A proteomic repertoire of autoantigens identified from the classic autoantibody clinical test substrate HEp-2 cells

Wang, Julia Y.; Zhang, Wei; Rho, Jung-hyun; Roehrl, Michael W.; Roehrl, Michael H.

doi:10.1186/s12014-020-09298-3

Clinical Proteomics

Table 1 Proteins identified from DS-affinity enrichment of HEp-2 cell extract

From: A proteomic repertoire of autoantigens identified from the classic autoantibody clinical test substrate HEp-2 cells

Pept. #^a	Gene	Protein	H	M	L	pI	Ref.
		Nuclear/Chromosome/Mitotic Cell Cycle
10	HIST1H4A	Histone H4	+	+		11.36	[18]
3	HIST2H2BE	Histone H2B type 2-E	+	+		10.31	[19]
4	H1-2	Histone H1.2 (H1F2, HIST1H1C)		+		10.94	[20]
3	H2AFY	Core histone macro-H2A.1		+		9.80	[21]
2	H1-5	Histone H1.5 (H1F5, HIST1H1B, DNMT3A)		+		10.91	[20]
2	H1F0	Histone H1.0		+		10.84	[22]
2	H2AFV	Histone H2A.V		+		10.58	[23]
2	HIST2H3A	Histone H3.2		+		11.27	[24]
Ab	TOP1	DNA topoisomerase I (Scl-70 autoantigen)	+				[2, 25]
5	SET	Protein SET (Inhibitor of granzyme A-activated DNase, HLA-DR-associated protein II)		+		4.22	?
Ab	TRIM21	E3 ubiquitin-protein ligase TRIM21 (Ro/SS-A autoantigen)	+				[2, 26]
4	SSB	Lupus La protein		+	+	6.68	[27]
4	ANP32B	Acidic leucine-rich nuclear phosphoprotein 32 family member B (putative HLA-DR-associated protein I-2)		+		3.93	?
2	PRMT1	Protein arginine N-methyltransferase 1 (Histone-arginine N-methyltransferase PRMT1)			+	5.18	?
28	DDB1	Damage-specific DNA-binding protein 1			+	5.14	[2]
2	NPM1	Nucleophosmin		+		4.64	[28]
4	KPNB1	Importin subunit beta-1 (pore targeting complex 97 kDa subunit)			+	4.68	[29]
3	PTMA	Prothymosin alpha			+	3.66	[30]
3	HDGF	Hepatoma-derived growth factor (High mobility group protein 1-like 2)			+	4.70	[31]
12	ENO1	Alpha-enolase			+	7.01	[2, 32]
3	MYBBP1A	Myb-binding protein 1A		+		9.34	?
4	YBX3	Y-box-binding protein 3 (Single-strand DNA-binding protein)		+		9.77	[2, 33]
10	YWHAE	14-3-3 protein epsilon			+	4.63	[34]
5	YWHAZ	14-3-3 protein zeta/delta			+	4.73	[35]
4	YWHAG	14-3-3 protein gamma			+	4.80	[34]
3	YWHAQ	14-3-3 protein theta			+	4.68	[36]
2	YWHAB	14-3-3 protein beta/alpha (Protein kinase C inhibitor protein 1)			+	4.76	?
4	SFN	14-3-3 protein sigma (Stratifin)			+	4.68	?
Ab	PCNA	Proliferating cell nuclear antigen		+			[2, 37]
21	XRCC6	Ku70 (X-ray repair cross-complementing protein 6, ATP-dependent DNA helicase 2 subunit 1)		+	+	6.23	[38]
10	XRCC5	Ku80 (Ku86, X-ray repair cross-complementing protein 5, ATP-dependent DNA helicase 2 subunit 2)		+	+	5.55	[39]
4	PRKDC	DNA-dependent protein kinase catalytic subunit (DNA-PKcs)		+		6.75	[40]
2	MCM6	DNA replication licensing factor MCM6			+	5.28	?
2	MCM2	DNA replication licensing factor MCM2			+	5.34	?
2	MCM3	DNA replication licensing factor MCM3			+	5.53	?
		RNA Metabolism/Ribonucleoprotein Granule
3	RPL6	60S ribosomal protein L6	+			10.59	[41]
2	RPS9	40S ribosomal protein S9	+			10.66	[42]
2	RPL7	60S ribosomal protein L7	+			10.66	[43]
16	RPL5	60S ribosomal protein L5		+		9.73	[44]
2	MRPL39	39S ribosomal protein L39, mitochondrial		+		7.56	?
16	PABP4	Poly(A)-binding protein 4		+		9.31	[2]
9	PABP3	Poly(A)-binding protein 3		+		9.68	[2]
12	NCL	Nucleolin		+	+	4.60	[45]
3	ANP32A	Acidic leucine-rich nuclear phosphoprotein 32 family member A (putative HLA-DR-associated protein I)		+		3.98	?
3	DHX9	ATP-dependent RNA helicase A (DEAH box protein 9)		+		6.41	[46]
4	HNRNPCL1	Heterogeneous nuclear ribonucleoprotein C-like 1		+		4.93	?
3	HNRNPU	Heterogeneous nuclear ribonucleoprotein U (Scaffold-attachment factor A)		+	+	5.76	?
2	HNRNPA3	Heterogeneous nuclear ribonucleoprotein A3		+		9.10	[47]
4	SYNCRIP	Heterogeneous nuclear ribonucleoprotein Q (Synaptotagmin binding cytoplasmic RNA interacting protein)			+	8.68	?
3	HNRNPA1	Heterogeneous nuclear ribonucleoprotein A1			+	9.17	[48]
2	HNRNPR	Heterogeneous nuclear ribonucleoprotein R			+	8.23	[49]
2	HNRNPA2B1	Heterogeneous nuclear ribonucleoprotein A2/B1			+	8.97	[50]
3	C1QBP	Complement component 1 Q subcomponent-binding protein, mitochondrial (Hyaluronan-binding protein) (Mitochondrial)			+	4.74	[51]
2	SUB1	Activated RNA polymerase II transcriptional coactivator p15 (PC4, RPO2TC1)			+	9.60	?
12	PRPF8	Pre-mRNA-processing-splicing factor 8 (U5 snRNP-specific protein 220 kDa)			+	8.95	[2]
2	EFTUD2	116 kDa U5 small nuclear ribonucleoprotein component			+	4.84	[52]
11	SF3B3	Splicing factor 3B subunit 3			+	5.13	[2, 53]
3	SFRS7	Serine/arginine-rich splicing factor 7			+	11.83	[2, 54]
3	VIM	Vimentin (Cytoskeleton)			+	5.05	[55]
4	IQGAP1	Ras GTPase-activating-like protein IQGAP1 (Membrane)			+	6.08	[56]
		Vesicle/ER/Mitochondrion
51	CLTC	Clathrin heavy chain 1			+	5.57	[2]
2	CLTCL1	Clathrin heavy chain 2			+	4.29	?
15	HSPA8	Heat shock cognate 71 kDa protein (LPS-associated protein 1, HSP7C) (ER)		+		5.37	[57]
34	HSPA5	Endoplasmic reticulum chaperone BiP (Grp-78, Immunoglobulin heavy chain-binding protein)			+	5.07	[58]
25	HSPA9	Stress-70 protein, mitochondrial (GRP-75, Mortalin)			+	5.87	[2, 57]
9	HSP90AA1	Heat shock protein HSP 90-alpha (Hsp86, NY-REN-38, LPS-associated protein 2) (Membrane)			+	4.94	[59]
7	HSP90AB1	Heat shock protein HSP 90-beta (Hsp84, HSP90B, HSPC2) (Membrane)			+	4.96	[60]
5	HSP90B1	Endoplasmin (GRP-94, Tumor rejection antigen 1)			+	4.76	[61]
4	HSP90AA2P	Heat shock protein HSP 90-alpha A2 (HSP90AA2, HSPCAL3)			+	4.57	[62]
19	CALR	Calreticulin (Calregulin, ER resident protein 60)			+	6.19	[63]
12	P4HB	Protein disulfide-isomerase (cellular thyroid hormone-binding protein)			+	4.76	[64]
6	PDIA6	Protein disulfide-isomerase A6 (ER protein 5)			+	4.95	?
6	PDIA4	Protein disulfide-isomerase A4			+	4.96	?
10	VCP	Transitional endoplasmic reticulum ATPase (Valosin-containing protein)			+	5.14	[65]
5	CALM1	Calmodulin-1			+	4.09	[66]
3	LRPPRC	Leucine-rich PPR motif-containing protein, mitochondrial (GP130)			+	5.81	[67]
3	CANX	Calnexin (Major MHC class I antigen-binding protein p88)			+	4.46	[68]
2	ERO1A	ERO1-like protein alpha (ER oxidoreductase alpha, disulfide bond formation in ER)			+	5.48	?
2	AHSG	Alpha-2-HS-glycoprotein (FETUA, fetuin-A)			+	5.43	[2, 69]
2	COPG1	Coatomer subunit gamma-1 (Golgi)			+	5.32	?
2	COPB2	Coatomer subunit beta			+	5.14	[70]
3	CAPN2	Calpain-2 catalytic subunit (Calcium-activated neutral proteinase 2) (Membrane)			+	4.87	?
2	PRKCSH	Glucosidase 2 subunit beta (Protein kinase C substrate 60.1 kDa protein heavy chain)		+	+	4.33	?
2	PPM1G	Protein phosphatase 1G (PPM1C)			+	4.27	[71]
15	UBA1	Ubiquitin-like modifier-activating enzyme 1 (Mitochondrion)			+	5.49	[2, 72]
2	PSMA7	Proteasome subunit alpha type-7			+	8.60	[73]
2	PSMA2	Proteasome subunit alpha type-2			+	6.91	?
2	PSMA5	Proteasome subunit alpha type-5			+	4.74	?
3	PSMD6	26S proteasome non-ATPase regulatory subunit 6			+	5.45	?
2	PSMD13	26S proteasome non-ATPase subunit 13			+	5.53	[74]
		Cytoskeleton
21	FLNA	Filamin-A (Actin-binding protein 280)		+	+	5.70	[2, 75]
17	FLNB	Filamin-B (Thyroid autoantigen)		+		5.47	[2]
3	LMNA	Lamin-A/C (Renal carcinoma antigen NY-REN-32)		+	+	6.57	[76]
28	ACTN1	Alpha-actinin-1 (Membrane)			+		[77]
22	ACTN4	Alpha-actinin-4 (Nucleus)			+		[2, 78]
2	ACTA2	Actin, aortic smooth muscle (alpha-actin 2, cell growth-inhibiting gene 46 protein)			+	5.24	?
2	ACTB	Actin, cytoplasmic 1 (Beta-actin) (Nucleus)			+	5.29	[79]
2	ACTBL2	Beta-actin-like protein 2 (Kappa-actin)			+	5.39	?
17	SPTAN1	Spectrin alpha chain non-erythrocytic 1, fodrin alpha chain			+	5.22	[80]
7	MYH9	Myosin-9			+	5.50	[81]
4	TPM4	Tropomyosin alpha-4 chain			+	4.67	[82]
3	TPM1	Tropomyosin alpha-1 chain			+	4.69	[83]
2	TPM3	Tropomyosin alpha-3 chain			+	4.68	[84]
2	TPM2	Tropomyosin beta chain			+	4.66	?
3	BASP1	Brain acid soluble protein 1 (Neuronal axonal membrane protein NAP-22)			+	4.62	?
3	TUBA1C	Tubulin alpha-1C chain (alpha-tublin 6)			+	4.96	[85]
2	TUBB4B	Tubulin beta-2C chain			+	4.79	[86]

^aColumns left to right: Number of peptides detected by mass spectrometry sequencing (Ab, confirmed by autoantibody staining [2]); Gene name; Protein name; H (high affinity): eluted with 1.0 M salt; M (medium affinity): eluted with 0.6 M salt; L (low affinity): eluted with 0.4 M salt; Predicted isoelectric point (pI); Literature reference reporting autoantibodies against the protein (“?”: no literature evidence found)

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ISSN: 1559-0275

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