Proteomic Analysis Identifies Distinct Glomerular Extracellular Matrix In

Home , ACO1, ACTA2, Annexin A11, Annexin A2, Annexin A3, Annexin A4

CLINICAL RESEARCH www.jasn.org

Proteomic Analysis Identiﬁes Distinct Glomerular Extracellular Matrix in Collapsing Focal Segmental Glomerulosclerosis

Michael L. Merchant,1 Michelle T. Barati,1 Dawn J. Caster ,1 Jessica L. Hata,2 Liliane Hobeika,3 Susan Coventry,2 Michael E. Brier,1 Daniel W. Wilkey,1 Ming Li,1 Ilse M. Rood,4 Jeroen K. Deegens,4 Jack F. Wetzels,4 Christopher P. Larsen,5 Jonathan P. Troost,6 Jeffrey B. Hodgin,7 Laura H. Mariani,8 Matthias Kretzler ,8 Jon B. Klein,1,9 and Kenneth R. McLeish1

Due to the number of contributing authors, the afﬁliations are listed at the end of this article.

ABSTRACT Background The mechanisms leading to extracellular matrix (ECM) replacement of areas of glomerular capillaries in histologic variants of FSGS are unknown. This study used proteomics to test the hypothesis that glomerular ECM composition in collapsing FSGS (cFSGS) differs from that of other variants. Methods ECM proteins in glomeruli from biopsy specimens of patients with FSGS not otherwise specified (FSGS-NOS) or cFSGS and from normal controls were distinguished and quantified using mass spectrometry, verified and localized using immunohistochemistry (IHC) and confocal microscopy, and assessed for gene expression. The analysis also quantified urinary excretion of ECM proteins and peptides. Results Of 58 ECM proteins that differed in abundance between cFSGS and FSGS-NOS, 41 were more abundant in cFSGS and 17 in FSGS-NOS. IHC showed that glomerular tuft staining for cathepsin B, cathepsin C, and annexin A3 in cFSGS was significantly greater than in other FSGS variants, in minimal change disease, or in membranous nephropathy. Annexin A3 colocalized with cathepsin B and C, claudin-1, phos- phorylated ERK1/2, and CD44, but not with synaptopodin, in parietal epithelial cells (PECs) infiltrating cFSGS glomeruli. Transcripts for cathepsins B and C were increased in FSGS glomeruli compared with normal controls, and urinary excretion of both cathepsins was significantly greater in cFSGS compared with FSGS-NOS. Urinary excretion of ECM-derived peptides was enhanced in cFSGS, although in silico analysis did not identify enhanced excretion of peptides derived from cathepsin B or C. Conclusions ECM differences suggest that glomerular sclerosis in cFSGS differs from that in other FSGS variants. Infiltration of activated PECs may disrupt ECM remodeling in cFSGS. These cells and their cathepsins may be therapeutic targets.

JASN 31: ccc–ccc, 2020. doi: https://doi.org/10.1681/ASN.2019070696

Received July 14, 2019. Accepted April 13, 2020.

FSGS is the most common glomerular disorder lead- Published online ahead of print. Publication date available at 1,2 ing to ESKD in North America. FSGS consists of a www.jasn.org. spectrum of histopathology with multiple causes, Correspondence: Dr. Kenneth R. McLeish, Division of Nephrol- various presentations, and different outcomes and ogy and Hypertension, Department of Medicine, University of responses to therapy. The Columbia classification de- Louisville, Baxter I Research Building, Rm 102 South, 570 S. fines five patterns of histopathologic changes Preston Street, Louisville, KY 40202, or Dr. Michael L. Merchant, Division of Nephrology and Hypertension, Department of Med- in FSGS: collapsing variant (collapse of the glo- icine, University of Louisville, Baxter I Research Building, Rm 202 merulartuftwithepithelialcellhyperplasia),tip South, 570 S. Preston Street, Louisville, KY 40202. E-mail: k. variant (lesions at the urinary pole), perihilar var- [email protected] or [email protected] iant (lesions at the vascular pole), cellular variant Copyright © 2020 by the American Society of Nephrology

JASN 31: ccc–ccc, 2020 ISSN : 1046-6673/3108-ccc 1 CLINICAL RESEARCH www.jasn.org

(endocapillary hypercellularity), and FSGS not otherwise Significance Statement specified (FSGS-NOS) for lesions that do not meet the criteria for the other four classes.3 The collapsing FSGS Extracellular matrix (ECM) replaces glomerular capillaries in FSGS. (cFSGS) variant defines a group of patients with more se- To evaluate differences in ECM remodeling between collapsing fi vere nephrotic syndrome, lower eGFR at presentation, and a FSGS (cFSGS) and FSGS not otherwise speci ed (FSGS-NOS), we performed a proteomic analysis of glomerular ECM composition 4–7 higher likelihood of progression to ESKD. Additionally, using human biopsies. Abundance of 58 ECM proteins differed: 41 cFSGS is associated with proliferation of parietal epithelial were more abundant in cFSGS and 17 in FSGS-NOS. Increased cells (PECs) and altered podocyte differentiation.8–10 The abundance and coexpression of cathepsin B, cathepsin C, and an- unique histologic and clinical characteristics suggest the nexin A3 characterized cells infiltrating glomerular tufts in cFSGS. pathophysiology of cFSGS differs from other FSGS variants. These cells expressed markers of activated parietal epithelial cells, fi but not markers of podocytes. This work demonstrates multiple A histopathologic nding common to all variants of FSGS mechanisms of how dysregulated ECM remodeling underlies focal is focal and segmental deposition of new extracellular matrix sclerosis. The work supports the important role of parietal epithelial (ECM) that obliterates glomerular capillaries. ECM is a com- cells in disease histopathology and identifies them as a possible plex molecular structure that provides a physical scaffold for therapeutic target, particularly for cFSGS. all tissues and regulates cell and tissue physiology. ECM com- fi position is tissue speci c and undergoes continuous 13 Halt Protease and Phosphatase Inhibitor [78442; Thermo 11–15 16 remodeling. Proteomic studies by our group and by Fisher Scientific, Waltham, MA]) and stored at 280°C. Lennon et al.17 identified about 250 proteins that comprise the normal glomerular ECM. Although alterations in glomer- Urine Collection ular ECM components occur in FSGS,9,18–21 a comprehensive Single void urine samples were centrifuged at 1200 3 g for analysis of ECM composition and differences among FSGS 15 minutes at 4°C to remove cellular debris. Supernatants were variants has not been performed. Thus, the contribution aliquoted into 15 ml vials and stored at 280°C until used for of abnormal ECM composition to development and pro- sample preparation. Urine was diluted with an equal volume gression of FSGS remains unclear. Based on the unique char- of 0.5% trifluoroacetic acid and then transferred to a Sartorius acteristics of cFSGS, we postulated that glomerular ECM Vivaspin-2 concentrator (Vivaproducts, Littleton, MA) composition in cFSGS differs from the other variants, and with a 5000 Da mol wt cutoff Hydrosart membrane. The those differences may contribute to the unique characteris- Vivaspin-2wasspunat32203 g for 15 minutes at 4°C in an tics of cFSGS. To address this hypothesis, proteomic and Eppendorf 5810R centrifuge. Peptides were concentrated transcriptomic analysis of glomeruli isolated from human and desalted using 1 ml Oasis HLB (Waters Corporation, biopsies was performed. Milford, MA) solid phase extraction cartridges as previously described.22 The ultrafiltrate was rinsed three times using 10 mM HEPES/0.5 mM EDTA, pH 7.6, and recovered by METHODS pipetting. The peptide and protein sample concentrations were determined by determined using a mBCA kit (Pierce, Study Approval Rockford, IL). The University of Louisville Human Studies Committee ap- proved sample collection and use of de-identified samples ECM Enrichment and Protein Extraction provided by coauthors’ institutions. All study subjects pro- Protein extraction was performed using a two-step procedure vided informed consent before sample collection, except previously reported.16 Isolated glomerular sections were de- where samples were deemed exempt. All studies were conduc- cellularized with 25 mM ammonium hydroxide/0.5% Triton ted in compliance with the Declaration of Helsinki. X-100 plus HALT Protease and Phosphatase Inhibitor Cock- tail (Thermo Fisher Scientific) followed by protein extraction Tissue Collection of residual ECM-enriched pellet using an acid-labile surfac- De-identified, formalin-fixed, paraffin-embedded renal tissue tant (0.1% ProteaseMAX Surfactant in 0.05 M ammonium was provided by collaborating pathologists after confirmation bicarbonate) with heating for 5 minutes at 95°C. The isolated of the diagnosis based on the Columbia classification criteria.3 proteins were digested overnight at 37°C with 20 ng Kidney tissue was cut into 10-mm sections on polyethylene sequencing-grade modified trypsin in 100 ml of 1 M urea terephthalate membrane frame slides and stained with Mayer with 0.1 M Tris hydrochloride, pH 8.5. The digests were fil- hematoxylin following Leica LMD6500 Laser Microdissection tered using the YM-10 (10,000 Da mol wt cutoff) device. The System staining protocol. Laser capture microdissection of filtered and digested samples were desalted and concentrated glomeruli was performed such that the Bowman’scapsule using a reversed phase C18 PROTO Ultra MicroSpin desalting was excluded from samples (Supplemental Figure 1). Between column (Nest Group, Southborough, MA). The recovered 38 and 124 glomerular sections from 12 to 26 glomeruli for peptides were lyophilized and resuspended in 2% acetoni- each subject were collected into tubes containing 20 ml trile/0.1% formic acid before quantification using a Nano- of storage buffer (10 mM HEPES pH 7.0, 0.67 mM EDTA, Drop 2000 (Thermo Fisher Scientific) at 205 nm.

2 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH

Proteomic Liquid Chromatography Mass Spectrometry of an EASY-nLC 1000 UHPLC system (Thermo Fisher Scien- Data Collection tific) and separated using a 50 cm Acclaim PepMap RSLC Glomerular ECM-Enriched Samples column (Thermo Fisher Scientific) before transfer by Nano- Methods for the analysis of ECM-enriched, Triton X-100– spray Flex source (Thermo Fisher Scientific) into an Orbitrap insoluble pellet digests using liquid chromatography (LC) Elite electron-transfer dissociation mass spectrometer mass spectrometry (LCMS) were conducted as previously de- (Thermo Fisher Scientific). An Nth Order Double Play (Xca- scribed.16 Peptide values were estimated using absorbance libur version 2.2) was used to collect Orbitrap MS1 scans measurements at 205 nm by NanoDrop 2000. Peptide samples (60,000 resolution) for the range 300–2000 m/z and FTMS were separated with a 170 minute LC gradient using a Proxeon MS2 scans (higher-energy collisional dissociation activation; EASY-nLC 1000 (Thermo Fisher Scientific) ultra-high-perfor- 60,000 resolution) on up to ten peaks that had a minimum mance LC (UHPLC) system and Dionex (Sunnyvale, CA) Ac- signal threshold of 5000 counts from scan event one. claim PepMap 100 75 mm32 cm, nanoViper (C18, 3 mm, 100 Å) trap, and a Dionex Acclaim PepMap RSLC Mass Spectrometry Data Analysis m 3 m 50 m 15 cm, nanoViper (C18, 2 m, 100 Å) separating col- Tissue Proteomics umn. The eluate was introduced via a Nanospray Flex source The individual cFSGS, FSGS-NOS, or normal control (NC) (Thermo Fisher Scientific) into an Orbitrap Elite electron- LCMS data sets were analyzed by Proteome Discoverer version transfer dissociation mass spectrometer (Thermo Fisher). Data 1.4.1.14 using Mascot version 2.5.1 and SequestHT searches were acquired using an Nth Order Double Play (Xcalibur version with the December 18, 2019 version of the UniprotKB Homo 2.2; Thermo Fisher Scientific) with Fourier transform mass sapiens reviewed reference proteome canonical and isoform spectrometry (FTMS) MS1 scans (240,000 resolution) collected sequences. Search parameters included: variable methionine from 300 to 2000 m/z and ion trap mass spectrometry MS2 scans or proline oxidation (116 Da), fixed cysteine carbamidome- collected on up to 20 peaks having a minimum signal threshold thylation (157 Da), up to two missed tryptic cleavages, 50 of 5000 counts from the MS1 scan event. ppm precursor error for MS1 Orbitrap FTMS data, 1 Da error for MS2 data sets, and minimum peptide length of four amino Urine Peptidomics acids. To estimate the false discovery rate (FDR), a Target Urine peptide samples were diluted to a final common con- Decoy PSM Validator node was included in the Proteome centration of 0.2 mg/ml in 2% acetonitrile/0.1% formic acid Discoverer workflow. The resulting .msf files from Proteome and loaded into autosampler vials before transfer to an Easy- Discoverer were loaded into Scaffold Q1S version 4.4.5 for nLC 1000 System. Peptides (500 ng) were separated using a 12 comparative proteomics. Scaffold was used to calculate the cm, 360 mmOD3100 mm ID fused silica tip packed with Aeris FDR (strict, 1% FDR; relaxed, 5% FDR) using the Peptide Peptide 3.6 mm XB-C18 100 Å material (Phenomenex, Tor- and Protein Prophet algorithms. The Scaffold Local FDR rance, CA) and high-resolution, label-free LCMS data col- algorithm was enabled during loading to accommodate in- lected as described above. strumental mass measurement drift in Orbitrap data. Final peptide level information used to build quantitative results Urine Proteomics were filtered by a 2 ppm precursor mass accuracy. Accepted Urine protein samples (50 mg) were reduced with dithiothrei- protein-level data were annotated with human gene ontology tol, alkylated using iodoacetamide, and digested using 2 mg information from the Gene Ontology Annotations Database mass spectrometry–grade trypsin/Lys-C protease mixture (geneontology.org). Protein intensity-based absolute quanti- (Promega, Madison, WI). Protein digests were quantified by fication (iBAQ) scores were exported as Excel files for statis- A205 nm measurements on a NanoDrop 2000 and 25 mgof tical analysis. As described previously,23 missing values were each sample was used for labeling with one isobaric tagging imputed and data normalized before statistical testing by AN- reagent from a Tandem Mass Tag (TMT) 10-plex kit (Thermo OVA analysis (one-way ANOVA in R version 3.5.0, using the R Fisher Scientific) according to the manufacturer’sinstruc- script aov) with Benjamini–Hochberg correction for multiple tions. A pooled internal standard comprising 5 mg admixtures comparisons and post hoc t tests. Missing values were imputed from all sample digests was used as a reference normalization by singular value decomposition using “impute.MAR” func- of TMT reporter ions between separate LCMS experiments. tion of the R package “imputeLCMD.” iBAQ scores were nor- TMT10-plex–labeled admixtures of patient urine protein di- malized by variance stabilizing normalization by applying the gests were separated using high pH reversed-phase chroma- “justvsn” function available in R package “vsn.” tography with fraction concatenation using an Ultimate 3000SD UHPLC system (Thermo Fisher Scientific) with an Urine Peptidomics XBridge BEH C18 130 Å, 5 mm33150 mm column (Waters Peptidomic data sets were recalibrated postacquisition (Reca- Corporation) and 5%–90% acetonitrile/ammonium formate, lOffline, Xcalibur version 2.2) to the 12 charge state of the pH 10 gradient. The concatenated samples were lyophilized uromodulin peptide SVIDQSRVLNLGPITR, a urinary pep- and resuspended in 50 ml 2% acetonitrile/0.01% formic acid. tide consistently identified at high confidence in all samples. The TMT-labeled samples were loaded into the autosampler The recalibrated files were researched in Peaks Studio X

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 3 CLINICAL RESEARCH www.jasn.org

(Bioinformatics Solutions Inc., Waterloo, ON, Canada) using the validation by the Human Proteome Atlas Project (https:// Denovo, PeaksDB, PeaksPTM, and Label-Free Q algorithms and www.proteinatlas.org).26 Primary antibodies to the following the August 8, 2018 version of the UniProtKB-reviewed reference proteins were used: cathepsin C (3 mg/ml, catalog AF1071; proteome canonical and isoform H. sapiens sequences (proteome R&D Systems, Minneapolis, MN), annexin A3 (1:2000, cata- identifier, UP000005640). Search parameters included: variable log HPA013398; Sigma, St. Louis, MO), cathepsin B (1:2000, methionine oxidation (115.9949 Da), no enzyme specified, 15 catalog 31817; Cell Signaling, Danvers, MA), CD44 (1:100, ppm precursor error for MS1 Orbitrap FTMS data, 0.5 Da error Cell Signaling 16728; Abcam, Cambridge, MA), and phos- for MS2 data sets, and common post-translational modifications phorylated ERK (pERK; 1:100, catalog 7383; Santa Cruz in the PeaksPTM algorithm. The peptide, feature, and protein- Biotechnology, Dallas, TX). Sections were incubated with peptide comma separated values files were exported from the primary antibodies overnight at 4°C. All sections, including Label-Free Q result into Microsoft Excel 2016 and normalized negative controls, were then incubated with biotinylated sec- to urine protein concentration. The statistical testing for signif- ondary antibodies (Vector Labs) for 30 minutes, followed by icant, differentially abundant urinary peptides was determined incubation in avidin/biotin enzyme complex (Vectastain Elite using the one-way ANOVA in R (version 3.5.0) using the R-script ABC Kit, Vector Labs) for 30 minutes. Proteins were detected aov. A P value ,0.05 was considered significant. after color development using 3,39-diaminobenzidine as substrate (Vector Labs). Digital images were acquired with a Q Urine Proteomics Color 5 camera attached to an Olympus BX51 microscope Proteomic data files were searched using Mascot version 2.5.1 using Image-Pro software. Cathepsin C and annexin A3 glo- and SequestHT against the August 8, 2018 version of merular tuft immunostaining was quantified with Image-Pro the UniprotKB-reviewed reference proteome canonical 6.2 software (Media Cybernetics, Silver Spring, MD) on im- and isoform H. sapiens sequences (proteome identifier, ages captured with a 403 objective. The percentage of immu- UP000005640) using Proteome Discoverer version 2.2.0.388 nostaining in each glomerular tuft was determined by the ratio (Thermo Fisher Scientific). Search parameters included: vari- of immunostained area to total glomerular tuft surface area. able methionine oxidation (115.9949 Da) and protein N-terminal acetylation (142.0106 Da), fixed cysteine carba- Matrisome Identification within Proteomic Data Sets midomethylation (157.0215 Da) and TMT6-plex modifica- Identification of ECM proteins was performed by comparing tion (1229.16293 at any N-terminal and K), up to two missed proteins expressed to the combination of the Matrisome da- tryptic cleavages, 10 ppm precursor error for MS1 Orbitrap FTMS data, 0.02 Da error for MS2 data sets, and minimum peptide length of six amino acids. A proteins text file was ex- 10 ported from Proteome Discoverer, data were normalized to INHBE urine protein concentration, and statistical tests were done in 8 UMOD APOC3 FGL1 AZU1 Microsoft Excel 2016 and R version 3.5.0. CTSL CST3 CTSG C1QB fi LGALS7 The statistical testing for signi cant, differentially abun- 6 PRG3 PRSS23 CTSC SERPINF2 IGFBP7 SERPIND1 dant proteins within glomerular tissue or urine was performed ELANE SAA1 ANXA3 ECM1 – LGALS3 F12 using the Kruskal Wallis ANOVA (H test) with post hoc cor- LMAN1 4 HTRA1 C1QC C1QA rection for multiple comparisons as provided within Scaffold HSD17B12 TTR Q1S. The statistical testing for significant, differentially abun- SERPINB12 IGHG4 -Log10(F adj p-value) FLG2 KNG1 LAMA3 COL12A1 2 PXDN S100A9 ITIH4 LAMB1 COL21A1 dant urinary peptides was performed using PeaksX data set MPO COL1A2 VWF normalized to urine protein concentration in Microsoft Excel 2016 by one-way ANOVA in R (version 3.5.0) using the 0 -5 0 5 R-script aov. A P value ,0.05 was considered significant. Log2 FC (cFSGS/FSGS-NOS)

Identification of Candidate Proteases Figure 1. Volcano plot shows significant differences in glomer- Urine peptides assigned with high confidence (PeaksX criteria) ular ECM protein expression between cFSGS and FSGS-NOS. Of were exported into comma separated values files for upload and 166 proteins, abundance of 42 proteins differed by ANOVA analysis by the Proteasix (http://www.proteasix.org/) algorithm analysis with Benjamini–Hochberg correction for multiple com- , fi 2 using the “peptide-centric” prediction tool based on curated, parisons (adjusted P 0.05). The y axis is de ned as the log10 known, and observed cleavage events enabling assignment of multiple comparisons adjusted P value(FadjP-value) and the x axis defined as the log fold change (Log FC) of ECM protein protease identities from the MEROPS database.24 2 2 abundance in isolated glomeruli from patients with cFSGS (n57), compared with those with FSGS-NOS (n56). Red symbols denote Immunohistochemistry increased abundance in cFSGS for 32 proteins. Blue symbols Immunohistochemistry (IHC) of paraffin-embedded renal denote increased abundance in FSGS-NOS for ten proteins. biopsy sections was performed as previously described.25 An- Symbols denoting differentially abundant proteins are annotated tibodies to identify glomerular proteins were chosen based on by gene name.

4 JASN JASN 31: ccc–ccc,2020 JASN Table 1. ECM proteins with differential abundance between cFSGS and FSGS-NOS 31: Protein Name Gene Name Log2 Fold Change P Value q Value Category Division ccc Proteins with greater abundance in cFSGS – ccc Annexin A3 ANXA3 3.04 1.96e207 1.69e206 ECM-afﬁliated proteins Matrisome associated

2020 , Apolipoprotein C3 APOC3 .5.0 1.92e211 5.65e210 ECM-affiliated proteins Matrisome associated Azurocidin AZU1 .5.0 3.81e208 3.92e207 ECM regulators Matrisome associated Complement C1q A chain C1QA .5.0 4.55e205 2.81e204 ECM-affiliated proteins Matrisome associated Complement C1q B chain C1QB .5.0 7.11e209 8.09e208 ECM-affiliated proteins Matrisome associated Complement C1q C chain C1QC 3.20 7.58e204 3.09e203 ECM-affiliated proteins Matrisome associated Collagen a-1 (XII) chain COL12A1 2.31 0.0443 0.1115 Collagens Structural matrisome Collagen a-1 (XXI) chain COL21A1 2.91 4.04e203 0.017 Collagens Structural matrisome Collagen a-1 (VII) chain COL7A1 3.30 0.0462 0.1149 Collagens Basement membrane Cysteine-rich transmembrane BMP regulator 1 CRIM1 4.58 8.05e212 3.23e210 ECM glycoproteins Structural matrisome Chondroitin sulfate proteoglycan 4 CSPG4 1.13 6.56e204 2.74e203 ECM-affiliated proteins Matrisome associated Cathepsin B CTSB 3.09 0.3219 0.4759 ECM regulators Matrisome associated Cathepsin C CTSC 3.61 4.21e207 3.41e206 ECM regulators Matrisome associated Cathepsin G CTSG 5.67 1.52e207 1.36e206 ECM regulators Matrisome associated Cathepsin L CTSL 4.96 5.06e208 ECM regulators Matrisome associated ECM protein 1 ECM1 4.10 4.31e205 2.24e204 ECM glycoproteins Structural matrisome Neutrophil elastase ELANE 4.55 4.61e209 5.71e208 ECM regulators Matrisome associated Coagulation factor XII F12 4.15 4.21e205 2.21e204 ECM regulators Matrisome associated Fibrillin 2 FBN2 2.26 2.09e207 1.76e206 ECM glycoproteins Structural matrisome Fibrinogen-like protein 1 FGL1 4.25 1.69e209 3.35e208 ECM glycoproteins Structural matrisome Hydroxysteroid 17-b dehydrogenase 12 HSD17B12 3.09 1.12e204 6.69e204 ECM-affiliated proteins Matrisome associated Insulin-like growth factor binding protein acid-labile subunit IGFALS .5.0 0.1133 0.2317 ECM glycoproteins Structural matrisome Insulin-like growth factor binding protein 7 IGFBP7 2.77 2.71e209 3.64e208 ECM glycoproteins Structural matrisome Inter-a-trypsin inhibitor heavy chain 5 ITIH5 2.85 1.09e203 4.25e203 ECM regulators Matrisome associated Kininogen 1 KNG1 1.63 5.74e205 2.91e204 ECM regulators Matrisome associated Laminin subunit a 3 LAMA3 2.57 2.42e203 0.011 ECM glycoproteins Basement membrane Laminin subunit b 1 LAMB1 1.85 3.78e203 0.013 ECM glycoproteins Basement membrane Galectin 3 LGALS3 2.53 4.76e209 5.74e208 ECM-affiliated proteins Matrisome associated Galectin 7 LGALS7 3.67 2.62e206 1.72e205 ECM-affiliated proteins Matrisome associated www.jasn.org Lectin, mannose binding 1 LMAN1 2.26 3.98e208 4.00e207 ECM-affiliated proteins Matrisome associated Matrix metalloproteinase 9 MMP9 .5.0 0.0978 0.2216 ECM regulators Matrisome associated Myeloperoxidase MPO 3.25 1.77e203 6.53e203 ECM regulators Matrisome associated lmrlrEMi FSGS in ECM Glomerular Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 PLOD3 2.54 0.0115 0.0353 ECM regulators Matrisome associated Proteoglycan 3 PRG3 .5.0 9.77e212 3.39e210 Proteoglycans Structural matrisome

Serine protease 23 PRSS23 4.22 6.04e207 4.58e206 ECM regulators Matrisome associated RESEARCH CLINICAL S100 calcium binding protein A8 S100A8 2.18 0.0492 0.121 Secreted factors Matrisome associated S100 calcium binding protein A9 S100A9 .5.0 2.31e207 1.93e206 Secreted factors Matrisome associated Serpin family D member 1 SERPIND1 4.12 3.88e208 3.96e207 ECM regulators Matrisome associated Transthyretin TTR 2.88 2.18e204 1.20e203 ECM regulators Matrisome associated Serpin family F member 2 SERPINF2 4.18 6.47e209 7.65e208 ECM regulators Matrisome associated Uromodulin UMOD 4.66 5.75e212 2.48e210 ECM glycoproteins Structural matrisome 5 6 LNCLRESEARCH CLINICAL JASN www.jasn.org

Table 1. Continued

Protein Name Gene Name Log2 Fold Change P Value q Value Category Division Proteins with greater abundance in FSGS-NOS Biglycan BGN 2.98 2.12e209 2.97e208 Proteoglycans Structural matrisome Collagen a-1 (I) chain COL1A1 3.71 4.08e203 0.0139 Collagens Structural matrisome Collagen a-2 (I) chain COL1A2 2.66 4.24e203 0.0143 Collagens Structural matrisome Collagen a-1 (XV) chain COL15A1 3.28 0.2057 0.3533 Collagens Basement membrane Collagen a-1 (III) chain COL3A1 1.70 0.4772 0.6235 Collagens Basement membrane Cystatin-C CST3 4.37 1.05e208 1.57e207 ECM regulators Matrisome associated Fibulin 5 FBLN5 0.76 0.0327 0.0859 ECM glycoproteins Structural matrisome Filaggrin family member 2 FLG2 1.22 0.0161 0.0475 Secreted factors Matrisome associated HtrA serine peptidase 1 HTRA1 4.10 3.58e206 2.29e205 ECM regulators Matrisome associated Inhibin b E chain INHBE 4.32 6.17e211 2.22e209 Secreted factors Matrisome associated Inter-a-trypsin inhibitor heavy chain H4 ITIH4 1.68 3.03e203 0.0131 ECM regulators Matrisome associated Lipoprotein(a) LPA 1.86 1.81e204 8.30e204 ECM regulators Matrisome associated Peroxidasin PXDN 3.07 5.59e203 0.0227 ECM glycoproteins Structural matrisome Serum amyloid A1 SAA1 5.65 1.01e205 5.97e205 ECM regulators Matrisome associated Serpin family B member 12 SERPINB12 2.18 1.22e203 5.90e203 ECM regulators Matrisome associated Serpin family G member 1 SERPING1 3.34 0.8085 0.8878 ECM regulators Matrisome associated von Willebrand factor VWF 1.92 0.0118 0.0362 ECM glycoproteins Structural matrisome JASN 31: ccc – ccc ,2020 www.jasn.org CLINICAL RESEARCH tabase (http://matrisomeproject.mit.edu/analytical-tools/ t test without multiple comparisons test corrections. A P value matrisome-annotator/)27 and previously published glomeru- ,0.05 was considered significant. lar ECM databases.16,17 Statistical Analysis Confocal Microscopy Differences in glomerular tissue proteomes and transcrip- Renal biopsy sections were cleared of paraffin, rehydrated, and tomes and urine proteome and peptidome were determined subjected to antigen retrieval and blocking with 5% horse by ANOVA and post hoc t tests. Significance for P values and serum as described above for IHC. Biopsy sections were in- multiple comparisons–adjusted P values (q values) by cubated simultaneously with anti–cathepsin C and anti– Benjamini–Hochberg correction were aprioriset at ,0.05. annexin A3 antibodies or anti-synaptopodin (1:100, catalog Statistical significance estimates and fold-change values were sc21537; Santa Cruz Biotechnology) and anti–annexin A3 an- used to identify candidates for IHC or confocal micros- tibodies, at the antibody dilutions described above, overnight copy tissue confirmation studies. Area under the curve at 4°C. Sections were incubated with anti-rabbit Alexa Fluor (AUC) of the receiver operator characteristic plots were used 488 for detection of annexin A3, followed by anti-goat Alexa to determine the classification model performance of glomer- Fluor 546 to detect cathepsin C or synaptopodin. For costain- ular cathepsin C and annexin A3 staining to accurately classify ing of annexin A3 with claudin-1 (1:250, catalog 211737; patient biopsy specimen diagnoses. Abcam) or cathepsin B, sections were first incubated with anti–annexin A3 overnight at 4°C, followed by incubation with anti-rabbit Alexa Fluor 488. Sections were again blocked RESULTS with 5% horse serum, followed by incubation with anti–claudin-1 antibody or anti–cathepsin B, overnight at 4° Glomerular ECM in FSGS C. Claudin-1 or cathepsin B were detected with anti-rabbit To identify glomerular ECM proteins, enrichment of glomer- Alexa Fluor 546. Nuclei were stained with 49,6-diamidino- ular sections was performed by sequential extraction with am- 2-phenylindole. Images were acquired using an Olympus monium hydroxide/Triton X-100 to disrupt cells followed by Fluoview FV-1000 confocal coupled to an Olympus 1381 protein extraction with ProteaseMAX (Promega).16 Prelimi- inverted microscope, a PlanApoN 603 objective, and FV-10 nary studies showed this procedure increased the number and ASW 2.1 software. A multichannel scanning configuration quantity of ECM proteins identified from patients without with sequential line scanning was set up for acquisition of renal disease (NC) and FSGS-NOS glomerular sections 49,6-diamidino-2-phenylindole, AF488, and AF546. The op- (Supplemental Figure 2). Glomerular ECM proteins were timal brightness setting for each channel was configured by identified from 38 to 124 glomerular sections from each of determining the HV setting yielding maximal intensity seven patients diagnosed with cFSGS, six with FSGS-NOS, and without saturation. Each of the settings was tested against two NCs.16 The number of glomeruli per patient from which negative control sections to ensure exclusion of nonspecific sections were obtained was 1962(mean6SEM; range, emission. 12–26). A total of 1402 unique proteins were identified by combining results of all 15 patients, of which 1148 were iden- Glomerular Transcriptome tified from cFSGS, 1104 from FSGS-NOS, and 900 from NCs Quantitative microarray (European Renal cDNA Bank; ERCB) (Supplemental Table 1). ECM proteins were identified from a and RNA-sequencing (RNA-seq; Nephrotic Syndrome Re- combined list of the Matrisome database27 and ECM proteins search Network, NEPTUNE) expression data from available previously identified from human glomeruli.16,17 Atotalof ERCB data sets were accessed through the Nephroseq platform 166 ECM proteins were identified (Supplemental Table 2), and from NEPTUNE data sets accessed through an Ancillary of which 158 ECM proteins were identified from cFSGS glo- Studies award.28,29 In brief, the ERCB data were developed meruli, 136 from FSGS-NOS, and 109 from NCs. The relative using RNA extracted from microdissected glomeruli to gen- abundance of 32 basement membrane matrisome proteins, 33 erate cDNA libraries that were sequenced by the University of structural matrisome proteins, and 101 matrisome-associated Michigan DNA Sequencing Core Facility on a HiSeq 4000. proteins, based on established categories,27,31 is shown in Quality control was performed to examine read quality, du- Supplemental Table 3. Differences in abundance of individual plication rates, GC content, adapter content, and nucleotide proteins were analyzed by ANOVA with post hoc determina- distribution using the FastQC toolkit. Reads were aligned to tion of q value by Benjamini–Hochberg analysis and by the the GRCh38 genome with the STAR aligner (2.5.2), and fold differences based on iBAQ between NCs and cFSGS or transcript-level quantification was performed using Kallisto.30 FSGS-NOS. A total of 79 ECM proteins demonstrated a sig- NEPTUNE RNA-seq ENST data were converted to gene nificant difference in abundance between FSGS and NCs. An names. The ERCB and NEPTUNE data were filtered for glo- additional 25 ECM proteins demonstrated a fivefold or greater merular transcripts by matching with the gene name of the difference in abundance between FSGS and NCs in the ab- identified regulated matrisome proteomic data. The differ- sence of statistical significance. Of those 104 proteins, 85 ences in transcript expression means were compared by showed enhanced abundance in FSGS, of which 31 were

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 7 CLINICAL RESEARCH www.jasn.org

ANXA3 CTSC CTSB A BC Normal

D EF FSGS-NOS

G HI

* cFSGS

J KL

* * * cFSGS

MN O cFSGS

Figure 2. Glomerular tufts stain for annexin A3, cathepsin B, and cathepsin C in cFSGS. Glomerular expression of annexin A3, cathepsin C, and cathepsin B was visualized by IHC. Representative photomicrographs of glomeruli are shown for protein staining in (A–C) NCs, (D–F) FSGS-NOS, and (G–O) cFSGS. Arrows identify PECs along Bowman’s capsule showing hypertrophy and enlarged nuclei. (M–O) Show enlargements of the boxes in (J–L) showing inﬁltration of glomerular tufts by stained cells (arrowheads). The asterisk marks areas of glomerular tuft staining. Scale bars, 30 mm. Original magniﬁcation, 403.

8 JASN JASN 31: ccc–ccc,2020 htmcorpso igepaecnoa mgso tiigfr(,D n )anxnA ny o B ,adH ahpi or C cathepsin H) and with E, colocalization (B, B JASN cathepsin for and only, C A3 cathepsin annexin demonstrate images G) merged and The D, images. 30 (A, merged bars, I) for Scale and staining A3. F, of (C, annexin and images only, confocal B plane cathepsin single of photomicrographs (A 3. Figure – )cSS (D cFSGS, C) 31: ccc nei 3c-olie ihctesnCadctesnBi SSgoeui etoso ea ipisfo ainswith patients from biopsies renal of Sections glomeruli. FSGS in B cathepsin and C cathepsin with co-loclaizes A3 Annexin – ccc 2020 , –

)FG-O,ad(G and FSGS-NOS, F) NC FSGS-NOS cFSGS NC FSGS-NOS cFSGS HI GH D A I GH D A m .Oiia magni Original m. Annexin A3 Annexin A3 – )Nswr tie o nei 3 ahpi rctesnB n uli h aesshow panels The nuclei. and B, cathepsin or C cathepsin A3, annexin for stained were NCs I) ﬁ ain 60 cation, EF BC EF BC 3 . Cathepsin C Cathepsin B www.jasn.org Merged Merged lmrlrEMi FSGS in ECM Glomerular LNCLRESEARCH CLINICAL 9 CLINICAL RESEARCH www.jasn.org

annexin A3 claudin-1 merged ABC cFSGS

D E F FSGSNOS

G H I NC

annexin A3 synaptopodin merged ABC cFSGS

D E F cFSGS

G H I cFSGS

Figure 4. Annexin A3 colocalizes with claudin-1, but not synaptopodin in cFSGS. (A) Sections of renal biopsies from patients with (A–C) cFSGS, (D–F) FSGS-NOS, and (G–I) NCs immunostained for annexin A3, claudin-1, and nuclei stained with 49,6-diamidino-2-phenylindole. The panels show staining for (A, D, and G) annexin A3 only, for (B, E, and H) claudin-1 only, and (C, F, and I) merged images. The merged images show that annexin A3 and claudin-1 colocalize. Photomicrographs are 1-mm, single-plane images acquired by confocal

10 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH

cFSGScFSGS cFSGS cFSGS A D F H ANXA3

B E G I CD44

C pERK

Figure 5. Annexin A3–stained PECs express CD44 and pERK in cFSGS. Photomicrographs show IHC staining patterns for (A) annexin A3, (B) CD44, and (C) pERK in serial sections of a cFSGS glomerulus. PECs showed hypertrophy/hyperplasia, enlarged nuclei, and adhesions to glomerular tufts. Annexin A3, CD44, and pERK showed the same staining pattern. (D and E) Serial sections of a single cFSGS glomerulus with annexin A3–stained PECs infiltrating the glomerular tuft, demonstrating CD44 staining of plasma membranes (E). (F–I) Enlarged portions of the same glomerulus as in (D and E). Scale bars, 30 mm. Original magnification, 1003 for (A–C) and (F–I), and 403 for (D and E). increased in both cFSGS and FSGS-NOS, 37 in cFSGS only, the average of iBAQ scores. Table 1 lists those 58 ECM pro- and 17 in FSGS-NOS only. A total of 19 proteins showed re- teins, of which 41 were more abundant in cFSGS and 17 were duced abundance in FSGS, five in both cFSGS and FSGS-NOS, more abundant in FSGS-NOS. five in cFSGS, and nine in FSGS-NOS. To identify ECM proteins with differential abundance be- Validation of ECM Protein Abundance Differences tween cFSGS and FSGS-NOS, three separate screens were ap- To validate differences in ECM protein abundance, IHC was plied to the 104 ECM proteins with altered abundance in performed on a separate cohort of human biopsies diagnosed FSGS. First, iBAQ parameters from high-resolution proteo- as cFSGS, FSGS-NOS, and NC for 15 of 41 ECM proteins more mic data sets were analyzed by ANOVA followed by a post abundant in cFSGS: annexin A3, azurocidin, cathepsin B, ca- hoc Benjamini–Hochberg test (q value).23 A total of 48 ECM thepsin C, cathepsin G, neutrophil elastase, coagulation factor proteins were significantly different (q#0.05), of which abun- XII, IGF binding protein acid-labile subunit, IGF binding pro- dance was greater in cFSGS for 35 proteins and in FSGS-NOS tein 7, kininogen 1, myeloperoxidase, lectin mannose binding for 13 proteins. A volcano plot of that analysis is shown in 1, proteoglycan 3, serpin D1, and transthyretin. A visually ob- Figure 1. Second, four ECM proteins analyzed by ANOVA vious increase in expression and difference in staining pattern without correction for multiple comparisons showed statisti- for annexin A3, cathepsin C, and cathepsin B were observed cally significant differences between cFSGS and FSGS-NOS. (Figure 2). All three proteins stained PECs with normal Finally, six glomerular ECM proteins demonstrated a three- morphology lining Bowman’s capsule in all three groups of fold or greater difference in protein abundance, determined by patients. Cells lining Bowman’s capsule with an abnormal

microscopy. Original magniﬁcation of all images, 603. Scale bars, 30 mm. (B) Sections of a renal biopsy from a patient with cFSGS immunostained for annexin A3, synaptopodin, and nuclei stained with 49,6-diamidino-2-phenylindole. The panels show staining for (A, D, and G) annexin A3 only, for (B, E, and H) synaptopodin only, and (C, F, and I) merged images, in three different glomeruli from the same patient. The merged images show that annexin A3 and synaptopodin do not colocalize. Photomicrographs are 1-mm, single- plane images acquired by confocal microscopy. Original magniﬁcation of all images, 603. Scale bars, 30 mm.

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 11 CLINICAL RESEARCH www.jasn.org

Cathepsin C 100

PEC Staining (%) 80

60 Activated PEC Staining (%) 40

Glomerular Tuft Staining (%) 20 0 Collapsing NOS TipPerihilar MCD MN NC

Annexin - A3 100

PEC Staining (%) 80

60 Activated PEC Staining (%) 40

Glomerular Tuft Staining (%) 20 0 Collapsing NOS Tip Perihilar MCD MN NC

Figure 6. Enhanced annexin A3 and cathepsin C staining in glomerular tufts in cFSGS, compared to other proteinuric glomerular diseases. Heat maps show the percentage of glomeruli with annexin A3 and cathepsin C staining of PECs with normal or hyperplastic morphology and cells infiltrating glomerular tufts for all patients with FSGS variants, MCD, MN, or no glomerular disease (NC). morphology characterized by cytoplasmic hyperplasia and en- cells with abnormal morphology stained for CD44 and pERK. larged nuclei typical of activated PECs19,32 also stained for the Additionally, annexin A3–positive cells infiltrating glomeru- three proteins in glomeruli from patients with cFSGS and lar tufts stained for CD44 (Figure 5, D–I). FSGS-NOS (Figure 2, D and E). Obvious staining in and around cells infiltrating glomerular tufts was seen in about Cathepsin C and Annexin A3 Expression in Proteinuric half of cFSGS glomeruli (Figure 2, J–O). Examples of staining Glomerular Diseases for the other proteins is shown in Supplemental Figure 3. Due to limited human kidney biopsy tissue, comparison of The staining patterns suggested cathepsin B and cathepsin protein expression in proteinuric glomerular diseases focused C were expressed by normal PECs, and their expression was on cathepsin C and annexin A3. IHC was performed on 64 increased in activated PECs. Colocalization of cathepsin C and kidney biopsy specimens containing at least four nonsclerotic cathepsin B with annexin A3 was confirmed by confocal mi- glomeruli diagnosed with various histologic classes of FSGS, croscopy (Figure 3). That colocalization occurred in cells with minimal change disease (MCD), membranous nephropathy normal and abnormal morphology lining Bowman’scapsule (MN), or NC. The number of glomeruli evaluated per patient and in cells within glomerular tufts. To confirm that annexin was 1267 (mean6SD; range, 4–35). Figure 6 illustrates the A3–stained cells expressed markers of PECs, and not podo- percentage of glomeruli with staining of normal PECs, staining cytes, colocalization of annexin A3 with claudin-1 and synap- of PECs with abnormal morphology, and staining of cells in- topodin was examined. Annexin A3 and claudin-1 extensively filtrating glomerular tufts for individual patients with each colocalized in cells lining Bowman’scapsuleandinfiltrating glomerular disease; Figure 7 shows representative photomicro- glomeruli in cFSGS (Figure 4A). Syndaptopodin did not co- graphs. The numeric data are shown in Supplemental Table 4. localize to annexin A3–stained cells, whether lining Biopsies from all patients showed annexin A3 and cathepsin C Bowman’s capsule or infiltrating glomeruli (Figure 4B). Taken staining of morphologically normal PECs lining Bowman’s together, the staining patterns suggest that cells infiltrating capsule in .80% of glomeruli. Staining for both cathepsin C glomeruli in cFSGS represent PECs. and annexin A3 of PECs with hyperplastic morphology lining In addition to altered morphology, PEC activation is associ- Bowman’s capsule occurred in 35%–65% of glomeruli from ated with ERK1/2-dependent expression of CD44.9,18–20,33,34 To patients with glomerular disease and in 10%–25% of glomeruli determine if annexin A3–positive cells with abnormal mor- obtained from patients without known renal disease. phology expressed activation markers, IHC for annexin A3, All patients with cFSGS exhibited the presence of cells CD44, and pERK was performed on serial cFSGS biopsy sec- staining for cathepsin C and annexin A3 within glomerular tions. Figure 5, A–C, shows that many annexin A3–positive tufts in 51%610% of glomeruli (mean6SEM; range,

12 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH

Annexin A3 Cathepsin C A B

C D

cFSGS

FSGS-NOS

G H

Tip Lesion

I J

Tip Lesion

Figure 7. Glomerular tuft staining for annexin A3 and cathepsin C is prominent in cFSGS, compared to other proteinuria glomerular diseases. Representative images of IHC staining for annexin A3 and cathepsin C in biopsies from (A and B) NCs, (C and D) cFSGS, (E and F) FSGS-NOS, (G–J) FSGS tip lesion, (K and L) FSGS perihilar lesion, (M and N) MCD, and (O and P) MN. Scale bars, 30 mm. Original magniﬁcation, 403.

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 13 CLINICAL RESEARCH www.jasn.org

Perihilar FSGS

MCD

Figure 7. Continued.

17%–85%). As shown in Figure 7 and Supplemental Table 4, for percentage of glomeruli stained was 0.91660.054 staining for cathepsin C and annexin A3 covered a large por- (P50.0006) for cathepsin C (Figure 8A) and 0.91860.049 tion of glomerular surface area in affected cFSGS glomeruli. (P50.0005) for annexin A3 (Figure 8B) when cFSGS was com- Glomerular tuft staining for cathepsin C and annexin A3 in pared with other FSGS variants. These classifications were op- biopsies from other classes of FSGS was much less common timal at 29% of glomerular tufts stained for cathepsin C with a and covered a smaller percentage of surface area. Fewer than resulting sensitivity of diagnosing cFSGS of 87.5% and a spec- 20% of glomeruli demonstrated cathepsin C or annexin A3 ificity to exclude other diseases of 91.3%. For annexin A3, 10% staining within glomerular tufts of biopsies from patients with of glomerular tuft staining provided a sensitivity of 87.5% and FSGS-NOS and perihilar or tip lesions. In the tip lesion, glo- a specificity of 88%. When compared with FSGS variants, merular tuft staining occurred in areas of adhesion at the uri- MCD, and MN, the AUC for cathepsin C was 0.94760.032 nary pole (Figure 7, G–J) and positive glomerular staining in (P50.0001) with a sensitivity of 87.5% and a specificity of perihilar FSGS was observed near the vascular pole (Figure 7, 93.8%. For annexin A3, AUC was 0.94060.031 (P50.0001) K and L). Minimal tuft staining was rarely seen in patients with a sensitivity of 87.5% and a specificity of 88%. Thus, diagnosed with MN and MCD and was absent in NCs. detection of glomerular tuft infiltration by cells containing By regression analysis, both the percentage of glomeruli per markers for PECs may improve the sensitivity of biopsy di- biopsy with tuft staining for cathepsin C and annexin A3 and agnosis of cFSGS. the percentage of glomerular surface area staining for cathepsin C were significantly different between cFSGS and other Evidence for Differences in Synthesis and Degradation histologic classes of FSGS (P,0.000015). Classification of bi- of ECM Proteins in FSGS opsy glomerular tuft staining by receiver operator character- The differential abundance of glomerular ECM proteins be- istic curves for percentage of glomeruli stained separated tween cFSGS and FSGS-NOS could be due to differences in cFSGS from the other histologic FSGS variants and from all matrix production and/or degradation. To define the basis for proteinuric glomerular diseases studied (Figure 8). The AUC differential ECM protein abundance, gene expression, urine

14 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH

A B 100 100

80 80

60 60

40 Sensitivity% Sensitivity%

20 20 AUC = 0.916 AUC = 0.940 p = 0.0006 p < 0.0001 0 0 0 20406080100 0 20406080100 100% - Specificity% 100% - Specificity%

C D 100 100

80 80

60 60

40 40 Sensitivity% Sensitivity%

20 20 AUC = 0.946 AUC = 0.918 p < 0.0001 p = 0.0005 0 0 0 20406080100 0 20406080100 100% - Specificity% 100% - Specificity%

Figure 8. Receiver operating characteristic (ROC) curves showing glomerular tuft staining for cathepsin C and annexin A3 predict cFSGS. ROC plots showing predictive capability of the percentage of glomeruli with tuft staining for cathepsin C or annexin A3. (A) The ROC curve for the percentage of glomeruli with cathepsin C staining of glomerular tufts comparing cFSGS to all other variants of FSGS. (B) The ROC curve for percentage of glomeruli with annexin A3 staining of glomerular tufts comparing cFSGS to all other variants of FSGS. (C) The ROC curve for the percentage of glomeruli with cathepsin C staining comparing cFSGS with other FSGS variants, MCD, and MN. (D) The ROC curve for annexin A3 staining comparing cFSGS with other FSGS variants, MCD, and MN. The AUC analysis and P value are in the box accompanying each panel. Patients with cFSGS had a mean6SEM serum creatinine of 3.8160.67 mg/dl and mean6SEM urine protein excretion of 9.5461.97 mg/24 h. Patients with the other variants had a mean6SEM serum creatinine of 1.8260.24 mg/dl and mean6SEM urine protein excretion of 8.161.95 gm/24 h. excretion of intact proteins, and urine excretion of peptides NOS, RNA-seq–based transcriptomic data obtained from from differentially abundant ECM proteins were compared the NEPTUNE database (https://www.rarediseasesnetwork. among patients with cFSGS, FSGS-NOS, and NCs. Table 2 org/cms/neptune) were analyzed for patients with cFSGS shows differences in gene expression between FSGS and NC (n511) and FSGS-NOS (n521). Due to the small sample and between cFSGS and FSGS-NOS for ECM proteins size, unadjusted P values were used to rank order transcript identified as differentially abundant by mass spectrometry. differential abundance between groups. Table 2 shows that, of Glomerular gene expression comparing FSGS with NC was the 38 genes observed for ECM proteins more abundant in performed for 32 of the 58 ECM proteins with differential cFSGS, five genes showed greater expression in cFSGS at the abundance between cFSGS and FSGS-NOS (Table 2). Tran- P,0.05 level, including CTSB. Of the 15 genes observed for scripts for 16 of 32 genes examined showed a significantly ECM proteins more abundant in FSGS-NOS, three genes greater expression in FSGS glomeruli, including CTSC. showed greater expression at the P,0.05 level. To determine if there was gene expression differential As additional support for increased production of ECM abundance of ECM proteins between cFSGS and FSGS- proteins in cFSGS, quantitative urine excretion of ECM pro-

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 15 CLINICAL RESEARCH www.jasn.org

Table 2. Transcript analysis for ECM proteins with differential abundance between cFSGS and FSGS-NOS Gene Log Fold Change (FSGS q Log Fold Change (cFSGS to P Protein Name 2 2 Name to NC) Value FSGS- NOS) Value Proteins with greater abundance in cFSGS Annexin A3 ANXA3 1.13 0.070 0.80 0.068 Apolipoprotein C3 APOC3 0.61 0.030 20.72 0.091 Azurocidin AZU1 1.03 0.380 0.122 0.852 Complement C1q A chain C1QA ND 0.30 0.473 Complement C1q B chain C1QB ND 0.28 0.556 Complement C1q C chain C1QC ND 0.40 0.089 Collagen a-1 (XII) chain COL12A1 ND 0.40 0.034 Collagen a-1 (XXI) chain COL21A1 ND 20.19 0.527 Collagen a-1(VII) chain COL7A1 1.28 0.001 0.07 0.505 Cysteine-rich transmembrane BMP CRIM1 0.86 0.001 20.10 0.524 regulator 1 Chondroitin sulfate proteoglycan 4 CSPG4 1.07 0.080 0.00 1.000 Cathepsin B CTSB ND 0.54 0.043 Cathepsin C CTSC 1.5 0.001 0.54 0.252 Cathepsin G CTSG 0.96 0.190 0.29 0.722 Cathepsin L CTSL ND 20.20 0.166 ECM protein 1 ECM1 2.67 0.001 20.10 0.834 Neutrophil elastase ELANE ND 0.17 0.577 Coagulation factor XI F12 0.94 0.090 20.06 0.858 Fibrillin 2 FBN2 1.35 0.001 0.26 0.373 Fibrinogen-like protein 1 FGL1 ND ND Hydroxysteroid 17-b dehydrogenase 12 HSD17B12 ND 0.40 0.047 Insulin-like growth factor binding protein IGFALS 0.92 0.030 0.07 0.704 acid labile Insulin-like growth factor binding protein 7 IGFBP7 1.06 0.070 20.20 0.483 Inter-a-trypsin inhibitor heavy chain 5 ITIH5 ND 20.29 0.363 Kininogen 1 KNG1 0.71 0.001 0.27 0.614 Laminin subunit a 3 LAMA3 ND 0.31 0.162 Laminin subunit b 1 LAMB1 1.11 0.160 0.13 0.447 Galectin 3 LGALS3 ND 0.52 0.025 Galectin 7 LGALS7 ND 20.39 0.924 Lectin, mannose binding 1 LMAN1 0.88 0.010 0.00 1.000 Matrix metalloproteinase 9 MMP9 ND 20.10 0.799 Myeloperoxidase MPO ND 20.08 0.880 Procollagen-lysine,2-oxoglutarate 5- PLOD3 1.13 0.001 0.84 0.090 dioxygenase 3 Proteoglycan 3 PRG3 0.95 0.080 ND Serine protease 23 PRSS23 1.48 0.001 1.15 0.050 S100 calcium binding protein S100A8 0.91 0.320 20.35 0.412 S100 calcium binding protein S100A9 0.88 0.290 20.31 0.344 Serpin family D member 1 SERPIND1 1.13 0.060 20.35 0.224 Transthyretin TTR ND 20.25 0.619 Serpin family F member 2 SERPINF2 ND 0.00 1.000 Uromodulin UMOD 0.69 0.001 20.50 0.510 Proteins with greater abundance in FSGS- NOS Biglycan BGN 1.2 0.020 20.02 0.560 Collagen a-1 (I) chain COL1A1 1.49 0.001 1.80 0.004 Collagen a-2 (I) chain COL1A2 2.82 0.001 0.70 0.160 Collagen a-1 (XV) chain COL15A1 1.94 0.001 0.09 0.824 Collagen a-1 (III) chain COL3A1 ND 0.20 0.640 Cystatin-C CST3 ND 0.30 0.409 Fibulin 5 FBLN5 0.95 0.230 20.30 0.389 Filaggrin family member 2 FLG2 ND 0.00 1.000

16 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH

Table 2. Continued

Gene Log Fold Change (FSGS q Log Fold Change (cFSGS to P Protein Name 2 2 Name to NC) Value FSGS- NOS) Value HtrA serine peptidase 1 HTRA1 0.97 0.280 20.75 0.236 Inhibin b E chain INHBE ND 0.05 0.990 Inter-a-trypsin inhibitor heavy chain H4 ITIH4 ND 20.53 0.642 Lipoprotein(a) LPA 0.93 0.070 20.36 0.465 Peroxidasin PXDN ND 1.00 0.015 Serum amyloid A1 SAA1 ND 20.14 0.827 Serpin family B member 12 SERPINB12 ND ND Serpin family G member 1 SERPING1 1.05 0.160 0.5 0.044 von Willebrand factor VWF 1.00 0.280 0.10 0.680 ND, not determined. teins was determined by mass spectrometry in three patients Peptides with cathepsin cleavage sites and increased abun- each with cFSGS and FSGS-NOS, and the relative abundances dance in urine from patients with cFSGS were derived from were compared. A total of 93 ECM proteins showed a signif- cathepsin D or cathepsin L. A list of all protease groups pre- icantly greater abundance in urine from patients with cFSGS, dicted to be responsible for cleavage sites on urine ECM pro- whereas 21 ECM proteins were significantly more abundant in teins is shown in Supplemental Table 7. urine from FSGS-NOS patients (Supplemental Table 5). Only eight of the 93 ECM proteins more abundant in cFSGS urine were also more abundant in glomeruli, including cathepsin B DISCUSSION and cathepsin C. On the other hand, seven ECM proteins more abundant in cFSGS urine were present in greater abun- We performed a proteomic and transcriptomic analysis of hu- dance in FSGS-NOS glomeruli. Similarly, three of 21 ECM man ECM constituents to gain an understanding of the dif- proteins more abundant in urine from patients with FSGS- ferences in ECM remodeling that distinguishes cFSGS from NOS were present in greater abundance in cFSGS glomeruli. other FSGS variants. Significant differences were identified in Thus, urine excretion of ECM proteins appears to be a poor cFSGS glomerular ECM composition. Proteomic analysis predictor of glomerular ECM composition. Because both found 41 ECM proteins with increased abundance in cFSGS cathepsin B and C were present in tubular cells (Figure 3), and 17 with increased abundance in FSGS-NOS. Those enhanced urine excretion cannot be conclusively linked to proteins included members of all categories of matrisome pro- glomerular abundance of those proteins. teins, including basement membrane, structural, ECM- To screen for degradation of ECM proteins by cathepsin B affiliated, and ECM regulators. IHC and confocal microscopy and C in cFSGS glomeruli, excretion of urine peptides of confirmed the enhanced expression and colocalization of ,5000 kDa was quantified for each of three patients with three proteins—cathepsin B, cathepsin C, and annexin A3— cFSGS, FSGS-NOS, and MCD. MCD was used as the control in cells lining Bowman’s capsule and infiltrating capillary tufts to account for filtered peptides due to increased glomerular in cFSGS. Those three proteins were not seen in normal glo- basement membrane permeability and degradation of filtered merular tufts and were uncommon in glomerular tufts from serum proteins by tubule cells. A total of 902 peptides from other FSGS variants, MCD, and MN. 152 unique proteins was identified, 45 of which were ECM Although the origin of cells infiltrating glomerular tufts in proteins represented by 365 peptides. Comparing the three cFSGS cannot be stated with certainty, substantial evidence patients with MCD to all six patients with FSGS, 34 peptides indicates they are activated PECs. A number of reports indi- derived from 25 ECM proteins showed significantly enhanced cated a contribution of PECs to the development of FSGS in abundance in urine from patients with FSGS (Supplemental humans and animal models, including their proliferation in Table 6). Of the 35 peptides with significantly different abun- cFSGS and increased synthesis of ECM.9,18,19,32,33 Consistent dance between cFSGS and FSGS-NOS, all showed greater with a previous study of human FSGS,9 we found that infil- abundance in cFSGS. To examine the potential role of cathep- trating cells expressed markers of PECs (claudin-1 and an- sin B and cathepsin C in ECM degradation in cFSGS, protease nexin A3), whereas a marker of podocytes (synaptopodin) prediction with Proteasix (www.proteasix.org) was performed was absent. PEC activation depends on ERK1/2-mediated ex- for urine peptides from ECM proteins, only accepting prote- pression of CD44, an adhesion receptor for hyaluronic acid ases with experimentally observed cleavage sites. No peptides and other ECM proteins.18,19,32,33,35–37 Colocalization of an- with cleavage sites for cathepsin C were identified. A total of nexin A3, CD44, and pERK1/2 in our study is also consistent eight peptides with cleavage sites for cathepsin B were identi- with a PEC origin of cells infiltrating cFSGS glomeruli. Both fied, none of which showed differential urine excretion. cathepsin B and C were detected in PECs of normal glomeruli,

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 17 CLINICAL RESEARCH www.jasn.org and both proteases were present in infiltrating cells. Finally, a role for PRSS23 in the development of a migratory PEC lineage tracing studies in mice show PECs contribute to pro- phenotype.49 The absence of increased gene expression for liferating epithelial cells within glomeruli in mouse models of the majority of differentially abundant ECM proteins suggests FSGS.18,38 The basis for PEC migration into glomerular tufts that transcriptional regulation of protein synthesis is not re- in cFSGS remains to be determined. Because CD44 is a recep- sponsible for most differences in ECM protein abundance in tor for a number of ECM components, it is possible that al- FSGS. Differential ECM protein abundance could be due to tered glomerular ECM composition in cFSGS contributes to altered degradation rates or to increased translational regula- PEC migration into glomeruli. tion of ECM synthesis, as has been described in idiopathic Migration of PECs into glomerular tufts introduced two pulmonary fibrosis.50 Differences in urinary peptide excretion proteases, cathepsin B and cathepsin C, not normally present. derived from ECM proteins in our study indicate ECM deg- Our study suggests that PEC activation increases expression of radation is increased in cFSGS. Because the ECM peptides both cathepsins. Glomerular transcript expression for cathep- were not derived from the proteins showing differential abun- sin C was increased in FSGS, compared with NC. Transcript dance, it is possible those proteins are more resistant to expression for cathepsin B was increased in cFSGS, compared proteolysis. with FSGS-NOS. IHC staining for both proteases was more A number of limitations to our study exist. Heterogeneity intense in PECs with hyperplastic morphology. Additionally, of glomerular changes in FSGS limits identification of the focal urine proteomic analysis showed significantly greater urinary and local changes in ECM composition. Because our proteo- excretion of both cathepsins in patients with FSGS, compared mic approach combined sections from 12 to 26 glomeruli with those with no renal disease. Those findings are consistent from each patient, our data present average differences in with single nephron proteomics performed in two mouse ECM composition. The application of proteomics to single models of FSGS showing that cathepsin B was significantly glomeruli with defined histologic changes will improve detec- increased in glomeruli.39 A potential role for cathepsin B in tion of altered ECM protein expression. Confirmation studies mediating FSGS was suggested by the resistance of cathepsin B that visualize the protein of interest are needed to determine knockout mice to nephrotoxic serum-induced proteinuria.39 the pattern of expression within abnormal glomeruli. It is Cathepsin B and C are members of a family of 11 cysteine possible that IHC validation of our proteomic findings from proteases.40 Cathepsins are normally present in high concen- Triton X-100–insoluble pellets failed due to differences in trations in lysosomes, where they are crucial for protein pro- sample handling. The inability to perform lineage tracing cessing and degradation.41 Cathepsins are also secreted into studies in humans resulted in using expression of markers the extracellular space, where they participate in ECM remod- presumed to be specific for PECs and podocytes to identify eling, receptor and adhesion molecule shedding, activation of the cell type infiltrating glomeruli in cFSGS. Marker expres- cytokines and growth factors, generation of bioactive frag- sion, coupled with previous animal studies, justifies the ments from ECM proteins, cleavage of cell junction proteins, preliminary conclusion that infiltrating cells are primarily and cell migration.12–14,41–43 Cathepsin B degrades a number composed of PECs. The possibility exists, however, that de- of basement membrane proteins, including laminins, and de- differentiation of podocytes results in altered expression of the grades intact glomerular basement membrane.41,44 In silico markers used in this study. The use of urine protein and pep- protease prediction, however, failed to identify increased urine tide excretion to reflect ECM expression and protease activity excretion of peptides generated by either cathepsin. Those in glomeruli has a number of limitations. Blood could be the findings suggest the possibility that increased glomerular ex- source of proteins and peptides in the urine due to altered pression of cathepsin B and C function differently from ECM glomerular filtration barrier in FSGS. That possibility was remodeling in cFSGS. Several cathepsins, including cathepsin addressed by using urine from MCD as a control for urine B, differentially regulate TGFb signaling that is linked to ECM peptide excretion. Although 114 ECM proteins showed differ- production. Altered cathepsin activity was observed in unilat- ential urine excretion between cFSGS and FSGS-NOS, only 18 eral ureteral obstruction–mediated renal fibrosis, and inhibi- of those proteins were differentially abundant in glomeruli. tion of cathepsin activity altered the degree of fibrosis.45 As Additionally, ten of those 18 ECM proteins showed increased pharmacologic inhibitors of specific cathepsins are being de- urine excretion in the patient group with a relative decrease in veloped,46 defining the role of cathepsins in cFSGS could pro- glomerular abundance. The expression of cathepsin B and C vide new therapeutic approaches. by renal tubule cells provides another source for increased Only five of 38 transcripts from proteins with increased urine excretion of those proteases. We conclude that technical abundance in cFSGS showed increased expression. In addition and biologic considerations limit the ability of urine excretion to cathepsin B, a transcript for PRSS23 was among those in- of ECM proteins to predict glomerular ECM composition. creased. Two previous studies showed increased gene expres- Similarly, urinary peptide excretion may not accurately reflect sion for PRSS23 in FSGS.47,48 Increased expression of PRSS23 the level of glomerular ECM degradation due to peptide pro- in PECs was associated with proteinuria and loss of renal func- cessing or reabsorption by renal tubules. The predictive algo- tion in FSGS, lupus nephritis, diabetic nephropathy, and rithms for protease cleavage sites may miss noncanonical MN,49 and evidence from a mouse model of FSGS suggested amino acid sequences identified by cathepsins, because

18 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH candidate proteases were not identified for 40% of peptides coordinator) at Emory University (Atlanta, GA); S. Adler (principal with differential urine excretion. investigator), C. Nast (principal investigator; Cedars-Sinai Medical In summary, a proteomic analysis of glomerular ECM Center, Los Angeles, CA), and J. LaPage (study coordinator) at composition shows distinct differences between cFSGS and Harbor-University of California Los Angeles Medical Center; A. FSGS-NOS, suggesting the mechanisms of abnormal ECM Athavale (principal investigator) at John H. Stroger Jr. Hospital of remodeling differ. Our data indicate that both enhanced Cook County (Chicago, IL); A. Neu (principal investigator) and S. ECM protein synthesis and altered degradation contribute Boynton (study coordinator) at Johns Hopkins Medicine (Baltimore, to abnormal ECM remodeling in FSGS. Extensive glomerular MD); F. Fervenza (principal investigator), M. Hogan (coinvestigator), tuft infiltration of cells with an activated PEC phenotype dif- J. Lieske (principal investigator), and V. Chernitskiy (study co- ferentiates cFSGS from other FSGS variants and other protei- ordinator) at Mayo Clinic (Rochester, MN); F. Kaskel (principal in- nuric glomerular diseases. Those cells introduce a new set of vestigator), N. Kumar (principal investigator), and P. Flynn (study proteases, cathepsins B and C, into glomeruli. Evidence from coordinator) at Montefiore Medical Center (Bronx, NY); J. Kopp animal studies suggests those proteases contribute to develop- (principal investigator) and J. Blake (study coordinator) at National ment of FSGS. Whereas podocyte injury likely initiates FSGS, Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) our data support the concept that PEC activation and migra- Intramural (Bethesda, MD); H. Trachtman (principal investigator), tion determine disease severity. Targeting PECs for therapeu- O. Zhdanova (coinvestigator), F. Modersitzki (study coordinator), tic intervention may alter disease progression, particularly in and S. Vento (study coordinator) at New York University Medical cFSGS. Multiple pathways leading to focal sclerotic lesions Center (New York, NY); R. Lafayette (principal investigator) and K. complicate identification of therapeutic targets for disruption Mehta (study coordinator) at Stanford University (Stanford, CA); C. of ECM deposition in FSGS. Our data point to cathepsin pro- Gadegbeku (principal investigator), D. Johnstone (coinvestigator), teases as possible candidates for pharmacologic intervention. and S. Quinn-Boyle (study coordinator) at Temple University (Philadelphia, PA); D. Cattran (principal investigator), M. Hladu- newich (coinvestigator), H. Reich (coinvestigator), P. Ling (study DATA SHARING STATEMENT coordinator), and M. Romano (study coordinator) at University Health Network Toronto; A. Fornoni (principal investigator) and C. Data files for acquired LCMS data (.RAW), for peak lists Bidot (study coordinator) at University of Miami (Miami, FL); M. (.mgf), and compressed search results (.mzIdentML) were de- Kretzler (principal investigator), D. Gipson (principal investigator), posited in MassIVE (http://massive.ucsd.edu/) data repository A. Williams (study coordinator), and J. LaVigne (study coordinator) (MassIVE identifier, MSV000079914) of the Center for Com- at University of Michigan (Ann Arbor, MI); V. Derebail (principal putational Mass Spectrometry at the University of California, investigator), K. Gibson (principal investigator), E. Cole (study co- San Diego and shared with the ProteomeXchange (www. ordinator), and S. Grubbs (study coordinator) at University of North proteomexchange.org). The data files for ERCB microarray Carolina (Chapel Hill, NC); L. Holzman (principal investigator), K. data are available at Gene Expression Omnibus (GEO; www. Meyers (coinvestigator), K. Kallem (study coordinator), and J. Lalli ncbi.nlm.nih.gov/geo/) under GEO numbers GSE47183, (study coordinator) at University of Pennsylvania (Philadelphia, PA); GSE32591, and GSE104948. K. Sambandam (principal investigator), Z. Wang (study coordinator), and F. Chambers (study coordinator) at University of Texas Southwestern (Dallas, TX); A. Jefferson (principal investigator), S. Hingorani (coinvestigator), K. Tuttle (coinvestigator; ACKNOWLEDGMENTS Providence Medical Research Center, Spokane, WA), N. Johnson (study coordinator), S. Dismuke (study coordinator), and A. Cooper We would like to thank all members of the NEPTUNE consortium (study coordinator; Providence Medical Research Center, Spokane, listed below. WA) at University of Washington (Seattle, WA); and B. Freedman From the NEPTUNE enrolling centers: J. Sedor (principal in- (principal investigator), J.J. Lin (coinvestigator), and S. Gray (study vestigator), K. Dell (principal investigator), M. Schachere (study coordinator) at Wake Forest University Baptist Health (Winston- coordinator), and J. Negrey (study coordinator) at Cleveland Clinic Salem, NC). (Cleveland, OH); K. Lemley (principal investigator) and S. Tang From the data analysis and coordinating center: M. Kretzler, L. (study coordinator) at Children’s Hospital Los Angeles (Los Angeles, Barisoni, C. Gadegbeku, B. Gillespie, D. Gipson, L. Holzman, L. CA); T. Srivastava (principal investigator) and A. Garrett (study co- Mariani, M. Sampson, P.Song, J. Troost, J. Zee, E. Herreshoff, S. Li, C. ordinator) at Children’s Mercy Hospital (Kansas City, MO); C. Lienczewski, T. Mainieri, M. Wladkowski, A. Williams, and D. Sethna (principal investigator) and R. Odusayana (study co- Zinsser. ordinator) at Cohen Children’s Hospital (New Hyde Park, NY); G. From the digital pathology committee: Carmen Avila-Casado Appel (principal investigator) and M. Toledo (study coordinator) at (University Health Network Toronto), Serena Bagnasco (Johns Columbia University (New York, NY); L. Barisoni (principal in- Hopkins), Joseph Gaut (Washington University), Stephen Hewitt vestigator) at Duke University (Durham, NC); L. Greenbaum (National Cancer Institute), Jeff Hodgin (University of Michigan), (principal investigator), C. Wang (coinvestigator), and B. Lee (study Kevin Lemley (Children’s Hospital Los Angeles), Laura Mariani

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 19 CLINICAL RESEARCH www.jasn.org

(University of Michigan), Matthew Palmer (University of Pennsyl- 92003587 to I. Rood; the James Y. McCullough Award Fund to M Merchant, vania), Avi Rosenberg (NIDDK), Virginie Royal (Montreal), David M. Barati, and K. McLeish; and the National Center for Advancing Thomas (University of Miami), Jarcy Zee (Arbor Research), and Translational Sciences grant UL1TR002240 for the Michigan Institute for Clinical and Health Research. cochairs Laura Barisoni (Duke University) and Cynthia Nast (Cedar Sinai). From the NIDDK program office: C. Roy and S. Mendley. SUPPLEMENTAL MATERIAL From the National Center for Advancing Translational Sciences program office: T. Urv and P.J. Brooks. This article contains the following supplemental material online at Dr. Kenneth McLeish and Dr. Michael Merchant conceived and http://jasn.asnjournals.org/lookup/suppl/doi:10.1681/ASN.2019070696/-/ designed the study; Dr. Michelle Barati, Dr. Liliane Hobeika, Dr. DCSupplemental. Jeffrey Hodgin, Dr. Jon Bernard Klein, Dr. Matthias Kretzler, Ms. Supplemental Figure 1. Laser capture of glomeruli excludes Ming Li, Dr. Laura Mariani, Dr. Michael Merchant, Dr. Johnathan Bowman’s capsule. Troost, and Mr. Daniel Wilkey performed and interpreted experi- Supplemental Figure 2. Comparison of ECM protein enrichment ments; Dr. Susan Coventry, Dr. Jessica Hata, and Dr. Christopher by extraction method. Patrick Larsen evaluated and provided anonymous renal biopsy Supplemental Figure 3. Immunohistochemistry of cFSGS, FSGS- material; Dr. Dawn Caster, Dr. Jeroen Deegens, Dr. Ilse Rood, and Dr. NOS, and NC for selected glomerular ECM proteins. Jack Wetzels collected and provided anonymous urine samples; Dr. Supplemental Table 1. All glomerular proteins identified from Michael Brier performed statistical analyses; Dr. Michelle Barati and cFSGS, FSGS-NOS, and NC. (Mass spectrometry data contained in a Dr. Michael Merchant prepared figures; Dr. Michelle Barati, Dr. supplemental spreadsheet.) Michael Merchant, and Dr. Kenneth McLeish wrote the manuscript; Supplemental Table 2. Gene names of glomerular ECM proteins Dr. Michael Brier, Dr. Jon Bernard Klein, Dr. Matthias Kretzler, Dr. identified in NC, FSGS-NOS, and cFSGS. Liliane Hobeika, and Dr. Johnathan Troost assisted in editing the Supplemental Table 3. Relative abundance of glomerular ECM manuscript. proteins. Supplemental Table 4. Glomerular cathepsin and annexin A3 staining of various proteinuric glomerular diseases. DISCLOSURES Supplemental Table 5. Comparison of urinary excretion of ECM proteins. D. Caster reports grant support from Aurinia and Mallinckrodt; personal (Mass spectrometry data contained in a supplemental spreadsheet.) fees from Retrophin; being site principal investigator for clinical trials from Aurinia, Calliditas, Mallinckrodt, and Retrophin; and being on the advisory Supplemental Table 6. Peptides derived from ECM proteins board for Retrophin; outside the submitted work. J. Hodgin reports grant showing increased urine excretion. (Mass spectrometry data con- support from Complexa Inc., Goldfinch Bio, and Pfizer Inc. M. Kretzler retained in a supplemental spreadsheet.) ports grants from Astra-Zeneca, Boehringer Ingelheim, Certa, Chan Zucker- Supplemental Table 7. Proteases associated with urine ECM berg Initiative, Complexa Inc., Eli Lilly, Elpidera, European Union Innovative peptides. Medicine Initiative, Gilead, Goldfinch Bio, Janssen, JDRF, Merck, NovoNor- disc, and Pfizer Inc., outside the submitted work. M. Kretzler also reports nonfinancial support from the University of Michigan and has a patent PCT/EP2014/073413 “Biomarkers and methods for progression prediction REFERENCES for CKD” issued. L. Mariani reports grants from Boehringer Ingelheim, Com- plexa Inc., Goldfinch Bio, NIDDK (during the conduct of the study), and 1. Rosenberg AZ, Kopp JB: Focal segmental glomerulosclerosis. Clin Pfizer Inc., and personal fees from Reata Pharmaceuticals, outside the sub- J Am Soc Nephrol 12: 502–517, 2017 mitted work. J. Troost reports grant support from Complexa Inc., Goldfinch 2. Sim JJ, Bhandari SK, Batech M, Hever A, Harrison TN, Shu YH, et al.: Bio, and Pfizer Inc.; other from General Electric; and other from Procter & End-stage renal disease and mortality outcomes across different glo- Gamble; outside the submitted work. J. Wetzels reports support and honoraria merulonephropathies in a large diverse US population. Mayo Clin Proc from Achillion, Chemocentryx, Shire, and Virfor Pharma; personal fees from 93: 167–178, 2018 Novartis; personal fees from Retrophin; and personal fees from Shire; outside 3. D’Agati VD, Fogo AB, Bruijn JA, Jennette JC: Pathologic classification the submitted work. All remaining authors have nothing to disclose. of focal segmental glomerulosclerosis: A working proposal. Am J Kidney Dis 43: 368–382, 2004 4. Stokes MB, D’Agati VD: Morphologic variants of focal segmental glomerulosclerosis and their significance. Adv Chronic Kidney Dis 21: FUNDING 400–407, 2014 5. Laurin L-P, Gasim AM, Derebail VK, McGregor JG, Kidd JM, Hogan SL, NEPTUNE is a part of the NIH Rare Disease Clinical Research Network, et al.: Renal survival in patients with collapsing compared with not supported through a collaboration between the Office of Rare Diseases Re- otherwise specified FSGS. Clin J Am Soc Nephrol 11: 1752–1759, 2016 search, National Center for Advancing Translational Sciences, and the 6. Raja R, Nada R, Yadav AK, Kumar A, Goyal A, Kumar V, et al.: A pro- NIDDK, grant U54‐DK‐083912. Additional funding and/or programmatic spective study of collapsing focal segmental glomerulosclerosis. Ren support for this project was also provided by the University of Michigan, Fail 38: 894–898, 2016 NephCure Foundation, and the Halpin Foundation. This project was suppor- 7. Tsuchimoto A, Matsukuma Y, Ueki K, Tanaka S, Masutani K, Nakagawa ted by NIH grant R01DK110077 to J. Klein; NIH grant R01DK091584 to M. K, et al.: Utility of Columbia classification in focal segmental glomer- Merchant; NIH grant 1K08DK102542 to D. Caster; ZonMw AGIKO grant ulosclerosis: Renal prognosis and treatment response among the

20 JASN JASN 31: ccc–ccc,2020 www.jasn.org CLINICAL RESEARCH

pathological variants [published online ahead of print January 11, 27. Naba A, Clauser KR, Ding H, Whittaker CA, Carr SA, Hynes RO: The 2019]. Nephrol Dial Transplant extracellular matrix: Tools and insights for the “omics” era. Matrix Biol 8. Albaqumi M, Soos TJ, Barisoni L, Nelson PJ: Collapsing glomerulop- 49: 10–24, 2016 athy. J Am Soc Nephrol 17: 2854–2863, 2006 28. Gadegbeku CA, Gipson DS, Holzman LB, Ojo AO, Song PX, Barisoni L, 9. Dijkman H, Smeets B, van der Laak J, Steenbergen E, Wetzels J: The et al.: Design of the Nephrotic Syndrome Study Network (NEPTUNE) to parietal epithelial cell is crucially involved in human idiopathic focal evaluate primary glomerular nephropathy by a multidisciplinary ap- segmental glomerulosclerosis. Kidney Int 68: 1562–1572, 2005 proach. Kidney Int 83: 749–756, 2013 10. Dijkman HB, Weening JJ, Smeets B, Verrijp KC, van Kuppevelt TH, 29. Ju W, Nair V, Smith S, Zhu L, Shedden K, Song PXK, et al; ERCB, Assmann KK, et al.: Proliferating cells in HIV and pamidronate- C-PROBE, NEPTUNE, and PKU-IgAN Consortium: Tissue associated collapsing focal segmental glomerulosclerosis are parietal transcriptome-driven identification of epidermal growth factor as a epithelial cells. Kidney Int 70: 338–344, 2006 chronic kidney disease biomarker. Sci Transl Med 7: 316ra193, 2015 11. Theocharis AD, Skandalis SS, Gialeli C, Karamanos NK: Extracellular 30. Bray NL, Pimentel H, Melsted P, Pachter L: Near-optimal probabilistic matrix structure. Adv Drug Deliv Rev 97: 4–27, 2016 RNA-seq quantification. Nat Biotechnol 34: 525–527, 2016 12. Fonovic M, Turk B: Cysteine cathepsins and extracellular matrix deg- 31. Randles MJ, Humphries MJ, Lennon R: Proteomic definitions of base- radation. Biochim Biophys Acta 1840: 2560–2570, 2014 ment membrane composition in health and disease. Matrix Biol 57–58: 13. Menou A, Duitman J, Crestani B: The impaired proteases and anti- 12–28, 2017 proteases balance in Idiopathic Pulmonary Fibrosis. Matrix Biol 32. Smeets B, Stucker F, Wetzels J, Brocheriou I, Ronco P, Gröne HJ, et al.: 68–69: 382–403, 2018 Detection of activated parietal epithelial cells on the glomerular tuft 14. Ricard-Blum S, Vallet SD: Fragments generated upon extracellular distinguishes early focal segmental glomerulosclerosis from minimal matrix remodeling: Biological regulators and potential drugs. Matrix change disease. Am J Pathol 184: 3239–3248, 2014 Biol 75–76: 170–189, 2019 33. Smeets B, Te Loeke NA, Dijkman HBPM, Steenbergen MLM, Lensen 15. Vizovišek M, Fonovic M, Turk B: Cysteine cathepsins in extracellular JFM, Begieneman MPV, et al.: The parietal epithelial cell: A key player matrix remodeling: Extracellular matrix degradation and beyond. Ma- in the pathogenesis of focal segmental glomerulosclerosis in Thy-1.1 trix Biol 75–76: 141–159, 2019 transgenic mice. JAmSocNephrol15: 928–939, 2004 16. Hobeika L, Barati MT, Caster DJ, McLeish KR, Merchant ML: Char- 34. Eymael J, Sharma S, Loeven MA, Wetzels JF, Mooren F, Florquin S, acterization of glomerular extracellular matrix by proteomic analysis et al.: CD44 is required for the pathogenesis of experimental crescentic of laser-captured microdissected glomeruli. Kidney Int 91: 501–511, glomerulonephritis and collapsing focal segmental glomerulosclerosis. 2017 Kidney Int 93: 626–642, 2018 17. Lennon R, Byron A, Humphries JD, Randles MJ, Carisey A, Murphy S, 35. Roeder SS, Stefanska A, Eng DG, Kaverina N, Sunseri MW, McNicholas et al.: Global analysis reveals the complexity of the human glomerular BA, et al.: Changes in glomerular parietal epithelial cells in mouse extracellular matrix. JAmSocNephrol25: 939–951, 2014 kidneys with advanced age. Am J Physiol Renal Physiol 309: F164–F178, 18. Smeets B, Kuppe C, Sicking EM, Fuss A, Jirak P, van Kuppevelt TH, 2015 et al.: Parietal epithelial cells participate in the formation of sclerotic 36. Aruffo A, Stamenkovic I, Melnick M, Underhill CB, Seed B: CD44 is the lesions in focal segmental glomerulosclerosis. JAmSocNephrol22: principal cell surface receptor for hyaluronate. Cell 61: 1303–1313, 1262–1274, 2011 1990 19. Kuppe C, Gröne HJ, Ostendorf T, van Kuppevelt TH, Boor P, Floege J, 37. Goodison S, Urquidi V, Tarin D: CD44 cell adhesion molecules. Mol et al.: Common histological patterns in glomerular epithelial cells in Pathol 52: 189–196, 1999 secondary focal segmental glomerulosclerosis. Kidney Int 88: 990–998, 38. Kuppe C, Leuchtle K, Wagner A, Kabgani N, Saritas T, Puelles VG, et al.: 2015 Novel parietal epithelial cell subpopulations contribute to focal seg- 20. Roeder SS, Barnes TJ, Lee JS, Kato I, Eng DG, Kaverina NV, et al.: mental glomerulosclerosis and glomerular tip lesions. Kidney Int 96: Activated ERK1/2 increases CD44 in glomerular parietal epithelial cells 80–93, 2019 leading to matrix expansion. Kidney Int 91: 896–913, 2017 39. Höhne M, Frese CK, Grahammer F, Dafinger C, Ciarimboli G, Butt L, 21. Chan GC, Eng DG, Miner JH, Alpers CE, Hudkins K, Chang A, et al.: et al.: Single-nephron proteomes connect morphology and function in Differential expression of parietal epithelial cell and podocyte extra- proteinuric kidney disease. Kidney Int 93: 1308–1319, 2018 cellular matrix proteins in focal segmental glomerulosclerosis and di- 40. Rossi A, Deveraux Q, Turk B, Sali A: Comprehensive search for cysteine abetic nephropathy. Am J Physiol Renal Physiol 317: F1680–F1694, cathepsins in the human genome. Biol Chem 385: 363–372, 2004 2019 41. Vidak E, Javoršek U, Vizovišek M, Turk B: Cysteine cathepsins and their 22. Merchant ML, Perkins BA, Boratyn GM, Ficociello LH, Wilkey DW, extracellular Roles: Shaping the microenvironment. Cells 8: E264, 2019 Barati MT, et al.: Urinary peptidome may predict renal function decline 42. Tong B, Wan B, Wei Z, Wang T, Zhao P, Dou Y, et al.: Role of cathepsin B in type 1 diabetes and microalbuminuria. J Am Soc Nephrol 20: in regulating migration and invasion of fibroblast-like synoviocytes into 2065–2074, 2009 inflamed tissue from patients with rheumatoid arthritis. Clin Exp Im- 23. Srivastava S, Merchant M, Rai A, Rai SN: Standardizing proteomics munol 177: 586–597, 2014 workflow for liquid chromatography-mass spectrometry: Technical 43. Wolters PJ, Laig-Webster M, Caughey GH: Dipeptidyl peptidase I and statistical considerations. J Proteomics Bioinform 12: 48–55, cleaves matrix-associated proteins and is expressed mainly by mast 2019 cells in normal dog airways. Am J Respir Cell Mol Biol 22: 183–190, 24. Klein J, Eales J, Zürbig P, Vlahou A, Mischak H, Stevens R: Proteasix: A 2000 tool for automated and large-scale prediction of proteases involved in 44. Baricos WH, Cortez SL, Le QC, Zhou YW, Dicarlo RM, O’Connor SE, naturally occurring peptide generation. Proteomics 13: 1077–1082, et al.: Glomerular basement membrane degradation by endogenous 2013 cysteine proteinases in isolated rat glomeruli. Kidney Int 38: 395–401, 25. Barati MT, Powell DW, Kechavarzi BD, Isaacs SM, Zheng S, Epstein PN, 1990 et al.: Differential expression of endoplasmic reticulum stress-response 45. Zhang X, Zhou Y, Yu X, Huang Q, Fang W, Li J, et al.: Differential roles of proteins in different renal tubule subtypes of OVE26 diabetic mice. Cell cysteinyl cathepsins in TGF-b signaling and tissue fibrosis. iScience 19: Stress Chaperones 21: 155–166, 2016 607 –622, 2019 26. Uhlén M, Fagerberg L, Hallström BM, Lindskog C, Oksvold P, 46. Korkmaz B, Caughey GH, Chapple I, Gauthier F, Hirschfeld J, Jenne DE, Mardinoglu A, et al.: Proteomics. Tissue-based map of the human et al.: Therapeutic targeting of cathepsin C: From pathophysiology to proteome. Science 347: 1260419, 2015 treatment. Pharmacol Ther 190: 202–236, 2018

JASN 31: ccc–ccc, 2020 Glomerular ECM in FSGS 21 CLINICAL RESEARCH www.jasn.org

47. Hodgin JB, Borczuk AC, Nasr SH, Markowitz GS, Nair V, Martini S, et al.: 49. Harder JL, Menon R, Otto EA, Zhou J, Eddy S, Wys NL, et al; European A molecular profile of focal segmental glomerulosclerosis from formalin- Renal cDNA Bank (ERCB); Nephrotic Syndrome Study Network (NEP- fixed, paraffin-embedded tissue. Am J Pathol 177: 1674–1686, 2010 TUNE): Organoid single cell profiling identifies a transcriptional sig- 48. Bennett MR, Czech KA, Arend LJ, Witte DP, Devarajan P, Potter SS: nature of glomerular disease. JCI Insight 4: e122697, 2019 Laser capture microdissection-microarray analysis of focal segmental 50. Parker MW, Rossi D, Peterson M, Smith K, Sikström K, White ES, et al.: glomerulosclerosis glomeruli. Nephron, Exp Nephrol 107: e30–e40, Fibrotic extracellular matrix activates a profibrotic positive feedback 2007 loop. J Clin Invest 124: 1622–1635, 2014

AFFILIATIONS

1Division of Nephrology and Hypertension, Department of Medicine, University of Louisville, Louisville, Kentucky 2Pathology Department, Norton Children’s Hospital, Louisville, Kentucky 3Division of Nephrology, Department of Medicine, Temple University, Philadelphia, Pennsylvania 4Department of Nephrology, Radboud University Medical Center, Nijmegen, The Netherlands 5Arkana Laboratories, Little Rock, Arkansas 6Michigan Institute for Clinical and Health Research, University of Michigan, Ann Arbor, Michigan 7Division of Pathology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 8Division of Nephrology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 9Robley Rex Veterans Affairs Medical Center, Louisville, Kentucky

22 JASN JASN 31: ccc–ccc,2020 Table of Contents for Supplemental Material:

1. Supplemental Figure 1. Laser Capture of Glomeruli Excludes Bowman’s Capsule.

Page 3.

2. Supplemental Figure 2. Comparison of ECM Protein Enrichment by Extraction Method.

Page 4.

3. Supplemental Figure 3. Immunohistochemistry of cFSGS, FSGS-NOS, and NC for

Selected Glomerular ECM Proteins.

Page 5-10.

4. Supplemental Table 1. All Glomerular Proteins Identified from cFSGS, FSGS-NOS, and

NC. (Mass Spectrometry data contained in a supplemental spreadsheet).

Pages 11-56.

5. Supplemental Table 2. Gene Names of Glomerular ECM Proteins Identified in NC,

FSGS-NOS, and cFSGS

Pages 57-60.

6. Supplemental Table 3. Relative Abundance of Glomerular ECM Proteins.

Pages 61-68.

7. Supplemental Table 4. Glomerular Cathepsin and Annexin A3 Staining of Various

Proteinuric Glomerular Diseases.

Page 69.

8. Supplemental Table 5. Comparison of Urinary Excretion of ECM Proteins.

Pages 70-73. (Mass Spectrometry data contained in a supplemental spreadsheet).

9. Supplemental Table 6. Peptides derived from ECM Proteins Showing Increased Urine

Excretion. (Mass Spectrometry data contained in a supplemental spreadsheet).

Page 74.

10. Supplemental Table 7. Proteases Associated with Urine ECM Peptides.

Page 75.

Supplemental Figure 1.

A B

Images of glomeruli collected by laser capture microdissection (LCMD). Panel A, image taken from a region of the kidney biopsy prior to dissection of glomeruli by LCMD. Panel B, image taken from the same region as in panel A, demonstrating outlines of dissection for each glomerulus. Panel B also demonstrates that Bowman’s capsule was not dissected with the captured glomeruli and is still intact/retained in the section.

Supplemental Figure 2.

p<0.030

80 NOS 70 NORMAL

Observed proteins-ECM Observed 40 GEF PMAX

p=0.110

2.5×10 8 NOS NORMAL 2×108

1.5×10 8

1×108

5×107

0 Observed proteins-ECM (TPI) GEF PMAX

Plots of proteomic analysis of glomerular ECM enrichment. Panel A shows the number of ECM proteins identified from isolated glomerular sections from normal or FSGS-NOS biopsies by 0.1% Protease MAX alone (PMAX) or sequential decellularization with 25 mM NH4OH/ 0.5% TritonX-100 followed protein extraction by PMAX. Sequential ECM enrichment significantly increased the number of ECM proteins identified. Panel B shows the total quantity of ECM proteins, expressed as total precursor intensity (TPI), for each extraction methods for normal and FSGS-NOS glomeruli. The quantity of ECM proteins identified was greater for sequential EMC enrichment, although the difference did not reach statistical significance for the 3 samples in each group.

Supplemental Figure 3A..

A Azurocidin (100×) Serpin D1 (40×) Cathepsin G (40×)

cFSGS

FSGSNOS

Supplemental Figure 3B.

B Elastase (40×) Elastase (40×) Elastase (100×)

cFSGS

FSGSNOS

Supplemental Figure 3C.

C IGFALS (40×) IGFALS (100×)

cFSGS

FSGSNOS

Supplemental Figure 3D.

D IGFBP7 (100×) F12 (100×) PRG3 (40×)

cFSGS

FSGSNOS

Supplemental Figure 3E.

E LMAN1 (40×) kininogen (100×) MPO (100×)

cFSGS

FSGSNOS

Supplemental Figure 3. Immunostaining of renal biopsy sections from patients with cFSGS, FSGS-NOS, and normal controls. A, immunohistochemistry for azurocidin (AZU1), serpin D1, and cathepsin G (CTSG). B, Immunohistochemistry for elastase (ELANE). Black arrows indicate positive staining of neutrophils using anti-elastase antibody. C, immunohistochemistry for HTRA1. D, IGFALS immunohistochemistry. E, IGFBP7, F12, and PRG3 immunohistochemistry. F, LMAN1, kininogen, and MPO immunohistochemistry. G, immunohistochemistry of fibulin 5. Original magnification of images indicated above panels. Immunohistochemistry was performed as described in methods section using the following primary antibodies: Azurocidin (1:100; #181989, Abcam), serpin D1 (1:200; #HPA055767, Sigma), cathepsin G (1:25; #PA5 83878, ThermoFisher, Waltham, MA), neutrophil elastase (1:200; #21595, Abcam), GFALS (1:100; #HPA040948, Sigma), IGFBP7 (1:100; #HpA002196, Sigma), F12 (1:20; #HPA003825, Sigma), PRG3 (1:2500; #204606, Abcam), LMAN1 (1:500; #13364-1, ProteinTech), kininogen 1 (1:100; #AF1569, R&D Systems), and MPO (1:200; #9535, Abcam),

Supplemental Table 1. All Glomerular Proteins Identified and Statistical Evaluation of Abundance among cFSGS, FSGS‐NOS, and NC Log2 q‐ q‐ Log2 FC FC value value Gene (cFSGS: Log2 FC q‐value Protein (FSGS‐ (cFSGS: (FSGS‐ Name FSGS‐ (cFSGS:NC) (cFSGS:NC) NOS: FSGS‐ NOS: NOS) NC) NOS) NC)

Alpha‐1B‐glycoprotein A1BG 1.0151 ‐0.4909 ‐1.1737 0.5259 0.7695 0.4500 Cluster of Alpha‐2‐macroglobulin A2M 2.6992 ‐1.4578 ‐3.2707 0.0561 0.3078 0.0239 Isoform 2 of Alanine‐‐tRNA ligase, cytoplasmic AARS ‐0.5617 1.4098 1.7672 0.7504 0.3238 0.2300 4‐aminobutyrate aminotransferase, mitochondrial ABAT ‐8.6382 ‐5.7429 0.2465 0.0000 0.0003 0.8888 Isoform 9 of Multidrug resistance‐ associated protein 1 ABCC1 0.0563 ‐0.7461 ‐0.7710 0.9724 0.6423 0.6393 ATP‐binding cassette sub‐family E member 1 ABCE1 ‐3.2356 ‐0.2629 1.9465 0.0227 0.8708 0.1824 ATP‐binding cassette sub‐family F member 1 ABCF1 ‐0.1855 1.9472 2.0385 0.9225 0.1611 0.1586 Protein ABHD14B ABHD14B 3.0129 ‐4.7312 ‐6.6989 0.0334 0.0017 0.0001 Isoform 11 of Abl interactor 1 ABI1 ‐4.9137 6.0089 9.2488 0.0011 0.0002 0.0000 3‐ketoacyl‐CoA thiolase, peroxisomal ACAA1 ‐4.3481 ‐0.2332 2.7337 0.0030 0.8857 0.0560 3‐ketoacyl‐CoA thiolase, mitochondrial ACAA2 1.8356 0.5284 ‐0.7318 0.2036 0.7497 0.6557 Isoform 2 of Medium‐chain specific acyl‐CoA dehydrogenase, mitochondrial ACADM 0.3254 0.3337 0.1059 0.8591 0.8411 0.9517 Short/branched chain specific acyl‐CoA dehydrogenase, mitochondrial ACADSB ‐7.3467 ‐1.4250 3.6066 0.0000 0.3175 0.0146 Cluster of Very long‐chain specific acyl‐CoA dehydrogenase, mitochondrial ACADVL 1.5174 4.5788 3.4624 0.3051 0.0021 0.0180 Acetyl‐CoA acetyltransferase, mitochondrial ACAT1 ‐2.4956 ‐2.9313 ‐1.1781 0.0765 0.0339 0.4488 Golgi resident protein GCP60 ACBD3 ‐2.8733 0.0967 2.0528 0.0422 0.9509 0.1553 Isoform 4 of Apoptotic chromatin condensation inducer in the nucleus ACIN1 ‐0.9614 ‐0.9029 ‐0.2315 0.5498 0.5568 0.8968 ATP‐citrate synthase ACLY ‐1.0130 ‐0.6777 0.0248 0.5264 0.6724 0.9870 Cytoplasmic aconitate hydratase ACO1 0.3244 ‐2.1433 ‐2.3257 0.8592 0.1199 0.1022 Aconitate hydratase, mitochondrial ACO2 ‐1.3953 ‐2.6893 ‐1.6901 0.3499 0.0513 0.2535 Acyl‐coenzyme A thioesterase 2, mitochondrial ACOT2 ‐7.6752 1.0843 6.2945 0.0000 0.4689 0.0002 Acyl‐coenzyme A thioesterase 9, mitochondrial ACOT9 5.8542 3.2381 ‐0.8093 0.0002 0.0199 0.6242 Isoform 3 of Medium‐chain acyl‐ CoA ligase ACSF2, mitochondrial ACSF2 ‐0.8032 ‐1.3565 ‐0.7847 0.6339 0.3469 0.6346

Cluster of Actin, aortic smooth muscle ACTA2 0.3967 ‐1.2321 ‐1.4802 0.8249 0.3982 0.3246 Cluster of Alpha‐actinin‐4 ACTN4 ‐2.1496 ‐3.2524 ‐1.7290 0.1288 0.0194 0.2407 Alpha‐centractin ACTR1A ‐0.1514 ‐0.7853 ‐0.6679 0.9388 0.6214 0.6868 Beta‐centractin ACTR1B 1.0611 1.1467 0.4030 0.5029 0.4383 0.8208 Actin‐related protein 2 ACTR2 0.3351 ‐1.0787 ‐1.2876 0.8538 0.4710 0.3993 Cluster of Actin‐related protein 3 ACTR3 ‐0.4561 ‐1.5688 ‐1.2297 0.7998 0.2646 0.4244 Aminoacylase‐1 ACY1 ‐2.2095 ‐8.9696 ‐7.3025 0.1188 0.0000 0.0000 Isoform 2 of Alpha‐adducin ADD1 ‐4.7832 ‐2.2626 1.0373 0.0014 0.1000 0.5078 Isoform 1 of Gamma‐adducin ADD3 2.5534 0.9597 ‐0.7975 0.0696 0.5291 0.6296 Cluster of Alcohol dehydrogenase 1C ADH1C ‐28.5069 0.5603 19.9744 0.0000 0.7291 0.0000 Isoform 2 of All‐trans‐retinol dehydrogenase [NAD(+)] ADH4 ADH4 ‐15.5666 ‐1.3800 9.2518 0.0000 0.3354 0.0000 Alcohol dehydrogenase class‐3 ADH5 2.1858 1.2415 ‐0.2702 0.1223 0.3947 0.8827 Adipogenesis regulatory factor ADIRF ‐0.5879 0.5712 0.9616 0.7395 0.7234 0.5389 Afamin AFM 7.9925 4.7584 ‐0.7733 0.0000 0.0016 0.6387 Agmatinase, mitochondrial AGMAT ‐24.3199 ‐17.2970 ‐0.4141 0.0000 0.0000 0.8142 Isoform 6 of Agrin AGRN 1.2671 ‐1.4182 ‐2.2561 0.4033 0.3198 0.1147 Angiotensinogen AGT 0.4952 0.3063 ‐0.0366 0.7785 0.8524 0.9804 Serine‐‐pyruvate aminotransferase AGXT ‐15.0317 ‐2.7725 7.5198 0.0000 0.0449 0.0000 Adenosylhomocysteinase AHCY ‐7.6873 ‐4.0515 1.2595 0.0000 0.0052 0.4117 Cluster of Neuroblast differentiation‐associated protein AHNAK AHNAK 0.5324 ‐0.7235 ‐1.0733 0.7673 0.6504 0.4918 Alpha‐2‐HS‐glycoprotein AHSG 6.2917 ‐3.5884 ‐7.8108 0.0001 0.0113 0.0000 Cluster of Allograft inflammatory ‐ factor 1 AIF1 ‐0.5635 ‐11.8705 11.2726 0.7504 0.0000 0.0000 Isoform 2 of Allograft inflammatory factor 1‐like AIF1L ‐0.5319 ‐8.9853 ‐8.4609 0.7673 0.0000 0.0000 Isoform 3 of Apoptosis‐inducing factor 1, mitochondrial AIFM1 ‐4.3816 ‐0.8210 2.1794 0.0029 0.6018 0.1284 AH receptor‐interacting protein AIP ‐1.9584 2.1171 3.4134 0.1721 0.1236 0.0193 Adenylate kinase isoenzyme 1 AK1 ‐1.3917 ‐3.3940 ‐2.3845 0.3506 0.0153 0.0931 Cluster of Isoform 2 of Adenylate kinase 2, mitochondrial AK2 ‐2.4020 ‐0.6430 1.0052 0.0887 0.6919 0.5195 GTP:AMP phosphotransferase AK3, mitochondrial AK3 1.0924 0.2234 ‐0.5250 0.4868 0.8897 0.7630 Isoform 2 of A‐kinase anchor protein 12 AKAP12 3.3245 1.8221 ‐0.4760 0.0195 0.1938 0.7812 Isoform 2 of A‐kinase anchor protein 2 AKAP2 ‐0.0556 ‐0.5220 ‐0.4747 0.9724 0.7521 0.7812 Aldo‐keto reductase family 1 member A1 AKR1A1 ‐2.5097 ‐4.7174 ‐2.9223 0.0747 0.0017 0.0409 Aflatoxin B1 aldehyde reductase member 2 AKR7A2 ‐0.2926 ‐1.0266 ‐0.8087 0.8710 0.4957 0.6242 Isoform 2 of Delta‐aminolevulinic ‐ acid dehydratase ALAD ‐0.5061 ‐12.0505 11.4884 0.7769 0.0000 0.0000 Serum albumin ALB 0.5758 ‐2.9058 ‐3.2458 0.7463 0.0354 0.0248

Cluster of Aldehyde dehydrogenase family 16 member A1 ALDH16A1 ‐4.3485 ‐2.4012 0.6051 0.0030 0.0810 0.7208 Retinal dehydrogenase 1 ALDH1A1 ‐2.5779 ‐0.8398 0.9318 0.0677 0.5909 0.5553 Isoform 2 of Retinal dehydrogenase 2 ALDH1A2 0.8712 ‐0.9081 ‐1.4853 0.5979 0.5537 0.3234 Aldehyde dehydrogenase X, mitochondrial ALDH1B1 ‐1.3535 3.1433 4.0089 0.3657 0.0233 0.0072 Isoform 3 of Cytosolic 10‐ formyltetrahydrofolate dehydrogenase ALDH1L1 ‐13.8453 ‐0.5788 8.8656 0.0000 0.7196 0.0000 Aldehyde dehydrogenase, mitochondrial ALDH2 ‐2.0134 ‐2.0998 ‐0.6900 0.1592 0.1268 0.6726 Isoform 3 of Delta‐1‐pyrroline‐5‐ carboxylate dehydrogenase, mitochondrial ALDH4A1 ‐1.0092 ‐0.5134 0.1835 0.5273 0.7579 0.9143 Isoform 2 of Methylmalonate‐ semialdehyde dehydrogenase [acylating], mitochondrial ALDH6A1 ‐10.4455 ‐0.8204 6.3118 0.0000 0.6018 0.0002 Alpha‐aminoadipic semialdehyde dehydrogenase ALDH7A1 ‐1.1658 ‐3.4421 ‐2.5857 0.4486 0.0141 0.0690 Isoform 3 of 4‐ trimethylaminobutyraldehyde dehydrogenase ALDH9A1 0.3762 ‐5.4678 ‐5.6256 0.8347 0.0005 0.0005 Fructose‐bisphosphate aldolase A ALDOA 0.9186 ‐2.5717 ‐3.1513 0.5695 0.0615 0.0288 Fructose‐bisphosphate aldolase B ALDOB ‐1.5029 ‐3.0196 ‐1.9411 0.3121 0.0289 0.1836 Fructose‐bisphosphate aldolase C ALDOC 3.0791 ‐0.4710 ‐2.5606 0.0297 0.7796 0.0715 Protein AMBP AMBP ‐0.3624 1.6890 1.9055 0.8423 0.2275 0.1924 Isoform 2 of Anaphase‐promoting complex subunit 7 ANAPC7 ‐1.3244 ‐0.9641 ‐0.0443 0.3792 0.5273 0.9771 Angiopoietin‐related protein 6 ANGPTL6 2.5380 2.8739 1.0928 0.0713 0.0376 0.4839 Acidic leucine‐rich nuclear phosphoprotein 32 family member A ANP32A ‐10.5988 ‐0.3903 6.8386 0.0000 0.8180 0.0001 Aminopeptidase N ANPEP ‐0.4024 ‐3.5025 ‐3.1653 0.8234 0.0128 0.0282 Annexin A1 ANXA1 ‐0.6835 2.3181 2.7421 0.6939 0.0920 0.0554 Isoform 2 of Annexin A11 ANXA11 ‐0.2915 ‐0.0563 0.1433 0.8710 0.9683 0.9298 Isoform 2 of Annexin A2 ANXA2 0.9514 ‐0.3682 ‐1.0098 0.5558 0.8268 0.5174 Annexin A3 ANXA3 8.3276 5.3101 ‐0.4599 0.0000 0.0006 0.7890 Annexin A4 ANXA4 0.2195 1.6441 1.4648 0.9047 0.2417 0.3299 Annexin A5 ANXA5 1.2337 ‐0.0677 ‐0.9070 0.4182 0.9614 0.5699 Annexin A6 ANXA6 0.0450 0.7661 0.7217 0.9751 0.6331 0.6595 Isoform 2 of Annexin A7 ANXA7 0.1648 5.8962 5.6776 0.9318 0.0003 0.0005 Isoform 2 of AP‐1 complex subunit gamma‐1 AP1G1 2.6435 ‐0.1170 ‐1.9161 0.0614 0.9410 0.1900 Cluster of Isoform B of AP‐2 complex subunit alpha‐1 AP2A1 0.2831 ‐1.4202 ‐1.5875 0.8743 0.3192 0.2869 Cluster of Isoform 2 of AP‐2 complex subunit beta AP2B1 0.5719 ‐2.6394 ‐2.9816 0.7463 0.0557 0.0380 Isoform 5 of AP‐3 complex subunit delta‐1 AP3D1 1.0411 ‐1.1085 ‐1.7980 0.5122 0.4555 0.2233

Serum amyloid P‐component APCS ‐0.5919 2.5343 2.8919 0.7388 0.0653 0.0427 Acylamino‐acid‐releasing enzyme APEH ‐5.0774 ‐0.0595 3.4012 0.0008 0.9664 0.0194 DNA‐(apurinic or apyrimidinic site) lyase APEX1 1.4445 1.2552 0.2483 0.3307 0.3888 0.8888 Adipocyte plasma membrane‐ associated protein APMAP ‐1.1919 ‐1.0786 ‐0.2471 0.4378 0.4710 0.8888 Apolipoprotein A‐I APOA1 1.9958 ‐1.0651 ‐2.4058 0.1633 0.4755 0.0913 Apolipoprotein A‐II APOA2 1.5341 ‐2.6289 ‐3.6268 0.3002 0.0565 0.0141 Apolipoprotein A‐IV APOA4 0.7671 0.7852 0.2484 0.6530 0.6214 0.8888 Apolipoprotein B‐100 APOB 2.1637 1.2362 ‐0.2604 0.1266 0.3970 0.8853 Apolipoprotein C‐III APOC3 13.4802 8.4259 ‐0.9111 0.0000 0.0000 0.5675 Apolipoprotein D APOD 0.6937 5.8298 5.2521 0.6887 0.0003 0.0009 Apolipoprotein E APOE 0.6407 1.8742 1.4038 0.7156 0.1800 0.3533 Beta‐2‐glycoprotein 1 APOH 1.3239 ‐0.0197 ‐0.9215 0.3792 0.9880 0.5616 Apolipoprotein L2 APOL2 0.8392 0.8128 0.2264 0.6146 0.6054 0.8976 Adenine phosphoribosyltransferase APRT 1.1287 ‐0.9639 ‐1.7156 0.4689 0.5273 0.2452 Isoform 2 of Aquaporin‐1 AQP1 1.6824 4.4002 3.1745 0.2490 0.0029 0.0277 Cluster of ADP‐ribosylation factor 3 ARF3 2.0879 ‐1.7903 ‐3.1808 0.1430 0.2003 0.0276 ADP‐ribosylation factor 6 ARF6 ‐21.9569 ‐14.0280 1.1858 0.0000 0.0000 0.4463 Isoform 2 of Arginase‐1 ARG1 ‐7.8676 ‐1.1293 4.2520 0.0000 0.4459 0.0049 Rho GTPase‐activating protein 1 ARHGAP1 0.7988 1.2063 0.6403 0.6356 0.4096 0.7033 Rho GDP‐dissociation inhibitor 1 ARHGDIA 0.3364 ‐2.1512 ‐2.3417 0.8538 0.1187 0.0995 Rho GDP‐dissociation inhibitor 2 ARHGDIB 1.3795 ‐3.2528 ‐4.1341 0.3551 0.0194 0.0059 Rho guanine nucleotide exchange factor 12 ARHGEF12 ‐0.3434 ‐0.1057 0.1302 0.8507 0.9469 0.9349 Rho guanine nucleotide exchange factor 15 ARHGEF15 ‐0.8780 ‐1.6218 ‐0.9943 0.5939 0.2490 0.5240 Rho guanine nucleotide exchange factor 17 ARHGEF17 ‐0.2922 ‐0.3746 ‐0.1687 0.8710 0.8251 0.9236 PRA1 family protein 3 ARL6IP5 0.1944 11.5574 11.2166 0.9192 0.0000 0.0000 Isoform 2 of Actin‐related protein ‐ 2/3 complex subunit 1A ARPC1A ‐0.7039 ‐12.1002 11.4026 0.6868 0.0000 0.0000 Actin‐related protein 2/3 complex subunit 1B ARPC1B ‐1.2899 4.3147 5.1159 0.3932 0.0033 0.0011 Actin‐related protein 2/3 complex subunit 2 ARPC2 ‐1.1726 ‐1.0906 ‐0.2719 0.4458 0.4661 0.8827 Actin‐related protein 2/3 complex subunit 3 ARPC3 ‐1.8801 ‐2.3415 ‐1.0182 0.1915 0.0894 0.5159 Cluster of Isoform 3 of Actin‐ related protein 2/3 complex subunit 4 ARPC4 1.3566 8.6270 7.5472 0.3651 0.0000 0.0000 Isoform 2 of Actin‐related protein 2/3 complex subunit 5 ARPC5 ‐0.2299 11.2647 11.2183 0.8996 0.0000 0.0000 Isoform 1B of Beta‐arrestin‐1 ARRB1 ‐1.1414 ‐2.5952 ‐1.7707 0.4624 0.0595 0.2293 Isoform 3 of Acid ceramidase ASAH1 8.7929 5.3324 ‐0.7550 0.0000 0.0006 0.6439 Argininosuccinate synthase ASS1 ‐0.3724 ‐4.5406 ‐4.2051 0.8366 0.0023 0.0053

Isoform 2 of Bifunctional purine biosynthesis protein PURH ATIC 2.8201 0.7295 ‐1.2052 0.0457 0.6499 0.4361 Cluster of Sodium/potassium‐ transporting ATPase subunit alpha‐2 ATP1A2 ‐20.5250 ‐2.0909 11.9322 0.0000 0.1282 0.0000 Sodium/potassium‐transporting ATPase subunit alpha‐4 ATP1A4 ‐3.5869 ‐0.2962 2.1532 0.0122 0.8561 0.1335 Isoform 2 of Sodium/potassium‐ transporting ATPase subunit beta‐ 1 ATP1B1 0.3273 ‐0.2866 ‐0.5045 0.8582 0.8599 0.7716 Isoform 2 of Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 ATP2A2 0.9844 1.1159 0.4250 0.5387 0.4522 0.8077 Cluster of Isoform XG of Plasma membrane calcium‐transporting ATPase 3 ATP2B3 ‐3.4688 ‐0.7640 1.6133 0.0148 0.6341 0.2782 ATP synthase subunit alpha, mitochondrial ATP5F1A 0.3367 ‐0.1574 ‐0.3840 0.8538 0.9183 0.8288 ATP synthase subunit beta, mitochondrial ATP5F1B ‐0.1567 ‐0.4901 ‐0.3745 0.9364 0.7696 0.8348 Cluster of ATP synthase subunit gamma, mitochondrial ATP5F1C 0.3428 ‐0.9206 ‐1.1376 0.8507 0.5484 0.4639 ATP synthase subunit delta, mitochondrial ATP5F1D 13.8534 8.3876 ‐1.2031 0.0000 0.0000 0.4365 Isoform 2 of ATP synthase subunit f, mitochondrial ATP5MF ‐1.7155 0.8504 2.0040 0.2386 0.5852 0.1669 ATP synthase subunit d, mitochondrial ATP5PD ‐0.4815 ‐0.6060 ‐0.2670 0.7863 0.7083 0.8827 ATP synthase subunit O, mitochondrial ATP5PO 0.9632 0.5987 ‐0.0685 0.5496 0.7093 0.9656 V‐type proton ATPase catalytic subunit A ATP6V1A ‐1.0111 ‐0.8972 ‐0.1920 0.5264 0.5584 0.9101 Cluster of V‐type proton ATPase subunit B, brain isoform ATP6V1B2 ‐2.6154 ‐2.8100 ‐0.9773 0.0638 0.0421 0.5316 Zinc‐alpha‐2‐glycoprotein AZGP1 1.4836 0.2085 ‐0.8062 0.3177 0.8954 0.6255 Azurocidin AZU1 12.4662 8.2989 ‐0.3449 0.0000 0.0000 0.8452 Beta‐2‐microglobulin B2M ‐4.6045 10.3908 13.3410 0.0019 0.0000 0.0000 BAG family molecular chaperone regulator 3 BAG3 4.1458 2.1141 ‐0.7489 0.0045 0.1239 0.6470 Isoform 5 of Large proline‐rich protein BAG6 BAG6 6.0238 3.6648 ‐0.5058 0.0002 0.0100 0.7716 Barrier‐to‐autointegration factor BANF1 1.2776 ‐0.8889 ‐1.7434 0.3988 0.5629 0.2362 Brain acid soluble protein 1 BASP1 ‐0.5271 1.8084 2.1350 0.7688 0.1960 0.1373 Isoform Epsilon of Apoptosis regulator BAX BAX 7.3761 3.7373 ‐1.3560 0.0000 0.0089 0.3712 Basal cell adhesion molecule BCAM ‐0.1787 ‐3.3822 ‐3.1995 0.9267 0.0156 0.0266 Bcl‐2‐like protein 13 BCL2L13 0.7391 2.4051 1.8582 0.6696 0.0805 0.2058 3‐hydroxybutyrate dehydrogenase type 2 BDH2 3.5290 7.2248 4.6900 0.0134 0.0000 0.0024 Biglycan BGN ‐0.0659 2.9734 2.9647 0.9677 0.0314 0.0388 Betaine‐‐homocysteine S‐ methyltransferase 1 BHMT ‐2.3332 ‐2.9920 ‐1.3483 0.0987 0.0304 0.3747 Bleomycin hydrolase BLMH ‐0.4315 2.8208 3.0640 0.8111 0.0414 0.0328

Flavin reductase (NADPH) BLVRB ‐9.4825 ‐9.0625 ‐2.4380 0.0000 0.0000 0.0865 Isoform 2 of ADP‐ribosyl cyclase/cyclic ADP‐ribose hydrolase 2 BST1 ‐1.0074 ‐7.5032 ‐6.6815 0.5280 0.0000 0.0001 Isoform 2 of Ester hydrolase C11orf54 C11orf54 ‐3.5505 ‐5.5669 ‐3.0473 0.0129 0.0004 0.0335 Complement C1q subcomponent subunit A C1QA 5.6799 0.4666 ‐3.4120 0.0003 0.7820 0.0193 Complement C1q subcomponent subunit B C1QB 11.2660 0.3460 ‐7.3367 0.0000 0.8348 0.0000 Complement component 1 Q subcomponent‐binding protein, mitochondrial C1QBP 8.3834 ‐1.5717 ‐7.2557 0.0000 0.2637 0.0000 Complement C1q subcomponent subunit C C1QC 5.7094 0.6256 ‐3.2760 0.0003 0.7004 0.0239 Complement C1r subcomponent C1R 17.0424 9.5813 ‐2.2038 0.0000 0.0000 0.1250 Complement C1s subcomponent C1S 9.6355 5.2744 ‐1.3861 0.0000 0.0007 0.3601 Complement C3 C3 2.2095 0.1593 ‐1.3491 0.1188 0.9182 0.3747 Cluster of Complement C4‐B C4B 4.5798 0.1814 ‐2.9424 0.0020 0.9077 0.0401 C4b‐binding protein alpha chain C4BPA 3.9987 4.0702 1.2722 0.0058 0.0051 0.4063 Isoform 2 of C4b‐binding protein beta chain C4BPB 11.6033 7.9793 ‐0.0707 0.0000 0.0000 0.9647 Complement C5 C5 0.9183 2.2800 1.6132 0.5695 0.0977 0.2782 Complement component C6 C6 1.4245 1.2451 0.2520 0.3382 0.3935 0.8881 Complement component C7 C7 0.6379 0.8778 0.4273 0.7168 0.5705 0.8071 Complement component C8 alpha chain C8A 0.5318 1.8183 1.4232 0.7673 0.1938 0.3471 Complement component C8 beta chain C8B 0.6091 2.1306 1.6772 0.7343 0.1214 0.2571 Complement component C8 gamma chain C8G 1.1325 1.0840 0.2928 0.4669 0.4689 0.8769 Complement component C9 C9 1.1164 0.6296 ‐0.1424 0.4730 0.6991 0.9298 Carbonic anhydrase 1 CA1 ‐3.0935 ‐4.0035 ‐1.8235 0.0289 0.0057 0.2160 Carbonic anhydrase 2 CA2 ‐0.0530 ‐2.6731 ‐2.5888 0.9730 0.0526 0.0689 ‐ Calbindin CALB1 ‐0.2473 ‐12.4635 12.0704 0.8904 0.0000 0.0000 Caldesmon CALD1 ‐1.7124 ‐0.1583 1.0114 0.2391 0.9183 0.5174 Calmodulin‐2 CALM2 1.4613 ‐0.9122 ‐1.8915 0.3258 0.5526 0.1959 Calmodulin‐like protein 5 CALML5 2.8236 5.4686 3.4461 0.0455 0.0005 0.0184 Calreticulin CALR 2.6809 ‐0.7296 ‐2.5432 0.0579 0.6499 0.0733 Cullin‐associated NEDD8‐ dissociated protein 1 CAND1 2.0014 ‐2.0920 ‐3.4181 0.1625 0.1282 0.0192 Isoform 2 of Cullin‐associated NEDD8‐dissociated protein 2 CAND2 0.1868 0.4537 0.3182 0.9221 0.7895 0.8617 Isoform 2 of Calnexin CANX ‐0.7186 ‐0.3107 0.1845 0.6787 0.8505 0.9142 Cluster of Adenylyl cyclase‐ associated protein 1 CAP1 0.5333 ‐0.4628 ‐0.8179 0.7673 0.7845 0.6202 Cluster of Isoform 2 of Macrophage‐capping protein CAPG 16.6289 10.3974 ‐1.1206 0.0000 0.0000 0.4728 Calpain‐1 catalytic subunit CAPN1 1.9592 ‐1.5928 ‐2.8991 0.1721 0.2572 0.0422

Cluster of Calpain‐2 catalytic subunit CAPN2 1.0418 ‐2.6993 ‐3.3605 0.5122 0.0504 0.0205 Calpain small subunit 1 CAPNS1 1.1331 ‐1.5931 ‐2.3365 0.4669 0.2572 0.1003 Caprin‐1 CAPRIN1 4.7379 2.6202 ‐0.6554 0.0015 0.0570 0.6934 F‐actin‐capping protein subunit alpha‐1 CAPZA1 ‐1.3324 ‐0.5822 0.3361 0.3756 0.7182 0.8500 F‐actin‐capping protein subunit alpha‐2 CAPZA2 0.1442 ‐1.9060 ‐1.9700 0.9409 0.1709 0.1767 Isoform 2 of F‐actin‐capping protein subunit beta CAPZB ‐1.2723 ‐3.8580 ‐2.9215 0.4011 0.0073 0.0409 Isoform 2 of Peripheral plasma membrane protein CASK CASK ‐1.1069 ‐1.8444 ‐1.0570 0.4784 0.1878 0.5006 Caspase‐14 CASP14 ‐1.0237 ‐0.2384 0.4634 0.5219 0.8842 0.7874 Catalase CAT ‐1.5935 ‐3.3289 ‐2.1831 0.2794 0.0170 0.1283 Caveolae‐associated protein 1 CAVIN1 3.1578 11.9789 9.6114 0.0259 0.0000 0.0000 Caveolae‐associated protein 2 CAVIN2 0.8873 ‐0.5279 ‐1.1230 0.5885 0.7497 0.4717 Cluster of Carbonyl reductase [NADPH] 1 CBR1 ‐1.2578 ‐1.0700 ‐0.1937 0.4057 0.4739 0.9094 Cluster of Chromobox protein homolog 3 CBX3 1.6214 1.4041 0.2740 0.2695 0.3259 0.8827 Isoform 2 of Cell cycle and apoptosis regulator protein 2 CCAR2 ‐4.3483 ‐0.4284 2.5422 0.0030 0.7991 0.0733 Coiled‐coil domain‐containing protein 22 CCDC22 ‐3.0982 ‐0.4592 1.6601 0.0288 0.7862 0.2636 Cluster of T‐complex protein 1 subunit beta CCT2 0.1399 ‐0.9223 ‐1.0010 0.9420 0.5484 0.5203 T‐complex protein 1 subunit gamma CCT3 ‐0.1285 ‐0.8370 ‐0.7343 0.9468 0.5920 0.6551 Isoform 2 of T‐complex protein 1 subunit delta CCT4 ‐0.5107 ‐1.4394 ‐1.0654 0.7759 0.3130 0.4957 Cluster of Isoform 2 of T‐complex protein 1 subunit epsilon CCT5 7.8255 5.1522 ‐0.2729 0.0000 0.0008 0.8827 Cluster of T‐complex protein 1 subunit zeta CCT6A 1.9930 ‐1.4218 ‐2.7542 0.1639 0.3188 0.0542 T‐complex protein 1 subunit eta CCT7 2.1321 ‐0.1156 ‐1.5664 0.1328 0.9410 0.2934 T‐complex protein 1 subunit theta CCT8 ‐0.2049 ‐3.1286 ‐2.9327 0.9141 0.0239 0.0403 Isoform 3 of CD276 antigen CD276 13.7137 8.0973 ‐1.3929 0.0000 0.0000 0.3581 CD2‐associated protein CD2AP ‐1.1207 ‐0.1750 0.5917 0.4705 0.9109 0.7284 Isoform 5 of CD44 antigen CD44 ‐4.1384 ‐0.2818 2.5431 0.0045 0.8626 0.0733 CD5 antigen‐like CD5L 8.5403 4.6190 ‐1.2835 0.0000 0.0020 0.4008 CD81 antigen CD81 ‐17.3127 ‐11.1998 0.7986 0.0000 0.0000 0.6296 Hsp90 co‐chaperone Cdc37 CDC37 1.4144 1.4463 0.4565 0.3419 0.3103 0.7900 Cell division control protein 42 homolog CDC42 ‐0.8620 ‐2.3169 ‐1.6878 0.6021 0.0920 0.2541 Isoform 4 of Cadherin‐13 CDH13 2.5603 2.5540 0.7634 0.0688 0.0632 0.6422 Isoform 2 of Cadherin‐5 CDH5 ‐7.1495 ‐1.9671 2.9399 0.0000 0.1567 0.0401 Isoform 2 of CDK5 regulatory subunit‐associated protein 3 CDK5RAP3 2.6439 0.7621 ‐1.0531 0.0614 0.6348 0.5028 Cyclin‐dependent kinase inhibitor 1B CDKN1B ‐0.2701 ‐5.7506 ‐5.4630 0.8806 0.0003 0.0007

Corneodesmosin CDSN ‐21.7780 ‐2.3285 12.5526 0.0000 0.0908 0.0000 Cluster of Isoform 3 of Protein CDV3 homolog CDV3 ‐19.4650 0.2973 13.5551 0.0000 0.8558 0.0000 Isoform 2 of Liver carboxylesterase 1 CES1 ‐24.9126 ‐1.5880 15.4157 0.0000 0.2590 0.0000 Complement factor B CFB 2.8647 ‐0.1702 ‐2.1190 0.0427 0.9131 0.1407 Complement factor D CFD ‐13.3153 ‐1.3804 7.7173 0.0000 0.3354 0.0000 Complement factor H CFH 0.4007 ‐0.0404 ‐0.3127 0.8234 0.9767 0.8657 Complement factor H‐related protein 1 CFHR1 ‐0.4110 0.5247 0.7953 0.8205 0.7508 0.6305 Isoform Short of Complement factor H‐related protein 2 CFHR2 ‐0.9231 2.9766 3.5520 0.5675 0.0313 0.0157 Complement factor H‐related protein 5 CFHR5 0.1634 ‐1.2319 ‐1.3211 0.9322 0.3982 0.3850 Cluster of Cofilin‐1 CFL1 0.8665 0.7465 0.1426 0.5998 0.6423 0.9298 Properdin CFP 2.5635 3.2563 1.4509 0.0685 0.0194 0.3347 Cingulin‐like protein 1 CGNL1 ‐0.0623 ‐3.0965 ‐2.9982 0.9691 0.0252 0.0368 Putative coiled‐coil‐helix‐coiled‐ coil‐helix domain‐containing protein CHCHD2P9, mitochondrial CHCHD2P9 ‐20.6813 ‐0.2135 13.8823 0.0000 0.8938 0.0000 MIC complex subunit MIC19 CHCHD3 2.9336 3.5502 1.4873 0.0378 0.0120 0.3234 Charged multivesicular body protein 5 CHMP5 0.1871 ‐2.3894 ‐2.4738 0.9221 0.0825 0.0812 Isoform 2 of Cold‐inducible RNA‐ binding protein CIRBP 0.9620 ‐0.8895 ‐1.5290 0.5498 0.5629 0.3079 Cytoskeleton‐associated protein 4 CKAP4 1.3561 ‐1.7740 ‐2.6661 0.3651 0.2042 0.0615 Creatine kinase B‐type CKB ‐2.0990 ‐4.2005 ‐2.6946 0.1403 0.0041 0.0586 Chloride intracellular channel protein 1 CLIC1 1.8630 ‐1.1849 ‐2.4330 0.1951 0.4198 0.0872 Chloride intracellular channel ‐ protein 4 CLIC4 14.3336 ‐1.3976 11.1391 0.0000 0.3286 0.0000 Isoform 1 of Chloride intracellular channel protein 5 CLIC5 ‐0.7561 ‐4.4927 ‐3.8966 0.6608 0.0025 0.0087 Isoform Non‐brain of Clathrin light chain A CLTA 9.3246 5.6015 ‐0.8531 0.0000 0.0004 0.6033 Cluster of Isoform 2 of Clathrin heavy chain 1 CLTC 0.2313 ‐0.9531 ‐1.0935 0.8991 0.5330 0.4839 Isoform 2 of Clusterin CLU 0.5847 0.6696 0.2591 0.7408 0.6765 0.8856 Isoform 3 of UMP‐CMP kinase CMPK1 ‐2.3823 ‐5.4118 ‐3.6910 0.0912 0.0005 0.0126 UMP‐CMP kinase 2, mitochondrial CMPK2 10.6491 6.6151 ‐0.7602 0.0000 0.0001 0.6422 Cluster of Isoform 4 of Cellular nucleic acid‐binding protein CNBP ‐6.3750 ‐0.5373 3.8163 0.0001 0.7439 0.0101 Cytosolic non‐specific dipeptidase CNDP2 ‐1.5011 ‐3.7602 ‐2.6697 0.3126 0.0086 0.0613 Calponin‐2 CNN2 2.6126 ‐0.1475 ‐1.9250 0.0640 0.9226 0.1883 Calponin‐3 CNN3 2.0771 ‐1.6851 ‐3.0701 0.1448 0.2280 0.0325 Isoform 2 of Bifunctional coenzyme A synthase COASY 7.7026 4.6477 ‐0.6845 0.0000 0.0019 0.6758 Collagen alpha‐1(XII) chain COL12A1 3.8349 2.6167 ‐0.0435 0.0078 0.0573 0.9771 Collagen alpha‐1(XV) chain COL15A1 ‐2.0472 2.9388 4.2808 0.1513 0.0334 0.0047

Cluster of Collagen alpha‐1(XVIII) chain COL18A1 0.6526 0.6525 0.1960 0.7091 0.6880 0.9094 Collagen alpha‐1(I) chain COL1A1 ‐1.4400 ‐0.4323 0.5567 0.3318 0.7991 0.7456 Collagen alpha‐2(I) chain COL1A2 ‐3.0553 ‐2.3329 ‐0.2091 0.0309 0.0903 0.9038 Cluster of Isoform 3 of Collagen alpha‐1(XXI) chain COL21A1 3.3964 2.0730 ‐0.2786 0.0171 0.1311 0.8827 Isoform 1 of Collagen alpha‐1(II) chain COL2A1 1.5342 2.1415 1.0576 0.3002 0.1199 0.5006 Cluster of Collagen alpha‐1(III) chain COL3A1 ‐0.5720 ‐0.0451 0.3454 0.7463 0.9743 0.8452 Collagen alpha‐1(IV) chain COL4A1 ‐0.6056 0.5735 0.9758 0.7347 0.7222 0.5318 Collagen alpha‐2(IV) chain COL4A2 ‐1.0910 0.1162 0.8574 0.4868 0.9410 0.6017 Cluster of Collagen alpha‐3(IV) chain COL4A3 0.9354 0.9917 0.3365 0.5611 0.5128 0.8500 Collagen alpha‐4(IV) chain COL4A4 0.4966 1.3963 1.0327 0.7785 0.3288 0.5094 Isoform 2 of Collagen alpha‐5(IV) chain COL4A5 0.7552 0.2945 ‐0.2254 0.6608 0.8568 0.8978 Collagen alpha‐1(VI) chain COL6A1 0.0070 ‐1.2307 ‐1.2133 0.9980 0.3984 0.4324 Cluster of Collagen alpha‐2(VI) chain COL6A2 ‐0.2955 ‐0.8340 ‐0.6176 0.8710 0.5936 0.7143 Isoform 2 of Collagen alpha‐3(VI) chain COL6A3 ‐0.5125 ‐1.0697 ‐0.7012 0.7755 0.4739 0.6686 Isoform 2 of Collagen alpha‐1(VII) chain COL7A1 1.8894 0.8958 ‐0.4077 0.1902 0.5588 0.8176 Isoform Soluble of Catechol O‐ methyltransferase COMT 0.4080 ‐0.9782 ‐1.2386 0.8208 0.5203 0.4209 Isoform 2 of Coatomer subunit alpha COPA 0.4272 ‐3.5240 ‐3.7516 0.8134 0.0125 0.0113 Coatomer subunit beta COPB1 1.4531 ‐0.0886 ‐1.0772 0.3284 0.9509 0.4902 Isoform 2 of Coatomer subunit beta' COPB2 0.1725 ‐2.0116 ‐2.0929 0.9290 0.1453 0.1458 Coatomer subunit epsilon COPE 1.4058 ‐0.4439 ‐1.3938 0.3450 0.7945 0.3581 Coatomer subunit gamma‐1 COPG1 0.5031 ‐2.4049 ‐2.7044 0.7769 0.0805 0.0579 Isoform 2 of COP9 signalosome complex subunit 4 COPS4 ‐0.1490 ‐0.7242 ‐0.6096 0.9398 0.6504 0.7191 COP9 signalosome complex subunit 7a COPS7A ‐2.7295 0.7098 2.5568 0.0532 0.6575 0.0719 Coronin‐1A CORO1A 7.5307 5.4805 0.2505 0.0000 0.0005 0.8887 Coronin‐1B CORO1B ‐0.4226 ‐1.5804 ‐1.2639 0.8143 0.2609 0.4105 Isoform 3 of Coronin‐1C CORO1C 1.6011 2.7674 1.6265 0.2765 0.0452 0.2744 Coronin‐2B CORO2B ‐3.7900 2.2707 4.8122 0.0085 0.0991 0.0019 Coactosin‐like protein COTL1 1.4752 5.5963 4.4903 0.3212 0.0004 0.0033 Cytochrome c oxidase subunit 5A, ‐ mitochondrial COX5A 16.4927 ‐0.3196 11.5517 0.0000 0.8457 0.0000 Cytochrome c oxidase subunit 6B1 COX6B1 ‐18.5672 ‐17.3596 ‐4.3954 0.0000 0.0000 0.0038 Ceruloplasmin CP 2.2188 ‐0.9872 ‐2.4812 0.1174 0.5144 0.0804 Carboxypeptidase M CPM 9.8248 5.6875 ‐1.1094 0.0000 0.0004 0.4765 Copine‐1 CPNE1 1.7863 ‐0.3434 ‐1.5544 0.2165 0.8356 0.2976 Cluster of Copine‐3 CPNE3 ‐1.6208 ‐0.9673 0.1545 0.2695 0.5260 0.9252

Cluster of Isoform 3 of Carbamoyl‐ phosphate synthase [ammonia], mitochondrial CPS1 ‐23.0164 ‐1.6832 14.0302 0.0000 0.2285 0.0000 Cluster of Isoform 3 of Cleavage and polyadenylation specificity factor subunit 6 CPSF6 ‐3.5533 ‐0.4309 1.9980 0.0129 0.7991 0.1681 Isoform 2 of Carnitine O‐ palmitoyltransferase 1, liver isoform CPT1A 3.1299 2.4481 0.2713 0.0272 0.0752 0.8827 Cluster of Complement receptor type 1 CR1 ‐1.1547 ‐3.2250 ‐2.3801 0.4545 0.0202 0.0934 Cluster of Protein crumbs homolog 2 CRB2 ‐1.3868 ‐3.2507 ‐2.2472 0.3519 0.0195 0.1164 Cysteine‐rich motor neuron 1 protein CRIM1 2.5655 1.1322 ‐0.6363 0.0685 0.4445 0.7047 Isoform 2 of Cysteine‐rich protein 2 CRIP2 ‐1.2575 ‐1.7452 ‐0.8569 0.4057 0.2111 0.6017 Isoform Crk‐I of Adapter molecule crk CRK 0.6679 0.3234 ‐0.1375 0.7032 0.8449 0.9316 C‐reactive protein CRP ‐12.2265 ‐1.0631 7.2870 0.0000 0.4763 0.0000 Alpha‐crystallin B chain CRYAB 2.1542 1.7232 0.2243 0.1284 0.2168 0.8979 Isoform 2 of Lambda‐crystallin homolog CRYL1 ‐0.4780 ‐0.7499 ‐0.4107 0.7866 0.6411 0.8158 Isoform 3 of Quinone oxidoreductase CRYZ ‐2.1002 ‐1.4482 0.0089 0.1403 0.3103 0.9937 Citrate synthase, mitochondrial CS 0.4989 ‐0.8509 ‐1.1756 0.7785 0.5852 0.4493 Isoform 3 of Exportin‐2 CSE1L 0.7038 ‐0.3757 ‐0.8485 0.6868 0.8248 0.6052 Chondroitin sulfate proteoglycan 4 CSPG4 ‐0.3980 1.2805 1.5287 0.8245 0.3789 0.3079 Cysteine and glycine‐rich protein 1 CSRP1 ‐1.6163 ‐3.9041 ‐2.7325 0.2711 0.0068 0.0560 Cysteine and glycine‐rich protein 2 CSRP2 9.6445 6.2532 ‐0.4311 0.0000 0.0002 0.8046 Cystatin‐C CST3 ‐11.3358 ‐2.1749 5.5883 0.0000 0.1147 0.0005 Cystatin‐A CSTA ‐0.6020 5.7793 6.0853 0.7358 0.0003 0.0002 Cystatin‐B CSTB 2.2049 ‐2.2146 ‐3.6770 0.1193 0.1083 0.0129 Catenin alpha‐1 CTNNA1 1.2144 ‐3.3729 ‐4.1396 0.4269 0.0158 0.0059 Isoform 2 of Catenin alpha‐2 CTNNA2 ‐3.1681 0.3175 2.4704 0.0254 0.8460 0.0816 Catenin beta‐1 CTNNB1 ‐0.7007 ‐0.9358 ‐0.4415 0.6868 0.5409 0.7992 Isoform 1AC of Catenin delta‐1 CTNND1 ‐0.9402 1.9351 2.5409 0.5592 0.1637 0.0733 Cathepsin B CTSB ‐0.5312 0.3736 0.7288 0.7673 0.8252 0.6567 Dipeptidyl peptidase 1 CTSC 8.7091 5.7434 ‐0.2944 0.0000 0.0003 0.8763 Cathepsin D CTSD ‐1.4501 ‐0.3495 0.6449 0.3291 0.8337 0.7008 Cathepsin G CTSG 11.7588 7.7294 ‐0.4221 0.0000 0.0000 0.8088 Cathepsin L1 CTSL 12.4592 7.6436 ‐0.9837 0.0000 0.0000 0.5283 Cathepsin Z CTSZ 0.7236 0.8557 0.3472 0.6765 0.5840 0.8452 Cluster of Src substrate cortactin CTTN ‐0.7363 0.2724 0.7692 0.6712 0.8663 0.6395 Cubilin CUBN ‐1.6560 ‐0.0907 1.0393 0.2597 0.9509 0.5073 Isoform 2 of Cytochrome b5 CYB5A ‐20.3286 ‐0.0621 13.7906 0.0000 0.9651 0.0000 Isoform 2 of NADH‐cytochrome b5 reductase 3 CYB5R3 1.1999 0.9119 0.0778 0.4349 0.5526 0.9633

Cytochrome c1, heme protein, mitochondrial CYC1 ‐0.6003 ‐5.7252 ‐5.2130 0.7365 0.0003 0.0010 Cluster of Cytoplasmic FMR1‐ interacting protein 1 CYFIP1 ‐3.8764 ‐1.7417 0.9310 0.0072 0.2116 0.5553 Dystroglycan DAG1 ‐2.6370 ‐0.3280 1.4747 0.0619 0.8438 0.3261 Aspartate‐‐tRNA ligase, cytoplasmic DARS ‐0.7296 1.2174 1.6926 0.6741 0.4037 0.2532 Isoform 2 of DAZ‐associated protein 1 DAZAP1 8.9770 5.0616 ‐1.1464 0.0000 0.0010 0.4607 Cluster of Isoform 4 of Acyl‐CoA‐ ‐ binding protein DBI ‐0.1681 ‐13.8341 13.4703 0.9306 0.0000 0.0000 Isoform 2 of Drebrin DBN1 3.0250 1.8661 ‐0.2286 0.0326 0.1817 0.8970 Cluster of Isoform 2 of Drebrin‐like protein DBNL ‐1.5194 ‐1.4477 ‐0.3863 0.3049 0.3103 0.8275 Dermcidin DCD ‐0.4038 3.9625 4.1663 0.8234 0.0061 0.0056 Cluster of Isoform 3 of Dynactin subunit 1 DCTN1 ‐1.3625 0.6509 1.5675 0.3629 0.6880 0.2934 Isoform 2 of Dynactin subunit 2 DCTN2 ‐1.5710 ‐0.2989 0.7769 0.2881 0.8551 0.6381 Isoform 2 of Dynactin subunit 4 DCTN4 ‐0.9963 ‐5.4604 ‐4.6831 0.5326 0.0005 0.0024 L‐xylulose reductase DCXR ‐24.1547 ‐2.1224 14.3745 0.0000 0.1230 0.0000 N(G),N(G)‐dimethylarginine dimethylaminohydrolase 2 DDAH2 1.4130 0.4604 ‐0.5107 0.3419 0.7859 0.7702 Dendrin DDN ‐7.5455 ‐8.8555 ‐3.5545 0.0000 0.0000 0.0157 Cluster of Dolichyl‐ diphosphooligosaccharide‐‐ protein glycosyltransferase 48 kDa subunit DDOST 12.0493 7.0473 ‐1.2899 0.0000 0.0000 0.3984 DDRGK domain‐containing protein 1 DDRGK1 8.4711 4.8240 ‐1.0350 0.0000 0.0014 0.5089 ATP‐dependent RNA helicase DDX1 DDX1 0.8232 ‐0.6012 ‐1.1513 0.6229 0.7089 0.4582 Cluster of Isoform 4 of Probable ATP‐dependent RNA helicase DDX17 DDX17 16.5665 9.6136 ‐1.8478 0.0000 0.0000 0.2082 Cluster of Isoform 2 of Spliceosome RNA helicase DDX39B DDX39B 0.8337 ‐0.7471 ‐1.3017 0.6182 0.6423 0.3922 Cluster of Isoform 2 of ATP‐ dependent RNA helicase DDX3X DDX3X ‐0.7151 2.5158 2.9577 0.6802 0.0670 0.0392 Probable ATP‐dependent RNA helicase DDX5 DDX5 1.7165 8.4887 7.1662 0.2386 0.0000 0.0000 Probable ATP‐dependent RNA helicase DDX6 DDX6 ‐0.6151 ‐1.2996 ‐0.8570 0.7314 0.3714 0.6017 Isoform 2 of 2,4‐dienoyl‐CoA reductase, mitochondrial DECR1 ‐17.0172 1.8347 13.3970 0.0000 0.1902 0.0000 Protein DEK DEK 7.8724 4.9046 ‐0.5480 0.0000 0.0013 0.7489 Isoform 2 of DENN domain‐ containing protein 4C DENND4C ‐1.5299 ‐1.7841 ‐0.7095 0.3015 0.2021 0.6631 Deoxyribose‐phosphate aldolase DERA ‐8.2658 ‐0.4052 5.2343 0.0000 0.8095 0.0010 Pre‐mRNA‐splicing factor ATP‐ dependent RNA helicase DHX15 DHX15 4.6351 2.9487 ‐0.2627 0.0018 0.0328 0.8840 ATP‐dependent RNA helicase A DHX9 1.6821 0.5984 ‐0.5585 0.2490 0.7093 0.7447

Dihydrolipoyllysine‐residue acetyltransferase component of pyruvate dehydrogenase complex, mitochondrial DLAT ‐0.9179 2.8327 3.4072 0.5695 0.0405 0.0194 Isoform 2 of Dihydrolipoyl dehydrogenase, mitochondrial DLD ‐0.8233 0.0263 0.5869 0.6229 0.9857 0.7295 Cluster of Dihydrolipoyllysine‐ residue succinyltransferase component of 2‐oxoglutarate dehydrogenase complex, mitochondrial DLST ‐0.0837 5.7091 5.6632 0.9634 0.0003 0.0005 DnaJ homolog subfamily A member 2 DNAJA2 ‐0.4322 0.0947 0.3874 0.8111 0.9509 0.8275 Isoform 6 of Dynamin‐1‐like protein DNM1L 1.1992 ‐0.7071 ‐1.5115 0.4349 0.6575 0.3145 Aspartyl aminopeptidase DNPEP 1.6527 0.1186 ‐1.0097 0.2600 0.9410 0.5174 2'‐deoxynucleoside 5'‐phosphate ‐ N‐hydrolase 1 DNPH1 ‐0.3350 ‐10.4708 10.0539 0.8538 0.0000 0.0000 Dipeptidase 1 DPEP1 ‐14.7904 ‐3.7729 6.3730 0.0000 0.0085 0.0002 Isoform 4 of Dipeptidyl peptidase 3 DPP3 ‐0.9344 ‐0.4382 0.2064 0.5612 0.7972 0.9038 Dipeptidyl peptidase 4 DPP4 8.6919 5.3026 ‐0.7155 0.0000 0.0006 0.6617 Isoform DPPX‐S of Dipeptidyl aminopeptidase‐like protein 6 DPP6 ‐0.0953 ‐4.0944 ‐3.9557 0.9589 0.0049 0.0079 Dihydropyrimidinase DPYS ‐8.4139 ‐7.2444 ‐1.3807 0.0000 0.0000 0.3607 Dihydropyrimidinase‐related protein 2 DPYSL2 ‐0.6721 ‐3.4891 ‐2.9682 0.7017 0.0131 0.0386 Isoform LCRMP‐4 of Dihydropyrimidinase‐related protein 3 DPYSL3 ‐0.4531 ‐2.3732 ‐2.0216 0.8004 0.0848 0.1624 Isoform 1B of Desmocollin‐1 DSC1 ‐7.5328 ‐0.7377 4.4084 0.0000 0.6459 0.0038 Desmoglein‐1 DSG1 ‐1.6214 ‐0.9094 0.2118 0.2695 0.5533 0.9035 Desmoplakin DSP 0.7952 ‐0.7401 ‐1.2687 0.6378 0.6452 0.4080 Cluster of Dystonin DST ‐0.0292 ‐0.8471 ‐0.8119 0.9849 0.5871 0.6229 Isoform 2 of Destrin DSTN 1.0785 ‐1.0535 ‐1.7694 0.4945 0.4813 0.2294 Dual specificity protein phosphatase 3 DUSP3 1.2244 6.0024 5.0599 0.4225 0.0002 0.0013 Cytoplasmic dynein 1 heavy chain 1 DYNC1H1 0.6076 ‐0.6100 ‐1.0130 0.7343 0.7076 0.5173 Isoform 2B of Cytoplasmic dynein 1 intermediate chain 2 DYNC1I2 ‐0.3135 ‐0.6196 ‐0.3949 0.8646 0.7041 0.8251 Isoform 2 of Cytoplasmic dynein 1 light intermediate chain 2 DYNC1LI2 ‐0.3790 1.8730 2.0975 0.8330 0.1800 0.1448 ‐ Dynein light chain 1, cytoplasmic DYNLL1 ‐0.4646 ‐11.2538 10.7344 0.7960 0.0000 0.0000 Dynein light chain roadblock‐type 1 DYNLRB1 ‐2.1508 ‐0.8526 0.6282 0.1287 0.5846 0.7087 Isoform 10 of Dysferlin DYSF 0.7815 ‐0.0694 ‐0.6006 0.6458 0.9607 0.7238 Delta(3,5)‐Delta(2,4)‐dienoyl‐CoA isomerase, mitochondrial ECH1 0.5733 0.4789 0.0797 0.7463 0.7782 0.9633 Ethylmalonyl‐CoA decarboxylase ECHDC1 ‐2.8905 ‐4.6378 ‐2.5847 0.0410 0.0019 0.0690

Enoyl‐CoA hydratase, mitochondrial ECHS1 ‐2.3108 ‐0.0081 1.5667 0.1020 0.9937 0.2934 Isoform 2 of Enoyl‐CoA delta isomerase 1, mitochondrial ECI1 0.0486 3.4729 3.3772 0.9744 0.0133 0.0201 Isoform 4 of Extracellular matrix protein 1 ECM1 7.1760 4.4143 ‐0.5548 0.0000 0.0028 0.7458 Enhancer of mRNA‐decapping protein 4 EDC4 7.1172 3.6618 ‐1.2538 0.0000 0.0100 0.4148 Early endosome antigen 1 EEA1 ‐0.0820 ‐3.4839 ‐3.3652 0.9634 0.0131 0.0204 Cluster of Elongation factor 1‐ alpha 1 EEF1A1 0.1909 ‐0.2216 ‐0.3477 0.9202 0.8905 0.8452 Elongation factor 1‐beta EEF1B2 0.2205 ‐1.7355 ‐1.8545 0.9046 0.2131 0.2068 Cluster of Isoform 2 of Elongation factor 1‐delta EEF1D 2.3082 0.4099 ‐1.1702 0.1023 0.8062 0.4506 Isoform 2 of Elongation factor 1‐ gamma EEF1G 0.4336 ‐0.7258 ‐1.0081 0.8107 0.6504 0.5180 Elongation factor 2 EEF2 2.2862 0.1935 ‐1.3678 0.1052 0.9040 0.3657 Isoform 2 of EGF‐containing fibulin‐like extracellular matrix protein 1 EFEMP1 ‐0.6535 5.8722 6.2116 0.7090 0.0003 0.0002 Cluster of EF‐hand domain‐ containing protein D1 EFHD1 0.4619 1.3102 0.9719 0.7977 0.3684 0.5336 Ephrin‐B1 EFNB1 1.3849 10.7678 9.6301 0.3525 0.0000 0.0000 Isoform 2 of 116 kDa U5 small nuclear ribonucleoprotein component EFTUD2 0.9495 2.2909 1.6026 0.5564 0.0963 0.2814 EH domain‐containing protein 2 EHD2 0.9392 2.2101 1.5303 0.5593 0.1090 0.3079 Cluster of EH domain‐containing protein 3 EHD3 ‐1.6388 ‐1.3044 ‐0.1642 0.2650 0.3697 0.9236 EH domain‐containing protein 4 EHD4 ‐2.5846 ‐1.7413 0.0512 0.0672 0.2116 0.9730 Peroxisomal bifunctional enzyme EHHADH ‐12.9141 ‐2.1185 6.7192 0.0000 0.1236 0.0001 Eukaryotic translation initiation factor 1A, Y‐chromosomal EIF1AY 9.9406 7.9048 0.9890 0.0000 0.0000 0.5262 Isoform 2 of Interferon‐induced, double‐stranded RNA‐activated protein kinase EIF2AK2 ‐1.4283 ‐2.6048 ‐1.5847 0.3368 0.0585 0.2875 Eukaryotic translation initiation factor 2 subunit 1 EIF2S1 8.0877 5.7904 0.1753 0.0000 0.0003 0.9197 Isoform 2 of Eukaryotic translation initiation factor 3 subunit A EIF3A 0.0742 3.6135 3.4978 0.9659 0.0108 0.0171 Eukaryotic translation initiation factor 3 subunit I EIF3I 2.8624 ‐1.0463 ‐2.9778 0.0428 0.4847 0.0381 Cluster of Isoform 2 of Eukaryotic initiation factor 4A‐II EIF4A2 2.5823 0.7846 ‐0.9890 0.0672 0.6214 0.5262 Eukaryotic initiation factor 4A‐III EIF4A3 1.8228 0.0715 ‐1.1718 0.2076 0.9602 0.4501 Eukaryotic translation initiation factor 4B EIF4B ‐0.3918 2.1760 2.4037 0.8256 0.1147 0.0913 Isoform 7 of Eukaryotic translation initiation factor 4 gamma 1 EIF4G1 1.9968 1.9360 0.5405 0.1633 0.1637 0.7539 Isoform Short of Eukaryotic translation initiation factor 4H EIF4H 0.2960 ‐0.1896 ‐0.3879 0.8710 0.9044 0.8275

Isoform 2 of Eukaryotic translation initiation factor 5A‐1 EIF5A ‐1.8833 ‐1.2517 0.0541 0.1913 0.3905 0.9729 Neutrophil elastase ELANE 8.3978 5.5548 ‐0.2674 0.0000 0.0004 0.8827 Isoform 2 of ELAV‐like protein 1 ELAVL1 3.3553 11.9475 9.4460 0.0184 0.0000 0.0000 Engulfment and cell motility protein 2 ELMO2 ‐1.1027 ‐0.2510 0.5049 0.4802 0.8771 0.7716 Emerin EMD ‐1.5522 5.3298 6.2914 0.2939 0.0006 0.0002 Cluster of EMILIN‐1 EMILIN1 0.2830 3.3359 3.0830 0.8743 0.0169 0.0318 Isoform 2 of Echinoderm microtubule‐associated protein‐ like 2 EML2 0.6495 ‐2.1421 ‐2.5461 0.7111 0.1199 0.0732 Isoform 2 of Echinoderm microtubule‐associated protein‐ like 4 EML4 ‐0.7031 ‐4.6909 ‐4.1273 0.6868 0.0018 0.0060 Endonuclease domain‐containing 1 protein ENDOD1 ‐0.4477 ‐0.1634 0.1446 0.8022 0.9155 0.9298 Isoform Short of Endoglin ENG ‐1.7541 ‐1.6483 ‐0.4234 0.2256 0.2406 0.8084 Alpha‐enolase ENO1 1.4838 ‐1.3857 ‐2.3718 0.3177 0.3332 0.0947 Glutamyl aminopeptidase ENPEP ‐1.6123 ‐4.6504 ‐3.4680 0.2718 0.0019 0.0179 Band 4.1‐like protein 2 EPB41L2 0.7905 1.7500 1.1798 0.6401 0.2101 0.4488 Cluster of Isoform 3 of Band 4.1‐ like protein 5 EPB41L5 1.2984 3.0491 2.1094 0.3904 0.0274 0.1424 Epoxide hydrolase 1 EPHX1 ‐3.2438 4.3371 6.4692 0.0226 0.0032 0.0001 Bifunctional epoxide hydrolase 2 EPHX2 2.2921 1.3931 ‐0.1938 0.1044 0.3296 0.9094 Isoform 2 of Epsin‐1 EPN1 0.7256 ‐8.7592 ‐9.0958 0.6759 0.0000 0.0000 Epiplakin EPPK1 ‐0.2739 0.3645 0.5446 0.8794 0.8268 0.7511 Bifunctional glutamate/proline‐‐ tRNA ligase EPRS ‐0.6848 ‐0.3359 0.1367 0.6935 0.8399 0.9316 Isoform 2 of Endoplasmic reticulum aminopeptidase 1 ERAP1 2.5672 2.5290 0.7342 0.0685 0.0657 0.6551 Isoform 2 of Endoplasmic reticulum‐Golgi intermediate compartment protein 1 ERGIC1 7.3014 3.7199 ‐1.3223 0.0000 0.0091 0.3849 Endoplasmic reticulum resident protein 29 ERP29 ‐0.2013 4.2295 4.2904 0.9164 0.0039 0.0046 Endoplasmic reticulum resident protein 44 ERP44 ‐1.3929 ‐1.0928 ‐0.1240 0.3506 0.4656 0.9385 Endothelial cell‐selective adhesion molecule ESAM ‐1.4022 ‐3.3328 ‐2.3173 0.3466 0.0169 0.1035 S‐formylglutathione hydrolase ESD 0.3306 ‐2.5519 ‐2.7312 0.8561 0.0633 0.0560 Isoform 2 of Extended synaptotagmin‐1 ESYT1 2.5376 0.6059 ‐1.1341 0.0713 0.7083 0.4652 Isoform 2 of Electron transfer flavoprotein subunit alpha, mitochondrial ETFA ‐7.0807 ‐1.2981 3.5500 0.0000 0.3714 0.0157 Isoform 2 of Electron transfer flavoprotein subunit beta ETFB ‐7.2630 0.2558 5.2001 0.0000 0.8753 0.0010 Isoform 2 of Electron transfer flavoprotein‐ubiquinone oxidoreductase, mitochondrial ETFDH ‐0.5053 ‐0.9366 ‐0.5754 0.7769 0.5409 0.7344 Protein eva‐1 homolog B EVA1B ‐2.3607 ‐4.0688 ‐2.3870 0.0945 0.0051 0.0931

Cluster of Isoform 3 of RNA‐ binding protein EWS EWSR1 0.1275 ‐1.4470 ‐1.5077 0.9469 0.3103 0.3152 Exocyst complex component 3‐like protein 2 EXOC3L2 ‐0.5902 ‐3.7642 ‐3.2942 0.7395 0.0086 0.0232 Ezrin EZR ‐0.7491 ‐3.8423 ‐3.2626 0.6632 0.0075 0.0242 Coagulation factor XII F12 7.1800 5.0731 0.0894 0.0000 0.0009 0.9590 Prothrombin F2 1.8782 ‐0.3378 ‐1.6115 0.1915 0.8390 0.2785 Coagulation factor IX F9 2.1709 1.1587 ‐0.3414 0.1251 0.4314 0.8469 Fatty acid‐binding protein, liver FABP1 ‐18.1435 ‐13.6510 ‐1.0423 0.0000 0.0000 0.5070 Fatty acid‐binding protein, adipocyte FABP4 1.1219 0.0836 ‐0.6824 0.4705 0.9542 0.6769 Fatty acid‐binding protein 5 FABP5 1.9247 8.6403 7.1732 0.1809 0.0000 0.0000 Fumarylacetoacetase FAH ‐2.2674 ‐1.6503 ‐0.0756 0.1084 0.2401 0.9633 Isoform D of Constitutive coactivator of PPAR‐gamma‐like protein 1 FAM120A ‐0.6607 ‐3.7913 ‐3.2728 0.7050 0.0082 0.0239 Protein FAM98B FAM98B 2.2574 1.1707 ‐0.3886 0.1101 0.4266 0.8275 Cluster of FERM, ARHGEF and pleckstrin domain‐containing protein 1 FARP1 ‐4.8561 ‐0.6187 2.7013 0.0012 0.7041 0.0581 Isoform 2 of Phenylalanine‐‐tRNA ligase alpha subunit FARSA ‐3.6449 1.1373 3.6004 0.0111 0.4427 0.0148 Fatty acid synthase FASN ‐0.5371 0.8106 1.1620 0.7673 0.6058 0.4529 Isoform 3 of Filamin‐binding LIM protein 1 FBLIM1 0.2675 0.3545 0.1659 0.8814 0.8324 0.9236 Cluster of Fibulin‐1 FBLN1 ‐1.7898 ‐0.8645 0.3706 0.2158 0.5785 0.8357 Fibulin‐5 FBLN5 ‐1.6791 2.9810 4.0714 0.2499 0.0311 0.0065 Fibrillin‐1 FBN1 1.5836 ‐0.5692 ‐1.6380 0.2833 0.7245 0.2711 Fibrillin‐2 FBN2 ‐1.2933 4.7971 5.5918 0.3917 0.0015 0.0005 Fructose‐1,6‐bisphosphatase 1 FBP1 ‐7.0298 ‐8.2100 ‐3.2720 0.0000 0.0000 0.0239 Cluster of Isoform 3 of Fermitin family homolog 2 FERMT2 0.0131 ‐3.4162 ‐3.3636 0.9947 0.0147 0.0204 Isoform 2 of Fermitin family homolog 3 FERMT3 ‐0.9153 0.7089 1.3198 0.5704 0.6575 0.3853 Isoform 2 of Fibrinogen alpha chain FGA ‐0.6078 ‐0.7253 ‐0.2981 0.7343 0.6504 0.8746 Fibrinogen beta chain FGB ‐0.8192 ‐0.7597 ‐0.1878 0.6243 0.6351 0.9128 Fibroblast growth factor 1 FGF1 1.5469 ‐1.1097 ‐2.1437 0.2960 0.4553 0.1354 Isoform Gamma‐A of Fibrinogen gamma chain FGG ‐1.0111 ‐1.2015 ‐0.4909 0.5264 0.4121 0.7763 Fibrinogen‐like protein 1 FGL1 12.9712 9.6351 0.6231 0.0000 0.0000 0.7114 Fumarate hydratase, mitochondrial FH ‐1.2464 1.7683 2.5857 0.4110 0.2054 0.0690 Cluster of Isoform 5 of Four and a half LIM domains protein 1 FHL1 2.3842 ‐1.4981 ‐3.0957 0.0911 0.2918 0.0312 Four and a half LIM domains protein 2 FHL2 0.8743 ‐1.4326 ‐2.0025 0.5961 0.3149 0.1670 Four and a half LIM domains protein 3 FHL3 3.8582 ‐2.6406 ‐5.2219 0.0075 0.0557 0.0010 Mitochondrial fission 1 protein FIS1 0.6346 ‐8.7825 ‐9.0567 0.7183 0.0000 0.0000

Peptidyl‐prolyl cis‐trans isomerase FKBP1A FKBP1A ‐1.8110 ‐1.5500 ‐0.2881 0.2109 0.2709 0.8795 Peptidyl‐prolyl cis‐trans isomerase FKBP2 FKBP2 ‐0.8972 ‐0.8422 ‐0.2157 0.5819 0.5897 0.9016 Cluster of Peptidyl‐prolyl cis‐trans isomerase FKBP3 FKBP3 3.6275 ‐1.4520 ‐3.8976 0.0114 0.3098 0.0087 Peptidyl‐prolyl cis‐trans isomerase FKBP5 FKBP5 ‐1.3916 2.3170 3.2235 0.3506 0.0920 0.0258 Filaggrin‐2 FLG2 ‐3.5117 ‐1.3351 1.0818 0.0138 0.3566 0.4898 Isoform 2 of Filamin‐A FLNA 0.2837 ‐0.1906 ‐0.3805 0.8743 0.9043 0.8304 Isoform 8 of Filamin‐B FLNB 2.2443 1.1861 ‐0.3645 0.1127 0.4198 0.8384 Isoform 2 of Filamin‐C FLNC 2.8793 ‐1.1846 ‐3.1252 0.0418 0.4198 0.0300 Isoform 2 of Flotillin‐1 FLOT1 ‐0.5939 ‐1.0125 ‐0.5895 0.7388 0.5041 0.7284 Flotillin‐2 FLOT2 ‐3.7450 ‐1.7617 0.8219 0.0092 0.2072 0.6188 Cluster of Vascular endothelial growth factor receptor 1 FLT1 ‐2.7641 ‐4.1377 ‐2.1797 0.0502 0.0045 0.1284 Isoform 17 of Fibronectin FN1 ‐0.2635 0.3192 0.4929 0.8834 0.8457 0.7755 Fascin FSCN1 ‐0.1739 ‐2.8824 ‐2.7120 0.9286 0.0370 0.0575 Isoform C of Formimidoyltransferase‐ cyclodeaminase FTCD ‐6.3733 ‐1.7721 2.6025 0.0001 0.2046 0.0677 Ferritin light chain FTL ‐4.4388 0.1872 3.2084 0.0026 0.9044 0.0263 Alpha‐ketoglutarate‐dependent dioxygenase FTO FTO ‐1.0204 ‐0.4263 0.2766 0.5238 0.7991 0.8827 Isoform 2 of Far upstream element‐binding protein 1 FUBP1 1.3896 ‐1.4339 ‐2.3549 0.3508 0.3149 0.0976 Isoform Short of RNA‐binding protein FUS FUS 0.7990 ‐1.8028 ‐2.3148 0.6356 0.1976 0.1038 Ras GTPase‐activating protein‐ binding protein 1 G3BP1 1.6517 3.6988 2.5067 0.2600 0.0094 0.0775 Lysosomal alpha‐glucosidase GAA ‐0.8986 2.3686 2.9382 0.5814 0.0853 0.0401 Aldose 1‐epimerase GALM ‐3.1937 ‐2.6767 ‐0.4523 0.0243 0.0525 0.7914 Neutral alpha‐glucosidase AB GANAB ‐0.0053 ‐1.0729 ‐1.0500 0.9987 0.4738 0.5043 Cluster of Isoform 2 of Glyceraldehyde‐3‐phosphate dehydrogenase GAPDH 0.1739 ‐2.6354 ‐2.7064 0.9286 0.0559 0.0578 Glycine‐‐tRNA ligase GARS1 3.2138 0.2784 ‐1.9164 0.0236 0.8640 0.1900 Growth arrest‐specific protein 2 GAS2 1.9357 ‐2.7590 ‐4.0282 0.1779 0.0457 0.0070 Isoform 2 of Glycine amidinotransferase, mitochondrial GATM ‐1.3110 ‐1.5125 ‐0.5920 0.3844 0.2861 0.7284 1,4‐alpha‐glucan‐branching enzyme GBE1 1.0640 ‐0.2107 ‐0.9319 0.5027 0.8954 0.5553 Guanylate‐binding protein 1 GBP1 6.9955 3.6677 ‐1.1651 0.0000 0.0100 0.4526 Isoform 3 of Vitamin D‐binding protein GC ‐0.3030 ‐3.5400 ‐3.2698 0.8704 0.0121 0.0239 eIF‐2‐alpha kinase activator GCN1 GCN1 0.8469 ‐0.6181 ‐1.1840 0.6097 0.7041 0.4470 Isoform 2 of Guanine deaminase GDA ‐0.4569 ‐0.4200 ‐0.1011 0.7998 0.7997 0.9542 Rab GDP dissociation inhibitor alpha GDI1 ‐0.7430 ‐3.4428 ‐2.8744 0.6676 0.0141 0.0438

Rab GDP dissociation inhibitor beta GDI2 0.7781 ‐2.0811 ‐2.5737 0.6478 0.1294 0.0701 Gamma‐glutamylcyclotransferase GGCT ‐9.4588 0.3892 6.8273 0.0000 0.8182 0.0001 GTPase IMAP family member 4 GIMAP4 ‐5.4695 ‐0.3036 3.4287 0.0004 0.8527 0.0189 GTPase IMAP family member 8 GIMAP8 ‐3.1307 ‐1.8410 0.3253 0.0272 0.1883 0.8578 Isoform 3 of ARF GTPase‐ activating protein GIT1 GIT1 0.7678 1.9391 1.3810 0.6530 0.1630 0.3607 Gap junction alpha‐5 protein GJA5 0.0605 ‐7.2598 ‐7.1702 0.9698 0.0000 0.0000 Isoform 2 of Golgi apparatus protein 1 GLG1 ‐1.4719 ‐0.9443 0.0756 0.3220 0.5377 0.9633 Isoform 2 of Lactoylglutathione lyase GLO1 ‐1.4228 ‐1.0085 ‐0.0209 0.3384 0.5052 0.9892 ‐ Glutaredoxin‐1 GLRX 0.4240 ‐11.9948 12.0676 0.8141 0.0000 0.0000 Isoform 3 of Glutaminase kidney isoform, mitochondrial GLS ‐0.8598 2.6743 3.2120 0.6032 0.0526 0.0262 Cluster of Glutamate dehydrogenase 1, mitochondrial GLUD1 ‐0.3005 ‐0.9024 ‐0.6814 0.8710 0.5568 0.6769 GDP‐mannose 4,6 dehydratase GMDS ‐0.5614 ‐3.5079 ‐3.0621 0.7504 0.0128 0.0328 Glia maturation factor beta GMFB ‐14.8455 ‐9.5348 0.7525 0.0000 0.0000 0.6453 Cluster of Guanine nucleotide‐ binding protein subunit alpha‐11 GNA11 0.5348 0.0107 ‐0.3540 0.7673 0.9923 0.8432 Cluster of Guanine nucleotide‐ binding protein G(i) subunit alpha‐ 2 GNAI2 ‐1.2963 ‐1.6851 ‐0.7715 0.3909 0.2280 0.6393 Isoform Alpha‐2 of Guanine nucleotide‐binding protein G(o) subunit alpha GNAO1 16.3511 9.5377 ‐1.7756 0.0000 0.0000 0.2281 Guanine nucleotide‐binding protein G(q) subunit alpha GNAQ ‐3.1054 ‐3.4946 ‐1.3157 0.0285 0.0130 0.3870 Isoform XLas‐2 of Guanine nucleotide‐binding protein G(s) subunit alpha isoforms XLas GNAS ‐0.1908 ‐1.3159 ‐1.1622 0.9202 0.3662 0.4529 Guanine nucleotide‐binding protein G(I)/G(S)/G(T) subunit beta‐1 GNB1 0.6364 ‐0.5782 ‐1.0014 0.7174 0.7196 0.5203 Cluster of Guanine nucleotide‐ binding protein G(I)/G(S)/G(T) subunit beta‐2 GNB2 0.4095 ‐2.0816 ‐2.3232 0.8205 0.1294 0.1025 Guanine nucleotide‐binding protein G(I)/G(S)/G(O) subunit ‐ gamma‐12 GNG12 ‐0.6471 ‐10.7874 10.1521 0.7119 0.0000 0.0000 Isoform 2 of Guanine nucleotide‐ binding protein‐like 1 GNL1 ‐1.2649 0.2082 1.0664 0.4036 0.8954 0.4956 Cluster of Glucosamine‐6‐ phosphate isomerase 1 GNPDA1 0.0488 ‐8.7364 ‐8.6123 0.9744 0.0000 0.0000 Isoform 3 of Golgi reassembly‐ stacking protein 2 GORASP2 1.0541 ‐1.9610 ‐2.6439 0.5074 0.1576 0.0634 Isoform 2 of Aspartate aminotransferase, cytoplasmic GOT1 ‐2.1745 ‐2.2501 ‐0.7278 0.1245 0.1021 0.6567 Aspartate aminotransferase, mitochondrial GOT2 0.0000 4.3848 4.3058 1.0000 0.0030 0.0045

Glycerol‐3‐phosphate dehydrogenase [NAD(+)], cytoplasmic GPD1 0.4001 1.8092 1.5040 0.8234 0.1960 0.3157 Isoform 2 of Gephyrin GPHN ‐0.3872 ‐4.6078 ‐4.2609 0.8274 0.0020 0.0048 Glucose‐6‐phosphate isomerase GPI 1.5188 ‐1.6167 ‐2.6225 0.3049 0.2497 0.0655 Isoform 2 of Transmembrane glycoprotein NMB GPNMB 1.2561 1.9048 1.0146 0.4058 0.1711 0.5173 Glutathione peroxidase 1 GPX1 ‐4.6776 2.5783 5.7191 0.0017 0.0609 0.0004 Glutathione peroxidase 3 GPX3 ‐2.6276 ‐3.1507 ‐1.3035 0.0627 0.0230 0.3922 Growth factor receptor‐bound protein 2 GRB2 ‐4.9071 0.1407 3.4818 0.0011 0.9270 0.0176 Glyoxylate reductase/hydroxypyruvate reductase GRHPR 1.8516 ‐3.1730 ‐4.3774 0.1988 0.0222 0.0040 Glycogen synthase kinase‐3 beta GSK3B ‐1.2652 0.2513 1.1089 0.4036 0.8771 0.4765 Isoform 2 of Gelsolin GSN ‐0.6655 ‐3.6400 ‐3.1210 0.7032 0.0104 0.0301 Glutathione reductase, mitochondrial GSR ‐7.4162 ‐7.7204 ‐2.5280 0.0000 0.0000 0.0748 Glutathione synthetase GSS ‐1.1737 ‐1.5506 ‐0.7229 0.4456 0.2709 0.6591 Isoform 4 of Glutathione S‐ transferase kappa 1 GSTK1 ‐13.7316 ‐1.5762 7.8087 0.0000 0.2624 0.0000 Glutathione S‐transferase Mu 3 GSTM3 ‐3.1266 ‐0.7388 1.4049 0.0274 0.6456 0.3533 Glutathione S‐transferase omega‐ 1 GSTO1 ‐0.5244 5.1046 5.3699 0.7697 0.0009 0.0008 Glutathione S‐transferase P GSTP1 1.2599 ‐2.2847 ‐3.1019 0.4057 0.0970 0.0310 Glutathione S‐transferase theta‐1 GSTT1 ‐4.6489 ‐3.5008 ‐0.2700 0.0018 0.0129 0.8827 Isoform 2 of General transcription factor II‐I GTF2I 0.6097 ‐0.3648 ‐0.7736 0.7343 0.8268 0.6387 Isoform 2 of Histone H1.0 H1‐0 ‐0.0678 1.0108 1.0388 0.9677 0.5042 0.5073 Cluster of Histone H1.4 H1‐4 0.3935 ‐1.6701 ‐1.9081 0.8252 0.2330 0.1921 Histone H1.5 H1‐5 1.8785 1.5957 0.2870 0.1915 0.2566 0.8797 Histone H1x H1FX ‐0.1955 ‐1.8187 ‐1.6527 0.9192 0.1938 0.2649 Histone H2A.V H2AFV 0.5679 ‐0.1658 ‐0.5498 0.7490 0.9144 0.7487 Isoform 1 of Core histone macro‐ H2A.1 H2AFY 0.5174 ‐1.0709 ‐1.4042 0.7734 0.4739 0.3533 Core histone macro‐H2A.2 H2AFY2 1.3102 ‐0.9376 ‐1.8135 0.3844 0.5409 0.2188 Cluster of Histone H2B type 1‐M H2BC14 13.0643 8.5443 ‐0.5114 0.0000 0.0000 0.7702 Cluster of Histone H3.3 H3‐3A 1.4850 1.2625 0.2279 0.3177 0.3862 0.8970 Histone H4 H4C1 2.0623 0.0709 ‐1.3356 0.1478 0.9602 0.3798 Cluster of 3‐hydroxyanthranilate 3,4‐dioxygenase HAAO 2.7650 0.4275 ‐1.4643 0.0502 0.7991 0.3299 Isoform 2 of Hydroxyacyl‐ coenzyme A dehydrogenase, mitochondrial HADH ‐6.0081 ‐4.1532 0.0154 0.0002 0.0044 0.9917 Trifunctional enzyme subunit alpha, mitochondrial HADHA 0.6951 1.6227 1.1198 0.6882 0.2489 0.4728 Trifunctional enzyme subunit beta, mitochondrial HADHB 0.2511 1.8229 1.6190 0.8898 0.1938 0.2771

Isoform 2 of Hydroxyacylglutathione hydrolase, mitochondrial HAGH ‐0.8017 ‐4.7270 ‐4.0955 0.6345 0.0017 0.0063 Isoform 2 of Histidine‐‐tRNA ligase, cytoplasmic HARS ‐2.8511 ‐0.6953 1.2599 0.0437 0.6632 0.4117 Hemoglobin subunit alpha HBA1 ‐1.7807 ‐4.3879 ‐3.0955 0.2182 0.0029 0.0312 Hemoglobin subunit beta HBB ‐1.4477 ‐3.9615 ‐2.9037 0.3299 0.0061 0.0421 Hemoglobin subunit delta HBD ‐1.7165 ‐3.7180 ‐2.4813 0.2386 0.0091 0.0804 Hemoglobin subunit gamma‐1 HBG1 ‐14.1692 ‐6.9054 2.8737 0.0000 0.0001 0.0438 Isoform 6 of Histone deacetylase 7 HDAC7 0.1170 0.5243 0.4351 0.9493 0.7508 0.8032 Isoform 2 of Hepatoma‐derived growth factor‐related protein 2 HDGFL2 1.5630 0.3511 ‐0.7203 0.2896 0.8337 0.6600 Vigilin HDLBP 2.3447 1.2587 ‐0.3616 0.0969 0.3872 0.8395 Heme‐binding protein 1 HEBP1 ‐0.5641 ‐8.1750 ‐7.6434 0.7504 0.0000 0.0000 Heme‐binding protein 2 HEBP2 ‐13.9018 ‐0.7069 8.7783 0.0000 0.6575 0.0000 3‐hydroxyisobutyrate dehydrogenase, mitochondrial HIBADH ‐8.5979 ‐0.2749 5.5886 0.0000 0.8656 0.0005 Histidine triad nucleotide‐binding protein 2, mitochondrial HINT2 ‐0.1653 ‐8.5169 ‐8.2508 0.9318 0.0000 0.0000 Cluster of Histone H2A type 1‐A HIST1H2AA 0.2954 ‐0.7084 ‐0.8969 0.8710 0.6575 0.5766 Putative histone H2B type 2‐C HIST2H2BC 0.4503 8.2682 7.8124 0.8013 0.0000 0.0000 Isoform 2 of Hexokinase‐1 HK1 ‐0.8296 1.2679 1.8103 0.6204 0.3841 0.2196 Cluster of Isoform 2 of HLA class I histocompatibility antigen, A alpha chain HLA‐A ‐1.8028 ‐2.7597 ‐1.4816 0.2130 0.0457 0.3243 HLA class I histocompatibility antigen, B alpha chain HLA‐B ‐2.4029 ‐1.3937 0.2688 0.0887 0.3296 0.8827 Cluster of HLA class II histocompatibility antigen, DR alpha chain HLA‐DRA ‐3.5094 ‐4.0651 ‐1.6005 0.0138 0.0051 0.2820 Cluster of HLA class II histocompatibility antigen, DRB1‐8 beta chain HLA‐DRB1 ‐1.4152 16.9294 17.5886 0.3419 0.0000 0.0000 Cluster of HLA class II histocompatibility antigen, DRB1‐ 13 beta chain HLA‐DRB1 ‐12.8701 ‐0.8099 7.9742 0.0000 0.6058 0.0000 HLA class II histocompatibility antigen, DRB1‐4 beta chain HLA‐DRB1 ‐9.9538 ‐7.7131 ‐0.7917 0.0000 0.0000 0.6305 Cluster of HLA class II histocompatibility antigen, DRB1‐7 beta chain HLA‐DRB1 ‐2.4724 7.5200 9.0692 0.0793 0.0000 0.0000 HLA class I histocompatibility antigen, alpha chain E HLA‐E 17.7177 11.1080 ‐1.1647 0.0000 0.0000 0.4526 Cluster of High mobility group protein B1 HMGB1 1.1853 ‐0.3495 ‐1.1509 0.4400 0.8337 0.4582 High mobility group protein B2 HMGB2 15.5830 10.1090 ‐0.6912 0.0000 0.0000 0.6726 Isoform 2 of Hydroxymethylglutaryl‐CoA synthase, mitochondrial HMGCS2 ‐8.0596 ‐0.2358 5.2601 0.0000 0.8850 0.0009 Histamine N‐methyltransferase HNMT 3.0002 1.4893 ‐0.5818 0.0339 0.2953 0.7311

Heterogeneous nuclear ribonucleoprotein A0 HNRNPA0 ‐0.6998 4.9394 5.3273 0.6868 0.0012 0.0008 Isoform A1‐A of Heterogeneous nuclear ribonucleoprotein A1 HNRNPA1 0.6855 0.3393 ‐0.1339 0.6935 0.8384 0.9325 Heterogeneous nuclear ribonucleoproteins A2/B1 HNRNPA2B1 1.8869 0.0452 ‐1.2413 0.1904 0.9743 0.4209 Isoform 2 of Heterogeneous nuclear ribonucleoprotein A3 HNRNPA3 ‐0.7923 1.1815 1.7001 0.6395 0.4208 0.2511 Isoform 2 of Heterogeneous nuclear ribonucleoprotein A/B HNRNPAB ‐4.0431 ‐0.7359 2.0323 0.0053 0.6467 0.1598 Cluster of Isoform C1 of Heterogeneous nuclear ribonucleoproteins C1/C2 HNRNPC 0.9766 0.3260 ‐0.3454 0.5426 0.8443 0.8452 Isoform 2 of Heterogeneous nuclear ribonucleoprotein D0 HNRNPD 1.7777 ‐0.2155 ‐1.4229 0.2184 0.8935 0.3471 Heterogeneous nuclear ribonucleoprotein D‐like HNRNPDL ‐4.5771 ‐3.4907 ‐0.3091 0.0020 0.0131 0.8681 Heterogeneous nuclear ribonucleoprotein F HNRNPF 1.1213 1.0651 0.2819 0.4705 0.4755 0.8827 Cluster of Heterogeneous nuclear ribonucleoprotein H HNRNPH1 2.2222 0.3197 ‐1.2003 0.1168 0.8457 0.4377 Isoform 2 of Heterogeneous nuclear ribonucleoprotein H3 HNRNPH3 0.7120 ‐0.3626 ‐0.8413 0.6821 0.8277 0.6084 Isoform 2 of Heterogeneous nuclear ribonucleoprotein K HNRNPK 1.7355 ‐1.2233 ‐2.3838 0.2323 0.4015 0.0931 Heterogeneous nuclear ribonucleoprotein L HNRNPL 1.5699 0.6044 ‐0.4761 0.2882 0.7088 0.7812 Isoform 2 of Heterogeneous nuclear ribonucleoprotein M HNRNPM 2.0173 0.3525 ‐1.0284 0.1584 0.8334 0.5114 Cluster of Isoform 2 of Heterogeneous nuclear ribonucleoprotein R HNRNPR 1.5264 8.4997 7.3065 0.3024 0.0000 0.0000 Heterogeneous nuclear ribonucleoprotein U HNRNPU 1.7978 ‐0.5919 ‐1.8063 0.2140 0.7134 0.2208 Isoform 2 of Heterogeneous nuclear ribonucleoprotein U‐like protein 1 HNRNPUL1 ‐0.4130 ‐0.8975 ‐0.5999 0.8201 0.5584 0.7238 Heterogeneous nuclear ribonucleoprotein U‐like protein 2 HNRNPUL2 1.1606 ‐2.4302 ‐3.1772 0.4516 0.0776 0.0277 Cluster of Isoform 2 of Haptoglobin HP 1.0176 ‐0.0912 ‐0.7830 0.5246 0.9509 0.6349 Heterochromatin protein 1‐ binding protein 3 HP1BP3 0.5856 0.3657 ‐0.0399 0.7408 0.8268 0.9789 Cluster of Isoform 5 of 15‐ hydroxyprostaglandin ‐ dehydrogenase [NAD(+)] HPGD ‐0.3190 ‐10.6764 10.2666 0.8624 0.0000 0.0000 Hemopexin HPX 1.7093 ‐1.0366 ‐2.1826 0.2401 0.4901 0.1283 Histidine‐rich glycoprotein HRG ‐0.4820 ‐1.1464 ‐0.7973 0.7863 0.4383 0.6296 Hornerin HRNR ‐1.3744 ‐1.4767 ‐0.5137 0.3575 0.3003 0.7702 HCLS1‐binding protein 3 HS1BP3 1.8170 ‐0.1871 ‐1.4218 0.2090 0.9044 0.3471 3‐hydroxyacyl‐CoA dehydrogenase type‐2 HSD17B10 0.9511 ‐0.2912 ‐0.9340 0.5558 0.8588 0.5548

Very‐long‐chain 3‐oxoacyl‐CoA reductase HSD17B12 5.1993 ‐0.9706 ‐4.4959 0.0007 0.5241 0.0033 Peroxisomal multifunctional enzyme type 2 HSD17B4 ‐0.0882 ‐0.6628 ‐0.5908 0.9625 0.6814 0.7284 Cluster of Isoform 2 of Heat shock protein HSP 90‐alpha HSP90AA1 1.4626 ‐0.6414 ‐1.6265 0.3256 0.6919 0.2744 Endoplasmin HSP90B1 2.1793 ‐0.4281 ‐1.9053 0.1236 0.7991 0.1924 Heat shock 70 kDa protein 12A HSPA12A ‐1.5644 ‐1.4744 ‐0.3819 0.2896 0.3011 0.8299 Heat shock 70 kDa protein 12B HSPA12B ‐2.1899 ‐2.2948 ‐0.7613 0.1216 0.0958 0.6422 Cluster of Heat shock 70 kDa protein 1B HSPA1B ‐0.8413 ‐1.7156 ‐1.1114 0.6135 0.2194 0.4758 Heat shock 70 kDa protein 4 HSPA4 0.9119 0.4688 ‐0.1611 0.5723 0.7808 0.9236 Endoplasmic reticulum chaperone BiP HSPA5 0.9426 ‐1.2392 ‐1.8591 0.5588 0.3957 0.2058 Cluster of Heat shock cognate 71 kDa protein HSPA8 0.3683 ‐0.3932 ‐0.6371 0.8387 0.8169 0.7047 Stress‐70 protein, mitochondrial HSPA9 0.1304 1.0070 0.8999 0.9459 0.5054 0.5748 Heat shock protein beta‐1 HSPB1 0.3591 0.4162 0.1641 0.8444 0.8015 0.9236 60 kDa heat shock protein, mitochondrial HSPD1 0.5520 ‐1.6975 ‐2.0430 0.7578 0.2248 0.1578 10 kDa heat shock protein, mitochondrial HSPE1 0.9749 ‐1.5613 ‐2.1974 0.5432 0.2672 0.1258 Basement membrane‐specific heparan sulfate proteoglycan core protein HSPG2 0.6977 0.0513 ‐0.4250 0.6868 0.9715 0.8077 Serine protease HTRA1 HTRA1 ‐5.9204 ‐0.9225 3.1283 0.0002 0.5484 0.0299 Isoform 2 of E3 ubiquitin‐protein ligase HUWE1 HUWE1 0.1150 ‐0.4301 ‐0.5007 0.9493 0.7991 0.7734 Hypoxia up‐regulated protein 1 HYOU1 ‐0.3901 ‐2.5547 ‐2.2428 0.8264 0.0632 0.1172 Isoamyl acetate‐hydrolyzing esterase 1 homolog IAH1 ‐7.2894 ‐1.4610 3.5322 0.0000 0.3066 0.0162 Isoleucine‐‐tRNA ligase, mitochondrial IARS2 ‐0.5657 0.1769 0.5592 0.7502 0.9107 0.7447 Intercellular adhesion molecule 1 ICAM1 ‐0.6541 ‐1.4514 ‐0.9796 0.7090 0.3098 0.5308 Isocitrate dehydrogenase [NADP] cytoplasmic IDH1 3.7773 1.0052 ‐1.5868 0.0087 0.5059 0.2869 Isocitrate dehydrogenase [NADP], mitochondrial IDH2 2.8415 4.1946 2.1828 0.0444 0.0041 0.1283 Interferon‐induced protein 44‐like IFI44L 8.9438 5.7018 ‐0.4952 0.0000 0.0003 0.7747 Isoform 2 of Interferon‐induced protein with tetratricopeptide repeats 1 IFIT1 6.6155 3.8177 ‐0.7588 0.0001 0.0078 0.6422 Isoform 2 of Insulin‐like growth factor‐binding protein complex acid labile subunit IGFALS 1.6891 ‐0.0902 ‐1.2395 0.2471 0.9509 0.4209 Isoform 2 of Insulin‐like growth factor‐binding protein 7 IGFBP7 8.6395 5.7731 ‐0.2178 0.0000 0.0003 0.9013 Cluster of Immunoglobulin heavy constant alpha 1 IGHA1 ‐0.4365 ‐1.0109 ‐0.6953 0.8090 0.5042 0.6718 Isoform 2 of Immunoglobulin heavy constant delta IGHD 12.8926 1.3127 ‐7.4957 0.0000 0.3676 0.0000

Immunoglobulin heavy constant gamma 1 IGHG1 0.2686 ‐1.0124 ‐1.1772 0.8812 0.5041 0.4488 Immunoglobulin heavy constant gamma 2 IGHG2 1.6525 ‐0.1537 ‐1.2770 0.2600 0.9199 0.4039 Immunoglobulin heavy constant gamma 3 IGHG3 0.2925 ‐0.6783 ‐0.8654 0.8710 0.6724 0.5978 Immunoglobulin heavy constant gamma 4 IGHG4 4.4820 ‐0.4248 ‐3.4711 0.0024 0.7997 0.0178 Immunoglobulin heavy constant mu IGHM 2.9442 0.0915 ‐1.9163 0.0372 0.9509 0.1900 Cluster of Immunoglobulin heavy ‐ variable 1‐18 IGHV1‐18 ‐0.6649 ‐12.8953 12.2099 0.7032 0.0000 0.0000 Immunoglobulin heavy variable 3‐ 66 IGHV3‐66 1.9654 ‐0.3197 ‐1.6531 0.1712 0.8457 0.2649 Immunoglobulin heavy variable 3‐ 72 IGHV3‐72 ‐14.1732 ‐1.4329 8.2504 0.0000 0.3149 0.0000 Immunoglobulin heavy variable 3‐ 9 IGHV3‐9 ‐9.6273 ‐6.5859 0.0927 0.0000 0.0001 0.9574 Immunoglobulin kappa constant IGKC 0.8204 ‐1.0863 ‐1.6257 0.6243 0.4684 0.2744 Cluster of Immunoglobulin kappa variable 2‐28 IGKV2‐28 5.3546 ‐2.1755 ‐5.7849 0.0005 0.1147 0.0004 Immunoglobulin kappa variable 3‐ 11 IGKV3‐11 2.4635 1.3363 ‐0.3664 0.0802 0.3564 0.8382 Immunoglobulin kappa variable 3‐ 15 IGKV3‐15 9.2811 ‐3.3036 ‐9.5681 0.0000 0.0178 0.0000 Cluster of Immunoglobulin kappa variable 3‐20 IGKV3‐20 1.1274 ‐0.0240 ‐0.7917 0.4693 0.9861 0.6305 Cluster of Immunoglobulin lambda‐like polypeptide 5 IGLL5 ‐0.1082 ‐1.2192 ‐1.1235 0.9526 0.4035 0.4717 Immunoglobulin lambda variable 1‐47 IGLV1‐47 0.0144 4.7237 4.6288 0.9943 0.0017 0.0026 Immunoglobulin superfamily member 8 IGSF8 ‐12.4505 ‐1.2613 7.2451 0.0000 0.3862 0.0000 Interleukin enhancer‐binding factor 2 ILF2 1.3024 ‐1.8736 ‐2.7272 0.3887 0.1800 0.0563 Isoform 7 of Interleukin enhancer‐ binding factor 3 ILF3 5.2008 ‐0.7165 ‐4.2473 0.0007 0.6542 0.0049 Cluster of Isoform 2 of Integrin‐ linked protein kinase ILK 1.2781 ‐0.6030 ‐1.4630 0.3988 0.7088 0.3301 Isoform 4 of MIC complex subunit MIC60 IMMT 0.9859 0.0429 ‐0.6296 0.5387 0.9754 0.7082 Inverted formin‐2 INF2 ‐1.5903 ‐0.5677 0.5262 0.2805 0.7246 0.7627 Inhibin beta E chain INHBE ‐16.4546 0.1491 11.3583 0.0000 0.9223 0.0000 Isoform 2 of Importin‐5 IPO5 2.5658 1.2740 ‐0.4973 0.0685 0.3819 0.7743 Importin‐9 IPO9 ‐0.7507 ‐1.5564 ‐1.0168 0.6626 0.2687 0.5163 Ras GTPase‐activating‐like protein IQGAP1 IQGAP1 2.5915 1.0914 ‐0.6941 0.0665 0.4660 0.6718 Ras GTPase‐activating‐like protein IQGAP2 IQGAP2 ‐2.1944 ‐3.4163 ‐1.8595 0.1211 0.0147 0.2058 Ubiquitin‐like protein ISG15 ISG15 16.7299 10.4144 ‐1.1728 0.0000 0.0000 0.4501 Isochorismatase domain‐ containing protein 2 ISOC2 ‐5.0430 ‐3.5594 ‐0.0591 0.0009 0.0118 0.9696 Isoform 2 of IST1 homolog IST1 4.0803 2.8564 0.0247 0.0050 0.0389 0.9870

Inositol‐3‐phosphate synthase 1 ISYNA1 2.3462 2.1163 0.4795 0.0968 0.1236 0.7812 E3 ubiquitin‐protein ligase Itchy homolog ITCH ‐0.3530 ‐0.8992 ‐0.6425 0.8482 0.5581 0.7021 Integrin alpha‐1 ITGA1 1.1813 ‐0.8654 ‐1.6547 0.4410 0.5784 0.2648 Cluster of Integrin alpha‐3 ITGA3 ‐0.7663 ‐3.7357 ‐3.1463 0.6530 0.0089 0.0289 Isoform Alpha‐6X1B of Integrin alpha‐6 ITGA6 2.7563 1.1219 ‐0.7765 0.0508 0.4493 0.6381 Integrin alpha‐8 ITGA8 ‐0.1795 0.7404 0.8494 0.9267 0.6452 0.6051 Isoform 3 of Integrin alpha‐V ITGAV ‐0.9487 ‐1.7560 ‐1.0779 0.5564 0.2090 0.4902 Integrin beta‐1 ITGB1 ‐1.7396 ‐4.9173 ‐3.6434 0.2309 0.0012 0.0137 Cluster of Integrin beta‐3 ITGB3 0.4522 0.6826 0.3622 0.8004 0.6709 0.8395 Integrin beta‐5 ITGB5 1.2311 ‐2.0892 ‐2.8904 0.4192 0.1282 0.0427 Inter‐alpha‐trypsin inhibitor heavy chain H1 ITIH1 2.7568 1.1851 ‐0.7147 0.0508 0.4198 0.6617 Inter‐alpha‐trypsin inhibitor heavy chain H2 ITIH2 0.1183 1.6177 1.5079 0.9493 0.2497 0.3152 Cluster of Isoform 2 of Inter‐alpha‐ trypsin inhibitor heavy chain H4 ITIH4 ‐3.5376 ‐0.9878 1.4405 0.0132 0.5144 0.3391 Cluster of Inter‐alpha‐trypsin inhibitor heavy chain H5 ITIH5 1.0178 ‐1.9466 ‐2.6051 0.5246 0.1611 0.0677 Integral membrane protein 2B ITM2B ‐2.5461 ‐4.1552 ‐2.3455 0.0704 0.0044 0.0990 Isoform 2 of Inosine triphosphate pyrophosphatase ITPA 7.5581 4.2055 ‐1.0203 0.0000 0.0040 0.5155 Junctional protein associated with coronary artery disease JCAD 0.9106 ‐1.1880 ‐1.7871 0.5727 0.4196 0.2254 Junction plakoglobin JUP 0.5296 1.3386 0.9536 0.7673 0.3555 0.5431 Cluster of KN motif and ankyrin repeat domain‐containing protein 2 KANK2 ‐2.2695 ‐2.6207 ‐1.0270 0.1082 0.0570 0.5118 Isoform 2 of KN motif and ankyrin repeat domain‐containing protein 3 KANK3 0.2588 ‐2.0722 ‐2.2112 0.8859 0.1311 0.1235 Lysine‐‐tRNA ligase KARS1 ‐0.6117 ‐0.0151 0.4020 0.7337 0.9903 0.8208 Kelch repeat and BTB domain‐ containing protein 11 KBTBD11 ‐4.5833 ‐1.1881 1.9563 0.0020 0.4196 0.1798 BTB/POZ domain‐containing protein KCTD12 KCTD12 ‐1.9061 ‐2.1967 ‐0.8583 0.1861 0.1116 0.6017 Isoform 2 of KH domain‐ containing, RNA‐binding, signal transduction‐associated protein 1 KHDRBS1 ‐0.4787 ‐3.4827 ‐3.0938 0.7866 0.0131 0.0312 Isoform A of Ketohexokinase KHK ‐3.4401 ‐1.4490 0.9211 0.0157 0.3103 0.5616 Far upstream element‐binding protein 2 KHSRP 2.0416 ‐0.4919 ‐1.8742 0.1525 0.7693 0.2018 Kinesin‐1 heavy chain KIF5B ‐0.0967 ‐1.4817 ‐1.3891 0.9585 0.2987 0.3588 Isoform 2 of Kin of IRRE‐like protein 1 KIRREL1 ‐1.0525 ‐6.7719 ‐5.9327 0.5079 0.0001 0.0003 Kininogen‐1 KNG1 3.5564 2.3959 ‐0.0705 0.0129 0.0816 0.9647 Importin subunit beta‐1 KPNB1 1.9843 0.4470 ‐0.9132 0.1659 0.7925 0.5671 Keratinocyte proline‐rich protein KPRP ‐1.8426 ‐0.5852 0.6809 0.2017 0.7177 0.6769 Keratin, type II cytoskeletal 1 KRT1 ‐0.2491 0.3880 0.5508 0.8898 0.8185 0.7486

Keratin, type I cytoskeletal 10 KRT10 ‐0.7216 0.0323 0.5234 0.6767 0.9822 0.7637 Cluster of Keratin, type I cytoskeletal 14 KRT14 0.1070 0.7107 0.6249 0.9529 0.6575 0.7108 Keratin, type I cytoskeletal 18 KRT18 ‐0.4941 3.6309 3.9021 0.7785 0.0105 0.0086 Cluster of Keratin, type II cytoskeletal 2 epidermal KRT2 ‐0.8705 ‐0.0892 0.5056 0.5979 0.9509 0.7716 Keratin, type I cytoskeletal 27 KRT27 0.7880 4.9941 4.3672 0.6411 0.0011 0.0040 Cluster of Keratin, type I cuticular Ha1 KRT31 14.5973 12.0663 1.9025 0.0000 0.0000 0.1931 Keratin, type I cuticular Ha4 KRT34 15.7543 19.7234 8.6332 0.0000 0.0000 0.0000 Keratin, type I cuticular Ha6 KRT36 23.3934 14.5084 ‐1.6929 0.0000 0.0000 0.2532 Keratin, type II cytoskeletal 4 KRT4 0.3050 1.5382 1.3026 0.8694 0.2755 0.3922 Cluster of Keratin, type II cytoskeletal 71 KRT71 1.1240 4.0614 3.2223 0.4705 0.0051 0.0258 Keratin, type II cytoskeletal 1b KRT77 ‐1.1207 15.5805 16.0633 0.4705 0.0000 0.0000 Keratin, type II cytoskeletal 78 KRT78 ‐0.1111 ‐0.5625 ‐0.4767 0.9517 0.7281 0.7812 Cluster of Isoform 2 of Keratin, type II cytoskeletal 8 KRT8 ‐0.2275 9.7466 9.7260 0.9009 0.0000 0.0000 Isoform 2 of Keratin, type II cytoskeletal 80 KRT80 ‐6.3298 ‐0.3828 3.9372 0.0001 0.8208 0.0081 Cluster of Keratin, type II cuticular Hb5 KRT85 12.7272 9.8921 1.0417 0.0000 0.0000 0.5070 Keratin, type I cytoskeletal 9 KRT9 0.0029 0.5839 0.5713 0.9997 0.7182 0.7372 Keratin‐associated protein 13‐1 KRTAP13‐1 25.8063 16.4066 ‐1.4730 0.0000 0.0000 0.3265 Keratin‐associated protein 13‐2 KRTAP13‐2 23.5866 16.5373 0.1678 0.0000 0.0000 0.9236 Keratin‐associated protein 13‐4 KRTAP13‐4 24.9529 17.0044 ‐0.3046 0.0000 0.0000 0.8712 Keratin‐associated protein 3‐3 KRTAP3‐3 30.8954 23.1512 1.6823 0.0000 0.0000 0.2552 Isoform 2 of Kinectin KTN1 2.0289 0.6296 ‐0.7642 0.1553 0.6991 0.6422 Laminin subunit alpha‐2 LAMA2 0.2724 1.2101 1.0027 0.8794 0.4077 0.5203 Cluster of Laminin subunit alpha‐3 LAMA3 3.6474 2.5174 ‐0.0133 0.0111 0.0669 0.9917 Isoform 2 of Laminin subunit alpha‐4 LAMA4 ‐1.1593 ‐1.2681 ‐0.4553 0.4519 0.3841 0.7900 Laminin subunit alpha‐5 LAMA5 1.4538 ‐0.3257 ‐1.3104 0.3284 0.8443 0.3889 Laminin subunit beta‐1 LAMB1 3.4717 2.7359 0.3211 0.0148 0.0473 0.8602 Laminin subunit beta‐2 LAMB2 2.0334 0.3035 ‐1.0875 0.1545 0.8527 0.4869 Laminin subunit gamma‐1 LAMC1 2.3973 0.2642 ‐1.3740 0.0891 0.8703 0.3630 Cluster of Lysosome‐associated membrane glycoprotein 1 LAMP1 1.3683 ‐0.1656 ‐1.0950 0.3601 0.9144 0.4839 Isoform LAMP‐2B of Lysosome‐ associated membrane glycoprotein 2 LAMP2 4.7113 1.5824 ‐1.6563 0.0016 0.2603 0.2645 Ragulator complex protein LAMTOR1 LAMTOR1 6.4316 3.5947 ‐0.8525 0.0001 0.0112 0.6033 Glutathione S‐transferase LANCL1 LANCL1 0.4529 ‐7.4603 ‐7.6344 0.8004 0.0000 0.0000 Cytosol aminopeptidase LAP3 2.1271 ‐1.1699 ‐2.5982 0.1336 0.4266 0.0681 Isoform 2 of Leucine‐‐tRNA ligase, cytoplasmic LARS ‐0.5142 ‐1.0798 ‐0.7099 0.7750 0.4710 0.6631 LIM and SH3 domain protein 1 LASP1 ‐0.6169 ‐1.8116 ‐1.3586 0.7309 0.1958 0.3702

Lipopolysaccharide‐binding protein LBP ‐14.0589 ‐2.2192 7.4003 0.0000 0.1077 0.0000 Neutrophil gelatinase‐associated lipocalin LCN2 12.9695 7.2246 ‐1.7428 0.0000 0.0000 0.2362 Plastin‐2 LCP1 ‐0.4712 ‐0.4760 ‐0.1463 0.7910 0.7782 0.9298 Cluster of Isoform 3 of L‐lactate dehydrogenase A chain LDHA 0.1541 ‐0.9874 ‐1.0746 0.9378 0.5144 0.4914 L‐lactate dehydrogenase B chain LDHB 1.6289 ‐2.9290 ‐3.9862 0.2684 0.0339 0.0075 Cluster of LEM domain‐containing protein 2 LEMD2 1.7687 3.8672 2.5924 0.2212 0.0072 0.0687 Galectin‐1 LGALS1 0.4214 0.3325 0.0394 0.8143 0.8414 0.9789 Galectin‐3 LGALS3 6.7819 4.4861 ‐0.2158 0.0000 0.0025 0.9016 Galectin‐3‐binding protein LGALS3BP 0.1701 ‐2.4512 ‐2.5229 0.9303 0.0749 0.0754 Galectin‐7 LGALS7 9.8737 5.8830 ‐0.9508 0.0000 0.0003 0.5439 Phospholysine phosphohistidine inorganic pyrophosphate phosphatase LHPP 0.2992 ‐9.4512 ‐9.4848 0.8710 0.0000 0.0000 Protein lin‐7 homolog C LIN7C ‐19.5131 ‐10.0691 3.4083 0.0000 0.0000 0.0194 Protein ERGIC‐53 LMAN1 6.3090 2.7213 ‐1.6267 0.0001 0.0485 0.2744 Cluster of Prelamin‐A/C LMNA 1.9512 0.3704 ‐0.9658 0.1736 0.8259 0.5363 Lamin‐B1 LMNB1 3.2880 5.9419 3.5945 0.0208 0.0002 0.0149 Lamin‐B2 LMNB2 2.6161 1.1413 ‐0.6618 0.0638 0.4411 0.6894 Cluster of Isoform 5 of LIM domain only protein 7 LMO7 ‐0.0272 ‐0.3820 ‐0.3566 0.9851 0.8208 0.8423 Apolipoprotein(a) LPA ‐1.6157 3.9730 5.0024 0.2711 0.0060 0.0014 Lipoma‐preferred partner LPP ‐0.0899 ‐2.0419 ‐1.9438 0.9618 0.1380 0.1830 Leucine‐rich alpha‐2‐glycoprotein LRG1 ‐0.6880 6.0730 6.4324 0.6922 0.0002 0.0001 Prolow‐density lipoprotein receptor‐related protein 1 LRP1 ‐1.0807 ‐0.1177 0.6208 0.4935 0.9410 0.7123 Low‐density lipoprotein receptor‐ related protein 2 LRP2 0.6401 ‐0.6815 ‐1.1053 0.7156 0.6709 0.4784 Leucine‐rich PPR motif‐containing protein, mitochondrial LRPPRC ‐1.4437 ‐0.8033 0.1949 0.3307 0.6085 0.9094 Isoform 2 of Leucine‐rich repeat‐ containing protein 15 LRRC15 20.6156 12.8949 ‐1.3846 0.0000 0.0000 0.3604 Leucine‐rich repeat‐containing protein 47 LRRC47 0.6662 5.6774 5.1211 0.7032 0.0004 0.0011 Isoform 2 of Leucine‐rich repeat flightless‐interacting protein 1 LRRFIP1 ‐1.0509 ‐0.2370 0.4833 0.5085 0.8846 0.7807 U6 snRNA‐associated Sm‐like protein LSm8 LSM8 9.5714 6.0697 ‐0.5615 0.0000 0.0002 0.7436 Cluster of Leukotriene A‐4 hydrolase LTA4H 6.8081 3.7313 ‐0.9748 0.0000 0.0090 0.5320 Lactotransferrin LTF 2.9840 1.0045 ‐1.0469 0.0349 0.5059 0.5056 Lumican LUM 0.2552 ‐0.4992 ‐0.6641 0.8882 0.7672 0.6881 Isoform 2 of Acyl‐protein thioesterase 1 LYPLA1 3.2022 0.9358 ‐1.2630 0.0240 0.5409 0.4106 Lysozyme C LYZ 1.2684 ‐0.7326 ‐1.5837 0.4030 0.6487 0.2875 Microtubule‐actin cross‐linking factor 1, isoforms 1/2/3/5 MACF1 ‐2.8233 ‐0.9111 1.0291 0.0455 0.5526 0.5114

Membrane‐associated guanylate kinase, WW and PDZ domain‐ containing protein 2 MAGI2 ‐1.6893 ‐5.9274 ‐4.6696 0.2471 0.0003 0.0024 Mesencephalic astrocyte‐derived neurotrophic factor MANF 12.8001 8.1338 ‐0.7346 0.0000 0.0000 0.6551 Cluster of Amine oxidase [flavin‐ containing] B MAOB ‐0.5120 2.2696 2.5776 0.7755 0.0991 0.0698 Isoform 2 of Microtubule‐ associated protein 1A MAP1A ‐0.5321 1.2982 1.6374 0.7673 0.3714 0.2711 Microtubule‐associated protein 1B MAP1B ‐1.1349 ‐0.1383 0.6375 0.4663 0.9283 0.7047 Microtubule‐associated protein 1S MAP1S ‐0.1424 ‐4.1345 ‐3.9629 0.9417 0.0045 0.0078 Isoform 3 of Microtubule‐ associated protein 2 MAP2 ‐0.3426 3.5373 3.7070 0.8507 0.0122 0.0122 Cluster of Isoform 4 of Microtubule‐associated protein 4 MAP4 1.5524 ‐2.5544 ‐3.5661 0.2939 0.0632 0.0155 Microtubule‐associated protein 6 MAP6 ‐4.1974 0.7073 3.5546 0.0041 0.6575 0.0157 Microtubule‐associated protein RP/EB family member 1 MAPRE1 ‐0.1007 ‐3.5075 ‐3.3757 0.9559 0.0128 0.0201 Cluster of Microtubule‐associated protein tau MAPT 0.2449 ‐3.9441 ‐4.0399 0.8913 0.0063 0.0069 Mitochondrial amidoxime reducing component 2 MARC2 ‐5.8633 0.9130 4.8917 0.0002 0.5526 0.0017 Microtubule‐associated serine/threonine‐protein kinase 4 MAST4 ‐3.4999 ‐0.3065 2.0838 0.0140 0.8524 0.1477 Matrin‐3 MATR3 ‐0.3945 ‐1.8082 ‐1.5068 0.8252 0.1960 0.3152 Cluster of Cell surface glycoprotein MUC18 MCAM ‐0.1379 2.3320 2.3839 0.9426 0.0903 0.0931 Isoform 3 of Malate dehydrogenase, cytoplasmic MDH1 0.2983 ‐4.3578 ‐4.4826 0.8710 0.0031 0.0034 Malate dehydrogenase, mitochondrial MDH2 0.8148 ‐0.8765 ‐1.4158 0.6271 0.5706 0.3495 Cluster of Isoform 3 of Methionine aminopeptidase 2 METAP2 0.6636 3.1499 2.6409 0.7032 0.0230 0.0635 Lactadherin MFGE8 0.4277 5.1396 4.7556 0.8134 0.0008 0.0021 Macrophage migration inhibitory factor MIF ‐0.9803 ‐3.0249 ‐2.3024 0.5403 0.0287 0.1056 Neprilysin MME ‐4.1673 ‐5.0311 ‐2.1009 0.0043 0.0010 0.1442 Matrix metalloproteinase‐9 MMP9 1.7666 1.6347 0.4015 0.2216 0.2445 0.8208 Multimerin‐2 MMRN2 0.3466 ‐1.5398 ‐1.7483 0.8495 0.2752 0.2354 Mannosyl‐oligosaccharide glucosidase MOGS ‐0.8675 ‐2.2219 ‐1.5908 0.5997 0.1074 0.2858 Isoform H7 of Myeloperoxidase MPO 3.0059 0.5514 ‐1.5068 0.0336 0.7348 0.3152 Isoform 3 of 55 kDa erythrocyte membrane protein MPP1 0.5409 ‐0.2254 ‐0.5899 0.7660 0.8894 0.7284 MAGUK p55 subfamily member 5 MPP5 ‐1.0424 ‐5.7269 ‐4.9134 0.5122 0.0003 0.0016 Isoform 2 of Myosin phosphatase Rho‐interacting protein MPRIP 3.1908 1.4081 ‐0.7914 0.0243 0.3242 0.6305 Isoform 2 of 3‐mercaptopyruvate sulfurtransferase MPST ‐6.5251 ‐0.5313 3.9243 0.0001 0.7482 0.0083 C‐type mannose receptor 2 MRC2 1.8085 ‐0.4969 ‐1.7202 0.2116 0.7678 0.2436

Mas‐related G‐protein coupled receptor member F MRGPRF ‐1.8975 ‐0.7772 0.5297 0.1884 0.6256 0.7603 DNA mismatch repair protein Msh2 MSH2 ‐1.1989 0.5866 1.3929 0.4349 0.7172 0.3581 Isoform 2 of RNA‐binding protein Musashi homolog 2 MSI2 11.2396 5.4063 ‐2.3496 0.0000 0.0005 0.0984 Moesin MSN ‐0.9677 ‐3.0995 ‐2.3843 0.5469 0.0251 0.0931 Cytochrome c oxidase subunit 2 MT‐CO2 ‐3.2387 ‐0.3480 1.8651 0.0227 0.8338 0.2044 Protein LYRIC MTDH ‐0.7747 1.2805 1.7853 0.6487 0.3789 0.2255 C‐1‐tetrahydrofolate synthase, cytoplasmic MTHFD1 ‐0.1233 ‐3.6316 ‐3.4822 0.9483 0.0105 0.0176 Myotubularin MTM1 ‐0.4369 ‐0.4169 ‐0.1117 0.8090 0.8015 0.9477 Myotrophin MTPN 11.8925 6.9262 ‐1.3020 0.0000 0.0001 0.3922 Major vault protein MVP 2.3051 1.5326 ‐0.0657 0.1027 0.2778 0.9671 Interferon‐induced GTP‐binding protein Mx2 MX2 1.2766 3.8722 2.9325 0.3989 0.0071 0.0403 Myeloid‐associated differentiation marker MYADM 7.6443 5.4026 0.0966 0.0000 0.0006 0.9557 Isoform 4 of Myosin‐10 MYH10 ‐0.5745 ‐0.6211 ‐0.2185 0.7463 0.7035 0.9013 Isoform 2 of Myosin‐11 MYH11 2.2956 15.6269 13.7811 0.1042 0.0000 0.0000 Myosin‐13 MYH13 ‐3.6642 ‐2.1626 0.3731 0.0107 0.1168 0.8353 Myosin‐9 MYH9 ‐1.6839 ‐3.2415 ‐2.0357 0.2489 0.0198 0.1591 Cluster of Myosin regulatory light chain 12B MYL12B ‐0.6741 ‐0.9498 ‐0.4734 0.7012 0.5348 0.7816 Cluster of Myosin light polypeptide 6 MYL6 ‐0.6894 ‐1.6171 ‐1.1182 0.6916 0.2497 0.4734 Isoform 2 of Myosin light chain kinase, smooth muscle MYLK ‐2.5245 ‐2.0356 ‐0.2787 0.0727 0.1394 0.8827 Isoform 2 of Unconventional myosin‐Ib MYO1B 0.9441 ‐1.1662 ‐1.7884 0.5587 0.4280 0.2253 Isoform 3 of Unconventional myosin‐Ic MYO1C ‐1.3600 ‐2.7517 ‐1.7754 0.3639 0.0463 0.2281 Unconventional myosin‐Id MYO1D ‐1.5224 0.1008 1.1363 0.3039 0.9502 0.4642 Unconventional myosin‐Ie MYO1E 1.1968 ‐0.6872 ‐1.4903 0.4357 0.6691 0.3225 Unconventional myosin‐If MYO1F ‐3.1993 ‐0.2888 1.8963 0.0241 0.8588 0.1949 Cluster of Isoform 6 of Myoferlin MYOF ‐0.7010 3.7241 4.1347 0.6868 0.0090 0.0059 Nascent polypeptide‐associated complex subunit alpha, muscle‐ specific form NACA 1.8781 1.0544 ‐0.2443 0.1915 0.4812 0.8897 Isoform 2 of NEDD8‐activating enzyme E1 regulatory subunit NAE1 ‐0.5060 ‐1.8200 ‐1.4425 0.7769 0.1938 0.3384 Isoform 2 of N‐acetyl‐D‐ glucosamine kinase NAGK 0.9842 ‐0.7569 ‐1.4138 0.5387 0.6367 0.3501 Sialic acid synthase NANS ‐0.4014 0.2288 0.4982 0.8234 0.8880 0.7743 Isoform 2 of Nucleosome assembly protein 1‐like 1 NAP1L1 ‐2.1303 8.2887 9.5910 0.1330 0.0000 0.0000 Alpha‐soluble NSF attachment protein NAPA 3.5920 1.9958 ‐0.4877 0.0121 0.1491 0.7783 Isoform 3 of Nicotinate phosphoribosyltransferase NAPRT 3.9468 1.7763 ‐0.9450 0.0063 0.2037 0.5471 NAD(P)H‐hydrate epimerase NAXE ‐3.5402 ‐0.6493 1.7746 0.0132 0.6886 0.2281

Isoform 2 of Nck‐associated protein 1 NCKAP1 ‐0.3625 ‐0.0894 0.1592 0.8423 0.9509 0.9243 Nucleolin NCL 2.4457 ‐1.7961 ‐3.4302 0.0823 0.1993 0.0189 Protein NDRG1 NDRG1 ‐0.4589 ‐4.5992 ‐4.2037 0.7996 0.0020 0.0053 Isoform 2 of Protein NDRG2 NDRG2 0.1192 ‐4.7036 ‐4.7001 0.9493 0.0017 0.0023 Isoform 2 of NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 10, mitochondrial NDUFA10 ‐6.9077 ‐1.5850 3.1504 0.0000 0.2596 0.0288 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 2 NDUFA2 13.0288 9.7725 0.7188 0.0000 0.0000 0.6606 NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 9, mitochondrial NDUFA9 1.4997 0.1999 ‐0.8256 0.3129 0.9001 0.6171 Isoform 2 of NADH‐ubiquinone oxidoreductase 75 kDa subunit, mitochondrial NDUFS1 ‐1.2457 2.4394 3.2442 0.4110 0.0763 0.0248 Isoform 2 of NADH dehydrogenase [ubiquinone] iron‐sulfur protein 2, mitochondrial NDUFS2 ‐0.3714 ‐1.2436 ‐0.9681 0.8367 0.3939 0.5352 NADH dehydrogenase [ubiquinone] iron‐sulfur protein 3, mitochondrial NDUFS3 2.4766 10.6524 8.7730 0.0788 0.0000 0.0000 Isoform 2 of NADH dehydrogenase [ubiquinone] flavoprotein 1, mitochondrial NDUFV1 ‐5.9006 0.2494 4.2655 0.0002 0.8771 0.0048 Isoform 2 of Nebulette NEBL ‐4.1455 ‐4.8806 ‐1.9680 0.0045 0.0013 0.1770 Cluster of Neurofilament heavy polypeptide NEFH 17.5472 11.6564 ‐0.5101 0.0000 0.0000 0.7702 Nestin NES ‐2.1950 ‐1.6018 ‐0.0773 0.1211 0.2551 0.9633 Isoform 11 of Neurofascin NFASC 1.7975 0.4759 ‐0.7575 0.2140 0.7782 0.6425 Isoform 2 of NHL repeat‐ containing protein 2 NHLRC2 0.0417 ‐4.8345 ‐4.7758 0.9771 0.0014 0.0020 Isoform 2 of Protein Niban 2 NIBAN2 1.5668 3.9387 2.8001 0.2893 0.0063 0.0499 Nidogen‐1 NID1 2.0869 ‐0.2896 ‐1.7064 0.1430 0.8588 0.2488 Nidogen‐2 NID2 1.4348 ‐0.3582 ‐1.3294 0.3342 0.8307 0.3815 Protein NipSnap homolog 3A NIPSNAP3A ‐1.0630 ‐7.8021 ‐6.9372 0.5027 0.0000 0.0001 Isoform 1 of Deaminated glutathione amidase NIT1 ‐0.3566 ‐0.1470 0.0986 0.8459 0.9226 0.9548 Omega‐amidase NIT2 NIT2 ‐7.0028 ‐7.1106 ‐2.2108 0.0000 0.0000 0.1235 Neurolysin, mitochondrial NLN 2.6635 0.6701 ‐1.1569 0.0595 0.6765 0.4556 Isoform 3 of Nucleoside diphosphate kinase B NME2 0.7698 1.3072 0.7591 0.6521 0.3689 0.6422 NAD(P) transhydrogenase, mitochondrial NNT 2.2113 1.3213 ‐0.2093 0.1188 0.3636 0.9038 Nodal modulator 3 NOMO3 0.5229 ‐0.6811 ‐1.0251 0.7703 0.6709 0.5126 Non‐POU domain‐containing octamer‐binding protein NONO 0.2644 ‐0.0151 ‐0.1950 0.8833 0.9903 0.9094 Neurogenic locus notch homolog protein 4 NOTCH4 0.4484 ‐0.7214 ‐1.0139 0.8022 0.6515 0.5173

Puromycin‐sensitive aminopeptidase NPEPPS ‐0.2073 ‐1.8579 ‐1.6831 0.9128 0.1842 0.2552 Isoform 2 of Nephrin NPHS1 0.3107 ‐1.7504 ‐1.9306 0.8652 0.2101 0.1868 Podocin NPHS2 ‐1.2556 ‐3.6292 ‐2.7083 0.4058 0.0105 0.0577 ‐ Isoform 2 of Nucleophosmin NPM1 18.8567 ‐0.8130 13.6470 0.0000 0.6054 0.0000 Cluster of Isoform 6 of Nephronectin NPNT ‐1.3459 0.5785 1.4851 0.3696 0.7196 0.3234 Ribosyldihydronicotinamide dehydrogenase [quinone] NQO2 ‐0.0660 ‐8.3478 ‐8.1524 0.9677 0.0000 0.0000 Isoform 2 of Nuclear receptor‐ interacting protein 2 NRIP2 ‐1.8310 ‐1.0362 0.2301 0.2049 0.4901 0.8970 Isoform 2 of Neuropilin‐1 NRP1 ‐4.0827 0.0316 2.8129 0.0050 0.9822 0.0489 Isoform 3 of NSFL1 cofactor p47 NSFL1C 1.0633 ‐0.3490 ‐1.0672 0.5027 0.8337 0.4956 5'(3')‐deoxyribonucleotidase, cytosolic type NT5C ‐0.9320 0.1702 0.8022 0.5618 0.9131 0.6276 Cytosolic purine 5'‐nucleotidase NT5C2 0.2915 0.7771 0.5644 0.8710 0.6256 0.7424 Isoform 3 of Netrin‐4 NTN4 ‐1.0614 2.7772 3.4504 0.5029 0.0447 0.0183 Nucleobindin‐1 NUCB1 1.3371 0.4368 ‐0.4821 0.3733 0.7977 0.7808 U8 snoRNA‐decapping enzyme NUDT16 1.8019 ‐1.2984 ‐2.5028 0.2130 0.3714 0.0779 Nucleoredoxin NXN 2.2416 1.3986 ‐0.1540 0.1130 0.3284 0.9252 Isoform p41 of 2'‐5'‐ oligoadenylate synthase 1 OAS1 ‐4.8176 ‐0.6554 2.6390 0.0013 0.6868 0.0636 2'‐5'‐oligoadenylate synthase 2 OAS2 1.9902 3.1768 1.7635 0.1644 0.0221 0.2307 Isoform B of Inositol polyphosphate 5‐phosphatase OCRL OCRL ‐0.2369 1.1819 1.3220 0.8958 0.4208 0.3849 Isoform 2 of 2‐oxoglutarate dehydrogenase, mitochondrial OGDH 0.5035 0.8773 0.5184 0.7769 0.5705 0.7672 Obg‐like ATPase 1 OLA1 0.8632 ‐0.1887 ‐0.7735 0.6018 0.9044 0.6387 Isoform 2 of Optineurin OPTN ‐0.9721 ‐2.0822 ‐1.3823 0.5441 0.1294 0.3607 Alpha‐1‐acid glycoprotein 1 ORM1 0.2492 4.6008 4.3480 0.8898 0.0020 0.0042 Alpha‐1‐acid glycoprotein 2 ORM2 1.5774 7.6639 6.4510 0.2854 0.0000 0.0001 Osteoclast‐stimulating factor 1 OSTF1 ‐2.0582 ‐3.2641 ‐1.8028 0.1487 0.0191 0.2218 Ubiquitin thioesterase OTUB1 OTUB1 ‐1.2979 3.7608 4.5774 0.3904 0.0086 0.0029 Succinyl‐CoA:3‐ketoacid coenzyme A transferase 1, mitochondrial OXCT1 6.7689 2.7375 ‐1.9241 0.0000 0.0473 0.1883 Protein disulfide‐isomerase P4HB 2.7302 1.1647 ‐0.7166 0.0532 0.4285 0.6617 Isoform 2 of Proliferation‐ associated protein 2G4 PA2G4 ‐2.9167 2.1304 4.0794 0.0390 0.1214 0.0064 Cluster of Polyadenylate‐binding protein 3 PABPC3 13.6214 8.9751 ‐0.4681 0.0000 0.0000 0.7848 Cluster of Platelet‐activating factor acetylhydrolase IB subunit alpha PAFAH1B1 2.7356 4.4649 2.5205 0.0528 0.0026 0.0756 Cluster of Platelet‐activating factor acetylhydrolase IB subunit beta PAFAH1B2 0.1463 ‐1.5869 ‐1.6580 0.9399 0.2591 0.2641 Isoform 2 of Serine/threonine‐ protein kinase PAK 1 PAK1 4.0378 2.3383 ‐0.4552 0.0054 0.0898 0.7900

Palladin PALLD ‐0.3864 ‐0.8548 ‐0.5760 0.8274 0.5840 0.7344 Cluster of Papilin PAPLN 0.6166 ‐0.9353 ‐1.3386 0.7309 0.5409 0.3790 Bifunctional 3'‐phosphoadenosine 5'‐phosphosulfate synthase 1 PAPSS1 0.3474 ‐0.1523 ‐0.3863 0.8495 0.9204 0.8275 Isoform 2 of Partitioning defective 3 homolog B PARD3B ‐1.9711 ‐4.3909 ‐2.9687 0.1697 0.0029 0.0386 Protein/nucleic acid deglycase DJ‐ 1 PARK7 ‐0.2093 ‐2.8388 ‐2.6451 0.9119 0.0401 0.0634 Poly [ADP‐ribose] polymerase 1 PARP1 4.1385 1.8512 ‐1.0021 0.0045 0.1858 0.5203 Alpha‐parvin PARVA ‐0.9902 ‐3.6007 ‐2.8611 0.5366 0.0111 0.0448 InaD‐like protein PATJ 0.8268 1.4799 0.8898 0.6220 0.2992 0.5808 PRKC apoptosis WT1 regulator protein PAWR ‐0.9423 6.8431 7.3619 0.5588 0.0001 0.0000 Phenazine biosynthesis‐like domain‐containing protein PBLD 0.2316 ‐9.7399 ‐9.7222 0.8991 0.0000 0.0000 Pyruvate carboxylase, mitochondrial PC ‐0.3122 ‐0.7235 ‐0.4977 0.8647 0.6504 0.7743 Pterin‐4‐alpha‐carbinolamine dehydratase PCBD1 ‐1.6004 0.4398 1.5224 0.2765 0.7972 0.3107 Poly(rC)‐binding protein 1 PCBP1 ‐0.3131 ‐1.7927 ‐1.5471 0.8646 0.2000 0.3008 Isoform 2 of Poly(rC)‐binding protein 2 PCBP2 1.0344 ‐0.3001 ‐0.9995 0.5158 0.8549 0.5208 Isoform 2 of Propionyl‐CoA carboxylase beta chain, mitochondrial PCCB 1.6938 ‐0.6531 ‐1.7954 0.2459 0.6880 0.2240 Phosphoenolpyruvate carboxykinase [GTP], mitochondrial PCK2 ‐22.5599 ‐10.8067 4.7600 0.0000 0.0000 0.0021 Isoform 2 of Protein‐L‐ isoaspartate(D‐aspartate) O‐ methyltransferase PCMT1 ‐18.3185 ‐14.1704 ‐1.4331 0.0000 0.0000 0.3427 Prenylcysteine oxidase 1 PCYOX1 0.5072 ‐0.4216 ‐0.7597 0.7769 0.7997 0.6422 Programmed cell death protein 10 PDCD10 ‐7.2889 ‐0.2537 4.7174 0.0000 0.8763 0.0023 Isoform 2 of Programmed cell death protein 6 PDCD6 ‐0.0695 ‐2.8163 ‐2.7182 0.9677 0.0416 0.0572 Isoform 2 of Programmed cell death 6‐interacting protein PDCD6IP ‐1.2792 ‐2.5782 ‐1.6601 0.3988 0.0609 0.2636 Platelet‐derived growth factor receptor beta PDGFRB ‐0.4376 1.7412 2.0080 0.8090 0.2116 0.1659 Isoform 2 of Pyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrial PDHA1 ‐5.2044 ‐0.6120 2.9453 0.0007 0.7072 0.0401 Isoform 3 of Pyruvate dehydrogenase E1 component subunit beta, mitochondrial PDHB 1.0238 4.3201 3.5447 0.5219 0.0033 0.0159 Protein disulfide‐isomerase A3 PDIA3 1.6213 ‐1.3089 ‐2.3900 0.2695 0.3684 0.0931 Protein disulfide‐isomerase A4 PDIA4 1.1694 ‐2.5730 ‐3.3234 0.4468 0.0614 0.0220 Isoform 2 of Protein disulfide‐ isomerase A6 PDIA6 4.0557 ‐0.4479 ‐3.2033 0.0052 0.7924 0.0265 PDZ and LIM domain protein 1 PDLIM1 ‐0.4008 ‐0.6287 ‐0.3442 0.8234 0.6992 0.8452 Cluster of Isoform 5 of PDZ and LIM domain protein 2 PDLIM2 ‐3.0443 ‐2.3248 ‐0.2086 0.0315 0.0913 0.9038

Cluster of PDZ and LIM domain protein 5 PDLIM5 ‐3.4905 ‐3.4863 ‐1.0451 0.0143 0.0131 0.5063 Cluster of Isoform 2 of PDZ and LIM domain protein 7 PDLIM7 ‐1.4464 ‐1.7994 ‐0.7814 0.3302 0.1985 0.6354 Pyridoxal kinase PDXK 1.4563 ‐1.1392 ‐2.1110 0.3279 0.4420 0.1423 Phosphatidylethanolamine‐ binding protein 1 PEBP1 ‐2.2864 ‐5.2361 ‐3.5838 0.1052 0.0007 0.0151 Cluster of Isoform Delta13 of Platelet endothelial cell adhesion molecule PECAM1 4.9754 0.9132 ‐2.4934 0.0010 0.5526 0.0790 Peflin PEF1 ‐1.3189 ‐0.0772 0.8229 0.3812 0.9575 0.6186 Isoform 2 of Xaa‐Pro dipeptidase PEPD ‐2.9814 ‐2.1555 ‐0.0852 0.0350 0.1180 0.9607 Isoform 2 of ATP‐dependent 6‐ phosphofructokinase, liver type PFKL 1.5357 ‐0.4737 ‐1.5116 0.3002 0.7794 0.3145 ATP‐dependent 6‐ phosphofructokinase, platelet type PFKP 3.5945 2.2577 ‐0.2322 0.0121 0.1008 0.8968 Profilin‐1 PFN1 2.6301 0.0504 ‐1.7426 0.0626 0.9716 0.2362 Isoform IIb of Profilin‐2 PFN2 ‐0.0794 ‐3.5794 ‐3.4608 0.9646 0.0114 0.0180 Phosphoglycerate mutase 1 PGAM1 1.4912 ‐2.1816 ‐3.1584 0.3158 0.1139 0.0285 Isoform 2 of 6‐phosphogluconate dehydrogenase, decarboxylating PGD ‐0.2248 ‐3.1185 ‐2.9091 0.9017 0.0243 0.0417 Phosphoglycerate kinase 1 PGK1 ‐0.4429 ‐3.7496 ‐3.3802 0.8056 0.0087 0.0200 6‐phosphogluconolactonase PGLS 0.5885 ‐2.2891 ‐2.6489 0.7395 0.0965 0.0631 Isoform 2 of N‐acetylmuramoyl‐L‐ alanine amidase PGLYRP2 0.1192 0.6038 0.5117 0.9493 0.7088 0.7702 Isoform 2 of Phosphoglucomutase‐1 PGM1 ‐5.1139 ‐4.6467 ‐1.0785 0.0008 0.0019 0.4902 Phosphoglucomutase‐2 PGM2 5.6560 ‐0.8127 ‐4.6520 0.0003 0.6054 0.0025 Phosphoglucomutase‐like protein 5 PGM5 1.3551 ‐0.7035 ‐1.6141 0.3653 0.6580 0.2782 Membrane‐associated progesterone receptor component 1 PGRMC1 3.9072 0.9257 ‐1.7533 0.0068 0.5475 0.2345 Isoform 2 of Membrane‐ associated progesterone receptor component 2 PGRMC2 ‐2.4781 3.3911 5.0185 0.0788 0.0153 0.0014 Isoform 3 of Phosphatase and actin regulator 4 PHACTR4 ‐0.5169 ‐0.6395 ‐0.2757 0.7734 0.6929 0.8827 Prohibitin PHB ‐0.5491 ‐0.5424 ‐0.1585 0.7596 0.7409 0.9243 Isoform 2 of Prohibitin‐2 PHB2 ‐0.4954 ‐1.2715 ‐0.9110 0.7785 0.3829 0.5675 D‐3‐phosphoglycerate dehydrogenase PHGDH ‐0.2882 ‐1.9173 ‐1.6864 0.8727 0.1680 0.2543 Isoform 2 of Pleckstrin homology‐ like domain family B member 1 PHLDB1 ‐0.0022 ‐1.6248 ‐1.5940 0.9997 0.2484 0.2847 Cluster of Phosphatidylinositol 4‐ kinase alpha PI4KA 1.4311 ‐0.5114 ‐1.4773 0.3357 0.7589 0.3252 Isoform 2 of Phosphatidylinositol‐ binding clathrin assembly protein PICALM 0.9843 ‐2.7731 ‐3.3938 0.5387 0.0449 0.0196 Polymeric immunoglobulin receptor PIGR 10.9965 7.4327 ‐0.1941 0.0000 0.0000 0.9094

Prolactin‐inducible protein PIP ‐9.8637 ‐0.2264 6.4987 0.0000 0.8893 0.0001 Isoform 2 of Phosphatidylinositol 5‐phosphate 4‐kinase type‐2 gamma PIP4K2C ‐0.3519 ‐2.0245 ‐1.7482 0.8482 0.1421 0.2354 Phosphatidylinositol transfer protein alpha isoform PITPNA ‐6.8195 ‐0.8543 3.8078 0.0000 0.5840 0.0102 Pyruvate kinase PKM PKM 3.2399 0.4718 ‐1.7444 0.0227 0.7796 0.2362 Isoform 1 of Plakophilin‐1 PKP1 ‐2.8660 ‐1.7496 0.2348 0.0427 0.2101 0.8955 Isoform 2 of Plakophilin‐4 PKP4 0.4262 ‐1.4254 ‐1.6901 0.8134 0.3175 0.2535 Secretory phospholipase A2 receptor PLA2R1 4.0208 4.0980 1.2844 0.0056 0.0049 0.4008 1‐phosphatidylinositol 4,5‐ bisphosphate phosphodiesterase gamma‐2 PLCG2 ‐6.1081 ‐2.4149 1.7905 0.0001 0.0796 0.2253 Cluster of Plectin PLEC 0.9405 0.3707 ‐0.2768 0.5592 0.8259 0.8827 Pleckstrin homology domain‐ containing family O member 2 PLEKHO2 ‐0.3477 ‐0.6817 ‐0.4325 0.8495 0.6709 0.8041 Plasminogen PLG 2.3528 0.4956 ‐1.1165 0.0958 0.7683 0.4740 Cluster of Isoform 4 of Perilipin‐3 PLIN3 3.7827 3.0731 0.4402 0.0086 0.0262 0.7996 Multifunctional procollagen lysine hydroxylase and glycosyltransferase LH3 PLOD3 2.5640 0.9213 ‐0.8424 0.0685 0.5484 0.6081 Cluster of Plastin‐3 PLS3 0.6211 ‐0.1959 ‐0.6156 0.7284 0.9027 0.7150 Cluster of Isoform PML‐11 of Protein PML PML 3.9209 2.7401 0.0191 0.0067 0.0472 0.9900 Purine nucleoside phosphorylase PNP ‐0.0271 ‐4.0073 ‐3.9166 0.9851 0.0057 0.0084 Pyridoxine‐5'‐phosphate oxidase PNPO ‐3.2730 ‐0.4001 1.8372 0.0214 0.8124 0.2119 Isoform 2 of Podocalyxin PODXL ‐2.4075 ‐4.2798 ‐2.5623 0.0881 0.0035 0.0714 Protein O‐glucosyltransferase 3 POGLUT3 2.2993 1.3478 ‐0.2432 0.1036 0.3508 0.8899 Serum paraoxonase/arylesterase 1 PON1 2.7648 1.7541 ‐0.1614 0.0502 0.2093 0.9236 Isoform 1 of Serum paraoxonase/arylesterase 2 PON2 ‐0.1471 ‐3.2765 ‐3.1173 0.9399 0.0187 0.0301 NADPH‐‐cytochrome P450 reductase POR ‐5.1114 ‐0.1910 3.2953 0.0008 0.9043 0.0232 Periostin POSTN 2.3408 2.4784 0.8387 0.0974 0.0714 0.6086 Inorganic pyrophosphatase PPA1 8.5398 4.6615 ‐1.2414 0.0000 0.0019 0.4209 Cluster of Peptidyl‐prolyl cis‐trans isomerase A PPIA ‐0.1055 ‐2.1395 ‐2.0291 0.9533 0.1201 0.1605 Peptidyl‐prolyl cis‐trans isomerase B PPIB 3.8323 0.4513 ‐2.1680 0.0078 0.7908 0.1306 Protein phosphatase 1F PPM1F ‐1.7890 ‐1.6183 ‐0.3701 0.2158 0.2497 0.8357 Cluster of Serine/threonine‐ protein phosphatase PP1‐beta catalytic subunit PPP1CB 1.2172 0.2789 ‐0.5555 0.4256 0.8640 0.7458 Protein phosphatase 1 regulatory subunit 12A PPP1R12A 0.3748 3.1246 2.8129 0.8353 0.0241 0.0489 Protein phosphatase 1 regulatory subunit 26 PPP1R26 ‐1.1075 ‐1.4957 ‐0.7141 0.4784 0.2926 0.6617

Serine/threonine‐protein phosphatase 2A catalytic subunit beta isoform PPP2CB 0.8503 3.5746 2.9308 0.6094 0.0115 0.0404 Serine/threonine‐protein phosphatase 2A 65 kDa regulatory subunit A alpha isoform PPP2R1A 1.7912 ‐1.3759 ‐2.5717 0.2158 0.3371 0.0703 Isoform 2 of Serine/threonine‐ protein phosphatase 2A 65 kDa regulatory subunit A beta isoform PPP2R1B ‐0.8840 ‐5.5780 ‐4.8751 0.5897 0.0004 0.0017 PRA1 family protein 2 PRAF2 ‐0.4987 4.1746 4.4392 0.7785 0.0042 0.0036 Peroxiredoxin‐1 PRDX1 ‐1.7539 ‐3.3423 ‐2.0870 0.2256 0.0167 0.1471 Cluster of Peroxiredoxin‐2 PRDX2 ‐1.2936 ‐3.8954 ‐2.9438 0.3917 0.0068 0.0401 Isoform 2 of Thioredoxin‐ dependent peroxide reductase, mitochondrial PRDX3 ‐0.0519 ‐0.8435 ‐0.7930 0.9732 0.5893 0.6305 Peroxiredoxin‐4 PRDX4 ‐2.3299 11.0749 12.4629 0.0989 0.0000 0.0000 Cluster of Isoform Cytoplasmic+peroxisomal of Peroxiredoxin‐5, mitochondrial PRDX5 0.5040 ‐2.1036 ‐2.4091 0.7769 0.1261 0.0910 Peroxiredoxin‐6 PRDX6 ‐1.4653 ‐5.3031 ‐4.2091 0.3247 0.0006 0.0053 Prolyl endopeptidase PREP 2.0664 0.6712 ‐0.7490 0.1470 0.6765 0.6470 Bone marrow proteoglycan PRG2 2.0729 12.5644 10.9256 0.1457 0.0000 0.0000 Proteoglycan 3 PRG3 9.5456 6.4648 ‐0.1559 0.0000 0.0001 0.9252 Isoform 3 of 5'‐AMP‐activated protein kinase subunit gamma‐1 PRKAG1 ‐0.5187 1.7457 2.0677 0.7732 0.2111 0.1516 cAMP‐dependent protein kinase type I‐alpha regulatory subunit PRKAR1A ‐0.0691 0.4969 0.5351 0.9677 0.7678 0.7571 Isoform 2 of cAMP‐dependent protein kinase type II‐alpha regulatory subunit PRKAR2A ‐0.0676 ‐0.5486 ‐0.4927 0.9677 0.7364 0.7755 cAMP‐dependent protein kinase type II‐beta regulatory subunit PRKAR2B ‐0.5732 ‐9.0608 ‐8.5069 0.7463 0.0000 0.0000 Cluster of Protein kinase C alpha type PRKCA ‐0.9810 1.2264 1.8727 0.5403 0.4006 0.2019 Protein kinase C iota type PRKCI 0.9980 ‐1.1175 ‐1.7774 0.5324 0.4516 0.2281 Isoform 2 of Glucosidase 2 subunit beta PRKCSH ‐3.9532 ‐3.5735 ‐0.8155 0.0063 0.0115 0.6209 Isoform 2 of DNA‐dependent protein kinase catalytic subunit PRKDC 1.5779 1.3061 0.2074 0.2854 0.3691 0.9038 Vitamin K‐dependent protein S PROS1 4.1937 2.6210 ‐0.2837 0.0041 0.0570 0.8818 Pre‐mRNA‐processing‐splicing factor 8 PRPF8 ‐1.9216 ‐1.6380 ‐0.2992 0.1816 0.2438 0.8743 Serine protease 23 PRSS23 8.7998 4.8519 ‐1.2316 0.0000 0.0014 0.4244 Periaxin PRX 1.4515 ‐0.2021 ‐1.1875 0.3288 0.8990 0.4457 Phosphoserine aminotransferase PSAT1 0.1954 ‐3.7240 ‐3.7901 0.9192 0.0090 0.0105 Isoform Long of Proteasome subunit alpha type‐1 PSMA1 0.4808 ‐2.3693 ‐2.6542 0.7863 0.0853 0.0627 Proteasome subunit alpha type‐2 PSMA2 1.8949 ‐2.1335 ‐3.3862 0.1889 0.1211 0.0199 Proteasome subunit alpha type‐4 PSMA4 ‐0.3882 ‐8.1263 ‐7.7154 0.8273 0.0000 0.0000 Proteasome subunit alpha type‐5 PSMA5 2.3149 ‐1.8815 ‐3.4249 0.1016 0.1782 0.0190

Proteasome subunit alpha type‐6 PSMA6 ‐0.7251 0.0967 0.5890 0.6759 0.9509 0.7284 Cluster of Proteasome subunit alpha type‐7 PSMA7 5.1945 0.8232 ‐2.7311 0.0007 0.6009 0.0560 Proteasome subunit beta type‐1 PSMB1 ‐1.9027 ‐1.6024 ‐0.2771 0.1869 0.2551 0.8827 Proteasome subunit beta type‐2 PSMB2 ‐0.2516 ‐8.4868 ‐8.1625 0.8898 0.0000 0.0000 Proteasome subunit beta type‐3 PSMB3 2.4577 6.9469 5.1471 0.0808 0.0001 0.0011 Proteasome subunit beta type‐4 PSMB4 2.8406 0.7179 ‐1.2306 0.0444 0.6537 0.4244 Proteasome subunit beta type‐6 PSMB6 0.8498 ‐1.0475 ‐1.6076 0.6094 0.4844 0.2799 Proteasome subunit beta type‐7 PSMB7 ‐0.1395 ‐2.9629 ‐2.8144 0.9420 0.0320 0.0489 Proteasome subunit beta type‐8 PSMB8 ‐1.8412 2.6575 3.8642 0.2019 0.0541 0.0092 Proteasome subunit beta type‐9 PSMB9 13.1044 7.6021 ‐1.4641 0.0000 0.0000 0.3299 26S proteasome regulatory subunit 4 PSMC1 4.0590 2.5208 ‐0.2904 0.0052 0.0666 0.8783 26S proteasome regulatory subunit 7 PSMC2 ‐2.6760 ‐1.0266 0.8152 0.0583 0.4957 0.6209 26S proteasome regulatory subunit 6A PSMC3 ‐2.6652 ‐1.8543 ‐0.0048 0.0595 0.1850 0.9962 Isoform 2 of 26S proteasome regulatory subunit 6B PSMC4 ‐5.1158 ‐6.2637 ‐2.6651 0.0008 0.0002 0.0615 26S proteasome regulatory subunit 10B PSMC6 0.4576 2.1821 1.8309 0.7998 0.1139 0.2139 Isoform 2 of 26S proteasome non‐ ATPase regulatory subunit 11 PSMD11 ‐1.3383 ‐2.2874 ‐1.3343 0.3731 0.0966 0.3798 26S proteasome non‐ATPase regulatory subunit 12 PSMD12 2.9287 2.1736 0.1388 0.0381 0.1148 0.9316 26S proteasome non‐ATPase regulatory subunit 14 PSMD14 5.8390 3.3054 ‐0.7327 0.0002 0.0178 0.6556 Cluster of 26S proteasome non‐ ATPase regulatory subunit 2 PSMD2 3.2953 ‐0.4766 ‐2.7134 0.0206 0.7782 0.0575 26S proteasome non‐ATPase regulatory subunit 3 PSMD3 2.6483 1.6685 ‐0.1661 0.0611 0.2333 0.9236 26S proteasome non‐ATPase regulatory subunit 8 PSMD8 ‐0.1618 ‐3.7598 ‐3.5818 0.9329 0.0086 0.0151 Proteasome activator complex subunit 1 PSME1 ‐1.1873 ‐1.5639 ‐0.7267 0.4398 0.2664 0.6567 Proteasome activator complex subunit 2 PSME2 ‐0.8251 ‐1.7385 ‐1.1450 0.6227 0.2123 0.4611 Paraspeckle component 1 PSPC1 2.3946 1.2618 ‐0.3926 0.0894 0.3862 0.8256 Cluster of Isoform 2 of Polypyrimidine tract‐binding protein 1 PTBP1 ‐0.1395 ‐1.5271 ‐1.4046 0.9420 0.2800 0.3533 Isoform 3 of Prostaglandin E synthase 3 PTGES3 12.1134 0.4923 ‐7.7705 0.0000 0.7693 0.0000 Isoform 2 of Prostaglandin reductase 1 PTGR1 1.3704 7.1341 6.0718 0.3593 0.0000 0.0003 Isoform 1 of Serine/threonine‐ protein phosphatase 2A activator PTPA 2.2036 2.5001 0.9535 0.1194 0.0688 0.5431 Isoform 2 of Receptor‐type tyrosine‐protein phosphatase O PTPRO ‐0.1249 ‐0.0972 ‐0.0103 0.9482 0.9509 0.9933 Isoform 2 of Poly(U)‐binding‐ splicing factor PUF60 PUF60 ‐1.5326 ‐0.6419 0.4140 0.3005 0.6919 0.8142

Transcriptional activator protein Pur‐alpha PURA ‐0.6069 ‐2.2698 ‐1.8154 0.7343 0.0991 0.2184 Transcriptional activator protein Pur‐beta PURB 0.7167 0.3573 ‐0.1375 0.6796 0.8308 0.9316 Peroxidasin homolog PXDN ‐3.2371 ‐2.1166 0.1273 0.0227 0.1236 0.9365 Glycogen phosphorylase, brain form PYGB 7.6361 3.9000 ‐1.3734 0.0000 0.0068 0.3630 Isoform 2 of Glycogen phosphorylase, liver form PYGL 2.6901 3.5927 1.6949 0.0570 0.0112 0.2530 Sulfhydryl oxidase 2 QSOX2 ‐0.2122 ‐0.6103 ‐0.4547 0.9101 0.7076 0.7900 Isoform 2 of Ras‐related protein Rab‐11B RAB11B ‐0.5920 1.4514 1.8286 0.7388 0.3098 0.2144 Cluster of Ras‐related protein Rab‐ 14 RAB14 0.1048 ‐1.1728 ‐1.2231 0.9533 0.4258 0.4271 Isoform 2 of Ras‐related protein Rab‐5A RAB5A ‐7.4334 ‐6.7036 ‐1.5179 0.0000 0.0001 0.3122 Ras‐related protein Rab‐5B RAB5B ‐7.2298 ‐4.8667 0.1473 0.0000 0.0013 0.9298 Ras‐related protein Rab‐5C RAB5C 0.4784 ‐1.8665 ‐2.1588 0.7866 0.1817 0.1326 Isoform 2 of Ras‐related protein Rab‐6A RAB6A ‐2.7270 ‐1.5205 0.3650 0.0533 0.2827 0.8384 Ras‐related protein Rab‐7a RAB7A ‐0.4946 ‐1.3095 ‐0.9489 0.7785 0.3684 0.5448 Cluster of Ras‐related C3 botulinum toxin substrate 3 RAC3 13.7778 8.9638 ‐0.5857 0.0000 0.0000 0.7298 Receptor of activated protein C kinase 1 RACK1 0.7223 0.0108 ‐0.4816 0.6767 0.9923 0.7808 Isoform 3 of UV excision repair protein RAD23 homolog A RAD23A 0.5893 2.9166 2.4625 0.7395 0.0347 0.0827 Isoform 2 of UV excision repair protein RAD23 homolog B RAD23B ‐1.1451 ‐0.5249 0.2648 0.4604 0.7508 0.8833 Isoform 3 of Ankycorbin RAI14 3.4993 1.7116 ‐0.7036 0.0140 0.2206 0.6672 Ras‐related protein Ral‐A RALA 6.0233 4.6941 0.5053 0.0002 0.0018 0.7716 GTP‐binding nuclear protein Ran RAN 2.4508 0.9399 ‐0.7469 0.0817 0.5404 0.6473 Cluster of Ras‐related protein Rap‐ 1b RAP1B ‐2.1905 ‐3.6330 ‐2.0749 0.1216 0.0105 0.1499 Arginine‐‐tRNA ligase, cytoplasmic RARS 3.0045 2.3565 0.2668 0.0337 0.0871 0.8827 Ras‐interacting protein 1 RASIP1 ‐2.8308 ‐4.7958 ‐2.7805 0.0452 0.0015 0.0518 RNA‐binding protein 14 RBM14 3.6908 2.0881 ‐0.4644 0.0102 0.1283 0.7873 RNA‐binding protein 3 RBM3 0.8853 0.4496 ‐0.1617 0.5894 0.7916 0.9236 Isoform 2 of RNA‐binding protein 39 RBM39 1.9143 3.9645 2.5887 0.1837 0.0061 0.0689 Isoform 2 of RNA‐binding motif protein, X chromosome RBMX 2.4006 ‐1.0257 ‐2.6429 0.0888 0.4958 0.0634 Retinol‐binding protein 4 RBP4 2.4712 0.7054 ‐0.9912 0.0793 0.6580 0.5257 Reticulocalbin‐1 RCN1 8.8461 5.6721 ‐0.4577 0.0000 0.0004 0.7900 Isoform 2 of Reticulocalbin‐2 RCN2 7.8523 4.3305 ‐1.0980 0.0000 0.0032 0.4830 Isoform 5 of Radixin RDX ‐0.9606 ‐3.4285 ‐2.7122 0.5498 0.0144 0.0575 Isoform 2 of Renin REN ‐7.8431 ‐0.9447 4.4165 0.0000 0.5377 0.0038 Raftlin RFTN1 0.5927 1.9203 1.4818 0.7388 0.1677 0.3243 Cluster of Rho‐related GTP‐ binding protein RhoC RHOC 0.0001 ‐1.6443 ‐1.6147 1.0000 0.2417 0.2782

2‐iminobutanoate/2‐ iminopropanoate deaminase RIDA ‐29.8464 ‐24.1730 ‐3.4005 0.0000 0.0000 0.0194 Isoform 3 of Rho family‐ interacting cell polarization regulator 1 RIPOR1 3.5819 3.1860 0.6879 0.0123 0.0218 0.6737 Eosinophil cationic protein RNASE3 18.7327 11.4503 ‐1.5201 0.0000 0.0000 0.3114 Ribonuclease inhibitor RNH1 ‐0.4257 ‐1.6955 ‐1.3749 0.8134 0.2252 0.3630 Aminopeptidase B RNPEP ‐1.4760 0.5770 1.5723 0.3212 0.7200 0.2922 Isoform 3 of 60 kDa SS‐A/Ro ribonucleoprotein RO60 ‐0.6976 ‐2.4139 ‐1.8951 0.6868 0.0796 0.1950 Rho‐associated protein kinase 2 ROCK2 0.5968 ‐1.2839 ‐1.6674 0.7381 0.3779 0.2611 60S ribosomal protein L10 RPL10 8.9347 5.9386 ‐0.2564 0.0000 0.0002 0.8859 60S ribosomal protein L10a RPL10A 2.0468 0.1697 ‐1.2280 0.1513 0.9131 0.4245 Isoform 2 of 60S ribosomal protein L11 RPL11 1.8817 1.3694 0.0626 0.1915 0.3402 0.9675 60S ribosomal protein L12 RPL12 2.6064 0.3658 ‐1.4167 0.0647 0.8268 0.3494 60S ribosomal protein L13 RPL13 0.5615 ‐0.3856 ‐0.7613 0.7504 0.8198 0.6422 60S ribosomal protein L14 RPL14 0.8077 ‐0.1662 ‐0.7136 0.6322 0.9144 0.6617 60S ribosomal protein L15 RPL15 0.0543 0.1109 0.0719 0.9727 0.9441 0.9647 Isoform 3 of 60S ribosomal protein L17 RPL17 0.7418 2.7224 2.1679 0.6680 0.0485 0.1306 Isoform 2 of 60S ribosomal protein L18 RPL18 1.4727 2.4993 1.4508 0.3220 0.0688 0.3347 60S ribosomal protein L18a RPL18A ‐1.4989 4.6777 5.6148 0.3129 0.0018 0.0005 60S ribosomal protein L19 RPL19 12.5844 8.4746 ‐0.2529 0.0000 0.0000 0.8880 60S ribosomal protein L21 RPL21 7.8667 4.3001 ‐1.1376 0.0000 0.0034 0.4639 60S ribosomal protein L22 RPL22 2.0830 1.7063 0.2563 0.1438 0.2220 0.8859 60S ribosomal protein L23 RPL23 2.7925 ‐0.1565 ‐2.0564 0.0479 0.9184 0.1546 60S ribosomal protein L23a RPL23A ‐0.2424 1.2797 1.4218 0.8926 0.3790 0.3471 60S ribosomal protein L24 RPL24 ‐0.1231 12.8040 12.6572 0.9483 0.0000 0.0000 60S ribosomal protein L27a RPL27A 5.8282 3.7444 ‐0.2943 0.0002 0.0088 0.8763 Cluster of 60S ribosomal protein L3 RPL3 1.8876 ‐0.0946 ‐1.3790 0.1904 0.9509 0.3612 60S ribosomal protein L4 RPL4 1.3433 0.9968 0.0635 0.3707 0.5097 0.9674 60S ribosomal protein L5 RPL5 ‐0.6019 5.1678 5.4848 0.7358 0.0008 0.0006 60S ribosomal protein L6 RPL6 2.8248 2.7665 0.7919 0.0455 0.0452 0.6305 60S ribosomal protein L7 RPL7 0.4719 0.8117 0.4756 0.7910 0.6056 0.7812 60S ribosomal protein L7a RPL7A 2.1525 2.6575 1.1429 0.1286 0.0541 0.4620 60S ribosomal protein L8 RPL8 ‐1.0012 0.2751 0.9524 0.5307 0.8656 0.5433 60S ribosomal protein L9 RPL9 1.4839 3.5546 2.4794 0.3177 0.0119 0.0805 Cluster of 60S acidic ribosomal protein P0 RPLP0 1.7227 3.0479 1.8192 0.2368 0.0274 0.2173 60S acidic ribosomal protein P2 RPLP2 1.7779 0.6384 ‐0.5845 0.2184 0.6932 0.7301 Dolichyl‐ diphosphooligosaccharide‐‐ protein glycosyltransferase subunit 1 RPN1 0.8496 0.4924 ‐0.0954 0.6094 0.7693 0.9559

Dolichyl‐ diphosphooligosaccharide‐‐ protein glycosyltransferase subunit 2 RPN2 0.0331 ‐2.2146 ‐2.1972 0.9825 0.1083 0.1258 Cluster of 40S ribosomal protein S10 RPS10 1.1061 1.9551 1.1661 0.4784 0.1591 0.4526 40S ribosomal protein S13 RPS13 1.1220 8.5603 7.6416 0.4705 0.0000 0.0000 40S ribosomal protein S14 RPS14 ‐23.7466 ‐0.4004 15.7874 0.0000 0.8124 0.0000 40S ribosomal protein S15 RPS15 ‐4.6955 ‐0.0760 3.1249 0.0016 0.9575 0.0300 40S ribosomal protein S15a RPS15A 0.3316 ‐0.8308 ‐1.0419 0.8559 0.5955 0.5070 40S ribosomal protein S16 RPS16 1.7231 1.0067 ‐0.1855 0.2368 0.5054 0.9140 40S ribosomal protein S17 RPS17 1.6250 ‐0.4383 ‐1.5377 0.2695 0.7972 0.3051 40S ribosomal protein S18 RPS18 0.0847 ‐0.5146 ‐0.5631 0.9634 0.7576 0.7429 40S ribosomal protein S19 RPS19 ‐0.4951 3.8831 4.1505 0.7785 0.0070 0.0058 40S ribosomal protein S2 RPS2 ‐0.0824 0.6075 0.6527 0.9634 0.7083 0.6949 40S ribosomal protein S20 RPS20 0.9155 0.5590 ‐0.0749 0.5704 0.7291 0.9633 40S ribosomal protein S21 RPS21 14.8093 12.0969 1.7881 0.0000 0.0000 0.2253 40S ribosomal protein S23 RPS23 1.9306 12.1601 10.6255 0.1792 0.0000 0.0000 Isoform 3 of 40S ribosomal protein S24 RPS24 3.0303 1.7703 ‐0.3264 0.0324 0.2049 0.8575 40S ribosomal protein S26 RPS26 1.8692 1.7003 0.3960 0.1936 0.2240 0.8248 Ubiquitin‐40S ribosomal protein S27a RPS27A 0.2878 ‐1.6854 ‐1.8512 0.8727 0.2280 0.2073 40S ribosomal protein S28 RPS28 1.4657 8.8261 7.6684 0.3247 0.0000 0.0000 Cluster of 40S ribosomal protein S3 RPS3 1.5347 1.3342 0.2644 0.3002 0.3567 0.8833 40S ribosomal protein S3a RPS3A 1.9500 1.2625 ‐0.0890 0.1736 0.3862 0.9590 40S ribosomal protein S4, X isoform RPS4X 2.8026 ‐0.2238 ‐2.1294 0.0472 0.8897 0.1385 40S ribosomal protein S5 RPS5 3.0760 ‐0.2905 ‐2.3812 0.0298 0.8588 0.0934 40S ribosomal protein S6 RPS6 0.7004 0.3849 ‐0.0993 0.6868 0.8198 0.9548 40S ribosomal protein S7 RPS7 2.4971 ‐0.4541 ‐2.1475 0.0764 0.7895 0.1347 40S ribosomal protein S8 RPS8 2.7995 2.6494 0.6942 0.0474 0.0548 0.6718 40S ribosomal protein S9 RPS9 1.7642 11.1421 9.7393 0.2222 0.0000 0.0000 40S ribosomal protein SA RPSA 1.9977 0.6742 ‐0.6991 0.1633 0.6746 0.6696 Cluster of Ras‐related protein R‐ Ras RRAS ‐2.3105 ‐2.8019 ‐1.1771 0.1020 0.0427 0.4488 Ribosome‐binding protein 1 RRBP1 1.4557 3.1557 2.1069 0.3279 0.0229 0.1428 Isoform 2 of Remodeling and spacing factor 1 RSF1 ‐1.1838 ‐1.9990 ‐1.1564 0.4402 0.1484 0.4556 Ribosomal L1 domain‐containing protein 1 RSL1D1 3.2858 2.7506 0.4622 0.0209 0.0463 0.7877 Ras suppressor protein 1 RSU1 ‐1.0409 ‐2.5041 ‐1.7497 0.5122 0.0684 0.2354 tRNA‐splicing ligase RtcB homolog RTCB ‐2.9787 3.3296 5.2993 0.0351 0.0170 0.0009 Cluster of Reticulon‐4 RTN4 ‐0.0768 6.2540 6.1937 0.9648 0.0002 0.0002 RNA transcription, translation and transport factor protein RTRAF 1.6223 0.6423 ‐0.4747 0.2695 0.6919 0.7812 RuvB‐like 1 RUVBL1 ‐0.7326 3.9734 4.4010 0.6728 0.0060 0.0038

Protein S100‐A11 S100A11 0.9266 ‐0.3448 ‐0.9699 0.5654 0.8352 0.5344 Protein S100‐A16 S100A16 ‐0.7774 1.0547 1.5653 0.6478 0.4812 0.2935 Protein S100‐A8 S100A8 1.3202 5.0198 4.0298 0.3809 0.0010 0.0070 Protein S100‐A9 S100A9 3.5617 3.0883 0.6058 0.0128 0.0256 0.7208 Serum amyloid A‐1 protein SAA1 ‐7.6594 0.4712 5.6818 0.0000 0.7796 0.0005 Serum amyloid A‐2 protein SAA2 ‐9.1017 ‐0.6418 5.5715 0.0000 0.6919 0.0005 SUMO‐activating enzyme subunit 1 SAE1 ‐0.8476 ‐1.6568 ‐1.0494 0.6097 0.2378 0.5043 Isoform 3 of Deoxynucleoside triphosphate triphosphohydrolase SAMHD1 SAMHD1 ‐2.2815 1.1145 2.6490 0.1060 0.4526 0.0631 Isoform 2 of GTP‐binding protein SAR1a SAR1A ‐10.9643 ‐0.3053 7.1711 0.0000 0.8526 0.0000 SAP domain‐containing ribonucleoprotein SARNP 2.5313 5.5566 3.7317 0.0720 0.0004 0.0117 Suprabasin SBSN ‐4.1001 ‐0.5831 2.2212 0.0049 0.7182 0.1219 Somatomedin‐B and thrombospondin type‐1 domain‐ containing protein SBSPON 0.9723 ‐3.2242 ‐3.8286 0.5441 0.0202 0.0099 Secretory carrier‐associated membrane protein 3 SCAMP3 2.0661 4.5080 3.0190 0.1470 0.0024 0.0354 Lysosome membrane protein 2 SCARB2 ‐0.6675 1.7341 2.1576 0.7032 0.2133 0.1326 Isoform 2 of Sec1 family domain‐ containing protein 1 SCFD1 2.2928 1.4250 ‐0.1630 0.1044 0.3175 0.9236 Isoform 2 of Secernin‐1 SCRN1 ‐1.4407 ‐1.2320 ‐0.2281 0.3318 0.3982 0.8970 Isoform 2 of Secernin‐2 SCRN2 7.3231 5.2183 0.1344 0.0000 0.0007 0.9325 Isoform 2 of Syntenin‐1 SDCBP ‐8.7283 ‐2.3369 3.6525 0.0000 0.0898 0.0135 Cluster of Isoform 2 of Succinate dehydrogenase [ubiquinone] flavoprotein subunit, mitochondrial SDHA ‐1.3306 6.2299 7.0243 0.3762 0.0002 0.0001 Succinate dehydrogenase [ubiquinone] iron‐sulfur subunit, mitochondrial SDHB ‐4.6993 ‐0.3308 2.8771 0.0016 0.8421 0.0438 Vesicle‐trafficking protein SEC22b SEC22B ‐3.3246 5.3262 7.4956 0.0195 0.0006 0.0000 Cluster of Protein transport protein Sec23A SEC23A ‐3.7755 ‐1.8180 0.7873 0.0087 0.1938 0.6332 Protein transport protein Sec24C SEC24C ‐0.5300 ‐0.4217 ‐0.0529 0.7673 0.7997 0.9730 Protein transport protein Sec61 subunit alpha isoform 1 SEC61A1 2.3734 0.8042 ‐0.8275 0.0924 0.6085 0.6162 Methanethiol oxidase SELENBP1 0.2468 ‐4.4245 ‐4.5129 0.8904 0.0028 0.0032 Semenogelin‐1 SEMG1 ‐8.9927 0.1844 6.3086 0.0000 0.9060 0.0002 Semenogelin‐2 SEMG2 ‐11.1420 ‐0.8382 6.7689 0.0000 0.5916 0.0001 Cluster of Isoform 2 of Septin‐11 SEPTIN11 0.2733 ‐2.2636 ‐2.4090 0.8794 0.1000 0.0910 Cluster of Isoform 2 of Septin‐2 SEPTIN2 ‐18.7971 ‐12.4535 0.5789 0.0000 0.0000 0.7328 Isoform 2 of Septin‐7 SEPTIN7 ‐1.0121 ‐2.5885 ‐1.8522 0.5264 0.0601 0.2073 Cluster of Isoform 2 of Septin‐9 SEPTIN9 0.1167 6.4006 6.2058 0.9493 0.0001 0.0002 Isoform 2 of Plasminogen activator inhibitor 1 RNA‐binding protein SERBP1 0.3514 ‐0.6085 ‐0.8370 0.8482 0.7081 0.6092

Alpha‐1‐antitrypsin SERPINA1 1.1834 ‐1.1261 ‐1.9121 0.4402 0.4475 0.1911 Alpha‐1‐antichymotrypsin SERPINA3 1.4907 ‐0.0253 ‐1.0406 0.3158 0.9858 0.5072 Cluster of Leukocyte elastase inhibitor SERPINB1 ‐0.2412 ‐2.1679 ‐1.9645 0.8929 0.1158 0.1775 Isoform 2 of Serpin B12 SERPINB12 ‐3.9858 ‐2.5665 0.1956 0.0059 0.0620 0.9094 Serpin B6 SERPINB6 ‐0.8897 ‐1.8429 ‐1.2035 0.5872 0.1880 0.4365 Antithrombin‐III SERPINC1 1.9617 0.3665 ‐0.9769 0.1720 0.8268 0.5316 Heparin cofactor 2 SERPIND1 8.5443 5.8759 ‐0.0520 0.0000 0.0003 0.9730 Pigment epithelium‐derived factor SERPINF1 0.0637 1.1601 1.0957 0.9687 0.4309 0.4839 Isoform 2 of Alpha‐2‐antiplasmin SERPINF2 8.9638 0.6811 ‐5.4390 0.0000 0.6709 0.0007 Isoform 2 of Plasma protease C1 inhibitor SERPING1 ‐0.0765 8.2846 8.1874 0.9648 0.0000 0.0000 Serpin H1 SERPINH1 0.6425 ‐0.8582 ‐1.2805 0.7149 0.5828 0.4022 Splicing factor 3A subunit 1 SF3A1 ‐0.1349 ‐0.6153 ‐0.5123 0.9436 0.7052 0.7702 Splicing factor 3B subunit 1 SF3B1 0.7900 ‐0.4232 ‐0.9538 0.6401 0.7997 0.5431 Splicing factor 3B subunit 2 SF3B2 ‐3.6296 ‐0.7517 1.7349 0.0114 0.6402 0.2386 Splicing factor 3B subunit 3 SF3B3 0.0817 0.4776 0.4133 0.9634 0.7782 0.8142 Splicing factor 3B subunit 4 SF3B4 1.5287 ‐2.2492 ‐3.2503 0.3016 0.1021 0.0247 Splicing factor, proline‐ and glutamine‐rich SFPQ ‐0.2826 ‐1.5103 ‐1.2905 0.8743 0.2864 0.3984 Sideroflexin‐3 SFXN3 ‐10.6047 ‐0.9709 6.2725 0.0000 0.5241 0.0002 SH3 domain‐binding glutamic acid‐rich‐like protein SH3BGRL 1.2038 ‐0.7608 ‐1.5674 0.4332 0.6348 0.2934 SH3 domain‐binding glutamic acid‐rich‐like protein 2 SH3BGRL2 ‐1.1902 ‐3.4120 ‐2.5395 0.4384 0.0147 0.0733 Isoform 2 of Endophilin‐B1 SH3GLB1 1.8728 ‐2.1356 ‐3.3732 0.1926 0.1208 0.0201 SH3 and multiple ankyrin repeat domains protein 3 SHANK3 ‐1.6327 ‐1.5738 ‐0.4329 0.2674 0.2631 0.8041 Isoform 4 of Serine hydroxymethyltransferase, cytosolic SHMT1 ‐12.2012 ‐9.6016 ‐1.1149 0.0000 0.0000 0.4746 Isoform 3 of Serine hydroxymethyltransferase, cytosolic SHMT1 ‐10.9470 ‐6.0898 1.4790 0.0000 0.0002 0.3247 Isoform 2 of Serine hydroxymethyltransferase, mitochondrial SHMT2 ‐7.2390 0.7726 5.6912 0.0000 0.6286 0.0005 Isoform 2 of S‐phase kinase‐ ‐ associated protein 1 SKP1 ‐0.7348 ‐11.4265 10.7199 0.6718 0.0000 0.0000 Cluster of Isoform 2 of Calcium‐ binding mitochondrial carrier protein Aralar2 SLC25A13 ‐1.6128 ‐0.2651 0.8386 0.2718 0.8703 0.6086 Isoform B of Phosphate carrier protein, mitochondrial SLC25A3 13.3341 0.2342 ‐8.8557 0.0000 0.8856 0.0000 Cluster of ADP/ATP translocase 2 SLC25A5 ‐0.1754 ‐3.0768 ‐2.9018 0.9286 0.0261 0.0421 Cluster of Isoform 3 of Solute carrier family 27 member 3 SLC27A3 0.9358 ‐0.0764 ‐0.7127 0.5611 0.9575 0.6617 Bile acyl‐CoA synthetase SLC27A5 ‐0.9451 ‐0.3778 0.2730 0.5585 0.8237 0.8827 Isoform 2 of Choline transporter‐ like protein 2 SLC44A2 ‐0.2732 0.4201 0.5986 0.8794 0.7997 0.7243

Band 3 anion transport protein SLC4A1 ‐2.0314 ‐3.6491 ‐2.1992 0.1548 0.0102 0.1258 Na(+)/H(+) exchange regulatory cofactor NHE‐RF1 SLC9A3R1 ‐1.5426 ‐5.1093 ‐3.9661 0.2977 0.0009 0.0078 Cluster of Isoform 2 of Na(+)/H(+) exchange regulatory cofactor NHE‐RF2 SLC9A3R2 ‐3.9523 ‐3.3350 ‐0.5818 0.0063 0.0169 0.7311 Isoform 2 of STE20‐like serine/threonine‐protein kinase SLK ‐0.4091 ‐1.9184 ‐1.6050 0.8205 0.1679 0.2807 Structural maintenance of chromosomes protein 1A SMC1A 0.3503 ‐0.5012 ‐0.7308 0.8485 0.7669 0.6559 Staphylococcal nuclease domain‐ containing protein 1 SND1 1.4130 0.4223 ‐0.5481 0.3419 0.7997 0.7489 U5 small nuclear ribonucleoprotein 200 kDa helicase SNRNP200 ‐2.1622 ‐0.1343 1.3415 0.1267 0.9302 0.3778 Small nuclear ribonucleoprotein Sm D1 SNRPD1 ‐0.5041 ‐1.5117 ‐1.1410 0.7769 0.2861 0.4627 Small nuclear ribonucleoprotein Sm D3 SNRPD3 ‐1.6966 ‐0.4269 0.7368 0.2451 0.7991 0.6549 Cluster of Beta‐1‐syntrophin SNTB1 2.4585 1.3518 ‐0.3477 0.0808 0.3491 0.8452 Beta‐2‐syntrophin SNTB2 3.2072 ‐1.1222 ‐3.2873 0.0238 0.4493 0.0234 Cluster of Isoform 1A of Sorting nexin‐1 SNX1 ‐6.7735 ‐0.2177 4.4016 0.0000 0.8923 0.0038 Sorting nexin‐5 SNX5 7.2570 4.0073 ‐1.0097 0.0000 0.0057 0.5174 Isoform 4 of Superoxide dismutase [Mn], mitochondrial SOD2 1.3899 5.2557 4.2139 0.3508 0.0007 0.0052 Cluster of Isoform 11 of Sorbin and SH3 domain‐containing protein 2 SORBS2 ‐1.7731 2.5503 3.7125 0.2198 0.0634 0.0121 Vinexin SORBS3 0.0911 0.8038 0.7273 0.9615 0.6085 0.6567 Sortilin SORT1 4.8974 2.8502 ‐0.5382 0.0011 0.0393 0.7552 Cluster of Isoform 2 of C‐Jun‐ amino‐terminal kinase‐interacting protein 4 SPAG9 0.5336 ‐1.7955 ‐2.1267 0.7673 0.1993 0.1389 Isoform 3 of SPATS2‐like protein SPATS2L ‐0.4940 ‐1.6790 ‐1.3122 0.7785 0.2298 0.3883 Sepiapterin reductase SPR 2.2072 2.6373 1.0858 0.1191 0.0558 0.4875 Isoform 2 of Spectrin alpha chain, erythrocytic 1 SPTA1 ‐3.0591 ‐1.9123 0.2066 0.0308 0.1693 0.9038 Cluster of Isoform 3 of Spectrin alpha chain, non‐erythrocytic 1 SPTAN1 ‐0.2800 ‐3.1604 ‐2.9127 0.8758 0.0227 0.0415 Cluster of Isoform 2 of Spectrin beta chain, erythrocytic SPTB ‐5.1109 ‐1.7901 1.7247 0.0008 0.2003 0.2421 Cluster of Spectrin beta chain, non‐erythrocytic 1 SPTBN1 ‐0.9336 ‐3.5027 ‐2.8034 0.5612 0.0128 0.0497 Sulfide:quinone oxidoreductase, mitochondrial SQOR 1.1694 0.2687 ‐0.5330 0.4468 0.8680 0.7582 Sequestosome‐1 SQSTM1 6.1260 3.4180 ‐0.8177 0.0001 0.0147 0.6202 Isoform 2 of Sorcin SRI ‐0.2931 ‐4.7328 ‐4.4477 0.8710 0.0017 0.0036 Signal recognition particle 14 kDa protein SRP14 2.6606 7.8589 5.9044 0.0597 0.0000 0.0003 Signal recognition particle 9 kDa protein SRP9 0.4535 5.9973 5.5802 0.8004 0.0002 0.0005

Isoform 2 of Serrate RNA effector molecule homolog SRRT ‐0.4827 ‐2.1572 ‐1.7894 0.7863 0.1178 0.2253 Serine/arginine‐rich splicing factor 1 SRSF1 0.3419 0.1926 ‐0.0438 0.8507 0.9040 0.9771 Isoform 2 of Serine/arginine‐rich splicing factor 10 SRSF10 1.2890 5.8022 4.8193 0.3933 0.0003 0.0019 Cluster of Serine/arginine‐rich splicing factor 2 SRSF2 11.5821 0.1753 ‐7.7197 0.0000 0.9109 0.0000 Serine/arginine‐rich splicing factor 3 SRSF3 1.2596 6.1527 5.1836 0.4057 0.0002 0.0010 Serine/arginine‐rich splicing factor 7 SRSF7 2.3798 0.7404 ‐0.8945 0.0915 0.6452 0.5778 Lupus La protein SSB 3.0111 ‐0.7272 ‐2.7657 0.0334 0.6504 0.0532 Single‐stranded DNA‐binding protein, mitochondrial SSBP1 11.1479 7.4744 ‐0.2563 0.0000 0.0000 0.8859 Translocon‐associated protein subunit alpha SSR1 9.9302 ‐1.6038 ‐8.3412 0.0000 0.2549 0.0000 Translocon‐associated protein subunit delta SSR4 0.8481 9.8425 9.0873 0.6097 0.0000 0.0000 Hsc70‐interacting protein ST13 ‐0.1183 ‐3.5475 ‐3.4030 0.9493 0.0120 0.0194 Signal transducer and activator of transcription 1‐alpha/beta STAT1 2.5277 0.3973 ‐1.3322 0.0724 0.8141 0.3803 Isoform Del‐701 of Signal transducer and activator of transcription 3 STAT3 3.5540 2.5314 0.0642 0.0129 0.0655 0.9674 Statherin STATH 15.0103 9.5560 ‐0.8440 0.0000 0.0000 0.6075 Stromal interaction molecule 1 STIM1 2.2268 1.2185 ‐0.3208 0.1160 0.4035 0.8602 Isoform 2 of Stress‐induced‐ phosphoprotein 1 STIP1 ‐0.6034 ‐1.7787 ‐1.3355 0.7358 0.2032 0.3798 Serine/threonine‐protein kinase 10 STK10 ‐0.2249 2.5786 2.6854 0.9017 0.0609 0.0595 Serine/threonine‐protein kinase 24 STK24 2.7913 1.0755 ‐0.8458 0.0479 0.4726 0.6067 Isoform 2 of Serine/threonine‐ protein kinase 25 STK25 0.1337 0.2498 0.1543 0.9439 0.8771 0.9252 Erythrocyte band 7 integral membrane protein STOM 0.4217 ‐0.8048 ‐1.0776 0.8143 0.6085 0.4902 Stomatin‐like protein 2, mitochondrial STOML2 ‐0.1154 0.7040 0.7699 0.9493 0.6580 0.6395 Isoform 2 of Serine‐threonine kinase receptor‐associated protein STRAP 1.8630 1.5989 0.3007 0.1951 0.2556 0.8738 Steryl‐sulfatase STS 5.1647 3.2311 ‐0.3462 0.0007 0.0200 0.8452 Isoform 2 of Syntaxin‐7 STX7 ‐0.7267 ‐10.5895 ‐9.9035 0.6759 0.0000 0.0000 Isoform 2 of Syntaxin‐binding protein 1 STXBP1 ‐1.3150 1.4378 2.3080 0.3825 0.3134 0.1048 Activated RNA polymerase II transcriptional coactivator p15 SUB1 0.9975 ‐2.4204 ‐3.0565 0.5324 0.0789 0.0331 Succinate‐‐CoA ligase [GDP‐ forming] subunit beta, mitochondrial SUCLG2 ‐1.0331 ‐3.1649 ‐2.4040 0.5162 0.0225 0.0913 Cluster of Sulfotransferase 1A1 SULT1A1 ‐0.4097 ‐6.2911 ‐5.8985 0.8205 0.0001 0.0003

Cluster of Isoform 5 of SUN domain‐containing protein 1 SUN1 1.8731 0.8154 ‐0.4755 0.1926 0.6051 0.7812 Isoform 2 of SUN domain‐ containing protein 2 SUN2 ‐0.0698 ‐1.4652 ‐1.3913 0.9677 0.3048 0.3586 Isoform 2 of Heterogeneous nuclear ribonucleoprotein Q SYNCRIP 0.5250 3.0157 2.6036 0.7697 0.0291 0.0677 Nesprin‐1 SYNE1 ‐0.7545 ‐0.2728 0.2462 0.6608 0.8663 0.8888 Isoform 2 of Nesprin‐2 SYNE2 ‐1.6544 ‐1.2247 ‐0.0753 0.2600 0.4012 0.9633 Cluster of Isoform 2 of Synaptopodin SYNPO ‐2.9756 ‐3.2646 ‐1.1782 0.0352 0.0191 0.4488 Cluster of Synaptopodin‐2 SYNPO2 0.0090 0.0199 0.0134 0.9972 0.9880 0.9917 Isoform Short of TATA‐binding protein‐associated factor 2N TAF15 8.3824 ‐0.1069 ‐5.8166 0.0000 0.9467 0.0004 Transgelin TAGLN ‐1.2263 0.9213 1.7403 0.4218 0.5484 0.2367 Isoform 2 of Transgelin‐2 TAGLN2 ‐1.0022 ‐0.2143 0.4725 0.5306 0.8938 0.7818 Transaldolase TALDO1 0.1512 ‐2.1942 ‐2.2577 0.9388 0.1118 0.1146 Antigen peptide transporter 1 TAP1 4.7973 8.1919 4.7755 0.0014 0.0000 0.0020 Cluster of TAR DNA‐binding protein 43 TARDBP 2.9694 0.7021 ‐1.3338 0.0356 0.6583 0.3798 Isoform 2 of Threonine‐‐tRNA ligase 1, cytoplasmic TARS1 1.4240 0.3172 ‐0.6588 0.3382 0.8460 0.6912 Tax1‐binding protein 3 TAX1BP3 11.7836 6.5926 ‐1.5554 0.0000 0.0001 0.2975 Isoform 2 of TBC1 domain family member 9B TBC1D9B ‐0.3189 0.5406 0.7481 0.8624 0.7418 0.6470 Tubulin‐specific chaperone A TBCA 15.1820 9.0223 ‐1.4851 0.0000 0.0000 0.3234 T‐complex protein 1 subunit alpha TCP1 0.8036 ‐2.4761 ‐2.9790 0.6339 0.0716 0.0381 Isoform 2 of Angiopoietin‐1 receptor TEK 5.5414 3.7576 ‐0.0859 0.0004 0.0086 0.9607 Methylcytosine dioxygenase TET1 TET1 2.5840 1.7108 ‐0.0808 0.0672 0.2206 0.9633 Serotransferrin TF 1.7799 ‐2.3493 ‐3.5198 0.2182 0.0882 0.0166 Isoform 2 of Transforming growth factor beta‐1‐induced transcript 1 protein TGFB1I1 ‐1.9532 ‐1.1326 0.2186 0.1735 0.4445 0.9013 Transforming growth factor‐beta‐ induced protein ig‐h3 TGFBI 0.6641 ‐0.7246 ‐1.1641 0.7032 0.6504 0.4526 Protein‐glutamine gamma‐ glutamyltransferase 2 TGM2 2.4190 2.3812 0.6900 0.0866 0.0837 0.6726 Protein‐glutamine gamma‐ glutamyltransferase E TGM3 2.4639 3.0771 1.3428 0.0802 0.0261 0.3775 Thrombospondin‐1 THBS1 1.0717 ‐0.5957 ‐1.3153 0.4988 0.7109 0.3870 Thrombospondin type‐1 domain‐ containing protein 7A THSD7A ‐3.8943 ‐1.4686 1.2113 0.0070 0.3035 0.4332 Tubulointerstitial nephritis antigen TINAG ‐0.5970 ‐5.3601 ‐4.8568 0.7381 0.0006 0.0018 Cluster of Tubulointerstitial nephritis antigen‐like TINAGL1 0.3177 0.9971 0.7627 0.8624 0.5097 0.6422 Cluster of Tight junction protein ZO‐1 TJP1 ‐3.2181 ‐4.2185 ‐1.9497 0.0234 0.0039 0.1817 Triokinase/FMN cyclase TKFC ‐4.9617 ‐1.9655 1.4508 0.0010 0.1569 0.3347 Isoform 2 of Transketolase TKT 1.0478 ‐1.0703 ‐1.7650 0.5102 0.4739 0.2305

Cluster of Talin‐1 TLN1 ‐0.7321 ‐1.7787 ‐1.2478 0.6728 0.2032 0.4181 Transmembrane emp24 domain‐ containing protein 2 TMED2 9.8907 6.1835 ‐0.6673 0.0000 0.0002 0.6868 Stimulator of interferon genes protein TMEM173 4.5409 2.7734 ‐0.3707 0.0021 0.0449 0.8357 Transmembrane protein 43 TMEM43 10.9681 6.9765 ‐0.6228 0.0000 0.0001 0.7114 Tropomodulin‐1 TMOD1 0.2501 4.3571 4.1082 0.8898 0.0031 0.0062 Tropomodulin‐3 TMOD3 ‐1.3153 ‐3.4557 ‐2.4972 0.3825 0.0137 0.0786 Cluster of Lamina‐associated polypeptide 2, isoforms beta/gamma TMPO 8.0226 5.2087 ‐0.3516 0.0000 0.0007 0.8445 Thymosin beta‐4 TMSB4X 0.2604 ‐1.8208 ‐1.9654 0.8852 0.1938 0.1775 Cluster of Isoform 4 of Tenascin TNC 1.9606 0.9601 ‐0.3931 0.1721 0.5291 0.8256 182 kDa tankyrase‐1‐binding protein TNKS1BP1 ‐1.2581 ‐1.7288 ‐0.8404 0.4057 0.2150 0.6085 Tensin‐1 TNS1 ‐0.0865 ‐1.0650 ‐0.9869 0.9632 0.4755 0.5268 Isoform 4 of Tensin‐2 TNS2 ‐1.0641 ‐4.3669 ‐3.5631 0.5027 0.0031 0.0156 Tensin‐3 TNS3 ‐0.6989 ‐2.7039 ‐2.1790 0.6868 0.0500 0.1284 Toll‐interacting protein TOLLIP 7.0962 4.2473 ‐0.6645 0.0000 0.0037 0.6881 Isoform 5 of TOM1‐like protein 2 TOM1L2 ‐3.3703 ‐3.2195 ‐0.8650 0.0179 0.0204 0.5978 Isoform 3 of Torsin‐1A‐interacting protein 1 TOR1AIP1 1.7905 2.7193 1.4502 0.2158 0.0486 0.3347 Isoform 3 of Tumor protein D52 TPD52 ‐2.3309 5.9951 7.4754 0.0989 0.0002 0.0000 Isoform 2 of Triosephosphate isomerase TPI1 1.5625 ‐2.1943 ‐3.2195 0.2896 0.1118 0.0259 Isoform 5 of Tropomyosin alpha‐1 chain TPM1 0.1365 ‐1.0031 ‐1.0781 0.9430 0.5063 0.4902 Cluster of Isoform 2 of Tropomyosin alpha‐3 chain TPM3 ‐0.0457 ‐0.6514 ‐0.6085 0.9751 0.6880 0.7193 Tripeptidyl‐peptidase 1 TPP1 0.1937 ‐0.7612 ‐0.8794 0.9192 0.6348 0.5883 Tubulin polymerization‐promoting protein family member 3 TPPP3 ‐17.4048 ‐12.8974 ‐0.8056 0.0000 0.0000 0.6255 Nucleoprotein TPR TPR ‐1.4924 1.0441 2.0422 0.3158 0.4857 0.1578 Transformer‐2 protein homolog alpha TRA2A 10.2794 6.0201 ‐1.0926 0.0000 0.0002 0.4839 Isoform 3 of Transformer‐2 protein homolog beta TRA2B 0.5805 ‐0.6018 ‐0.9865 0.7438 0.7089 0.5268 Isoform Beta of E3 ubiquitin‐ protein ligase TRIM23 TRIM23 7.2391 3.3658 ‐1.6274 0.0000 0.0160 0.2744 E3 ubiquitin/ISG15 ligase TRIM25 TRIM25 3.0948 1.6368 ‐0.5014 0.0289 0.2440 0.7734 Transcription intermediary factor 1‐beta TRIM28 0.6719 ‐1.1352 ‐1.5726 0.7017 0.4435 0.2922 TSC22 domain family protein 1 TSC22D1 9.1469 ‐0.5675 ‐6.7898 0.0000 0.7246 0.0001 Thiosulfate sulfurtransferase TST 12.7779 8.7206 ‐0.1433 0.0000 0.0000 0.9298 Transthyretin TTR 4.8502 0.3711 ‐2.9404 0.0012 0.8259 0.0401 Cluster of Tubulin alpha‐1B chain TUBA1B 0.5730 ‐2.0419 ‐2.3956 0.7463 0.1380 0.0926 Cluster of Tubulin beta chain TUBB 0.0784 ‐1.7633 ‐1.7849 0.9647 0.2069 0.2255 Elongation factor Tu, mitochondrial TUFM ‐0.4158 2.1495 2.3941 0.8183 0.1189 0.0926

Isoform 4 of Twinfilin‐1 TWF1 ‐2.9682 3.7117 5.6673 0.0356 0.0092 0.0005 Twinfilin‐2 TWF2 2.5664 1.5994 ‐0.1781 0.0685 0.2556 0.9180 Thioredoxin TXN 0.3017 ‐3.8309 ‐3.9674 0.8708 0.0076 0.0078 Thioredoxin domain‐containing protein 17 TXNDC17 0.5311 ‐0.1370 ‐0.4965 0.7673 0.9286 0.7743 Isoform 2 of Thioredoxin domain‐ containing protein 5 TXNDC5 ‐7.9683 ‐0.4313 5.0060 0.0000 0.7991 0.0014 Thioredoxin‐like protein 1 TXNL1 6.3709 0.3240 ‐4.0229 0.0001 0.8449 0.0071 Cluster of Thioredoxin reductase 1, cytoplasmic TXNRD1 ‐5.8755 ‐0.2709 3.7375 0.0002 0.8669 0.0116 Isoform 2 of Thymidine phosphorylase TYMP 1.8199 1.2493 ‐0.0133 0.2083 0.3914 0.9917 Tyrosine‐protein kinase receptor TYRO3 TYRO3 ‐3.7344 ‐0.2617 2.2876 0.0093 0.8711 0.1084 Isoform 2 of Splicing factor U2AF 65 kDa subunit U2AF2 ‐2.6268 4.0295 5.7468 0.0627 0.0054 0.0004 Isoform 2 of Uveal autoantigen with coiled‐coil domains and ankyrin repeats UACA 1.1954 ‐0.4326 ‐1.2393 0.4361 0.7991 0.4209 Ubiquitin‐like modifier‐activating enzyme 1 UBA1 1.8033 ‐2.4075 ‐3.5929 0.2130 0.0804 0.0149 Isoform 2 of Ubiquitin‐associated protein 2‐like UBAP2L 3.2235 1.7826 ‐0.4459 0.0232 0.2023 0.7961 Isoform 2 of Ubiquitin‐conjugating enzyme E2 K UBE2K 4.2460 2.3198 ‐0.6152 0.0037 0.0920 0.7150 Cluster of Isoform 3 of Ubiquitin‐ conjugating enzyme E2 L3 UBE2L3 ‐8.9207 ‐8.2456 ‐2.0186 0.0000 0.0000 0.1630 Ubiquitin‐conjugating enzyme E2 N UBE2N ‐1.0065 ‐3.5037 ‐2.7548 0.5280 0.0128 0.0542 Cluster of Ubiquilin‐4 UBQLN4 ‐11.5393 ‐2.4615 5.4455 0.0000 0.0735 0.0007 Isoform 2 of UBX domain‐ containing protein 1 UBXN1 6.7558 3.4572 ‐1.2084 0.0000 0.0137 0.4346 Ubiquitin carboxyl‐terminal hydrolase isozyme L1 UCHL1 10.1611 6.5563 ‐0.4855 0.0000 0.0001 0.7795 Isoform 2 of E3 UFM1‐protein ligase 1 UFL1 ‐2.5639 ‐0.2470 1.5045 0.0685 0.8785 0.3157 ‐ Ubiquitin‐fold modifier 1 UFM1 ‐1.6475 ‐11.7516 10.4173 0.2614 0.0000 0.0000 UDP‐glucose 6‐dehydrogenase UGDH 6.4837 3.2360 ‐1.2402 0.0001 0.0199 0.4209 Isoform 2 of UDP‐ glucose:glycoprotein glucosyltransferase 1 UGGT1 0.7535 1.5604 1.0189 0.6609 0.2673 0.5159 Isoform 2 of UTP‐‐glucose‐1‐ phosphate uridylyltransferase UGP2 ‐6.7496 ‐0.0774 4.5231 0.0000 0.9575 0.0032 Cluster of UDP‐ glucuronosyltransferase 2B7 UGT2B7 ‐11.9495 0.2320 8.3700 0.0000 0.8861 0.0000 Isoform 4 of Uromodulin UMOD 14.5006 9.4147 ‐0.6354 0.0000 0.0000 0.7047 Protein unc‐45 homolog A UNC45A 0.1479 ‐1.2874 ‐1.3650 0.9399 0.3772 0.3669 Cytochrome b‐c1 complex subunit 1, mitochondrial UQCRC1 0.3174 0.4994 0.2741 0.8624 0.7672 0.8827 Cytochrome b‐c1 complex subunit 2, mitochondrial UQCRC2 ‐0.3931 ‐0.2451 0.0272 0.8252 0.8794 0.9864

Isoform 2 of General vesicular transport factor p115 USO1 1.9509 ‐0.2087 ‐1.5342 0.1736 0.8954 0.3064 Ubiquitin carboxyl‐terminal hydrolase 14 USP14 ‐1.2200 0.2055 1.0330 0.4248 0.8969 0.5094 Isoform Short of Ubiquitin carboxyl‐terminal hydrolase 5 USP5 ‐1.0444 ‐0.8991 ‐0.1712 0.5121 0.5581 0.9223 Isoform 2 of Probable ubiquitin carboxyl‐terminal hydrolase FAF‐X USP9X 0.0386 0.1325 0.1038 0.9788 0.9309 0.9527 Isoform 2 of Utrophin UTRN ‐0.8331 ‐3.6814 ‐3.0475 0.6182 0.0097 0.0335 Cluster of Vesicle‐associated membrane protein 3 VAMP3 ‐2.7228 17.4890 19.0291 0.0536 0.0000 0.0000 Valine‐‐tRNA ligase VARS 1.4077 ‐0.6151 ‐1.5632 0.3444 0.7052 0.2941 Vasorin VASN 0.1679 ‐2.6270 ‐2.6941 0.9306 0.0566 0.0586 Vasodilator‐stimulated phosphoprotein VASP 9.2910 5.1940 ‐1.2303 0.0000 0.0008 0.4244 Synaptic vesicle membrane protein VAT‐1 homolog VAT1 2.0787 0.3102 ‐1.1117 0.1447 0.8505 0.4758 Cluster of Isoform 1 of Vinculin VCL ‐1.2180 ‐2.0967 ‐1.2289 0.4256 0.1273 0.4244 Transitional endoplasmic reticulum ATPase VCP ‐0.0472 ‐2.1896 ‐2.1180 0.9748 0.1126 0.1407 Voltage‐dependent anion‐ selective channel protein 1 VDAC1 2.4081 ‐0.5597 ‐2.1905 0.0881 0.7291 0.1271 Isoform 1 of Voltage‐dependent anion‐selective channel protein 2 VDAC2 0.6694 ‐3.1003 ‐3.5006 0.7031 0.0251 0.0171 Cluster of Vimentin VIM ‐0.7016 ‐1.9199 ‐1.4073 0.6868 0.1677 0.3533 Vacuolar protein sorting‐ associated protein 26B VPS26B 3.6097 2.1423 ‐0.3559 0.0118 0.1199 0.8423 Vacuolar protein sorting‐ associated protein 35 VPS35 ‐0.3956 0.4286 0.6905 0.8251 0.7991 0.6726 Isoform 2 of Vacuolar protein sorting‐associated protein 52 homolog VPS52 0.6212 ‐1.0513 ‐1.4556 0.7284 0.4823 0.3336 Vitronectin VTN 1.0914 0.9748 0.2136 0.4868 0.5222 0.9027 von Willebrand factor A domain‐ containing protein 1 VWA1 1.1862 ‐2.0900 ‐2.8606 0.4400 0.1282 0.0448 von Willebrand factor VWF ‐2.9410 0.2189 2.2189 0.0374 0.8920 0.1221 Tryptophan‐‐tRNA ligase, cytoplasmic WARS 0.8191 ‐1.9624 ‐2.4851 0.6243 0.1575 0.0802 Wiskott‐Aldrich syndrome protein family member 2 WASF2 ‐0.6570 0.9592 1.3895 0.7075 0.5291 0.3588 WD repeat‐containing protein 1 WDR1 0.1087 ‐1.1662 ‐1.2193 0.9526 0.4280 0.4291 Skin‐specific protein 32 XP32 ‐20.8516 ‐0.2834 13.9296 0.0000 0.8619 0.0000 Isoform 3 of Xaa‐Pro aminopeptidase 1 XPNPEP1 ‐0.7765 ‐4.7186 ‐4.1044 0.6479 0.0017 0.0062 Exportin‐7 XPO7 0.6469 1.2841 0.8201 0.7119 0.3779 0.6196 X‐ray repair cross‐complementing protein 5 XRCC5 1.7141 0.3922 ‐0.7828 0.2388 0.8170 0.6349 X‐ray repair cross‐complementing protein 6 XRCC6 2.4830 ‐0.6267 ‐2.3072 0.0782 0.7002 0.1048 Y‐box‐binding protein 1 YBX1 0.4901 0.7032 0.3566 0.7811 0.6580 0.8423 Y‐box‐binding protein 2 YBX2 ‐13.0370 ‐9.0817 ‐0.0348 0.0000 0.0000 0.9811

Isoform 2 of Y‐box‐binding protein 3 YBX3 ‐1.0402 8.5390 9.0938 0.5122 0.0000 0.0000 Isoform 1 of YLP motif‐containing protein 1 YLPM1 ‐0.5958 ‐1.2847 ‐0.8556 0.7383 0.3779 0.6021 Isoform Short of 14‐3‐3 protein beta/alpha YWHAB 2.2573 ‐1.9701 ‐3.4727 0.1101 0.1560 0.0178 14‐3‐3 protein epsilon YWHAE 1.5628 ‐2.4868 ‐3.5068 0.2896 0.0704 0.0169 14‐3‐3 protein gamma YWHAG 0.8059 ‐2.5900 ‐3.0925 0.6330 0.0600 0.0312 14‐3‐3 protein eta YWHAH 2.6409 ‐0.6005 ‐2.3892 0.0615 0.7089 0.0931 14‐3‐3 protein theta YWHAQ 1.8926 ‐0.0927 ‐1.3806 0.1894 0.9509 0.3607 14‐3‐3 protein zeta/delta YWHAZ 1.6287 ‐2.0463 ‐3.1192 0.2684 0.1373 0.0301 Zymogen granule protein 16 homolog B ZG16B 12.8997 9.1917 0.2365 0.0000 0.0000 0.8948 Cluster of Isoform 6 of Zinc finger protein 185 ZNF185 ‐3.3623 ‐1.4401 0.8768 0.0182 0.3130 0.5897 Zyxin ZYX ‐0.1939 ‐0.7790 ‐0.6329 0.9192 0.6253 0.7062

Supplemental Table 2. Gene Names of Glomerular ECM Proteins Identified in NC, FSGS-NOS, and cFSGS Normal CFSGS FSGS-NOS A2M A2M A2M AGRN AGRN AGRN AGT AGT AGT ALB ALB ALB AMBP AMBP AMBP ANGPTL6 ANGPTL6 ANGPTL6 ANXA1 ANXA1 ANXA1 ANXA11 ANXA11 ANXA11 ANXA2 ANXA2 ANXA2 ANXA4 ANXA3 ANXA4 ANXA5 ANXA4 ANXA5 ANXA6 ANXA5 ANXA6 APCS ANXA6 ANXA7 APOA1 ANXA7 APCS APOA4 APCS APOA1 APOE APOA1 APOA4 C1QA APOA4 APOE C1QB APOC3 BGN C1QC APOE C1QA C3 AZU1 C1QB C5 C1QA C1QC C6 C1QB C3 C7 C1QC C5 C8A C3 C6 C8G C5 C7 C9 C6 C8A CFHR5 C7 C8B CLU C8A C8G COL18A1 C8B C9 COL1A1 C8G CFHR5 COL1A2 C9 CLU COL3A1 CFHR5 COL12A1 COL4A1 CLU COL15A1 COL4A2 COL12A1 COL18A1 COL4A3 COL15A1 COL1A1 COL4A4 COL18A1 COL1A2 COL4A5 COL1A1 COL2A1 COL6A1 COL1A2 COL3A1

COL6A2 COL2A1 COL4A1 COL6A3 COL3A1 COL4A2 COPA COL4A1 COL4A3 CSTB COL4A2 COL4A4 CTSD COL4A3 COL4A5 CTSZ COL4A4 COL6A1 EMILIN1 COL4A5 COL6A2 F2 COL6A1 COL6A3 F9 COL6A2 COL7A1 FBLN1 COL6A3 COPA FBN1 COL7A1 CSTA FGA COPA CSTB FGB CRIM1 CTSD FGF1 CSPG4 CTSZ FGG CSTA DCD FN1 CSTB DST GNAS CTSC EFEMP1 GPI CTSD EMILIN1 GPX3 CTSG F2 GSN CTSZ F9 HP DCD FBLN1 HPX ECM1 FBLN5 HRG EFEMP1 FBN1 HRNR ELANE FGA HSD17B12 EMILIN1 FGB HSPG2 F12 FGF1 IGHG4 F2 FGG ITIH1 F9 FLG2 ITIH2 FBLN1 FN1 ITIH4 FBLN5 GNAS LAMA2 FBN1 GPI LAMA5 FBN2 GPX3 LAMB1 FGA GSN LAMB2 FGB HP LAMC1 FGF1 HPX LGALS1 FGG HRG LGALS3BP FLG2 HRNR LUM FN1 HSD17B12 LYZ GNAS HSPG2 MMRN2 GPI HTRA1 MPO GPX3 IGHG4 NID1 GSN ITIH1 NID2 HP ITIH2

NPNT HPX ITIH4 PAPLN HRG LAMA2 PEBP1 HRNR LAMA5 PLG HSD17B12 LAMB1 POSTN HSPG2 LAMB2 PPIA IGFALS LAMC1 RBP4 IGFBP7 LGALS1 S100A11 IGHG4 LGALS3BP SBSPON ITIH1 LPA SERPINA1 ITIH2 LRG1 SERPINA3 ITIH4 LRP2 SERPINB1 ITIH5 LUM SERPINB12 KNG1 LYZ SERPINB6 LAMA2 MFGE8 SERPINC1 LAMA4 MMRN2 SERPINF1 LAMA5 MPO SERPINF2 LAMB1 NID1 SERPINH1 LAMB2 NID2 TGFBI LAMC1 NPNT TGM2 LGALS1 NTN4 THBS1 LGALS3 PAPLN TINAG LGALS3BP PEBP1 TINAGL1 LGALS7 PLG TNC LMAN1 POSTN TTR LPA PPIA VTN LRG1 PRG2 VWA1 LUM PXDN VWF LYZ RBP4 MFGE8 S100A11 MMRN2 S100A16 MPO S100A8 NID1 SAA1 NID2 SBSPON NPNT SERPINA1 PAPLN SERPINA3 PEBP1 SERPINB1 PLG SERPINB12 PLOD3 SERPINB6 POSTN SERPINC1 PPIA SERPINF1 PRG2 SERPINF2 PRG3 SERPING1 PRSS23 SERPINH1

PXDN TGFBI RBP4 TGM2 S100A11 TGM3 S100A16 THBS1 S100A8 TINAG S100A9 TINAGL1 SBSPON TNC SERPINA1 TTR SERPINA3 VTN SERPINB1 VWA1 SERPINB12 VWF SERPINB6 SERPINC1 SERPIND1 SERPINF1 SERPINF2 SERPING1 SERPINH1 TGFBI TGM2 TGM3 THBS1 TINAG TINAGL1 TNC TTR VTN UMOD VWA1 VWF

Supplemental Table 3. Relative Abundance of Glomerular ECM Proteins

Core Basement Membrane Matrisome

Protein Gene Matrisome Fold change log2FC Fold Log2FC Category cFSGS: NC change NOS: NC

Collagen alpha-1(XV) COL15A1 Collagens >10 >4.0 >10 >4.0

Collagen alpha-1(XVIII) COL18A1 Collagens 1.8 0.8 1.5 0.58

Collagen alpha-1(II) COL2A1 Collagens >10 >4.0 >10 >4.0

Collagen alpha-1 (III) COL3A1 Collagens 1.8 0.8 5.3 2.41

Collagen alpha-1 (IV) COL4A1 Collagens 1.0 0.0 1.8 0.85

Collagen alpha-2 (IV) COL4A2 Collagens 1.4 0.5 2.4 1.26

Collagen alpha-3 (IV) COL4A3 Collagens 1.4 0.5 1.4 0.49

Collagen alpha-4 (IV) COL4A4 Collagens 1.3 0.4 1.1 0.14

Collagen alpha-5 (IV) COL4A5 Collagens 1.0 0.0 0.8 0.32

Collagen alpha-1 (VII) COL7A1 Collagens >10 >4.0 >10 >4.0

Agrin AGRN ECM 1.2 0.3 1.2 0.26 Glycoproteins

EGF-containing fibulin-like EFEMP1 ECM >10 >4.0 >10 >4.0 extracellular matrix protein 1 Glycoproteins

Fibulin-1 FBLN1 ECM 0.8 -0.3 1.5 0.58 Glycoproteins

Fibrillin-1 FBN1 ECM 0.8 -0.3 0.8 0.32 Glycoproteins

Fibronectin FN1 ECM 1.6 0.7 1.5 0.58 Glycoproteins

Laminin subunit alpha-2 LAMA2 ECM 5.3 2.4 0.6 0.74 Glycoproteins

Laminin subunit alpha-4 LAMA4 ECM >10 >4.0 1.0 0.00 Glycoproteins

Laminin subunit alpha-5 LAMA5 ECM 1.0 0.0 0.9 0.15 Glycoproteins

Laminin subunit beta-1 LAMB1 ECM 3.6 1.8 1.0 0.00 Glycoproteins

Laminin subunit beta-2 LAMB2 ECM 1.1 0.1 1.1 0.14 Glycoproteins

Laminin subunit gamma-1 LAMC1 ECM 1.2 0.3 1.0 0.00 Glycoproteins

Multimerin-2 MMRN2 ECM 0.4 -1.3 0.4 1.30 Glycoproteins

Nidogen-1 NID1 ECM 1.1 0.1 1.1 0.14 Glycoproteins

Nidogen-2 NID2 ECM 1.0 0.0 1.0 0.00 Glycoproteins

Nephronectin NPNT ECM 1.1 0.1 2.4 1.26 Glycoproteins

Netrin-4 NTN4 ECM 1.0 0.0 1.0 0.00 Glycoproteins

Papilin PAPLN ECM 0.5 -1.0 0.9 0.15 Glycoproteins

Transforming growth factor-beta- TGFBI ECM 0.8 -0.3 0.8 0.32 induced protein ig-h3 Glycoproteins

Tenascin TNC ECM 2.6 1.4 1.6 0.68 Glycoproteins

von Willebrand factor A domain- VWA1 ECM 0.8 -0.3 0.8 0.32 containing protein 1 Glycoproteins

Basement membrane-specific HSPG2 Proteoglycan 1.0 0.0 1.0 0.00 heparan sulfate proteoglycan core s protein

Core Structural Matrisome

Collagen alpha-1 (XII) COL12A1 Collagens >10 >4.0 >10 >4.0

Collagen alpha-1 (I) COL1A1 Collagens 1.3 0.4 6.9 2.79

Collagen alpha-1 (I) COL1A2 Collagens 1.8 0.8 9.5 3.25

Collagen alpha-1 (VI) COL6A1 Collagens 0.8 -0.3 1.1 0.14

Collagen alpha-2 (VI) COL6A2 Collagens 0.8 -0.3 1.2 0.26

Collagen alpha-3 (VI) COL6A3 Collagens 0.8 -0.3 1.2 0.26

Cysteine-rich motor neuron 1 CRIM1 ECM >10 >4.0 1.0 0.00 protein Glycoproteins

Extracellular matrix protein 1 ECM1 ECM >10 >4.0 1.0 0.00 Glycoproteins

Elastin microfibril interfacer 1 EMILIN1 ECM 2.6 1.4 3.3 1.72 Glycoproteins

Fibulin-5 FBLN5 ECM >10 >4.0 >10 >4.0 Glycoproteins

Fibrillin-2 FBN2 ECM >10 >4.0 1.0 0.00 Glycoproteins

Fibrinogen alpha chain FGA ECM 1.0 0.0 3.0 1.58 Glycoproteins

Fibrinogen beta chain FGB ECM 0.9 -0.2 2.0 1.00 Glycoproteins

Fibrinogen gamma chain FGG ECM 0.8 -0.3 1.4 0.49 Glycoproteins

Insulin-like growth factor-binding IGFALS ECM >10 >4.0 1.0 0.00 protein complex acid labile Glycoproteins subunit

Insulin-like growth factor-binding IGFBP7 ECM >10 >4.0 1.0 0.00 protein 7 Glycoproteins

Leucine-rich alpha-2-glycoprotein LRG1 ECM >10 >4.0 >10 >4.0 Glycoproteins

Lactadherin MFGE8 ECM >10 >4.0 >10 >4.0 Glycoproteins

Periostin POSTN ECM 7.3 2.9 6.3 2.66 Glycoproteins

Peroxidasin PXDN ECM >10 >4.0 >10 >4.0 Glycoproteins

Somatomedin-B and SBSPON ECM 0.4 -1.3 0.4 1.32 thrombospondin type-1 domain- Glycoproteins containing protein

Thrombospondin-1 THBS1 ECM 1.0 0.0 0.8 0.32 Glycoproteins

Tubulointerstitial nephritis antigen- TINAGL1 ECM 1.4 0.5 1.6 0.68 like Glycoproteins

Uromodulin UMOD ECM >10 >4.0 1.0 0.00 Glycoproteins

Vitronectin VTN ECM 2.3 1.2 2.0 1.00 Glycoproteins

von Willebrand factor VWF ECM 7.0 2.8 >10 >4.0 Glycoproteins

Biglycan BGN Proteoglycan 1.0 0.0 >10 >4.0 s

Lumican LUM Proteoglycan 0.3 -1.7 1.8 0.85 s

Proteoglycan 2 PRG2 Proteoglycan >10 >4.0 >10 >4.0 s

Proteoglycan 3 PRG3 Proteoglycan >10 >4.0 1.0 0.00 s

Matrisome Associated

Alpha-2-macroglobulin A2M ECM 0.7 -0.5 0.5 1.00 Regulators

Angiotensinogen AGT ECM 1.8 0.8 0.7 0.51 Regulators

Alpha-1-microglobulin/bikunin AMBP ECM 4.7 2.2 7.4 2.89 precursor Regulators

Angiopoietin-related protein 6 ANGPTL6 ECM 0.9 -0.2 1.0 0.00 Regulators

Azurocidin AZU1 ECM >10 >4.0 1.0 0.00 Regulators

Cystatin-A CSTA ECM >10 >4.0 >10 >4.0 Regulators

Cystatin-B CSTB ECM 0.4 -1.3 0.4 1.32 Regulators

Cathepsin B CTSB ECM >10 >4.0 1.5 0.58 Regulators

Cathepsin C CTSC ECM >10 >4.0 1.0 0.00 Regulators

Cathepsin D CTSD ECM 1.2 0.3 3.0 1.58 Regulators

Cathepsin G CTSG ECM >10 >4.0 1.0 0.00 Regulators

Cathepsin Z CTSZ ECM 2.5 1.3 2.1 1.07 Regulators

Neutrophil elastase ELANE ECM >10 >4.0 1.0 0.00 Regulators

Coagulation factor XII F12 ECM >10 >4.0 1.0 0.00 Regulators

Prothrombin F2 ECM 2.2 1.1 1.0 0.00 Regulators

Coagulation factor IX F9 ECM 2.2 1.1 2.3 1.20 Regulators

Histidine-rich glycoprotein HRG ECM 0.7 -0.5 0.9 0.15 Regulators

HtrA serine peptidase 1 HTRA1 ECM 1.0 0.0 >10 >4.0 Regulators

Inter-alpha-trypsin inhibitor heavy ITIH1 ECM 1.4 0.5 0.7 0.51 chain H1 Regulators

Inter-alpha-trypsin inhibitor heavy ITIH2 ECM 1.0 0.0 0.6 0.74 chain H2 Regulators

Inter-alpha-trypsin inhibitor heavy ITIH4 ECM 0.6 -0.7 3.0 1.58 chain H4 Regulators

Inter-alpha-trypsin inhibitor heavy ITIH5 ECM >10 >4.0 1.0 0.00 chain H5 Regulators

Kininogen-1 KNG1 ECM >10 >4.0 1.0 0.00 Regulators

Apolipoprotein(a) LPA ECM >10 >4.0 >10 >4.0 Regulators

Myeloperoxidase MPO ECM >10 >4.0 7.9 2.98 Regulators

Plasminogen PLG ECM 8.7 3.1 4.6 2.20 Regulators

Procollagen-lysine,2-oxoglutarate PLOD3 ECM >10 >4.0 1.0 0.00 5-dioxygenase 3 Regulators

Serine protease 23 PRSS23 ECM >10 >4.0 1.0 0.00 Regulators

Serum amyloid A-1 protein SAA1 ECM 1.0 0.0 >10 >4.0 Regulators

Serpin family A member 1 SERPINA1 ECM 0.6 -0.7 1.1 0.14 Regulators

Serpin family A member 3 SERPINA3 ECM 1.4 0.5 2.2 1.14 Regulators

Serpin family B member 1 SERPINB1 ECM 0.5 -1.0 0.8 0.32 Regulators

Serpin family B member 12 SERPINB1 ECM 0.5 -1.0 1.1 0.14 2 Regulators

Serpin family B member 6 SERPINB6 ECM 0.4 -1.3 1.4 0.49 Regulators

Serpin family C member 1 SERPINC1 ECM 2.0 1.0 1.2 0.26 Regulators

Serpin family D member 1 SERPIND1 ECM >10 >4.0 1.0 0.00 Regulators

Serpin family F member 1 SERPINF1 ECM 1.1 0.1 1.5 0.58 Regulators

Serpin family F member 2 SERPINF2 ECM 1.4 0.5 <0.1 >4.0 Regulators

Serpin family G member 1 SERPING1 ECM >10 >4.0 >10 >4.0 Regulators

Serpin family H member 1 SERPINH1 ECM 0.9 -0.2 0.8 0.32 Regulators

Transglutaminase 2 TGM2 ECM 2.7 1.4 2.0 1.00 Regulators

Transglutaminase 3 TGM3 ECM >10 >4.0 >10 >4.0 Regulators

Transthyretin TTR ECM 1.8 0.8 0.3 1.74 Regulators

Annexin A1 ANXA1 ECM-affiliated 2.1 1.1 2.9 1.54 Proteins

Annexin A11 ANXA11 ECM-affiliated 0.9 -0.2 1.5 0.58 Proteins

Annexin A2 ANXA2 ECM-affiliated 1.1 0.1 1.2 0.26 Proteins

Annexin A3 ANXA3 ECM-affiliated >10 >4.0 1.0 0.00 Proteins

Annexin A4 ANXA4 ECM-affiliated 2.1 1.1 2.5 1.32 Proteins

Annexin A5 ANXA5 ECM-affiliated 1.0 0.0 1.0 0.00 Proteins

Annexin A6 ANXA6 ECM-affiliated 1.2 0.3 1.5 0.58 Proteins

Annexin A7 ANXA7 ECM-affiliated >10 >4.0 >10 >4.0 Proteins

Serum amyloid P-component APCS ECM-affiliated 8.3 3.1 8.4 3.07 Proteins

Apolipoprotein A-I APOA1 ECM-affiliated 0.6 -0.7 0.8 0.32 Proteins

Apolipoprotein A-IV APOA4 ECM-affiliated 2.7 1.4 5.2 2.38 Proteins

Apolipoprotein C-III APOC3 ECM-affiliated 1.0 0.0 1.0 0.00 Proteins

Apolipoprotein E APOE ECM-affiliated 2.4 1.3 2.9 1.54 Proteins

Complement C1q subcomponent C1QA ECM-affiliated 0.2 -2.3 <0.1 >4.0 subunit A Proteins

Complement C1q subcomponent C1QB ECM-affiliated 2.1 1.1 <0.1 >4.0 subunit B Proteins

Complement C1q subcomponent C1QC ECM-affiliated 1.2 0.3 <0.1 >4.0 subunit C Proteins

Complement C3 C3 ECM-affiliated 1.4 0.5 0.9 0.15 Proteins

Complement C5 C5 ECM-affiliated >10 >4.0 >10 >4.0 Proteins

Complement C6 C6 ECM-affiliated >10 >4.0 >10 >4.0 Proteins

Complement C7 C7 ECM-affiliated >10 >4.0 >10 >4.0 Proteins

Complement component C8 alpha C8A ECM-affiliated >10 >4.0 >10 >4.0 chain Proteins

Complement component C8 beta C8B ECM-affiliated >10 >4.0 >10 >4.0 chain Proteins

Complement component C8 C8G ECM-affiliated >10 >4.0 7.8 2.96 gamma chain Proteins

Complement component C9 C9 ECM-affiliated 3.8 1.9 3.8 1.93 Proteins

Complement factor H-related CFHR5 ECM-affiliated 0.5 -1.0 0.5 1.00 protein 5 Proteins

Clusterin CLU ECM-affiliated 2.3 1.2 2.5 1.32 Proteins

Coatomer subunit alpha COPA ECM-affiliated 2.1 1.1 0.9 0.15 Proteins

Chondroitin sulfate proteoglycan 4 CSPG4 ECM-affiliated >10 >4.0 1.0 0.00 Proteins

Dermcidin DCD ECM-affiliated >10 >4.0 >10 >4.0 Proteins

Dystonin DST ECM-affiliated 1.0 0.0 >10 >4.0 Proteins

Guanine nucleotide-binding GNAS ECM-affiliated 0.4 -1.3 0.5 1.00 protein G(s) subunit alpha Proteins isoforms XLas

Glucose-6-phosphate isomerase GPI ECM-affiliated 0.4 -1.3 0.5 1.00 Proteins

Glutathione peroxidase 3 GPX3 ECM-affiliated <0.1 >4.0 0.4 1.32 Proteins

Gelsolin GSN ECM-affiliated 0.5 -1.0 0.6 0.74 Proteins

Haptoglobin HP ECM-affiliated 1.6 0.7 1.6 0.68 Proteins

Hemopexin HPX ECM-affiliated 0.6 -0.7 0.5 1.00 Proteins

Very-long-chain 3-oxoacyl-CoA HSD17B12 ECM-affiliated 0.4 -1.3 <0.1 >4.0 reductase Proteins

Ig gamma-4 chain C region IGHG4 ECM-affiliated 0.3 -1.7 0.4 1.32 Proteins

Galectin-1 LGALS1 ECM-affiliated 1.2 0.3 1.5 0.58 Proteins

Galectin-3 LGALS3 ECM-affiliated >10 >4.0 1.0 0.00 Proteins

Galectin-7 LGALS7 ECM-affiliated >10 >4.0 1.0 0.00 Proteins

Lectin, mannose binding 1 LMAN1 ECM-affiliated >10 >4.0 1.0 0.00 Proteins

Low-density lipoprotein receptor- LRP2 ECM-affiliated 1.0 0.0 >10 >4.0 related protein 2 Proteins

Lysozyme C LYZ ECM-affiliated 0.4 -1.3 0.2 2.32 Proteins

Phosphatidylethanolamine- PEBP1 ECM-affiliated 0.3 -1.7 0.6 0.74 binding protein 1 Proteins

Peptidyl-prolyl cis-trans isomerase PPIA ECM-affiliated 0.5 -1.0 0.7 0.51 A Proteins

Retinol-binding protein 4 RBP4 ECM-affiliated 2.0 1.0 0.8 0.32 Proteins

Fibroblast growth factor 1 FGF1 Secreted 0.4 -1.3 <0.1 >4.0 Factors

Filaggrin-2 FLG2 Secreted >10 >4.0 >10 >4.0 Factors

Hornerin HRNR Secreted 1.6 0.7 0.5 1.00 Factors

S100 calcium binding protein A11 S100A11 Secreted 0.5 -1.0 0.4 1.32 Factors

S100 calcium binding protein A16 S100A16 Secreted >10 >4.0 >10 >4.0 Factors

S100 calcium binding protein A8 S100A8 Secreted >10 >4.0 >10 >4.0 Factors

S100 calcium binding protein A9 S100A9 Secreted >10 >4.0 1.0 0.00 Factors

Supplemental Table 4. Glomerular Cathepsin and Annexin A3 Staining of Various Diseases

Cathepsin C

Diagnosis # # #(%) # #(%) PEC # #(%) # Tuft Patients glomeruli PEC patients Hypertrophy/Proliferation patients Tuft patients staining (range/ staining staining area patient) (%) cFSGS 8 119 111 8 75 (63%) 8 47 (51 8 13.7 + (4-34) (93%) + 10%) 3.1 FSGS- 8 57 47 8 21 (37%) 5 4 (10 + 4 5.4 + NOS (4-14) (82%) 4%) 2.2 FSGS 7 110 110 7 69 (63%) 7 20 (19 6 7.6 + TIP (4-34) (100%) + 7%) 1.9 lesion FSGS 6 70 63 6 25 (36%) 5 7 (9 + 3 6.9 + perihilar (4-20) (90%) 4%) 2.0 MCD 9 87 83 9 34 (39%) 8 0 0 (4-17) (95%) MN 9 97 87 7 39 (40%) 7 6 (10 + 2 (4-14) (90%) 7%) NC 6 75 69 6 8 (11%) 2 0 0 (7-26) (92%)

Annexin A3

cFSGS 8 114 84 8 59 (52%) 8 26 (29 8 14.4 + (6-33) (74%) + 9%) 2.8 FSGS- 9 52 46 9 30 (58%) 7 0 0 0 NOS (4-13) (88%) FSGS 7 107 99 7 52 (48%) 7 5 (9 + 1 4.2 + TIP (7-37) (92%) 3%) 1.1 lesion FSGS 6 80 68 6 34 (42%) 6 7 (9 +/- 3 7.9 + perihilar (6-22) (85%) 5%) 5.6 MCD 8 91 85 8 35 (38%) 8 1 (2 + 1 (4-24) (93%) 2%) MN 9 111 106 9 53 (48%) 9 3 (3 + 2 (6-25) (95%) 3%)

NC 8 117 112 8 32 (27%) 8 0 0 (4-35) (96%)

Supplemental Table 5. Comparison of Urinary Excretion of ECM Proteins log2FC cFSGS: Protein Gene FSGS- q-value NOS ECM Proteins More Abundant in cFSGS Urine Syndecan-4 SDC4 6.37 9.97E‐08 Apolipoprotein(a) LPA 6.09 1.07E‐06 Matrix metalloproteinase-9 MMP9 6.09 2.83E‐05 Laminin subunit alpha-3 LAMA3 5.94 2.79E‐06 Fibulin-7 FBLN7 5.91 3.41E‐07 Insulin-like growth factor-binding protein 7 IGFBP7 5.90 9.97E‐08 Latent-transforming growth factor beta- binding protein 4 LTBP4 5.86 7.78E‐08 Hemicentin-1 HMCN1 5.46 1.93E‐07 Epidermal growth factor EGF 5.42 9.82E‐06 Secreted frizzled-related protein 4 SFRP4 5.39 9.97E‐08 Macrophage colony-stimulating factor 1 CSF1 5.34 2.02E‐06 C-type lectin domain family 14 member A CLEC14A 5.20 2.42E‐06 Fibrillin-1 FBN1 5.19 2.66E‐07 Cathepsin B CTSB 5.09 4.84E‐06 Collagen alpha-2(I) chain COL1A2 5.00 2.83E‐05 Chondroitin sulfate proteoglycan 4 CSPG4 4.95 2.02E‐06 Multiple epidermal growth factor-like domains protein 8 MEGF8 4.95 8.80E‐06 Semaphorin-5A SEMA5A 4.90 1.21E‐04 Brevican core protein BCAN 4.83 3.76E‐05 Stromal cell-derived factor 1 CXCL12 4.75 2.42E‐06 Serine protease HTRA1 HTRA1 4.74 5.66E‐04 Growth/differentiation factor 15 GDF15 4.66 4.84E‐06 Collagen alpha-2(VI) chain COL6A2 4.62 5.17E‐07 Mucin-like protein 1 MUCL1 4.60 2.94E‐04 Basement membrane-specific heparan sulfate proteoglycan core protein HSPG2 4.58 4.82E‐07 Hemicentin-2 HMCN2 4.57 3.57E‐07 Galectin-9 LGALS9 4.47 3.35E‐04 ADAMTS-like protein 2 ADAMTSL2 4.46 1.57E‐04 Collagen alpha-1(VI) chain COL6A1 4.41 6.19E‐06 Thrombospondin-1 THBS1 4.36 3.05E‐06 Cartilage intermediate layer protein 1 CILP 4.32 3.41E‐07 Fibulin-5 FBLN5 4.25 4.84E‐06 Agrin AGRN 4.14 7.10E‐04 Cartilage intermediate layer protein 2 CILP2 4.10 2.02E‐06

Collagen alpha-1(XV) chain COL15A1 3.97 6.53E‐05 Fibronectin FN1 3.94 2.42E‐06 Latent-transforming growth factor beta- binding protein 1 LTBP1 3.93 5.71E‐03 Protein S100-A6 S100A6 3.85 2.02E‐04 Thrombospondin-4 THBS4 3.82 4.84E‐06 Protein S100-A11 S100A11 3.61 8.72E‐04 Follistatin-related protein 1 FSTL1 3.60 1.08E‐04 C-C motif chemokine 25 CCL25 3.59 1.67E‐03 Dermatopontin DPT 3.58 2.83E‐05 Fibulin-1 FBLN1 3.57 3.65E‐05 Mucin-1 MUC1 3.57 1.32E‐04 Collagen alpha-1(I) chain COL1A1 3.52 9.38E‐04 Fibulin-2 FBLN2 3.50 7.10E‐04 Lithostathine-1-alpha REG1A 3.50 4.13E‐03 Collagen alpha-2(IV) chain COL4A2 3.50 2.02E‐06 Kininogen-1 KNG1 3.50 8.80E‐06 Extracellular sulfatase Sulf-2 SULF2 3.48 1.73E‐03 Neuroserpin SERPINI1 3.47 8.54E‐06 EGF-containing fibulin-like extracellular matrix protein 1 EFEMP1 3.46 1.78E‐05 Urokinase-type plasminogen activator PLAU 3.46 1.11E‐03 Cathepsin L1 CTSL 3.45 2.90E‐06 Bone marrow proteoglycan PRG2 3.32 2.83E‐05 Angiopoietin-related protein 2 ANGPTL2 3.30 5.97E‐05 Nidogen-1 NID1 3.29 7.45E‐04 Tetranectin CLEC3B 3.28 1.72E‐05 Mannan-binding lectin serine protease 2 MASP2 3.27 1.17E‐04 Phosphoinositide-3-kinase-interacting protein 1 PIK3IP1 3.22 7.65E‐04 Cystatin-M CST6 3.16 5.76E‐03 Proteoglycan 4 PRG4 3.13 4.43E‐03 Plasma serine protease inhibitor SERPINA5 3.11 3.47E‐04 Hyaluronidase-1 HYAL1 3.11 2.34E‐03 Laminin subunit alpha-4 LAMA4 3.08 2.94E‐04 Procollagen C-endopeptidase enhancer 1 PCOLCE 3.04 1.09E‐05 Plexin domain-containing protein 2 PLXDC2 3.02 4.76E‐05 Protein AMBP AMBP 2.98 1.66E‐04 Cartilage oligomeric matrix protein COMP 2.94 2.82E‐04 Collectin-12 COLEC12 2.74 6.86E‐03 Osteopontin SPP1 2.73 1.57E‐04 Collagen alpha-3(VI) chain COL6A3 2.62 0.0124 Trypsin-1 PRSS1 2.53 1.38E‐03

Metalloproteinase inhibitor 2 TIMP2 2.48 1.47E‐03 Cathepsin Z CTSZ 2.39 5.76E‐03 Multimerin-2 MMRN2 2.30 0.0104 EGF-containing fibulin-like extracellular matrix protein 2 EFEMP2 2.24 5.79E‐05 Elafin PI3 2.17 2.02E‐03 Plasma protease C1 inhibitor SERPING1 2.07 0.0126 Insulin-like growth factor-binding protein 2 IGFBP2 2.06 2.57E‐04 Glypican-3 GPC3 1.97 2.81E‐03 Cathepsin D CTSD 1.95 2.13E‐03 Cystatin-C CST3 1.94 0.0201 WNT1-inducible-signaling pathway protein 2 WISP2 1.82 0.0279 Cathepsin C CTSC 1.77 0.0258 Latent-transforming growth factor beta- binding protein 2 LTBP2 1.74 0.0311 Mucin-20 MUC20 1.73 0.0126 Tenascin-X TNXB 1.59 2.59E‐03 Cystatin-A CSTA 1.47 0.0771 Carboxypeptidase N subunit 2 CPN2 1.32 0.0465 Insulin-like growth factor-binding protein 6 IGFBP6 1.28 8.21E‐03 Fibrinogen alpha chain FGA 1.21 0.3079 Insulin-like growth factor II IGF2 1.20 0.0468 SPARC-like protein 1 SPARCL1 1.07 0.0315 Vitronectin VTN 0.99 0.1494 Inter-alpha-trypsin inhibitor heavy chain H4 ITIH4 0.75 0.3079 Hepatocyte growth factor activator HGFAC 0.64 0.2689 Protein S100-A9 S100A9 0.50 0.6984 Prothrombin F2 0.36 0.5848 Lysosomal protective protein CTSA 0.27 0.7104 Protein S100-A8 S100A8 0.09 0.9480 ECM Proteins More Abundant in FSGS-NOS Urine Coagulation factor XII F12 ‐0.04 0.9480 Leucine-rich alpha-2-glycoprotein LRG1 ‐0.09 0.9353 Cornulin CRNN ‐0.14 0.9350 Lumican LUM ‐0.43 0.5753 Serpin B4 SERPINB4 ‐1.10 0.3059 Extracellular matrix protein 1 ECM1 ‐1.41 0.0157 Hemopexin HPX ‐1.56 0.0774 Kallistatin SERPINA4 ‐1.92 0.0888 Plasminogen PLG ‐1.96 3.76E‐03 Hyaluronan-binding protein 2 HABP2 ‐2.24 8.14E‐03

Insulin-like growth factor-binding protein complex acid labile subunit IGFALS ‐2.41 1.15E‐03 Thyroxine-binding globulin SERPINA7 ‐2.43 2.98E‐03 Histidine-rich glycoprotein HRG ‐2.57 0.0435 Inter-alpha-trypsin inhibitor heavy chain H1 ITIH1 ‐2.61 0.0157 Fibrinogen beta chain FGB ‐2.65 0.0223 Alpha-2-antiplasmin SERPINF2 ‐2.72 3.73E‐04 Corticosteroid-binding globulin SERPINA6 ‐2.77 1.38E‐03 Alpha-1-antichymotrypsin SERPINA3 ‐2.77 6.04E‐05 Coagulation factor IX F9 ‐2.87 5.35E‐03 Alpha-2-macroglobulin A2M ‐2.91 7.12E‐03 Angiotensinogen AGT ‐3.05 3.61E‐03 Pigment epithelium-derived factor SERPINF1 ‐3.13 0.0129 Inter-alpha-trypsin inhibitor heavy chain H2 ITIH2 ‐3.31 3.47E‐04 Fibrinogen gamma chain FGG ‐3.42 3.84E‐03 Heparin cofactor 2 SERPIND1 ‐3.97 8.69E‐03 Antithrombin-III SERPINC1 ‐4.03 1.09E‐05 Alpha-1-antitrypsin SERPINA1 ‐4.51 1.65E‐06 Complement C3 C3 ‐4.88 5.47E‐04

Supplemental Table 6. Peptides derived from ECM Proteins Showing Increased Urine Excretion Gene Number of peptides Number of peptides (FSGS vs MCD) (cFSGS vs FSGS-NOS) ANXA1 1 0 COL18A1 2 0 COL1A1 2 2 COL1A2 3 2

COL4A1 1 0 COL5A2 2 1 F2 1 1

FGA 6 2 HPX 4 2 IGF2 2 2

INS 0 2 KNG1 1 0 LRG1 0 1

LTBP4 1 1 MASP2 6 1 MEP1A 1 1 MFAP5 0 1 NID1 2 1 PIK3IP1 1 1 PLG 5 1 S100A9 2 0 SERPINA1 11 10 SERPINA3 1 0 SERPINC1 1 0 SPP1 6 3

Patients with FSGS-NOS were 3 white females with mean + SEM serum creatinine of 0.96 + 0.27 mg/dl and mean + SEM urine protein/creatinine of 7463 + 1205 mg/gm. Patients with cFSGS were 2 males and 1 female, 2 of which were black with mean + SEM serum creatinine of 1.59 + 0.67 mg/dl and mean + SEM urine protein/creatinine of 7558 + 532 mg/gm.

Supplemental Table 7. Proteases Associated with Urine ECM Peptides Number of peptides with Peptides with similar urine increased urine excretion excretion between groups in FSGS or cFSGS (percent of total) Protease Group (percent of total) FSGS vs MCD Total = 66 Total = 299 matrix metalloproteinases (MMP) 13 (19.7) 105 (35.1) cathepsins (CTS) 7 (10.1) 29 (9.7) MMP + CTS 1 (1.5) 17 (5.7) MMP + misc 3 (4.5) 10 (3.3) Plasminogen (PLG) 0 (0) 18 (6.0) proprotein convertase subtilisin/kexin (PCSK) + misc 6 (9.1) 2 (0.7) misc 2 (3) 10 (3.3) All Proteases 32 (48.5) 191 (63.9)

cFSGS vs FSGS-NOS Total = 35 Total = 330 MMP 9 (25.7) 109 (33) CTS 4 (11.4) 32 (9.7) MMP + CTS 1 (2.8) 17 (5.2) MMP + misc 0 (0) 13 (3.9) PLG 0 (0) 18 (5.4) PCSK + misc 6 (17.1) 2 (0.6) misc 1 (2.8) 11 (3.3) All Proteases 21 (60) 202 (61.2)