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

Berge, Tone; Eriksson, Anna; Brorson, Ina Skaara; Høgestøl, Einar August; Berg-Hansen, Pål; Døskeland, Anne; Mjaavatten, Olav; Bos, Steffan Daniel; Harbo, Hanne F.; Berven, Frode

doi:10.1186/s12014-019-9241-5

Clinical Proteomics

Table 2 Top-hit list of differentially expressed proteins in CD4⁺ T cells

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 intensity MS (log2)	MS SD	Median intensity HC (log2)	HC SD	% seq cov	# pep	AUC
Q5JSL3	Dedicator of cytokinesis protein 11	DOCK11	4.69E−05	0.27405	22.73205	0.14968	22.458	0.11384	13	21	0.98
Q03252	Lamin-B2	LMNB2	0.000203	0.2023	26.23395	0.10367	26.03165	0.1219	58.1	42	0.94
Q14978	Nucleolar and coiled-body phosphoprotein 1	NOLC1	0.000306	0.67815	21.4053	0.26237	20.72715	0.36787	16.2	9	0.92
Q2M2I8; Q9NSY1	AP2-associated protein kinase 1	AAK1	0.000457	0.22605	23.1178	0.11404	22.89175	0.12897	33	20	0.92
Q13148	TAR DNA-binding protein 43	TARDBP	0.000642	0.29	23.3943	0.12816	23.1043	0.14754	39.4	11	0.89
P20963	T-cell surface glycoprotein CD3 zeta chain	CD247	0.000907	0.19535	23.48275	0.0965	23.2874	0.18125	60.4	11	0.88
P49959	Double-strand break repair protein MRE11A	MRE11A	0.001405	0.1957	21.44665	0.17074	21.25095	0.15881	21.6	11	0.88
P06239	Tyrosine-protein kinase Lck	LCK	0.001598	0.2009	24.642	0.12459	24.4411	0.13158	49.7	18	0.85
Q9NR56; Q5VZF2; Q9NUK0	Muscleblind-like protein 1	MBNL1	0.001651	0.3464	22.0867	0.19817	21.7403	0.24361	21.6	8	0.87
P35573	Glycogen debranching enzyme; 4-alpha-glucanotransferase; amylo-alpha-1,6-glucosidase	AGL	0.00177	0.32245	21.79335	0.29915	21.4709	0.18837	18.1	18	0.87
P18085	ADP-ribosylation factor 4	ARF4	0.00199	− 0.29765	21.6712	0.17375	21.96885	0.14457	64.4	10	0.86
O75131; Q96FN4; Q8IYJ1; Q9HCH3; Q9UBL6	Copine-3	CPNE3	0.002255	0.1118	23.9288	0.09682	23.817	0.07363	46.7	19	0.88
P27824	Calnexin	CANX	0.002331	− 0.2029	24.6288	0.09381	24.8317	0.13864	37.7	22	0.85
Q49A26	Putative oxidoreductase GLYR1	GLYR1	0.002442	0.2299	22.8002	0.15088	22.5703	0.13549	40	14	0.88
P12694	2-oxoisovalerate dehydrogenase subunit alpha, mitochondrial	BCKDHA	0.002513	0.2997	20.58005	0.14155	20.28035	0.16289	21.1	6	0.89
P16615	Sarcoplasmic/endoplasmic reticulum calcium ATPase 2	ATP2A2	0.002577	− 0.34015	20.91155	0.24663	21.2517	0.39528	22.5	15	0.85
P31146; REV__Q02818	Coronin-1A	CORO1A	0.002667	0.196	28.77805	0.04311	28.58205	0.14531	63.8	33	0.91
P29401	Transketolase	TKT	0.002709	0.18195	27.0961	0.16375	26.91415	0.08497	68.9	38	0.86
Q00610; P53675	Clathrin heavy chain 1	CLTC	0.00312	− 0.10695	26.3723	0.05858	26.47925	0.08019	58.7	80	0.83
P19971	Thymidine phosphorylase	TYMP	0.003318	− 0.6095	21.51775	0.63532	22.12725	0.52772	51	16	0.85
Q16401	26S proteasome non-ATPase regulatory subunit 5	PSMD5	0.003478	0.12765	23.7053	0.09891	23.57765	0.13094	58.9	21	0.86
Q15084	Protein disulfide-isomerase A6	PDIA6	0.003546	− 0.3043	23.5948	0.25739	23.8991	0.17192	45.9	13	0.86
P07237	Protein disulfide-isomerase	P4HB	0.003888	− 0.1857	25.1359	0.14266	25.3216	0.09151	56.1	27	0.85
O43665	Regulator of G-protein signaling 10	RGS10	0.003925	0.2594	23.5918	0.213	23.3324	0.14464	60.1	12	0.85
P27986; O00459	Phosphatidylinositol 3-kinase regulatory subunit alpha	PIK3R1	0.004008	0.2604	22.56095	0.17873	22.30055	0.21783	38.3	19	0.83
Q9Y4L1	Hypoxia up-regulated protein 1	HYOU1	0.004021	− 0.1815	23.00205	0.13058	23.18355	0.13156	31.8	20	0.83
O75306	NADH dehydrogenase [ubiquinone] iron-sulfur protein 2, mitochondrial	NDUFS2	0.004057	0.13545	22.6738	0.08259	22.53835	0.13156	34.8	12	0.83
Q8WUX9	Charged multivesicular body protein 7	CHMP7	0.004115	0.23275	21.9775	0.21092	21.74475	0.18291	37.1	13	0.81
P07602	Prosaposin; Saposin-A; Saposin-B-Val; Saposin-B; Saposin-C; Saposin-D	PSAP	0.004366	− 0.19325	22.296	0.18336	22.48925	0.42157	12.6	6	0.94
O00422	Histone deacetylase complex subunit SAP18	SAP18	0.004452	0.37715	20.6193	0.18761	20.24215	0.34985	41.8	5	0.87
Q9ULA0	Aspartyl aminopeptidase	DNPEP	0.004664	0.3613	23.6397	0.17228	23.2784	0.18788	53.3	18	0.82
O43681	ATPase ASNA1	ASNA1	0.004954	− 0.11665	22.25215	0.13672	22.3688	0.11129	50.6	10	0.83
O75832	26S proteasome non-ATPase regulatory subunit 10	PSMD10	0.004963	0.21305	21.312	0.24569	21.09895	0.12837	40.3	6	0.89
P30536	Translocator protein	TSPO	0.004964	0.5376	22.44845	0.37985	21.91085	0.337	23.1	3	0.82
P24666	Low molecular weight phosphotyrosine protein phosphatase	ACP1	0.005013	0.2241	22.8028	0.19373	22.5787	0.20543	72.2	8	0.88
Q4G176	Acyl-CoA synthetase family member 3, mitochondrial	ACSF3	0.005127	0.3234	20.8339	0.32659	20.5105	0.20115	19.3	7	0.83
P35611	Alpha-adducin	ADD1	0.005201	0.17245	23.941	0.12213	23.76855	0.20616	44.9	24	0.81
P19525	Interferon-induced, double-stranded RNA-activated protein kinase	EIF2AK2	0.005211	− 0.54585	20.65625	0.47474	21.2021	0.40633	20.1	9	0.87
O75791	GRB2-related adapter protein 2	GRAP2	0.00589	0.1927	23.58335	0.07421	23.39065	0.15601	43	13	0.84
Q16666; Q6N021	Gamma-interferon-inducible protein 16	IFI16	0.006051	− 0.27745	24.51685	0.24674	24.7943	0.12775	43.4	31	0.84
Q9HAV4	Exportin-5	XPO5	0.006457	− 0.402	18.4781	0.23884	18.8801	0.22546	5.1	4	0.87
Q9NRY5	Protein FAM114A2	FAM114A2	0.006779	0.4935	19.3331	0.23485	18.8396	0.34369	15.8	4	0.86
P11177	Pyruvate dehydrogenase E1 component subunit beta, mitochondrial	PDHB	0.006838	0.2322	24.05355	0.11379	23.82135	0.12468	52.9	13	0.83
Q9NZZ3	Charged multivesicular body protein 5	CHMP5	0.006962	− 0.28845	20.37145	0.31795	20.6599	0.20311	40.6	6	0.83
P53634	Dipeptidyl peptidase 1; dipeptidyl peptidase 1 exclusion domain chain; dipeptidyl peptidase 1 heavy chain; dipeptidyl peptidase 1 light chain	CTSC	0.006992	− 0.36305	20.5409	0.54754	20.90395	0.10359	19.9	7	0.81
Q06546	GA-binding protein alpha chain	GABPA	0.006996	0.2074	21.3763	0.1983	21.1689	0.20734	28	8	0.8
P21399	Cytoplasmic aconitate hydratase	ACO1	0.008051	0.1699	21.4757	0.14153	21.3058	0.20875	20.4	11	0.82
Q9H400	Lck-interacting transmembrane adapter 1	LIME1	0.008125	0.25515	21.11	0.19997	20.85485	0.21307	46.1	7	0.81
Q02750	Dual specificity mitogen-activated protein kinase kinase 1	MAP2K1	0.00822	0.1771	23.2231	0.13291	23.046	0.1348	42.2	14	0.8
O94826	Mitochondrial import receptor subunit TOM70	TOMM70A	0.008231	0.21725	22.34995	0.15186	22.1327	0.20502	34.5	13	0.81
O75475	PC4 and SFRS1-interacting protein	PSIP1	0.008443	0.1899	22.08185	0.1504	21.9335	0.15516	45.5	21	0.8
P02776	Platelet factor 4; platelet factor 4, short form	PF4	0.008535	− 1.5035	24.86845	1.22842	24.67855	1.48716	36.6	5	0.83
Q5XKP0	Protein QIL1	QIL1	0.008552	0.31595	22.7718	0.27181	24.2753	0.34286	62.7	3	0.84
Q9UGI8	Testin	TES	0.008688	0.14215	19.94335	0.09764	19.6274	0.12853	72	31	0.8
Q86VP6; O75155	Cullin-associated NEDD8-dissociated protein 1	CAND1	0.008724	0.11355	25.3342	0.10321	25.19205	0.08176	48.9	46	0.84
Q9C0K0	B-cell lymphoma/leukemia 11B	BCL11B	0.008892	0.2434	25.65085	0.17505	25.5373	0.22495	12.8	8	0.79
P13861; P31323	cAMP-dependent protein kinase type II-alpha regulatory subunit	PRKAR2A	0.008993	0.13145	21.90015	0.12538	21.65675	0.09173	62.1	20	0.81
P07741	Adenine phosphoribosyltransferase	APRT	0.008995	0.19165	23.14455	0.1699	23.0131	0.15824	91.1	17	0.83
P23246	Splicing factor, proline- and glutamine-rich	SFPQ	0.009648	0.12175	25.8719	0.14919	25.68025	0.09657	47.9	31	0.83
P49903	Selenide, water dikinase 1	SEPHS1	0.009747	0.2257	26.39505	0.15139	26.2733	0.15099	41.6	10	0.83
P62995	Transformer-2 protein homolog beta	TRA2B	0.009757	0.17515	22.6718	0.18232	22.4461	0.12504	30.9	8	0.8
Q86XP3	ATP-dependent RNA helicase DDX42	DDX42	0.009985	0.1467	23.91205	0.20211	23.7369	0.12402	22.7	13	0.85
P13010	X-ray repair cross-complementing protein 5	XRCC5	0.01116	0.2196	22.23445	0.1468	22.08775	0.12306	71.2	48	0.82
Q15428	Splicing factor 3A subunit 2	SF3A2	0.011498	0.30175	25.0703	0.2546	25.26055	0.28193	28.7	9	0.85
P37837	Transaldolase	TALDO1	0.011683	0.26525	24.0953	0.16309	23.9199	0.1934	47.2	19	0.8
O94973	AAK1	AP2A2	0.01208	0.40715	22.87215	0.18724	22.7054	0.31295	25	16	0.82
P16150	Leukosialin	SPN	0.012636	0.41995	27.0869	0.31488	26.8673	0.23838	19.5	5	0.8
Q9Y6K5	2-5-oligoadenylate synthase 3	OAS3	0.013062	− 0.58225	24.1071	0.61142	23.9796	0.40043	26.2	21	0.8
P13598	Intercellular adhesion molecule 2	ICAM2	0.013215	− 0.33575	22.4839	0.36073	22.18215	0.13532	14.9	3	0.81
O96000	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 10	NDUFB10	0.013266	0.2682	27.0077	0.2602	26.74245	0.17232	43	7	0.82
P48059; Q7Z4I7	LIM and senescent cell antigen-like-containing domain protein 1	LIMS1	0.013613	− 1.11835	22.2423	1.06748	22.4974	1.04857	45.8	13	0.83
P0DOX5; P01857	Ig gamma-1 chain C region	IGHG1	0.014981	− 0.8553	21.9197	0.96324	21.51255	0.41275	28.3	9	0.8
P67936	Tropomyosin alpha-4 chain	TPM4	0.015875	− 0.39585	22.849	0.50209	22.42905	0.33951	66.1	27	0.81
Q53QZ3	Rho GTPase-activating protein 15	ARHGAP15	0.016084	0.2283	22.7616	0.11442	22.6226	0.26067	28.8	10	0.8
Q93077; Q7L7L0; P04908	Histone H2A type 1-C; histone H2A type 3; histone H2A type 1-B/E	HIST1H2AC; HIST3H2A; HIST1H2AB	0.016472	0.5318	24.6077	0.68101	24.4913	0.51829	35.4	7	0.83
Q00341	Vigilin	HDLBP	0.017653	− 0.3557	22.1316	0.25975	22.71385	0.26847	5.3	5	0.8
Q9Y3C4	EKC/KEOPS complex subunit TPRKB	TPRKB	0.01784	0.33545	25.2378	0.31196	25.04925	0.2556	56.6	7	0.83
Q96I24	Far upstream element-binding protein 3	FUBP3	0.018912	0.2288	19.18425	0.18212	19.52	0.15408	24.7	9	0.81
P18206	Vinculin	VCL	0.019685	− 0.57615	22.07985	0.84436	21.81165	0.52692	64.2	60	0.83
Q96BW5	Phosphotriesterase-related protein	PTER	0.020487	0.35515	23.0556	0.21492	22.8575	0.29673	24.4	6	0.82
P02775	Platelet basic protein; connective tissue-activating peptide III; TC-2; connective tissue-activating peptide III(1-81); beta-thromboglobulin; neutrophil-activating peptide 2(74); neutrophil-activating peptide 2(73); neutrophil-activating peptide 2; TC-1; Neutrophil-activating peptide 2(1–66); neutrophil-activating peptide 2(1–63)	PPBP	0.022319	− 1.4945	21.6995	1.19479	21.55895	1.23096	38.3	5	0.81
P21333	Filamin-A	FLNA	0.023825	− 0.23365	21.21755	0.43258	22.3359	0.24022	71.6	137	0.81
Q01469; A8MUU1	Fatty acid-binding protein, epidermal	FABP5	0.024356	− 0.5329	26.41625	0.73245	26.33375	0.55502	76.3	11	0.83
O94903	Proline synthase co-transcribed bacterial homolog protein	PROSC	0.024792	0.27275	24.465	0.13221	24.3072	0.20226	37.8	8	0.8
P21291	Cysteine and glycine-rich protein 1	CSRP1	0.026425	− 0.2011	25.4829	0.36999	25.34655	0.16603	64.2	8	0.8
P53041	Serine/threonine-protein phosphatase 5	PPP5C	0.028586	0.2748	23.5436	0.14823	23.3623	0.29589	22.8	8	0.84
Q8WUM0	Nuclear pore complex protein Nup133	NUP133	0.030136	0.272	21.15755	0.26096	22.01285	0.19541	18.3	12	0.81
P09525	Annexin A4	ANXA4	0.032901	− 0.25805	26.25495	0.30546	26.6508	0.2431	47.6	13	0.82
Q04826	HLA class I histocompatibility antigen, B-40 alpha chain	HLA-B	0.033546	− 1.0305	21.98915	0.72834	21.76085	0.84434	44.5	13	0.81
O43704	Sulfotransferase family cytosolic 1B member 1	SULT1B1	0.035541	0.4495	26.00495	0.2866	26.19745	0.42792	39.2	9	0.82

The table displays proteins (n = 90) that are differentially expressed in CD4⁺ T cells from MS patients compared to healthy controls (HC). The proteins are extracted from Additional file 1: Table S1 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 are 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 (% seq cov) and number of peptides (# pep) identified for each protein

Back to article page

ISSN: 1559-0275

Contact us

Submission enquiries: journalsubmissions@springernature.com