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Table 3 Top-hit list of differentially expressed proteins in CD8+ T cells from MS patients compared healthy controls

From: Quantitative proteomic analyses of CD4+ and CD8+ T cells reveal differentially expressed proteins in multiple sclerosis patients and healthy controls

Accession Protein identity Gene names p-value FC MS versus HC (log2) Median intesity MS (log2) MS SD Median intensity HC (log2) HC SD % seq cov # pep AUC
P36915 Guanine nucleotide-binding protein-like 1 GNL1 0.000363 0.3823 22.9373 0.13239 22.555 0.19548 22.6 9 0.9
P57764 Gasdermin-D GSDMD 0.0004 − 0.247 23.0081 0.09966 23.2551 0.13969 27.9 8 0.91
Q15027 Arf-GAP with coiled-coil, ANK repeat and PH domain-containing protein 1 ACAP1 0.000818 0.3588 25.3317 0.13259 24.9729 0.21057 44.7 22 0.89
Q14240 Eukaryotic initiation factor 4A-II; eukaryotic initiation factor 4A-II, N-terminally processed EIF4A2 0.001679 0.2287 25.7838 0.1338 25.5551 0.31408 75.4 23 0.92
Q9GZP4 PITH domain-containing protein 1 PITHD1 0.001791 0.1974 22.8647 0.13746 22.3619 0.14509 47.9 8 0.91
P10155 60 kDa SS-A/Ro ribonucleoprotein TROVE2 0.001865 0.1765 25.7638 0.08234 25.9917 0.13787 37.4 16 0.87
P14174 Macrophage migration inhibitory factor MIF 0.002217 0.3238 23.462 0.21611 23.2646 0.28198 36.5 4 0.88
Q96ST3 Paired amphipathic helix protein Sin3a SIN3A 0.002395 0.2302 25.1124 0.11111 24.9359 0.14227 14.2 13 0.85
P06703 Protein S100-A6 S100A6 0.002446 − 0.7296 26.8304 0.62637 26.5066 0.61209 52.2 4 0.9
P51452 Dual specificity protein phosphatase 3 DUSP3 0.002706 − 0.5138 23.1048 0.19565 22.8746 0.4382 29.2 4 0.88
O75431 Metaxin-2 MTX2 0.002927 0.293 25.2256 0.21249 25.9552 0.11457 33.8 5 0.82
Q8TBC4 NEDD8-activating enzyme E1 catalytic subunit UBA3 0.002937 0.1439 24.5971 0.10266 24.3764 0.1286 51.6 13 0.85
P30405; Q6BAA4 Peptidyl-prolyl cis–trans isomerase F, mitochondrial PPIF 0.003314 − 1.0344 21.1705 0.33533 21.6843 0.63539 40.1 8 0.84
P21953 2-oxoisovalerate dehydrogenase subunit beta, mitochondrial BCKDHB 0.003651 0.2586 22.4515 0.21161 22.1585 0.24451 15.3 4 0.83
Q8TCD5 5(3)-deoxyribonucleotidase, cytosolic type NT5C 0.003791 0.3211 24.2434 0.14217 24.0995 0.45523 54.2 7 0.86
P57737 Coronin-7 CORO7 0.004431 0.147 23.7522 0.148 23.3999 0.0888 49.4 28 0.86
O94925 Glutaminase kidney isoform, mitochondrial GLS 0.0047 0.1506 22.33535 0.10161 22.9562 0.13926 45 22 0.85
Q3ZCW2 Galectin-related protein LGALSL 0.005089 − 2.2604 21.7926 0.93109 22.827 0.91857 61 8 0.86
P63151; Q00005; Q9Y2T4 Serine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform PPP2R2A 0.005319 0.243 21.8042 0.15983 21.5456 0.24976 48.1 12 0.84
O94826 Mitochondrial import receptor subunit TOM70 TOMM70A 0.005477 0.235 23.0302 0.0878 22.7091 0.2231 32.1 13 0.89
Q13586; Q9P246 Stromal interaction molecule 1 STIM1 0.005533 − 0.2404 26.1487 0.20417 26.0017 0.23545 32.7 16 0.82
P13224 Platelet glycoprotein Ib beta chain GP1BB 0.005768 − 1.9102 24.998 0.8499 24.8474 1.00102 23.8 5 0.82
O00186 Syntaxin-binding protein 3 STXBP3 0.005812 0.193 22.9285 0.11405 23.296 0.15529 10.5 5 0.87
P20645 Cation-dependent mannose-6-phosphate receptor M6PR 0.006115 − 0.1934 22.3302 0.22866 23.6924 0.17682 22 4 0.84
Q96RQ3 Methylcrotonoyl-CoA carboxylase subunit alpha, mitochondrial MCCC1 0.007633 0.5028 21.2898 0.19278 23.5502 0.34081 16.4 7 0.83
P78417 Glutathione S-transferase omega-1 GSTO1 0.007795 − 0.2279 23.6102 0.09562 23.1469 0.19987 59.3 14 0.79
P24666 Low molecular weight phosphotyrosine protein phosphatase ACP1 0.008395 0.2207 23.6258 0.18286 23.3828 0.19924 72.2 8 0.82
Q9H0R4 Haloacid dehalogenase-like hydrolase domain-containing protein 2 HDHD2 0.008617 0.3523 24.1578 0.21888 23.9228 0.23008 67.2 8 0.84
Q12913 Receptor-type tyrosine-protein phosphatase eta PTPRJ 0.008808 − 0.62085 24.2463 0.30864 24.4867 0.44153 10.9 11 0.83
P49327 Fatty acid synthase; [acyl-carrier-protein] S-acetyltransferase;[acyl-carrier-protein] S-malonyltransferase; 3-oxoacyl-[acyl-carrier-protein] synthase; 3-oxoacyl-[acyl-carrier-protein] reductase; 3-hydroxyacyl-[acyl-carrier-protein] dehydratase; enoyl-[acyl-carrier-protein] reductase; oleoyl-[acyl-carrier-protein] hydrolase FASN 0.009384 − 0.3675 23.3745 0.18085 25.2847 0.4045 10.9 18 0.8
P04275 von Willebrand factor; von Willebrand antigen 2 VWF 0.009824 − 1.3622 22.1391 1.21897 21.9461 1.05341 13 25 0.84
P35573 Glycogen debranching enzyme; 4-alpha-glucanotransferase; amylo-alpha-1,6-glucosidase AGL 0.010066 0.4633 21.956 0.26486 21.7305 0.29541 20.9 22 0.8
Q8TDQ7 Glucosamine-6-phosphate isomerase 2 GNPDA2 0.010164 0.2255 23.3542 0.28146 23.8593 0.21281 59.8 10 0.84
P16615 Sarcoplasmic/endoplasmic reticulum calcium ATPase 2 ATP2A2 0.010248 − 0.5051 24.5083 0.30171 24.3585 0.32708 28.7 21 0.81
Q13555; Q13554 Calcium/calmodulin-dependent protein kinase type II subunit gamma; calcium/calmodulin-dependent protein kinase type II subunit beta CAMK2G; CAMK2B 0.010445 0.2908 22.9757 0.12761 22.6849 0.25143 24.6 10 0.82
P12931; Q9H3Y6; P42685; P08581; Q04912 Proto-oncogene tyrosine-protein kinase Src SRC 0.01081 − 1.20015 22.8527 0.73685 24.05285 0.66689 37.5 15 0.81
Q15120 [Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrial PDK3 0.010829 0.24475 20.7149 0.28722 20.47015 0.26592 12.1 3 0.81
P05556 Integrin beta-1 ITGB1 0.010894 − 0.4327 24.5472 0.41637 24.9799 0.37748 32.8 19 0.81
Q9P0J1 [Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrial PDP1 0.011178 0.3474 22.5526 0.14746 22.2052 0.18283 16.9 7 0.82
P01137 Transforming growth factor beta-1; latency-associated peptide TGFB1 0.012983 − 0.87595 24.8165 0.44917 24.6229 0.65195 29.5 7 0.81
P14770 Platelet glycoprotein IX GP9 0.013113 − 1.25275 29.9764 0.73326 29.8298 0.84609 30.5 5 0.82
P05386 60S acidic ribosomal protein P1 RPLP1 0.014256 0.2666 22.157 0.16745 22.4676 0.17334 94.7 5 0.81
Q02083 N-acylethanolamine-hydrolyzing acid amidase; N-acylethanolamine-hydrolyzing acid amidase subunit alpha; N-acylethanolamine-hydrolyzing acid amidase subunit beta NAAA 0.014286 0.43565 23.0686 0.40847 23.6457 0.49594 27.9 8 0.87
P50148; P29992; O95837 Guanine nucleotide-binding protein G(q) subunit alpha GNAQ 0.014465 − 0.487 24.8592 0.48364 24.5987 0.51884 30.6 8 0.82
O14828 Secretory carrier-associated membrane protein 3 SCAMP3 0.014503 − 0.2404 22.5342 0.16111 22.3259 0.19252 22.8 5 0.8
P67936; Q2TAC2 Tropomyosin alpha-4 chain TPM4 0.015754 − 0.598 23.0621 0.52458 22.8134 0.46362 70.6 27 0.81
O14561 Acyl carrier protein, mitochondrial NDUFAB1 0.015958 0.2347 23.5152 0.23866 23.7086 0.12417 21.2 4 0.82
Q00653 Nuclear factor NF-kappa-B p100 subunit; nuclear factor NF-kappa-B p52 subunit NFKB2 0.016322 0.322 22.11305 0.2449 22.989 0.28366 15.8 9 0.81
P35244 Replication protein A 14 kDa subunit RPA3 0.016781 0.2976 23.4742 0.16891 24.72695 0.38956 86.8 7 0.8
O95379 Tumor necrosis factor alpha-induced protein 8 TNFAIP8 0.016869 0.2251 22.0409 0.1305 23.8998 0.38972 40.4 5 0.8
Q9NY12 H/ACA ribonucleoprotein complex subunit 1 GAR1 0.01728 0.2208 27.6053 0.18001 28.7912 0.21825 29 5 0.8
P16109 P-selectin SELP 0.017721 − 2.0401 24.1549 1.03363 23.9684 1.06785 29 14 0.81
Q96RP9 Elongation factor G, mitochondrial GFM1 0.020163 0.288 24.2375 0.19021 24.3248 0.22518 13.2 7 0.8
Q96F86 Enhancer of mRNA-decapping protein 3 EDC3 0.02024 0.44525 26.7743 0.34422 26.5077 0.41686 12.4 3 0.82
P08134 Rho-related GTP-binding protein RhoC RHOC 0.022534 0.3601 23.692 0.17871 23.25635 0.48992 65.8 10 0.81
Q15283 Ras GTPase-activating protein 2 RASA2 0.025799 0.2581 25.2002 0.25399 25.0644 0.3012 14.5 9 0.8
O95866 Protein G6b G6B 0.025824 − 1.4023 21.8137 0.77427 22.3007 0.97969 23.7 5 0.81
O75874 Isocitrate dehydrogenase [NADP] cytoplasmic IDH1 0.026221 − 0.3508 21.6884 0.25198 21.9288 0.44714 52.4 17 0.81
P09564 T-cell antigen CD7 CD7 0.027969 0.3583 22.542 0.19792 22.6533 0.35246 16.7 4 0.82
O75439 Mitochondrial-processing peptidase subunit beta PMPCB 0.031524 0.2241 22.4262 0.21703 24.1114 0.27829 22.1 7 0.83
P24158 Myeloblastin PRTN3 0.049099 − 0.55295 28.221 0.57502 28.819 0.84918 20.7 4 0.81
  1. The table displays proteins (n = 61) that are differentially expressed in CD8+ T cells from MS patients compared to healthy controls (HC). The proteins are extracted from Additional file 2: Table S2 and selected by fulfilling at least two of the three criteria: p-value (p < 0.01), area under the curve (AUC) (AUC > 0.8) and log fold-change (FC) > [0.2] between samples from MS patients and healthy controls. The log2-fold changes in MS versus HC is based on normalized values. Accession number, protein identity and gene names are indicated for each protein, in addition to median log2-transformed protein abundances with standard variation (SD) for each group, the percentage of sequence coverage (% sequence coverage) and number of peptides (# peptides) identified for each protein