(A) Sample Contribution to the PLS Model

SUPPLEMENTARY DATA

Supplementary Figure 1. Correlation of levels of auto-antibodies with disease duration. (A) Sample contribution to the PLS model. The bars represent the distances of individual samples to the PLS model, which represent the contribution of individual samples to the separation between T1DM and T2DM/NGT captured by the PLS model. A small distance indicates high contribution of the corresponding sample to the separation captured by the PLS model. The numbers in parenthesis in the x- axis labels of T1DM samples represent the disease durations in months. (B) Scatterplot of disease duration and sample contribution to the separation between T1DM and T2DM/NGT captured by the PLS model (i.e. distances of samples to the PLS model). The distances showed no significant correlation (r = –0.465 and P = 0.070) with disease durations of the individual samples.

Supplementary Figure 2. Expression of EEF1A1 and UBE2L3 in human tissues. Immunohistochemistry of tissue array showed that (A) EEF1A1 and (B) UBE2L3 were expressed in skin, liver, kidney, stomach, intestine, lung, adrenal gland, and thyroid gland as well as pancreas. Original magnification 400.

헑

Supplementary Figure 3. Detection of EEF1A1 and UBE2L3 auto-antibodies by immunoblotting. Three pairs of T1DM patient samples were selected from the second cohort based on their ELISA absorbance values categorized in three groups: high: >1.3, medium: <1.3 and >0.5, and low: <0.5 absorbance at 450 nm (A450nm). Immunoblots of EEF1A1 and UBE2L3 auto-antibodies of T1DM and NGT samples immunoprecipitated with EEF1A1-flag or UBE2L3-flag antigen are shown. (A) Heavy chain (HC) and light chain (LC) of EEF1A1-AAb from the T1DM sera with EEF1A1-AAb ELISA A450nm values of 2.4 and 1.8 (lane 1 and 2), 1.0 and 0.9 (lane 3 and 4), and 0.2 and 0.3 (lane 5 and 6). (B) HC and LC of UBE2L3-AAb from T1DM sera with UBE2L3-AAb ELISA A450nm values of 1.3 and 1.4 (lane 1 and 2), 0.6 and 0.5 (lane 3 and 4), and 0.3 and 0.2 (lane 5 and 6). Immunoblots of NGT with auto-antibody ELISA A450nm value of 0.2 in both EEF1A1 and UBE2L3 are shown in lane 8 and the control immunoprecipitates of human IgG are shown in lane 7 (A and B).

Supplementary Figure 4. Correlation of auto-antibody concentration estimated between ELISA and immunoprecipitation methods for EEF1A1-AAb and UBE2L3-AAb.Scatterplot depicting relative fold changes in A450nm of auto-antibody levels measured by ELISA (y-axis) compared to relative fold changes in density of auto-antibody levels measured by the immunoprecipitation method (x-axis). There are a significant correlation between them in both EEF1A1-AAb (r = 0.779, P = 0.039; A) and UBE2L3-AAb (r = 0.940, P = 0.002; B). Relative fold changes of auto-antibody levels were normalized to the levels of NGT.

Supplementary Figure 5. Positive correlation between the concentrations of EEF1A1-AAb and UBE2L3-AAb in the second cohort. The level of the auto-antibodies showed a significant correlation between EEF1A1-AAb and UBE2L3-AAb (r = 0.65, P<0.001).

Supplementary Figure 6. Auto-antibodies involved in T1DM-related pathophysiology in the pancreatic β-cells: insulin secretion, calcium ion homeostasis, cytokines, and glucose metabolism. The columns and rows in the heat map represent samples and auto-antibodies, respectively. Yellow and blue represent the increase and decrease in abundances, respectively. Color bar represents the gradient of the auto- scaled log2-intensities.See the legend of Fig. 1B for the descriptions of the heat map.

Supplementary Table 1. Previously reported auto-antigen in T1DM and their availability in ProtoArray.

Number of Signal with T1DM vs. T1DM Gene ProtoArray † T1DM Protein Header Reference Array ID Z>1.64 (NGT+T2DM) vs. Symbol (Y/N)* vs. NGT‡ NGT T1DM T2DM ‡ T2DM‡ glutamate decarboxylase 2 Baekkeskov et B11R21C09 0 7 0 <0.001 <0.001 0.001 GAD2 (pancreatic islets and brain, Y al.,1990 (1) 65kDa) B11R21C10 0 7 0 <0.001 <0.001 0.001 Palmer et al., B19R03C13 0 0 0 1 1 1 INS insulin Y 1983 (2) B19R03C14 0 0 0 1 1 1 Taniguchi et B19R14C17 0 0 0 1 1 1 CA2 carbonic anhydrase II (CA2) Y al., 2003 (3) B19R14C18 0 0 0 1 1 1 dopa decarboxylase (aromatic Rorsman et al., B14R21C03 0 0 0 1 1 1 DDC Y L-amino acid decarboxylase) 1995 (4) B14R21C04 0 0 0 1 1 1 heat shock 60kDa protein 1 Jones et al., B25R03C21 1 0 0 0.380 0.237 1 HSPD1 Y (chaperonin) 1990 (5) B25R03C22 2 0 0 0.380 0.237 1 regenerating islet-derived 3 Gurr et al., B18R05C03 0 0 0 0.528 0.628 0.500 REG3A Y alpha 2002 (6) B18R05C04 0 0 0 0.528 0.628 0.500 SLC30A8 solute carrier family 30 (zinc Wenzlau et al., N - (ZnT8A) transporter), member 8 2007 (7) Bottazo et al., ICA1 islet cell autoantigen 1 N - 1974 (8) PTPRN protein tyrosine phosphatase, Rabin et al., N - (IA-2A) receptor type, N 1994 (9) Castano et al., CPH carboxypeptidase H N - 1991 (10) PTPRN2 protein tyrosine phosphatase, Kawasaki et N - (IA-2beta) receptor type, N polypeptide 2 al., 1996 (11) solute carrier family 2 Inman et al., SLC2A2 (facilitated glucose N - 1993 (12) transporter), member 2 topoisomerase (DNA) II alpha Chang et al., TOP2A N - 170kDa 1996 (13) For the known auto-antibodies, the numbers of samples with Z >1.64 and P-values from M-tests were shown. *Whether auto-antigen is included in ProtoArray 5.0 platform. Y, included in ProtoArray; N, not included in ProtoArray †Z-score defined by (spot intensity - the averaged intensity of all probes) / the standard deviation of all probes ‡P-values from M-test T1DM, type 1 diabetes mellitus; T2DM, type 2 diabetes mellitus; NGT, subjects with normal glucose tolerance

Supplementary Table 2. Sixty nine auto-antibody candidates.

T1DM vs. (NGT+T2DM) T1DM vs. NGT T1DM vs. T2DM NGT+ Gene Symbol Protein Header Database ID Array ID T1DM T1DM NGT T1DM T2DM T2DM P-value† P-value† P-value† Count* Count* Count* Count* Count* Count* GAD2 Glutamate decarboxylase 2 NM_000818.1 B11R21C09 7 0 3.35E-05 7 0 3.55E-04 8 0 0.001 Coiled-coil domain-containing c7orf53 NM_182597.1 B31R08C07 5 0 0.001 5 0 0.005 5 0 0.022 transmembrane protein C7orf53 PRKCA protein kinase C, alpha (PRKCA) NM_002737.1 B21R02C15 5 0 0.001 5 0 0.005 5 0 0.022 cytoplasmic polyadenylation element CPEB1 BC035348.1 B30R20C01 4 0 0.017 6 0 0.007 2 0 0.242 binding protein 1 (CPEB1) ATP-binding cassette, sub-family F (GCN20), member 2 (ABCF2), nuclear ABCF2 NM_007189.1 B02R15C05 3 0 0.017 3 0 0.045 3 0 0.113 gene encoding mitochondrial protein, transcript variant 1 ATG16L1 Autophagy-related protein 16-1 NM_017974.2 B32R21C17 3 0 0.017 3 0 0.045 3 0 0.113 chromosome 2 open reading frame 47 C2orf47 BC017959.1 B41R05C05 3 0 0.017 3 0 0.045 3 0 0.113 (C2orf47) development and differentiation DDEFL1 BC060786.1 B07R02C21 3 0 0.017 3 0 0.045 3 0 0.113 enhancing factor-like 1 (DDEFL1) EEF1A1 Elongation factor 1-alpha 1 BC094687.1 B20R19C01 3 0 0.017 5 0 0.005 3 0 0.113 EXOSC5 exosome component 5 (EXOSC5) BC007742.1 B45R14C21 3 0 0.017 3 0 0.045 3 0 0.113 HES6 Transcription cofactor HES-6 NM_018645.3 B39R21C09 3 0 0.017 3 0 0.045 3 0 0.113 HIG1 domain family, member 2A HIGD2A NM_138820.1 B27R15C09 3 0 0.017 3 0 0.045 3 0 0.113 (HIGD2A) IGKC immunoglobulin kappa constant (IGKC) BC070334.1 B28R06C05 3 0 0.017 5 0 0.005 3 0 0.113 potassium inwardly-rectifying channel, KCNJ1 subfamily J, member 1 (KCNJ1), NM_153764.1 B16R08C11 3 0 0.017 3 0 0.045 3 0 0.113 transcript variant rom-k2 Smith-Magenis syndrome chromosome SMCR7 NM_139162.2 B25R03C15 3 0 0.017 3 0 0.045 3 0 0.113 region candidate gene 7 protein ubiquitin-conjugating enzyme E2L 3 UBE2L3 NM_198157.1 B46R08C03 3 0 0.017 3 0 0.045 3 0 0.113 (UBE2L3), transcript variant 2 ZNF434 zinc finger protein 434 (ZNF434) BC002859.1 B26R09C05 3 0 0.017 3 0 0.045 3 0 0.113 hypothetical protein MGC31957 MGC31957 BC005043.1 B04R08C11 6 1 0.001 6 0 0.001 6 1 0.041 (MGC31957) acidic (leucine-rich) nuclear ANP32B phosphoprotein 32 family, member B NM_006401.1 B18R03C13 6 1 0.003 6 0 0.001 6 0 0.110 (ANP32B) erythrocyte membrane protein band 4.9 EPB49 BC006318.1 B16R02C11 4 1 0.017 3 0 0.045 3 0 0.113 (dematin) (EPB49) FLJ21908 RNA polymerase II-associated protein 3 BC056415.1 B35R19C11 4 1 0.017 3 0 0.045 4 0 0.051 FLT3LG fms-related tyrosine kinase 3 ligand PHC1705 B40R16C01 4 1 0.017 4 0 0.015 3 0 0.113

(FLT3LG) retinoblastoma binding protein 4 RBBP4 NM_005610.1 B23R17C17 4 1 0.017 4 0 0.015 4 1 0.166 (RBBP4) FAM107A Protein FAM107A NM_007177.1 B40R21C05 5 2 0.028 3 0 0.045 5 1 0.086 leucine rich repeat containing 8 family, LRRC8D BC009486.1 B27R16C07 5 2 0.013 5 1 0.021 5 0 0.086 member D (LRRC8D) chromosome 10 open reading frame 91 C10orf91 NM_173541.1 B09R12C19 4 2 0.041 4 1 0.056 6 1 0.041 (C10orf91) immunoglobulin kappa variable 1-5 IGKV1-5 BC034142.1 B15R04C15 8 5 0.007 7 1 0.002 5 1 0.197 (IGKV1-5) IGHG1 Ig gamma-1 chain C region BC072419.1 B20R19C03 9 9 0.012 6 1 0.007 9 4 0.074 oxysterol binding protein-like 11 OSBPL11 NM_022776.3 B45R06C03 6 2 0.009 6 2 0.022 5 0 0.022 (OSBPL11) chromosome 3 open reading frame 36 C3orf36 NM_025041.2 B27R07C17 6 3 0.009 6 2 0.022 11 4 0.016 (C3orf36) ABI1 abl-interactor 1 (ABI1) BC024254.1 B23R18C05 5 3 0.028 7 2 0.020 4 2 0.327 Alcohol dehydrogenase class 4 ADH7 NM_000673.3 B05R18C13 6 4 0.018 9 2 0.002 5 2 0.197 mu/sigma chain p21(CDKN1A)-activated kinase 4 PAK4 BC002921.2 B37R19C19 8 5 0.007 7 2 0.008 7 2 0.057 (PAK4) Parkinson disease 7 domain containing 1 PDDC1 NM_182612.1 B45R08C17 11 8 0.021 11 2 0.001 4 1 0.327 (PDDC1) immunoglobulin heavy constant mu IGHM BC041037.1 B44R05C03 12 17 0.023 7 2 0.008 12 7 0.074 (IGHM) cDNA clone MGC:31944 CD247 BC022098.1 B28R14C09 3 0 0.017 9 3 0.006 3 0 0.113 IMAGE:4878869, complete cds CTLA-FC Recombinant human CTLA-4/Fc PHR5001 B40R16C05 6 1 0.001 9 3 0.002 7 2 0.057 chromosome 9 open reading frame 25 C9orf25 BC041009.2 B09R02C21 5 3 0.028 5 3 0.110 5 0 0.022 (C9orf25) glutamate-ammonia ligase (glutamine GLUL BC031964.1 B40R09C01 7 3 0.035 7 3 0.042 7 0 0.057 synthetase) (GLUL) GPI Glucose-6-phosphate isomerase NM_000175.2 B13R19C03 7 4 0.021 8 3 0.017 7 1 0.057 ACVR2B Activin receptor type-2B NM_001106.2 B01R09C17 6 5 0.033 6 3 0.049 6 2 0.110 EGF-like repeats and discoidin I-like EDIL3 BC053656.1 B24R17C13 11 7 4.98E-04 11 3 0.001 12 5 0.016 domains 3 (EDIL3) hydroxyacyl-Coenzyme A HADH BC000306.1 B22R13C09 8 7 0.021 8 3 0.007 8 4 0.236 dehydrogenase (HADH) immunoglobulin heavy constant gamma IGHG3 BC033178.1 B36R05C17 10 8 0.002 10 3 0.001 5 1 0.086 3 (G3m marker) (IGHG3) choline kinase alpha (CHKA), transcript CHKA NM_001277.1 B46R09C15 8 7 0.012 8 4 0.035 8 3 0.068 variant 1 cDNA clone MGC:12418 ENTPD1 BC005332.1 B01R04C07 9 9 0.045 9 4 0.027 2 0 0.242 IMAGE:3934658, complete cds dual specificity phosphatase 21 DUSP21 NM_022076.2 B42R07C21 12 11 0.033 12 4 0.002 3 1 0.300 (DUSP21) FANCM Fanconi anemia, complementation group BC036056.1 B10R09C09 15 24 0.050 8 4 0.035 15 8 0.019

M (FANCM) nudix (nucleoside diphosphate linked NUDT16L1 moiety X)-type motif 16-like 1 NM_032349.1 B33R04C05 15 29 0.050 8 4 0.017 15 9 0.019 (NUDT16L1) Spindle assembly abnormal protein 6 SASS6 BC101026.2 B16R21C07 9 7 0.004 9 5 0.014 9 2 0.012 homolog RAS-like, family 11, member B RASL11B NM_023940.1 B22R14C09 11 9 0.005 11 6 0.026 11 3 0.006 (RASL11B) immunoglobulin heavy variable 4-31 IGHV4-31 BC053984.1 B24R17C11 13 13 0.002 12 6 0.001 16 11 0.022 (IGHV4-31) cDNA clone MGC:40426 IGK@ BC032451.1 B10R15C05 12 13 0.004 12 6 0.001 15 11 0.086 IMAGE:5178085, complete cds potassium voltage-gated channel, shaker- KCNAB1 related subfamily, beta member 1 NM_172159.2 B13R09C13 13 21 0.024 9 6 0.027 13 6 0.015 (KCNAB1), transcript variant 3 MCM10 Protein MCM10 homolog BC004876.1 B35R16C17 8 8 0.033 8 7 0.103 8 1 0.027 hematopoietic SH2 domain containing HSH2D NM_032855.1 B10R14C03 14 18 0.004 14 7 2.67E-04 16 13 0.113 (HSH2D) cDNA clone IMAGE:3451214 MCM10 BC009108.1 B01R12C15 11 12 0.021 11 8 0.026 5 1 0.086 (MCM10) proteasome (prosome, macropain) 26S PSMD9 NM_002813.4 B17R03C17 13 13 0.003 14 8 0.001 13 6 0.068 subunit, non-ATPase, 9 (PSMD9) methyl-CpG binding domain protein 5 MBD5 NM_018328.1 B37R04C13 12 14 0.023 12 8 0.017 2 5 0.197 (MBD5) IGL@ immunoglobulin lambda locus (IGL@) BC032452.1 B27R05C05 12 19 0.033 12 10 0.017 12 9 0.229 TRIM21 tripartite motif-containing 21 (TRIM21) NM_003141.2 B31R18C03 15 29 0.050 12 10 0.017 15 10 0.041 mitochondrial trans-2-enoyl-CoA MECR BC001419.1 B13R18C07 12 17 0.016 12 11 0.030 8 1 0.008 reductase (MECR) ODF3L2 Outer dense fiber protein 3-like protein 2 BC104469.1 B16R20C17 13 22 0.034 13 13 0.032 14 9 0.057 MYOT myotilin (MYOT) NM_006790.1 B21R15C05 14 23 0.044 14 13 0.031 16 13 0.113 endoglin (Osler-Rendu-Weber syndrome ENG BC014271.2 B37R21C03 16 27 0.009 16 15 0.002 6 1 0.110 1) (ENG) chromosome 1 open reading frame 77 C1orf77 BC002733.2 B25R03C07 15 25 0.035 15 16 0.044 15 8 0.041 (C1orf77) phosphatase and actin regulator 1 PHACTR1 NM_030948.1 B09R08C01 16 31 0.021 15 16 0.044 16 11 0.022 (PHACTR1) LIM and senescent cell antigen-like- LIMS1 NM_004987.3 B48R17C17 15 28 0.025 15 17 0.026 15 11 0.086 containing domain protein 1 UBXD3 UBX domain containing 3 (UBXD3) NM_152376.2 B27R18C07 16 30 0.021 16 18 0.028 16 12 0.113 *Number of subjects with Z-score >1.64 for each candidate auto-antibody †P-values from T1DM, type 1 diabetes mellitus; T2DM, type 2 diabetes mellitus; NGT, subjects with normal glucose tolerance

Supplementary Table 3. Explained variance of X and Y blocks by individual latent variables (LV) in multivariate partial least square-discriminant analysis (PLS-DA).

X-block Y-block LV # Total Total This LV This LV 1 2.76 2.76 85.09 85.09 2 2.79 5.56 13.59 98.69 3 2.72 8.27 1.05 99.74 4 3.22 11.5 0.22 99.96 5 2.6 14.09 0.04 100 6 2.05 16.14 0 100 7 2.14 18.28 0 100 8 2.2 20.49 0 100 9 2.32 22.8 0 100 10 1.97 24.78 0 100 X and Y blocks are 59 (number of samples) by 9,480 (number of probes on the array) and 59 by 2 (group information) data matrixes, respectively. For each sample, the rows in Y block represent which group the sample belongs to: [1 0] for T1DM, [0 1] for T2DM, and [0 0] for NGT.

Supplementary Table 4. Variable importance in projection (VIP) values of the 69 auto-antibody candidates computed from PLS-DA.

Gene Signal Y/N (Z>1.6449) Protein Header Database ID Array ID VIP Symbol NGT T1DM T2DM cDNA clone MGC:12418 ENTPD1 BC005332.1 B01R04C07 2.292 18 14 12 IMAGE:3934658, complete cds cDNA clone MGC:12418 ENTPD1 BC005332.1 B01R04C08 2.193 17 14 12 IMAGE:3934658, complete cds ACVR2B Activin receptor type-2B NM_001106.2 B01R09C17 0.638 14 7 8 ACVR2B Activin receptor type-2B NM_001106.2 B01R09C18 0.698 14 7 7 cDNA clone IMAGE:3451214 MCM10 BC009108.1 B01R12C15 0.772 16 13 10 (MCM10) cDNA clone IMAGE:3451214 MCM10 BC009108.1 B01R12C16 1.062 18 14 10 (MCM10) submaxillary gland androgen SMR3B regulated protein 3 homolog B NM_006685.2 B02R13C16 3.094 0 1 0 (mouse) (SMR3B) ATP-binding cassette, subfamily F (GCN20), member 2 ABCF2 (ABCF2), nuclear gene encoding NM_007189.1 B02R15C05 1.441 8 5 6 mitochondrial protein, transcript variant 1 ATP-binding cassette, subfamily F (GCN20), member 2 ABCF2 (ABCF2), nuclear gene encoding NM_007189.1 B02R15C06 1.248 8 4 5 mitochondrial protein, transcript variant 1 hypothetical protein MGC31957 MGC31957 BC005043.1 B04R08C11 1.589 26 15 16 (MGC31957) hypothetical protein MGC31957 MGC31957 BC005043.1 B04R08C12 1.709 24 15 16 (MGC31957) Alcohol dehydrogenase class 4 ADH7 NM_000673.3 B05R18C13 2.389 2 6 2 mu/sigma chain Alcohol dehydrogenase class 4 ADH7 NM_000673.3 B05R18C14 2.377 2 6 2 mu/sigma chain development and differentiation DDEFL1 enhancing factor-like 1 BC060786.1 B07R02C21 1.512 0 1 0 (DDEFL1) development and differentiation DDEFL1 enhancing factor-like 1 BC060786.1 B07R02C22 2.159 0 1 0 (DDEFL1) chromosome 9 open reading C9orf25 BC041009.2 B09R02C21 1.142 3 5 0 frame 25 (C9orf25) chromosome 9 open reading C9orf25 BC041009.2 B09R02C22 1.083 3 5 0 frame 25 (C9orf25) phosphatase and actin regulator PHACTR1 NM_030948.1 B09R08C01 1.104 26 16 16 1 (PHACTR1) phosphatase and actin regulator PHACTR1 NM_030948.1 B09R08C02 1.089 27 16 15 1 (PHACTR1) chromosome 10 open reading C10orf91 NM_173541.1 B09R12C19 2.399 1 3 1 frame 91 (C10orf91)

chromosome 10 open reading C10orf91 NM_173541.1 B09R12C20 2.431 1 3 1 frame 91 (C10orf91) Fanconi anemia, FANCM complementation group M BC036056.1 B10R09C09 2.254 18 15 8 (FANCM) Fanconi anemia, FANCM complementation group M BC036056.1 B10R09C10 2.110 19 15 8 (FANCM) hematopoietic SH2 domain HSH2D NM_032855.1 B10R14C03 2.392 26 16 16 containing (HSH2D) hematopoietic SH2 domain HSH2D NM_032855.1 B10R14C04 2.501 27 16 16 containing (HSH2D) cDNA clone MGC:40426 IGK@ BC032451.1 B10R15C05 2.589 27 16 16 IMAGE:5178085, complete cds cDNA clone MGC:40426 IGK@ BC032451.1 B10R15C06 2.446 27 16 16 IMAGE:5178085, complete cds GAD2 Glutamate decarboxylase 2 NM_000818.1 B11R21C09 4.192 0 7 0 GAD2 Glutamate decarboxylase 2 NM_000818.1 B11R21C10 4.106 0 7 0 potassium voltage-gated channel, shaker-related KCNAB1 NM_172159.2 B13R09C13 1.836 27 16 16 subfamily, beta member 1 (KCNAB1), transcript variant 3 potassium voltage-gated channel, shaker-related KCNAB1 NM_172159.2 B13R09C14 1.785 27 16 16 subfamily, beta member 1 (KCNAB1), transcript variant 3 mitochondrial trans-2-enoyl- MECR BC001419.1 B13R18C07 2.410 27 16 16 CoA reductase (MECR) mitochondrial trans-2-enoyl- MECR BC001419.1 B13R18C08 2.446 27 16 16 CoA reductase (MECR) GPI Glucose-6-phosphate isomerase NM_000175.2 B13R19C03 2.675 2 3 0 GPI Glucose-6-phosphate isomerase NM_000175.2 B13R19C04 2.587 2 3 0 immunoglobulin kappa variable IGKV1-5 BC034142.1 B15R04C15 2.657 23 16 15 1-5 (IGKV1-5) immunoglobulin kappa variable IGKV1-5 BC034142.1 B15R04C16 2.666 23 16 15 1-5 (IGKV1-5) erythrocyte membrane protein EPB49 BC006318.1 B16R02C11 1.075 5 7 4 band 4.9 (dematin) (EPB49) erythrocyte membrane protein EPB49 BC006318.1 B16R02C12 1.732 6 7 4 band 4.9 (dematin) (EPB49) potassium inwardly-rectifying channel, subfamily J, member 1 KCNJ1 NM_153764.1 B16R08C11 2.959 1 4 0 (KCNJ1), transcript variant rom- k2 potassium inwardly-rectifying channel, subfamily J, member 1 KCNJ1 NM_153764.1 B16R08C12 3.083 0 5 0 (KCNJ1), transcript variant rom- k2 erythrocyte membrane protein EPB49 BC052805.1 B16R20C13 1.528 4 5 3 band 4.9 (dematin) (EPB49) erythrocyte membrane protein EPB49 BC052805.1 B16R20C14 1.765 4 5 3 band 4.9 (dematin) (EPB49)

Outer dense fiber protein 3-like ODF3L2 BC104469.1 B16R20C17 1.424 27 16 16 protein 2 Outer dense fiber protein 3-like ODF3L2 BC104469.1 B16R20C18 1.452 26 16 16 protein 2 Spindle assembly abnormal SASS6 BC101026.2 B16R21C07 2.644 19 15 11 protein 6 homolog Spindle assembly abnormal SASS6 BC101026.2 B16R21C08 2.445 19 14 11 protein 6 homolog proteasome (prosome, PSMD9 macropain) 26S subunit, non- NM_002813.4 B17R03C17 2.335 15 15 11 ATPase, 9 (PSMD9) proteasome (prosome, PSMD9 macropain) 26S subunit, non- NM_002813.4 B17R03C18 2.538 16 15 13 ATPase, 9 (PSMD9) acidic (leucine-rich) nuclear ANP32B phosphoprotein 32 family, NM_006401.1 B18R03C13 1.574 0 1 0 member B (ANP32B) acidic (leucine-rich) nuclear ANP32B phosphoprotein 32 family, NM_006401.1 B18R03C14 1.738 0 1 0 member B (ANP32B) IGHG1 Ig gamma-1 chain C region BC092518.1 B18R21C03 1.862 27 16 16 IGHG1 Ig gamma-1 chain C region BC092518.1 B18R21C04 0.843 27 16 16 p21(CDKN1A)-activated kinase PAK4 NM_005884.2 B20R09C21 2.371 1 5 4 4 (PAK4), transcript variant 1 p21(CDKN1A)-activated kinase PAK4 NM_005884.2 B20R09C22 2.214 1 5 4 4 (PAK4), transcript variant 1 EEF1A1 Elongation factor 1-alpha 1 BC094687.1 B20R19C01 3.551 0 1 0 EEF1A1 Elongation factor 1-alpha 1 BC094687.1 B20R19C02 2.986 0 1 0 IGHG1 Ig gamma-1 chain C region BC072419.1 B20R19C03 1.729 27 16 16 IGHG1 Ig gamma-1 chain C region BC072419.1 B20R19C04 2.077 27 16 16 IGHG1 Ig gamma-1 chain C region BC090938.1 B20R21C07 1.125 27 16 16 IGHG1 Ig gamma-1 chain C region BC090938.1 B20R21C08 1.272 27 16 16 protein kinase C, alpha PRKCA NM_002737.1 B21R02C15 2.593 0 5 1 (PRKCA) protein kinase C, alpha PRKCA NM_002737.1 B21R02C16 2.557 0 5 0 (PRKCA) immunoglobulin kappa variable IGKV1-5 BC030814.1 B21R12C17 1.939 27 16 16 1-5 (IGKV1-5) immunoglobulin kappa variable IGKV1-5 BC030814.1 B21R12C18 1.975 27 16 16 1-5 (IGKV1-5) MYOT myotilin (MYOT) NM_006790.1 B21R15C05 1.305 26 16 15 MYOT myotilin (MYOT) NM_006790.1 B21R15C06 1.489 25 16 15 hydroxyacyl-Coenzyme A HADH BC000306.1 B22R13C09 1.297 9 11 9 dehydrogenase (HADH) hydroxyacyl-Coenzyme A HADH BC000306.1 B22R13C10 1.321 8 11 9 dehydrogenase (HADH) RAS-like, family 11, member B RASL11B NM_023940.1 B22R14C09 2.557 10 11 3 (RASL11B) RAS-like, family 11, member B RASL11B NM_023940.1 B22R14C10 2.555 8 11 3 (RASL11B) retinoblastoma binding protein 4 RBBP4 NM_005610.1 B23R17C17 3.172 0 1 0 (RBBP4)

retinoblastoma binding protein 4 RBBP4 NM_005610.1 B23R17C18 1.566 0 1 0 (RBBP4) ABI1 abl-interactor 1 (ABI1) BC024254.1 B23R18C05 2.529 1 3 2 ABI1 abl-interactor 1 (ABI1) BC024254.1 B23R18C06 2.591 1 4 2 immunoglobulin heavy variable IGHV4-31 BC053984.1 B24R17C11 2.333 27 16 16 4-31 (IGHV4-31) immunoglobulin heavy variable IGHV4-31 BC053984.1 B24R17C12 2.465 27 16 16 4-31 (IGHV4-31) EGF-like repeats and discoidin EDIL3 BC053656.1 B24R17C13 3.025 27 16 16 I-like domains 3 (EDIL3) EGF-like repeats and discoidin EDIL3 BC053656.1 B24R17C14 3.045 27 16 16 I-like domains 3 (EDIL3) chromosome 1 open reading C1orf77 BC002733.2 B25R03C07 1.505 22 16 15 frame 77 (C1orf77) chromosome 1 open reading C1orf77 BC002733.2 B25R03C08 1.524 22 16 15 frame 77 (C1orf77) Smith-Magenis syndrome SMCR7 chromosome region candidate NM_139162.2 B25R03C15 1.805 0 3 0 gene 7 protein Smith-Magenis syndrome SMCR7 chromosome region candidate NM_139162.2 B25R03C16 1.609 0 3 0 gene 7 protein zinc finger protein 434 ZNF434 BC002859.1 B26R09C05 1.697 0 3 3 (ZNF434) zinc finger protein 434 ZNF434 BC002859.1 B26R09C06 1.932 0 3 2 (ZNF434) immunoglobulin lambda locus IGL@ BC032452.1 B27R05C05 1.773 27 16 16 (IGL@) immunoglobulin lambda locus IGL@ BC032452.1 B27R05C06 1.490 27 16 16 (IGL@) chromosome 3 open reading C3orf36 NM_025041.2 B27R07C17 2.148 27 15 14 frame 36 (C3orf36) chromosome 3 open reading C3orf36 NM_025041.2 B27R07C18 2.428 27 16 14 frame 36 (C3orf36) HIG1 domain family, member HIGD2A NM_138820.1 B27R15C09 1.297 3 4 2 2A (HIGD2A) HIG1 domain family, member HIGD2A NM_138820.1 B27R15C10 1.345 2 4 2 2A (HIGD2A) leucine rich repeat containing 8 LRRC8D BC009486.1 B27R16C07 2.527 2 4 0 family, member D (LRRC8D) leucine rich repeat containing 8 LRRC8D BC009486.1 B27R16C08 2.305 0 3 0 family, member D (LRRC8D) UBX domain containing 3 UBXD3 NM_152376.2 B27R18C07 0.901 21 16 12 (UBXD3) UBX domain containing 3 UBXD3 NM_152376.2 B27R18C08 1.038 20 16 12 (UBXD3) immunoglobulin kappa constant IGKC BC070334.1 B28R06C05 1.876 21 15 13 (IGKC) immunoglobulin kappa constant IGKC BC070334.1 B28R06C06 1.877 21 14 13 (IGKC) cDNA clone MGC:31944 CD247 BC022098.1 B28R14C09 2.459 25 16 16 IMAGE:4878869, complete cds

cDNA clone MGC:31944 CD247 BC022098.1 B28R14C10 2.278 25 16 16 IMAGE:4878869, complete cds immunoglobulin kappa constant IGKC BC034141.1 B29R04C21 2.067 27 16 16 (IGKC) immunoglobulin kappa constant IGKC BC034141.1 B29R04C22 2.069 27 16 16 (IGKC) immunoglobulin heavy constant IGHG1 gamma 1 (G1m marker) BC025314.1 B30R17C13 2.193 27 16 16 (IGHG1) immunoglobulin heavy constant IGHG1 gamma 1 (G1m marker) BC025314.1 B30R17C14 1.913 27 16 16 (IGHG1) cytoplasmic polyadenylation CPEB1 element binding protein 1 BC035348.1 B30R20C01 2.990 5 11 8 (CPEB1) cytoplasmic polyadenylation CPEB1 element binding protein 1 BC035348.1 B30R20C02 2.849 3 10 6 (CPEB1) Coiled-coil domain-containing FLJ39575 NM_182597.1 B31R08C07 2.136 0 5 0 transmembrane protein C7orf53 Coiled-coil domain-containing FLJ39575 NM_182597.1 B31R08C08 1.989 0 4 0 transmembrane protein C7orf53 tripartite motif-containing 21 TRIM21 NM_003141.2 B31R18C03 1.373 27 16 16 (TRIM21) tripartite motif-containing 21 TRIM21 NM_003141.2 B31R18C04 1.046 27 16 16 (TRIM21) cDNA clone MGC:27376 IGK@ BC016380.1 B32R12C13 1.658 27 16 16 IMAGE:4688477, complete cds cDNA clone MGC:27376 IGK@ BC016380.1 B32R12C14 1.350 27 16 16 IMAGE:4688477, complete cds ATG16L1 Autophagy-related protein 16-1 NM_017974.2 B32R21C17 1.328 0 3 0 ATG16L1 Autophagy-related protein 16-1 NM_017974.2 B32R21C18 0.963 0 3 0 nudix (nucleoside diphosphate NUDT16L1 linked moiety X)-type motif 16- NM_032349.1 B33R04C05 1.637 27 16 16 like 1 (NUDT16L1) nudix (nucleoside diphosphate NUDT16L1 linked moiety X)-type motif 16- NM_032349.1 B33R04C06 1.609 26 16 16 like 1 (NUDT16L1) potassium voltage-gated channel, shaker-related KCNAB1 NM_172160.1 B33R07C09 0.793 27 16 16 subfamily, beta member 1 (KCNAB1), transcript variant 1 potassium voltage-gated channel, shaker-related KCNAB1 NM_172160.1 B33R07C10 0.808 27 16 16 subfamily, beta member 1 (KCNAB1), transcript variant 1 immunoglobulin heavy constant IGHM BC016381.1 B34R14C09 1.962 27 16 16 mu (IGHM) immunoglobulin heavy constant IGHM BC016381.1 B34R14C10 1.242 27 16 16 mu (IGHM) MCM10 Protein MCM10 homolog BC004876.1 B35R16C17 1.537 6 9 1 MCM10 Protein MCM10 homolog BC004876.1 B35R16C18 1.476 6 9 2

RNA polymerase II-associated FLJ21908 BC056415.1 B35R19C11 0.622 1 4 1 protein 3 RNA polymerase II-associated FLJ21908 BC056415.1 B35R19C12 0.706 3 4 1 protein 3 immunoglobulin heavy constant IGHG3 gamma 3 (G3m marker) BC033178.1 B36R05C17 1.231 27 16 16 (IGHG3) immunoglobulin heavy constant IGHG3 gamma 3 (G3m marker) BC033178.1 B36R05C18 1.252 27 16 16 (IGHG3) methyl-CpG binding domain MBD5 NM_018328.1 B37R04C13 2.140 18 15 14 protein 5 (MBD5) methyl-CpG binding domain MBD5 NM_018328.1 B37R04C14 1.996 18 15 14 protein 5 (MBD5) p21(CDKN1A)-activated kinase PAK4 BC002921.2 B37R19C19 2.227 4 8 5 4 (PAK4) p21(CDKN1A)-activated kinase PAK4 BC002921.2 B37R19C20 1.914 4 8 4 4 (PAK4) endoglin (Osler-Rendu-Weber ENG BC014271.2 B37R21C03 2.912 27 16 16 syndrome 1) (ENG) endoglin (Osler-Rendu-Weber ENG BC014271.2 B37R21C04 2.895 27 16 16 syndrome 1) (ENG) HES6 Transcription cofactor HES-6 NM_018645.3 B39R21C09 2.339 0 3 0 HES6 Transcription cofactor HES-6 NM_018645.3 B39R21C10 2.116 1 3 0 p21(CDKN1A)-activated kinase PAK4 NM_005884.2 B40R03C09 1.960 18 15 8 4 (PAK4), transcript variant 1 p21(CDKN1A)-activated kinase PAK4 NM_005884.2 B40R03C10 1.914 17 14 8 4 (PAK4), transcript variant 1 glutamate-ammonia ligase GLUL BC031964.1 B40R09C01 1.782 2 2 0 (glutamine synthetase) (GLUL) glutamate-ammonia ligase GLUL BC031964.1 B40R09C02 1.971 1 1 0 (glutamine synthetase) (GLUL) fms-related tyrosine kinase 3 FLT3LG PHC1705 B40R16C01 2.287 21 14 13 ligand (FLT3LG) fms-related tyrosine kinase 3 FLT3LG PHC1705 B40R16C02 2.142 21 14 13 ligand (FLT3LG) CTLA-FC Recombinant human CTLA-4/Fc PHR5001 B40R16C05 0.963 27 16 16 CTLA-FC Recombinant human CTLA-4/Fc PHR5001 B40R16C06 0.933 27 16 16 FAM107A Protein FAM107A NM_007177.1 B40R21C05 1.820 0 4 1 FAM107A Protein FAM107A NM_007177.1 B40R21C06 1.795 0 2 1 chromosome 2 open reading C2orf47 BC017959.1 B41R05C05 2.473 0 2 0 frame 47 (C2orf47) chromosome 2 open reading C2orf47 BC017959.1 B41R05C06 2.206 0 3 0 frame 47 (C2orf47) dual specificity phosphatase 21 DUSP21 NM_022076.2 B42R07C21 2.090 10 12 12 (DUSP21) dual specificity phosphatase 21 DUSP21 NM_022076.2 B42R07C22 2.200 8 13 13 (DUSP21) NaN NaN CCP_1BSA B43R15C13 3.001 0 1 0 NaN NaN CCP_1BSA B43R15C14 2.852 0 1 0 immunoglobulin heavy constant IGHM BC041037.1 B44R05C03 1.819 27 16 16 mu (IGHM)

immunoglobulin heavy constant IGHM BC041037.1 B44R05C04 1.776 27 16 16 mu (IGHM) immunoglobulin heavy constant IGHG1 gamma 1 (G1m marker) BC014667.1 B45R04C19 1.642 27 16 16 (IGHG1) immunoglobulin heavy constant IGHG1 gamma 1 (G1m marker) BC014667.1 B45R04C20 1.523 27 16 16 (IGHG1) oxysterol binding protein-like 11 OSBPL11 NM_022776.3 B45R06C03 1.245 3 6 4 (OSBPL11) oxysterol binding protein-like 11 OSBPL11 NM_022776.3 B45R06C04 1.325 3 6 5 (OSBPL11) Parkinson disease 7 domain PDDC1 NM_182612.1 B45R08C17 2.228 17 13 13 containing 1 (PDDC1) Parkinson disease 7 domain PDDC1 NM_182612.1 B45R08C18 2.140 18 13 13 containing 1 (PDDC1) exosome component 5 EXOSC5 BC007742.1 B45R14C21 1.417 0 3 0 (EXOSC5) exosome component 5 EXOSC5 BC007742.1 B45R14C22 1.442 0 2 0 (EXOSC5) ubiquitin-conjugating enzyme UBE2L3 E2L 3 (UBE2L3), transcript NM_198157.1 B46R08C03 3.022 0 3 0 variant 2 ubiquitin-conjugating enzyme UBE2L3 E2L 3 (UBE2L3), transcript NM_198157.1 B46R08C04 3.091 0 3 0 variant 2 choline kinase alpha (CHKA), CHKA NM_001277.1 B46R09C15 1.657 4 8 3 transcript variant 1 choline kinase alpha (CHKA), CHKA NM_001277.1 B46R09C16 1.839 5 9 3 transcript variant 1 LIM and senescent cell antigen- LIMS1 NM_004987.3 B48R17C17 1.286 27 16 16 like-containing domain protein 1 LIM and senescent cell antigen- LIMS1 NM_004987.3 B48R17C18 1.130 27 16 16 like-containing domain protein 1 For each candidate, the number of samples with Z >1.64 and P-value from M-tests are shown. T1DM, type 1 diabetes mellitus; T2DM, type 2 diabetes mellitus; NGT, subjects with normal glucose tolerance

Supplementary Figure References

1. Schneider CA, Rasband WS, Eliceiri KW: NIH Image to ImageJ: 25 years of image analysis. Nature Methods 2012; 9: 671-675

Supplementary Table References

1. Baekkeskov S, Nielsen JH, Marner B, Bilde T, Ludvigsson J, Lernmark A: Autoantibodies in newly diagnosed diabetic children immunoprecipitate human pancreatic islet cell proteins. Nature 1982;298:167-169 2. Palmer JP, Asplin CM, Clemons P, Lyen K, Tatpati O, Raghu PK, Paquette TL: Insulin antibodies in insulin-dependent diabetics before insulin treatment. Science 1983;222:1337-1339 3. Taniguchi T, Okazaki K, Okamoto M, Seko S, Tanaka J, Uchida K, Nagashima K, Kurose T, Yamada Y, Chiba T, Seino Y: High prevalence of autoantibodies against carbonic anhydrase II and lactoferrin in type 1 diabetes: concept of autoimmune exocrinopathy and endocrinopathy of the pancreas. Pancreas 2003;27:26-30 4. Rorsman F, Husebye ES, Winqvist O, Bjork E, Karlsson FA, Kampe O: Aromatic-L-amino-acid decarboxylase, a pyridoxal phosphate-dependent enzyme, is a beta-cell autoantigen. Proc Natl Acad Sci U S A 1995;92:8626-8629 5. Jones DB, Hunter NR, Duff GW: Heat-shock protein 65 as a beta cell antigen of insulin-dependent diabetes. Lancet 1990;336:583-585 6. Gurr W, Yavari R, Wen L, Shaw M, Mora C, Christa L, Sherwin RS: A Reg family protein is overexpressed in islets from a patient with new-onset type 1 diabetes and acts as T-cell autoantigen in NOD mice. Diabetes 2002;51:339-346 7. Wenzlau JM, Juhl K, Yu L, Moua O, Sarkar SA, Gottlieb P, Rewers M, Eisenbarth GS, Jensen J, Davidson HW, Hutton JC: The cation efflux transporter ZnT8 (Slc30A8) is a major autoantigen in human type 1 diabetes. Proc Natl Acad Sci U S A 2007;104:17040-17045 8. Bottazzo GF, Florin-Christensen A, Doniach D: Islet-cell antibodies in diabetes mellitus with autoimmune polyendocrine deficiencies. Lancet 1974;2:1279-1283 9. Rabin DU, Pleasic SM, Shapiro JA, Yoo-Warren H, Oles J, Hicks JM, Goldstein DE, Rae PM: Islet cell antigen 512 is a diabetes-specific islet autoantigen related to protein tyrosine phosphatases. J Immunol 1994;152:3183-3188 10. Castano L, Russo E, Zhou L, Lipes MA, Eisenbarth GS: Identification and cloning of a granule autoantigen (carboxypeptidase-H) associated with type I diabetes. J Clin Endocrinol Metab 1991;73:1197-1201 11. Kawasaki E, Hutton JC, Eisenbarth GS: Molecular cloning and characterization of the human transmembrane protein tyrosine phosphatase homologue, phogrin, an autoantigen of type 1 diabetes. Biochem Biophys Res Commun 1996;227:440-447 12. Inman LR, McAllister CT, Chen L, Hughes S, Newgard CB, Kettman JR, Unger RH, Johnson JH: Autoantibodies to the GLUT-2 glucose transporter of beta cells in insulin-dependent diabetes mellitus of recent onset. Proc Natl Acad Sci U S A 1993;90:1281-1284 13. Chang YH, Hwang J, Shang HF, Tsai ST: Characterization of human DNA topoisomerase II as an autoantigen recognized by patients with IDDM. Diabetes 1996;45:408-414