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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]
  1. 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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Clinical Proteomics

ISSN: 1559-0275

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