDUFV1,NDUFB3,CYCS,ATP5A1,COX6C,NDUFS3,NDUFA 13,ATP5C1,NDUFS5,ND5,NDUFV2,ATP5B,NDUFA6,CAT,UQCRC2,NDUFB7,COX5A,NDUFA 12,CYC1,UQCRC1,COX5B,NDUFA7

TCA Cycle II (Eukaryotic) 17,6 SDHA,SDHB,IDH3G,ACO2,SUCLA2,CS,SUCLG1,DLST,DLD,IDH3A,FH,MDH2,OGDH,IDH3B

Glycolysis I 8,44 Pkm,PGK1,GPI,TPI1,ENO3,PGAM2,ALDOA,PFKM,FBP2

MYH4,TNNT1,MYL2,TNNI2,TNNC2,MYH8,TNNC1,ATP2A1,TPM3,TPM2,Tpm1,MYH7,ATP2 Calcium Signaling 8,29 A2,MYL1,MYH2,TNNT3,CASQ1,MYL4,RYR1,ACTC1,ACTA1,MYH1

Fatty Acid β-oxidation I 7,01 HSD17B10,HADHB,SLC27A1,ACADM,ACAA2,ECI1,ACSL1,HADHA,HADH

Glycolysis II 5,68 PGK1,GPI,ENO3,PGAM2,ALDOA,MDH2,FBP2

MYH4,PFN1,MYL2,MYH8,MYLPF,ACTN2,MYLK2,PPP1CB,MYH7,GSN,TTN,MYL1,MYH2,CFL Actin Cytoskeleton Signaling 5,11 2,MYL4,ACTC1,ACTA1,ACTN3,MYH1

Cellular Effects of Sildenafil 4,88 MYH4,MYH2,MYL2,MYH8,MYLPF,MYL4,PPP1CB,MYH7,ACTC1,MYL1,ACTA1,MYH1 (Viagra)

Glycogen Degradation II 4,65 PYGM,PGM1,PYGB,AGL

Glycogen Degradation III 4,19 PYGM,PGM1,PYGB,AGL

Valine Degradation I 4,11 HIBCH,HADHB,HIBADH,DLD,HADHA

2-ketoglutarate 4 DLST,DLD,OGDH Dehydrogenase Complex

Ketolysis 4 HADHB,OXCT1,HADHA

Aspartate Degradation II 4 GOT1,MDH2,GOT2

Isoleucine Degradation I 3,84 HSD17B10,HADHB,DLD,HADHA

Epithelial Adherens Junction MYH4,MYL2,MYH8,ACTN2,TUBA4A,MYH7,TUBB,MYL1,MYH2,MYL4,ACTC1,ACTN3,ACTA 3,8 Signaling 1,MYH1

RhoA Signaling 3,63 PFN1,CFL2,MYL2,MYLPF,MYLK2,MYL4,PPP1CB,ACTC1,TTN,MYL1,ACTA1

MAP2K6,MYH4,MYL2,MYH8,ACTN2,MYH7,MYL1,MYH2,CFL2,FLNC,MYL4,ACTC1,ACTA1, ILK Signaling 3,58 ACTN3,MYH1

Glutaryl-CoA Degradation 3,55 HSD17B10,HADHB,HADHA,HADH

Tryptophan Degradation III 3,55 HSD17B10,HADHB,HADHA,HADH (Eukaryotic)

Regulation of Actin-based 3,44 PFN1,MYL2,MYLPF,MYL4,PPP1CB,GSN,ACTC1,MYL1,ACTA1 Motility by Rho

Acetyl-CoA Biosynthesis I (Pyruvate Dehydrogenase 3,41 PDHA1,DLAT,DLD Complex) Diabetes Page 142 of 165

Mitochondrial L-carnitine 2,93 CPT1B,CPT2,SLC27A1,ACSL1 Shuttle Pathway

Superoxide Radicals 2,74 SOD1,SOD2,CAT Degradation

Methylglyoxal Degradation III 2,74 Akr1b10,FAM213B,AKR1B1

Creatine-phosphate 2,66 CKMT2,CKM Biosynthesis

Pyruvate Fermentation to 2,66 Ldhb,LDHA Lactate

Glycerol Degradation I 2,66 GPD1,GPD2

Glycerol-3-phosphate Shuttle 2,66 GPD1,GPD2

Glutamate Degradation II 2,66 GOT1,GOT2

Aspartate Biosynthesis 2,66 GOT1,GOT2

H1F0,MYH4,YWHAG,YWHAE,MYL2,TNNI2,YWHAB,MYLPF,MYLK2,GNB2L1,YWHAZ,PPP1C Protein Kinase A Signaling 2,61 B,PYGB,TTN,MYL1,MYH2,PYGM,FLNC,MYL4,RYR1

EIF2 Signaling 2,58 RPS7,RPS4Y1,RPS10,RPS18,RPS19,RPLP2,PPP1CB,RPL12,RPS3,RPLP0,RPL10A,RPSA

Phenylalanine Degradation IV 2,33 ALDH2,GOT1,GOT2 (Mammalian, via Side Chain)

Superpathway of Methionine 2,27 DLD,GOT1,MAT2A,GOT2 Degradation

Phenylethylamine Degradation 2,2 AOC3,ALDH2 I

L-cysteine Degradation I 2,2 GOT1,GOT2

Ethanol Degradation IV 2,17 ALDH2,CAT,ACSL1

Stearate Biosynthesis I 2,07 FAM213B,FASN,SLC27A1,ACSL1 (Animals)

Mevalonate Pathway I 1,91 HADHB,HADHA

Cell Cycle: G2/M DNA Damage 1,76 YWHAG,YWHAE,YWHAB,YWHAZ Checkpoint Regulation

Tight Junction Signaling 1,73 MYH4,MYH2,MYL2,MYH8,MYL4,MYH7,ACTC1,MYL1,ACTA1,MYH1

Remodeling of Epithelial 1,72 ACTN2,TUBA4A,TUBB,ACTC1,ACTA1,ACTN3 Adherens Junctions

Ketogenesis 1,71 HADHB,HADHA

Sucrose Degradation V 1,71 TPI1,ALDOA (Mammalian)

Superpathway of Geranylgeranyldiphosphate 1,71 HADHB,HADHA Biosynthesis I (via Mevalonate)

NRF2-mediated Oxidative 1,7 MAP2K6,GSTM1,SOD1,SOD2,GSTM5,PRDX1,STIP1,CAT,ACTC1,ACTA1,FTH1 Stress Response Page 143 of 165 Diabetes

Ethanol Degradation II 1,6 HSD17B10,ALDH2,ACSL1

Hepatic Fibrosis / Hepatic 1,6 COL1A2,MYH4,MYH2,MYL2,MYH8,MYL4,MYH7,MYL1,MYH1 Stellate Cell Activation

PPARα/RXRα Activation 1,47 MAP2K6,ACADL,GPD1,HSP90AB1,GPD2,FASN,CPT1B,CD36,SLC27A1,GOT2

Fatty Acid Activation 1,41 SLC27A1,ACSL1

Calcium Transport I 1,41 ATP2A1,ATP2A2

Colanic Acid Building Blocks 1,41 GPI,UGP2 Biosynthesis

Oxidative Ethanol Degradation 1,41 ALDH2,ACSL1 III

Myc Mediated Apoptosis 1,39 YWHAG,YWHAE,CYCS,YWHAB,YWHAZ Signaling

Glucose and Glucose-1- 1,33 PGM1 phosphate Degradation

Protein Citrullination 1,33 PADI2

Palmitate Biosynthesis I 1,33 FASN (Animals)

Fatty Acid Biosynthesis 1,33 FASN Initiation II

GDP-glucose Biosynthesis 1,33 PGM1

Glutamate Biosynthesis II 1,33 GLUD1

Glutamate Degradation X 1,33 GLUD1

Diabetes Page 144 of 165

Table S3B– Canonical pathways significantly affected by insulin treatment of STZ-animals (STZ+I vs. STZ-I comparison). Table lists pathway names as given by Ingenuity Pathway Analysis software, pathway p-value (score, as –Log10 p-value derivative) and significantly affected molecular members of a given pathway.

Pathway Name Score Significantly affected proteins

Glycolysis I 9,55 Pkm,PGK1,GPI,TPI1,ENO3,PGAM2,ALDOA,PFKM,FBP2

TCA Cycle II (Eukaryotic) 7,99 SDHA,SUCLA2,SDHB,CS,IDH3G,IDH3A,MDH2,IDH3B

Glycolysis II 7,99 PGK1,GPI,ENO3,PGAM2,ALDOA,ME1,MDH2,FBP2

Fatty Acid β-oxidation I 5,51 HADHB,SLC27A1,ACAA2,ECI1,ACSL1,HADHA,HADH

TNNT1,TNNI2,MYL2,TNNC2,ATP2A1,PRKAR2A,Tpm1,MYH7,ATP2A2,TNNT3,CASQ1,RYR1, Calcium Signaling 5,21 ASPH,ACTA1,MYH1

RPS4Y1,RPL22,RPL27,RPS18,RPS19,RPLP0,RPL10A,RPS10,RPS16,RPLP2,RPL12,RPS3,PPP1 EIF2 Signaling 4,98 CA,RPSA

Ketolysis 4,37 HADHB,OXCT1,HADHA

Aspartate Degradation II 4,37 GOT1,MDH2,GOT2

Mitochondrial Dysfunction 3,52 SDHA,NDUFV1,SDHB,NDUFS1,SOD2,ATP5B,PARK7,GPD2,ATP5A1,UQCRC2,CAT,UQCRFS1

Glycogen Degradation II 3,4 PYGM,PGM1,PYGB

Glycogen Degradation III 3,11 PYGM,PGM1,PYGB

Superoxide Radicals 3,11 SOD1,SOD2,CAT Degradation

Creatine-phosphate 2,91 CKMT2,CKM Biosynthesis

Pyruvate Fermentation to 2,91 Ldhb,LDHA Lactate

Glycerol Degradation I 2,91 GPD1,GPD2

Glycerol-3-phosphate Shuttle 2,91 GPD1,GPD2

Glutamate Degradation II 2,91 GOT1,GOT2

Aspartate Biosynthesis 2,91 GOT1,GOT2

Actin Cytoskeleton Signaling 2,73 PFN1,CFL2,MYL2,MYLPF,ACTN2,MYLK2,MYH7,GSN,TTN,ACTA1,ACTN3,MYH1

Glutaryl-CoA Degradation 2,68 HADHB,HADHA,HADH

Phenylalanine Degradation IV 2,68 ALDH2,GOT1,GOT2 (Mammalian, via Side Chain)

Tryptophan Degradation III 2,68 HADHB,HADHA,HADH (Eukaryotic)

RhoA Signaling 2,66 PFN1,CFL2,MYL2,MYLPF,MYLK2,Pfn2,TTN,ACTA1

Ethanol Degradation IV 2,52 ALDH2,CAT,ACSL1

H1F0,YWHAG,YWHAE,TNNI2,MYL2,YWHAB,MYLPF,MYLK2,YWHAZ,PRKAR2A,PYGB,TTN,P Protein Kinase A Signaling 2,45 YGM,PHKB,RYR1,PPP1CA Page 145 of 165 Diabetes

Phenylethylamine Degradation 2,45 AOC3,ALDH2 I

L-cysteine Degradation I 2,45 GOT1,GOT2

tRNA Charging 2,43 TARSL2,GARS,DARS,EPRS

Nitric Oxide Signaling in the 2,4 HSP90AB1,CACNA1S,ATP2A1,CAV1,PRKAR2A,ATP2A2 Cardiovascular System

Cellular Effects of Sildenafil 2,37 MYL2,MYLPF,CACNA1S,PRKAR2A,MYH7,ACTA1,MYH1 (Viagra)

Cell Cycle: G2/M DNA Damage 2,19 YWHAG,YWHAE,YWHAB,YWHAZ Checkpoint Regulation

Mevalonate Pathway I 2,16 HADHB,HADHA

Ketogenesis 1,94 HADHB,HADHA

Sucrose Degradation V 1,94 TPI1,ALDOA (Mammalian)

Superpathway of Geranylgeranyldiphosphate 1,94 HADHB,HADHA Biosynthesis I (via Mevalonate)

Ethanol Degradation II 1,94 ADH5,ALDH2,ACSL1

Regulation of eIF4 and p70S6K 1,83 RPS4Y1,RPS10,PPP2R2A,RPS16,RPS18,RPS19,RPS3,RPSA Signaling

PPARα/RXRα Activation 1,81 ACADL,GPD1,HSP90AB1,GPD2,ADIPOQ,PRKAR2A,CD36,SLC27A1,GOT2

Superpathway of Methionine 1,77 GOT1,MAT2A,GOT2 Degradation

Epithelial Adherens Junction 1,68 TUBA1A,MYL2,TUBB4B,ACTN2,MYH7,ACTA1,ACTN3,MYH1 Signaling

NRF2-mediated Oxidative 1,68 GSTM1,SOD1,SOD2,GSTM5,PRDX1,CAT,VCP,ACTA1,FTH1 Stress Response

Remodeling of Epithelial 1,67 TUBA1A,TUBB4B,ACTN2,ACTA1,ACTN3 Adherens Junctions

Fatty Acid Activation 1,64 SLC27A1,ACSL1

Isoleucine Degradation I 1,64 HADHB,HADHA

Calcium Transport I 1,64 ATP2A1,ATP2A2

Colanic Acid Building Blocks 1,64 GPI,UGP2 Biosynthesis

Oxidative Ethanol Degradation 1,64 ALDH2,ACSL1 III

Regulation of Actin-based 1,56 PFN1,MYL2,MYLPF,GSN,ACTA1 Motility by Rho

Cardiomyocyte Differentiation 1,53 MYL2,MYH7 via BMP Receptors

Glucose and Glucose-1- 1,46 PGM1 Diabetes Page 146 of 165 phosphate Degradation

Spermine Biosynthesis 1,46 SMS

GDP-glucose Biosynthesis 1,46 PGM1

Formaldehyde Oxidation II 1,46 ADH5 (Glutathione-dependent)

14-3-3-mediated Signaling 1,46 YWHAG,TUBA1A,YWHAE,TUBB4B,YWHAB,YWHAZ

γ-linolenate Biosynthesis II 1,43 SLC27A1,ACSL1 (Animals)

Cardiac β-adrenergic Signaling 1,38 PPP2R2A,CACNA1S,ATP2A1,PRKAR2A,PPP1CA,ATP2A2

ILK Signaling 1,32 CFL2,MYL2,PPP2R2A,ACTN2,MYH7,ACTA1,ACTN3,MYH1

Page 147 of 165 Diabetes

Table S3C– Canonical pathways significantly different between insulin treated and non-diabetic animals (STZ+I vs. ND comparison). Table lists pathway names as given by Ingenuity Pathway Analysis software, pathway p-value (score, as – Log10 p-value derivative) and significantly affected molecular members of a given pathway.

Pathway Name Score Significantly affected proteins

HSD17B10,SDHB,NDUFA9,NDUFA10,PRDX5,CPT1B,NDUFB5,COX2,NDUFA2,PDHA1,NDUF A5,NDUFS1,SOD2,GPD2,UQCRFS1,NDUFS2,OGDH,COX4I1,NDUFS4,NDUFA8,COX1,SDHA, Mitochondrial Dysfunction 27 NDUFV1,NDUFB3,CYCS,ATP5A1,NDUFA13,ATP5C1,NDUFS5,PRDX3,ATP5B,NDUFA6,UQC RC2,COX5A,CYC1,UQCRC1,COX5B

TCA Cycle II (Eukaryotic) 19.3 SDHA,SDHB,IDH3G,ACO2,SUCLA2,CS,SUCLG1,DLST,DLD,IDH3A,FH,MDH2,OGDH,IDH3B

MYH4,TNNT1,MYL2,TNNI2,TNNC2,MYH8,TNNC1,ATP2A1,PRKAR2A,TPM3,TPM2,Tpm1,A Calcium Signaling 9.65 TP2A2,MYL1,MYH2,TNNT3,MYL4,RYR1,ACTC1,ACTA1,MYH1

Fatty Acid β-oxidation I 8.01 HSD17B10,HADHB,SLC27A1,ACADM,ACAA2,ECI1,ACSL1,HADHA,HADH

Cellular Effects of Sildenafil 5.23 MYH4,MYH2,MYL2,MYH8,MYLPF,PRKAR2A,MYL4,ACTC1,MYL1,ACTA1,MYH1 (Viagra)

Valine Degradation I 4.66 HIBCH,HADHB,HIBADH,DLD,HADHA

2-ketoglutarate 4.34 DLST,DLD,OGDH Dehydrogenase Complex

Ketolysis 4.34 HADHB,OXCT1,HADHA

Aspartate Degradation II 4.34 GOT1,MDH2,GOT2

Isoleucine Degradation I 4.29 HSD17B10,HADHB,DLD,HADHA

Glutaryl-CoA Degradation 4 HSD17B10,HADHB,HADHA,HADH

Tryptophan Degradation III 4 HSD17B10,HADHB,HADHA,HADH (Eukaryotic)

Gluconeogenesis I 3.9 PGK1,ENO3,ALDOA,ME1,MDH2

Epithelial Adherens Junction 3.76 MYH4,MYH2,MYL2,MYH8,ACTN2,TUBA4A,MYL4,ACTC1,MYL1,ACTA1,ACTN3,MYH1 Signaling

Acetyl-CoA Biosynthesis I (Pyruvate Dehydrogenase 3.75 PDHA1,DLAT,DLD Complex) Diabetes Page 148 of 165

MYH4,MYL2,MYH8,MYLPF,ACTN2,GSN,TTN,MYL1,MYH2,MYL4,ACTC1,ACTN3,ACTA1,MY Actin Cytoskeleton Signaling 3.69 H1

MYH4,MYL2,MYH8,ACTN2,MYL1,PPP2R1A,MYH2,FLNC,MYL4,ACTC1,ACTA1,ACTN3,MYH ILK Signaling 3.67 1

Mitochondrial L-carnitine 3.36 CPT1B,CPT2,SLC27A1,ACSL1 Shuttle Pathway

Tight Junction Signaling 3.05 MYH4,PPP2R1A,MYH2,MYL2,MYH8,PRKAR2A,MYL4,ACTC1,MYL1,ACTA1,MYH1

NRF2-mediated Oxidative 3.04 GSTM1,SOD1,SOD2,GSTM5,PRDX1,STIP1,VCP,DNAJA2,ACTC1,ACTA1,MGST3,FTH1 Stress Response

Pyruvate Fermentation to 2.89 Ldhb,LDHA Lactate

Glycerol Degradation I 2.89 GPD1,GPD2

Glycerol-3-phosphate Shuttle 2.89 GPD1,GPD2

Glutamate Degradation II 2.89 GOT1,GOT2

Aspartate Biosynthesis 2.89 GOT1,GOT2

Glycolysis I 2.8 PGK1,ENO3,ALDOA,PFKM

Regulation of Actin-based 2.79 MYL2,MYLPF,MYL4,GSN,ACTC1,MYL1,ACTA1 Motility by Rho

Phenylalanine Degradation IV 2.65 ALDH2,GOT1,GOT2 (Mammalian, via Side Chain)

L-cysteine Degradation I 2.43 GOT1,GOT2

PPARα/RXRα Activation 2.21 ACADL,GPD1,HSP90AB1,GPD2,FASN,CPT1B,PRKAR2A,CD36,SLC27A1,GOT2

Mevalonate Pathway I 2.14 HADHB,HADHA

Glutathione-mediated 2.11 GSTM1,GSTM5,MGST3 Detoxification

RhoA Signaling 2.02 MYL2,MYLPF,MYL4,ACTC1,TTN,MYL1,ACTA1 Page 149 of 165 Diabetes

Ketogenesis 1.93 HADHB,HADHA

Glycogen Degradation II 1.93 PYGM,PGM1

Superpathway of Geranylgeranyldiphosphate 1.93 HADHB,HADHA Biosynthesis I (via Mevalonate)

Ethanol Degradation II 1.91 HSD17B10,ALDH2,ACSL1

Hepatic Fibrosis / Hepatic 1.8 COL1A2,MYH4,MYH2,MYL2,MYH8,MYL4,MYL1,MYH1 Stellate Cell Activation

Glycogen Degradation III 1.76 PYGM,PGM1

Superoxide Radicals 1.76 SOD1,SOD2 Degradation

Superpathway of Methionine 1.75 DLD,GOT1,GOT2 Degradation

LPS/IL-1 Mediated Inhibition 1.71 GSTM1,GSTM5,CPT1B,CPT2,FABP4,SLC27A1,FABP3,ACSL1,MGST3 of RXR Function

MYH4,YWHAG,MYL2,TNNI2,MYLPF,YWHAZ,PRKAR2A,TTN,MYL1,MYH2,PYGM,FLNC,MYL Protein Kinase A Signaling 1.65 4,RYR1

Remodeling of Epithelial 1.63 ACTN2,TUBA4A,ACTC1,ACTA1,ACTN3 Adherens Junctions

Fatty Acid Activation 1.62 SLC27A1,ACSL1

Calcium Transport I 1.62 ATP2A1,ATP2A2

Oxidative Ethanol Degradation 1.62 ALDH2,ACSL1 III

Stearate Biosynthesis I 1.61 FASN,SLC27A1,ACSL1 (Animals)

Glucose and Glucose-1- 1.45 PGM1 phosphate Degradation

Protein Citrullination 1.45 PADI2 Diabetes Page 150 of 165

Palmitate Biosynthesis I 1.45 FASN (Animals)

Fatty Acid Biosynthesis 1.45 FASN Initiation II

GDP-glucose Biosynthesis 1.45 PGM1

TR/RXR Activation 1.43 SLC16A3,COL6A3,FASN,ATP2A1,ME1

γ-linolenate Biosynthesis II 1.41 SLC27A1,ACSL1 (Animals)

Ethanol Degradation IV 1.41 ALDH2,ACSL1

Page 151 of 165 Diabetes

Table S4 –Individual mitochondrial protein data from Figure S3. Table lists 111 mitochondrial proteins, protein symbols, names and accession numbers as given by UniProt database, together with their expression ratio (in log2 scale), p-value (base and in –log10 scale) and Ingenuity IPA protein group affiliation (Group). Proteins are listed in alphabetical order by their symbols. Mitochondrial localization according to MitoCarta mitochondrial proteome database.

Log2 p-value Log2 p-value Symbol Entrez Gene Name Accession # (STZ-I vs (STZ-I vs (STZ+I vs (STZ+I vs Group ND) ND) ND) ND)

ACAA2 acetyl-CoA acyltransferase 2 Q8BWT1 -0.672 1.8E-42 -0.523 1.1E-27 Lipid metabolism

acyl-CoA dehydrogenase, long ACADL P51174 -0.461 4.7E-19 -0.510 3.7E-23 Lipid metabolism chain

acyl-CoA dehydrogenase, C-4 ACADM Q91WS8 -0.512 8.0E-13 -0.454 1.3E-13 Lipid metabolism to C-12 straight chain

acyl-CoA dehydrogenase, very ACADVL B1AR27 -0.246 2.2E-16 -0.301 4.4E-16 Lipid metabolism long chain

ACAT1 acetyl-CoA acetyltransferase 1 Q8QZT1 -0.440 7.89E-25 -0.295 1.12E-12 Lipid metabolism

ACO2 aconitase 2, mitochondrial Q99KI0 0.073 3.8E-08 0.050 1.4E-04 TCA Cycle

acyl-CoA synthetase long- ACSL1 P41216 -0.235 5.8E-19 -0.318 1.9E-42 Lipid metabolism chain family member 1

aarF domain containing Respiratory chain, ADCK3 Q60936 0.285 3.6E-03 -0.288 3.2E-02 kinase 3 realted

aldehyde dehydrogenase 2 ALDH2 P47738 -0.156 9.1E-03 -0.453 2.4E-13 Ethanol degradation family (mitochondrial)

ATP synthase, H+ transporting, mitochondrial ATP5A1 D3Z6F5 -0.185 1.0E-07 -0.118 7.0E-05 Respiratory chain F1 complex, alpha subunit 1, cardiac muscle

ATP synthase, H+ ATP5B transporting, mitochondrial P56480 -0.202 4.4E-16 -0.127 4.3E-07 Respiratory chain F1 complex, beta polypeptide

ATP synthase, H+ transporting, mitochondrial ATP5C1 A2AKU9 -0.150 5.2E-05 -0.144 2.4E-06 Respiratory chain F1 complex, gamma polypeptide 1 Diabetes Page 152 of 165

ATP synthase, H+ ATP5F1 transporting, mitochondrial Q5I0W0 -0.238 6.7E-08 -0.200 2.5E-06 Respiratory chain Fo complex, subunit B1

ATP synthase, H+ Atp5h transporting, mitochondrial Q9DCX2 -0.300 5.1E-12 -0.250 4.0E-11 Respiratory chain F0 complex, subunit d

ATP synthase, H+ ATP5I transporting, mitochondrial Q5EBI8 -0.211 2.9E-04 -0.177 1.4E-03 Respiratory chain Fo complex, subunit E

ATP synthase, H+ ATP5L transporting, mitochondrial Q9CPQ8 -0.286 1.3E-04 -0.261 2.7E-05 Respiratory chain Fo complex, subunit G

ATP synthase, H+ ATP5O transporting, mitochondrial Q9DB20 -0.201 2.9E-05 -0.161 9.0E-05 Respiratory chain F1 complex, O subunit

capping protein (actin CAPZA2 filament) muscle Z-line, alpha Q5DQJ3 0.707 5.6E-22 0.763 4.2E-23 2

coiled-coil-helix-coiled-coil- Mitochondrial cristae CHCHD3 Q9CRB9 -0.315 2.0E-04 -0.231 3.0E-02 helix domain containing 3 integrity

CISD1 CDGSH iron sulfur domain 1 Q91WS0 -0.130 2.6E-02 -0.145 3.8E-03 Mitochondrial

creatine kinase, mitochondrial Mitochondrial CKMT2 Q6P8J7 -0.646 4.5E-88 -0.379 2.6E-54 2 (sarcomeric) transport

coenzyme Q9 homolog (S. Ubiquinone COQ9 Q8K1Z0 -0.337 2.5E-09 -0.245 2.0E-05 cerevisiae) biosynthesis

cytochrome c oxidase subunit COX1 Q9MD68 -0.392 2.6E-09 -0.269 1.8E-04 Respiratory chain I

cytochrome c oxidase subunit COX2 P00405 -0.331 1.6E-05 -0.213 3.3E-04 Respiratory chain II

cytochrome c oxidase subunit COX4I1 P19783 -0.321 2.6E-04 -0.211 4.7E-03 Respiratory chain IV isoform 1

COX5A cytochrome c oxidase subunit P12787 -0.386 1.3E-02 -0.267 4.7E-03 Respiratory chain Page 153 of 165 Diabetes

cytochrome c oxidase subunit COX5B P19536 -0.374 1.5E-04 -0.256 4.4E-03 Respiratory chain Vb

carnitine palmitoyltransferase CPT1B Q3UIM5 -0.226 1.4E-10 -0.246 3.0E-12 Lipid metabolism 1B (muscle)

carnitine palmitoyltransferase CPT2 P52825 -0.345 1.0E-04 -0.324 3.8E-04 Lipid metabolism 2

CRAT carnitine O-acetyltransferase Q3V1Y3 -0.268 1.2E-10 -0.253 1.1E-06 Lipid metabolism

CS citrate synthase Q9CZU6 -0.211 3.0E-10 -0.123 2.2E-04 TCA Cycle

CYC1 cytochrome c-1 Q9D0M3 -0.365 1.3E-05 -0.266 1.9E-03 Respiratory chain

CYCS cytochrome c, somatic Q56A15 -0.259 7.8E-09 -0.229 5.1E-06 Respiratory chain

2,4-dienoyl CoA reductase 1, DECR1 Q4FJK0 -0.296 2.3E-07 -0.327 3.1E-10 Lipid metabolism mitochondrial

dihydrolipoamide S- DLAT Q8BMF4 -0.251 3.6E-19 -0.257 6.8E-20 Lipid metabolism acetyltransferase

dihydrolipoamide DLD O08749 -0.114 1.6E-04 -0.127 8.1E-06 Lipid metabolism dehydrogenase

dihydrolipoamide S- succinyltransferase (E2 DLST Q9D2G2 -0.318 1.1E-05 -0.295 2.8E-04 Lipid metabolism component of 2-oxo-glutarate complex)

ECI1 enoyl-CoA delta isomerase 1 Q8QZV3 -0.289 6.8E-08 -0.268 2.4E-08 Lipid metabolism

enoyl CoA hydratase, short ECHS1 Q8BH95 -0,310 7,98E-03 -0,292 1,21E-02 Lipid metabolism chain, 1, mitochondrial

electron-transfer- ETFA flavoprotein, alpha Q99LC5 -0.286 3.8E-10 -0.272 6.4E-30 Respiratory chain polypeptide

electron-transfer- ETFB flavoprotein, beta Q9DCW4 -0.373 3.6E-14 -0.315 5.1E-18 Respiratory chain polypeptide Diabetes Page 154 of 165

electron-transferring- ETFDH Q6PF96 -0.422 3.78E-08 -0.386 2.69E-07 Respiratory chain flavoprotein dehydrogenase

FH fumarate hydratase P97807 -0.237 3.2E-04 0.097 2.3E-03 TCA Cycle

glyceraldehyde-3-phosphate Glycolysis/Glycogen Gapdh P16858 0.102 1.28E-14 0.073 2.24E-13 dehydrogenase degradation

glutamic-oxaloacetic transaminase 2, GOT2 P05202 -0.377 1.1E-19 -0.251 9.7E-13 Lipid metabolism mitochondrial (aspartate aminotransferase 2)

glycerol-3-phosphate GPD2 dehydrogenase 2 Q64521 0.110 1.8E-02 0.225 3.5E-07 Lipid metabolism (mitochondrial)

Free Radical glutathione S-transferase mu Scavenging/Protein GSTM5 P10649 0.303 3.2E-07 0.149 1.2E-02 5 ubiquitination/Protein Folding

hydroxyacyl-CoA HADH Q61425 -0.334 8.7E-05 -0.361 2.4E-06 Lipid metabolism dehydrogenase

hydroxyacyl-CoA dehydrogenase/3-ketoacyl- HADHA CoA thiolase/enoyl-CoA Q8BMS1 0.179 4.4E-16 -0.255 6.9E-25 Lipid metabolism hydratase (trifunctional protein), alpha subunit

hydroxyacyl-CoA dehydrogenase/3-ketoacyl- HADHB CoA thiolase/enoyl-CoA Q99JY0 -0.162 2.1E-13 -0.235 8.5E-27 Lipid metabolism hydratase (trifunctional protein), beta subunit

3-hydroxyisobutyrate HIBADH Q99L13 -0.380 4.8E-03 -0.445 9.2E-04 Valine Degradation dehydrogenase

3-hydroxyisobutyryl-CoA HIBCH Q8QZS1 -0.255 1.7E-03 -0.179 4.2E-02 Valine Degradation hydrolase

HSD17B10 ; hydroxysteroid (17-beta) Q99N15 -0.162 3.3E-03 -0.137 3.1E-02 Lipid metabolism M/SCHAD dehydrogenase 10 Page 155 of 165 Diabetes

Free Radical heat shock protein 90kDa Scavenging/Protein HSP90AB1 alpha (cytosolic), class B Q71LX8 -0.291 1.4E-13 -0.110 4.1E-04 ubiquitination/Protein member 1 Folding

Free Radical heat shock 70kDa protein 9 Scavenging/Protein HSPA9 P38647 -0.423 9.3E-20 -0.265 8.5E-10 (mortalin) ubiquitination/Protein Folding

Free Radical heat shock 60kDa protein 1 Scavenging/Protein HSPD1 P63038 -0.248 3.1E-18 -0.216 5.1E-13 (chaperonin) ubiquitination/Protein Folding

Free Radical heat shock 10kDa protein 1 Scavenging/Protein HSPE1 Q4KL76 -0.348 7.8E-04 -0.238 4.1E-02 (chaperonin 10) ubiquitination/Protein Folding

isocitrate dehydrogenase 2 IDH2 P54071 0.472 3.9E-19 -0.242 2.9E-13 TCA Cycle (NADP+), mitochondrial

isocitrate dehydrogenase 3 IDH3A Q9D6R2 -0.303 4.2E-15 -0.181 7.4E-09 TCA Cycle (NAD+) alpha

isocitrate dehydrogenase 3 IDH3B Q91VA7 -0.319 3.5E-24 -0.212 1.7E-11 TCA Cycle (NAD+) beta

isocitrate dehydrogenase 3 IDH3G P70404 -0.392 2.1E-10 -0.235 1.1E-03 TCA Cycle (NAD+) gamma

Free Radical inner membrane protein, Scavenging/Protein IMMT Q3TEY5 -0.321 3.7E-39 -0.287 1.5E-31 mitochondrial ubiquitination/Protein Folding

leucine-rich LRPPRC pentatricopeptide repeat Q6PB66 -0.711 4.6E-04 -0.439 3.4E-02 Lipid metabolism containing

leucine zipper-EF-hand Putative LETM1 containing transmembrane Q9Z2I0 -0.5 9.38E-05 -0.402 1.28E-03 mitochondrial protein 1 Ca(2+)/H(+) antiporter

MDH2 malate dehydrogenase 2, P08249 -0.198 9.9E-14 -0.152 5.0E-11 TCA Cycle Diabetes Page 156 of 165

NAD (mitochondrial)

mitochondrial pyruvate Mitochondrial MPC2 Q9D023 -0.514 3.4E-06 -0.262 9.6E-03 carrier 2 transport

NADH dehydrogenase NDUFA10 (ubiquinone) 1 alpha Q99LC3 -0.334 4.9E-09 -0.226 2.1E-03 Respiratory chain subcomplex, 10, 42kDa

NADH dehydrogenase NDUFA13 (ubiquinone) 1 alpha Q9ERS2 -0.367 3.2E-05 -0.213 2.3E-03 Respiratory chain subcomplex, 13

NADH dehydrogenase NDUFA2 (ubiquinone) 1 alpha Q9CQ75 -0.485 8.4E-04 -0.281 2.1E-02 Respiratory chain subcomplex, 2, 8kDa

NADH dehydrogenase NDUFA5 (ubiquinone) 1 alpha Q9CPP6 -0.414 3.0E-08 -0.296 1.8E-05 Respiratory chain subcomplex, 5, 13kDa

NADH dehydrogenase NDUFA6 (ubiquinone) 1 alpha Q9CQZ5 -0.371 6.0E-12 -0.319 4.4E-07 Respiratory chain subcomplex, 6, 14kDa

NADH dehydrogenase NDUFA8 (ubiquinone) 1 alpha Q9DCJ5 -0.363 1.3E-05 -0.256 1.1E-03 Respiratory chain subcomplex, 8, 19kDa

NADH dehydrogenase NDUFA9 (ubiquinone) 1 alpha Q6GTD3 -0.435 1.6E-07 -0.317 3.9E-06 Respiratory chain subcomplex, 9, 39kDa

NADH dehydrogenase NDUFB3 (ubiquinone) 1 beta Q9D6H6 -0.432 1.8E-03 -0.311 2.0E-02 Respiratory chain subcomplex, 3, 12kDa

NADH dehydrogenase NDUFB5 (ubiquinone) 1 beta Q8BU20 -0.332 4.4E-10 -0.250 1.8E-05 Respiratory chain subcomplex, 5, 16kDa

NADH dehydrogenase (ubiquinone) Fe-S protein 1, NDUFS1 Q91VD9 -0.333 2.0E-15 -0.221 1.8E-10 Respiratory chain 75kDa (NADH-coenzyme Q reductase) Page 157 of 165 Diabetes

NADH dehydrogenase (ubiquinone) Fe-S protein 2, NDUFS2 Q91WD5 -0.327 2.9E-09 -0.248 5.9E-05 Respiratory chain 49kDa (NADH-coenzyme Q reductase)

NADH dehydrogenase (ubiquinone) Fe-S protein 4, NDUFS4 Q923F9 -0.312 3.0E-05 -0.201 3.5E-03 Respiratory chain 18kDa (NADH-coenzyme Q reductase)

NADH dehydrogenase (ubiquinone) Fe-S protein 5, NDUFS5 Q99LY9 -0.415 2.8E-03 -0.319 1.5E-02 Respiratory chain 15kDa (NADH-coenzyme Q reductase)

NADH dehydrogenase NDUFV1 (ubiquinone) flavoprotein 1, Q91YT0 -0.325 9.3E-14 -0.206 1.0E-05 Respiratory chain 51kDa

oxoglutarate (alpha- OGDH ketoglutarate) dehydrogenase Q60597 -0.215 6.7E-08 -0.212 1.0E-08 TCA Cycle (lipoamide)

OXCT1 3-oxoacid CoA transferase 1 Q9D0K2 -0.520 1.9E-21 -0.212 2.5E-06 Lipid metabolism

pyruvate dehydrogenase PDHA1 Q3UFJ3 -0.392 3.5E-04 -0.347 2.2E-03 Glycolysis, TCA Cycle (lipoamide) alpha 1

pyruvate dehydrogenase PDHB Q9D051 -0.233 2.71E-06 -0.189 2.45E-05 Glycolysis, TCA Cycle (lipoamide) beta

pyruvate dehydrogenase PDHX Q8BKZ9 -0.304 4.41E-09 -0.26 4.91E-07 Glycolysis, TCA Cycle complex, component X

pyruvate dehydrogenase PDPR phosphatase regulatory Q7TSQ8 -0.412 2.1E-10 -0.283 2.4E-06 Glycolysis, TCA Cycle subunit

Free Radical Scavenging/Protein PHB prohibitin P67778 -0.248 1.2E-04 -0.217 2.7E-04 ubiquitination/Protein Folding

Free Radical PRDX5 peroxiredoxin 5 P99029 -0.299 4.8E-08 -0.258 5.1E-06 Scavenging/Protein ubiquitination/Protein Diabetes Page 158 of 165

Folding

sorting and assembly Mitochondrial protein SAMM50 machinery component 50 Q8BGH2 -0.229 3.70E-03 -0.129 4.73E-02 complexes assembly homolog (S. cerevisiae)

succinate dehydrogenase SDHA complex, subunit A, Q8K2B3 -0.298 6.2E-21 -0.197 4.2E-12 Respiratory chain flavoprotein (Fp)

succinate dehydrogenase SDHB complex, subunit B, iron A2AA77 -0.302 1.4E-09 -0.167 3.6E-04 Respiratory chain sulfur (Ip)

succinate dehydrogenase SDHC complex, subunit C, integral Q5XK33 -0.522 3.18E-03 -0.378 2.13E-02 Respiratory chain membrane protein, 15kDa

solute carrier family 25 (mitochondrial carrier; Mitochondrial SLC25A11 Q5SX53 -0.388 7.8E-10 -0.220 2.5E-04 oxoglutarate carrier), member transport 11

solute carrier family 25 Mitochondrial SLC25A12 (aspartate/glutamate carrier), Q8BH59 -0.176 8.5E-19 -0.126 6.0E-12 transport member 12

solute carrier family 25 Mitochondrial SLC25A3 (mitochondrial carrier; Q3THU8 -0.348 8.6E-17 -0.248 3.0E-12 transport phosphate carrier), member 3

solute carrier family 25 (mitochondrial carrier; Mitochondrial SLC25A4 Q8BVI9 -0.233 1.0E-04 -0.138 4.3E-03 adenine nucleotide transport translocator), member 4

solute carrier family 25 (mitochondrial carrier; Mitochondrial SLC25A5 P51881 -0.209 4.86E-05 -0.149 6.23E-04 adenine nucleotide transport translocator), member 5

Free Radical superoxide dismutase 1, Scavenging/Protein SOD1 P08228 0.213 9.2E-07 -0.118 2.0E-02 soluble ubiquitination/Protein Folding Page 159 of 165 Diabetes

Free Radical superoxide dismutase 2, Scavenging/Protein SOD2 P09671 -0.305 8.3E-07 -0.173 6.3E-04 mitochondrial ubiquitination/Protein Folding

succinate-CoA ligase, ADP- SUCLA2 Q3U6C7 -0.240 3.2E-11 -0.186 6.3E-10 TCA Cycle forming, beta subunit

succinate-CoA ligase, alpha SUCLG1 Q9WUM5 -0.246 2.1E-11 -0.214 1.4E-07 TCA Cycle subunit

Tu translation elongation Mitochondrial protein TUFM Q8BFR5 -0.179 1.6E-05 0.107 7.9E-03 factor, mitochondrial translation

ubiquinol-cytochrome c UQCRB Q9D855 -0.399 2.07E-09 -0.336 2.25E-07 Respiratory chain reductase binding protein

ubiquinol-cytochrome c UQCRC1 Q3TIC8 -0.230 8.3E-07 -0.169 9.2E-05 Respiratory chain reductase core protein I

ubiquinol-cytochrome c UQCRC2 Q9DB77 -0.254 1.2E-19 -0.165 1.5E-12 Respiratory chain reductase core protein II

ubiquinol-cytochrome c UQCRFS1 reductase, Rieske iron-sulfur Q9CR68 -0.331 5.3E-31 -0.211 1.4E-10 Respiratory chain polypeptide 1

voltage-dependent anion Mitochondrial VDAC1 Q60932-2 -0.159 2.1E-05 -0.112 6.0E-03 channel 1 transport

voltage-dependent anion Mitochondrial VDAC2 Q60930 -0.165 3.6E-04 -0.119 1.0E-02 channel 2 transport

Free Radical tyrosine 3- Scavenging/Protein monooxygenase/tryptophan YWHAZ P63101 0.139 4.3E-03 -0.146 7.9E-03 ubiquitination/Protein 5-monooxygenase activation Folding/Mitochondrial protein, zeta polypeptide protein import

Diabetes Page 160 of 165

Figure S1. Effects of insulin on body composition, blood parameters, and whole-body energy metabolism. Insulin replacement restored body weight, lean mass, and fat mass in STZ-induced diabetic mice (A). Insulin replacement also corrected changes in total body water and bladder water volume observed with insulin deprivation (B), while not affecting body hydration ratio (C). Plasma glucose (D), ketones (E), free fatty acids (F) and percentage of HbA1C (G) were elevated by insulin deprivation and corrected by insulin treatment. Results of 24h indirect calorimetry indicate that although insulin treatment was unable to fully compensate for the decrease in respiratory quotient (RQ, J), total 24h energy expenditure (TEE, K) and physical activity (L), it was able to decrease resting metabolic rate (RMR, M). Both oxygen and carbon dioxide flux (H,I) lower in STZ+I and VO2 was lower in STZ-I than in ND. Data are means SEM. N=8 per group. * denotes p<0.05 vs. non-diabetic, # denotes p<0.05 vs. STZ-I group. Page 161 of 165 Diabetes

Figure S2. The effect of insulin deprivation and treatment on mitochondrial oxygen consumption (Panel A) ATP production (Panel B) and H2O2 emission (Panel C) as calculated per muscle tissue weight. Substrate combinations explained under materials and methods section. * - p<0.05 vs. ND group, # - p<0.05 vs. STZ+I group. Values are means +/- SEM N=13 (except panel C, N=8). Diabetes Page 162 of 165

A B

Upregulated in STZ-I Upregulated in STZ-I Downregulated in STZ+I Upregulated in STZ+I

NRF2 Oxidative Stress Response Calcium Signaling* DNA Damage Regulation Actin Cytoskeleton Signaling Fatty Acids Transport Glycerol-3-P Shuttle Glucose and GP1 Degradation

Downregulated in STZ-I Downregulated in STZ-I Downregulated in STZ+I Upregulated in STZ+I

Mitochondrial Dysfunction TCA Cycle Actin Cytoskeleton Signaling Fatty Acid β-oxidation Mitochondrial L-carnitine Shuttle

Figure S3. Insulin treatment does not fully corrects mitochondrial proteome changes induced by insulin deprivation. Panel A shows expression of 242 proteins significantly (p<0.05) different from non-diabetic (ND) group in both the STZ-I and STZ+I animals. Proteins not corrected by insulin treatment are located in quadrant III (down-regulated in both STZ-I and STZ+I, n=118 ) and in quadrant I (up-regulated in both STZ-I and D+,I n=58). Proteins in quadrants II (n=5) and IV (n=27) have the opposite expression pattern and are therefore regulated by insulin. Values from STZ+I vs. ND and STZ-I vs. ND comparison are given on X and Y axis, respectively. Panel B presents significantly altered pathways (p<0.05, -log10 p- value >1.3) associated with proteins from respective I-IV quadrants. Detailed expression data for individual mitochondrial proteins is presented in Table S4. Page 163 of 165 Diabetes

Figure S4. PPARK7 protein responsible for ROS-related mitophagy is up regulated within mitochondria of STZ-diabetic mice, despite overall decrease in mitochondrial protein content. Mitochondrial loading VDAC1 (non-selective mitochondrial anion channel) or COX41 (subunit of mitochondrial electron transport chain) was used to normalize mitochondrial expression of PARK7 across experimental groups. N=6 per group. Diabetes Page 164 of 165

Figure S5. Insulin deprivation increases the abundance of semi-tryptic peptides from mitochondrial proteins, which is corrected by insulin treatment. Panel A presents total number of semi-tryptic peptides from all skeletal muscle proteins, from both the experimental (light) and SILAC (heavy, graph bars to left) animals and from experimental animals only (light, bar graphs to right). Panel B presents total number of semi-tryptic peptides from proteins of mitochondrial origin. The increase in the number of semi-tryptic peptides is visible only for experimental animals in insulindeprived group N=3 per group. Values represent mean +/- SEM. * -p<0.0001 compared to non-diabetic (ND) group values; # -p<0.0001 as compared to diabetic, insulin treated group (STZ+I). Page 165 of 165 Diabetes

Figure S6. Insulin deprivation in STZ-diabetic animals significantly decreases mixed muscle protein (MMP) fractional synthesis rate (FSR) in different skeletal muscles, which is partially corrected by insulin treatment. Values are expressed as a mean % /day (N=3 per group), +/- SEM * -p<0.05 compared to non-diabetic (ND) group values; # -p<0.05 as compared to diabetic, insulin treated group (STZ+I).