Introduction
Materials and methods
Immunoglobulin sources
Main clinical characteristics | Autoimmunity | Number of pools tested
b |
---|---|---|
Healthy blood donors | No ANA | 1 |
dcSSc | ||
No visceral involvement | No ANA | 1 |
Interstitial lung disease | ATA | 1 |
Scleroderma renal crisis | Anti-RNA-pol III Abs | 1 |
lcSSc | ||
Pulmonary arterial hypertension | ACA | 1 |
No visceral involvement | ACA | 1 |
dcSSc | ||
Scleroderma renal crisis | ANA with unidentified specificity | 1 |
Pulmonary arterial hypertension | ANA with unidentified specificity | 1 |
Interstitial lung disease | ANA with unidentified specificity | 2 |
No visceral involvement | ANA with unidentified specificity | 1 |
lcSSc | ||
Digital ulcers | ANA with unidentified specificity | 1 |
Pulmonary arterial hypertension | ANA with unidentified specificity | 1 |
Interstitial lung disease | ANA with unidentified specificity | 1 |
No visceral involvement | ANA with unidentified specificity | 2 |
HEp-2 cell culture
Protein extraction
Two-dimensional electrophoresis
Electrotransfer and immunoblotting
In-gel trypsin digestion
Protein identification by mass spectrometry
Biological network analysis
Statistical analysis
Results
Analysis of HEp-2 cell proteomes
IgG reactivities shared between SSc patients
Protein | SwissProt accession number |
---|---|
Total protein extract | |
Heat shock 70-kDa protein 1b | [SwissProt:HSP71_HUMAN] |
Stress-induced phosphoprotein 1 | [SwissProt:STIP1_HUMAN] |
Protein disulfide-isomerase A3 precursor | [SwissProt:PDIA3_HUMAN] |
Glial fibrillary acidic proteinb | [SwissProt:GFAP_HUMAN] |
α-enolaseb | [SwissProt:ENOA_HUMAN] |
Mannose-6 phosphate receptor-binding protein 1 | [SwissProt:M6PBP_HUMAN] |
40S ribosomal protein SAb | [SwissProt:RSSA_HUMAN] |
Phosphoglycerate kinase 1 | [SwissProt:PGK1_HUMAN] |
Actin, cytoplasmic 1b | [SwissProt:ACTB_HUMAN] |
Glyceraldehyde-3-phosphate dehydrogenaseb | [SwissProt:G3P_HUMAN] |
Heterogeneous nuclear ribonucleoproteins A2/B1 | [SwissProt:ROA2_HUMAN] |
Triosephosphate isomeraseb | [SwissProt:TPIS_HUMAN] |
Peroxiredoxin 6 | [SwissProt:PRDX6_HUMAN] |
Superoxide dismutase [Mn], mitochondrial precursorb | [SwissProt:SODM_HUMAN] |
Enriched nuclear protein extract | |
Heterogeneous nuclear ribonucleoprotein Lb | [SwissProt:HNRPL_HUMAN] |
Pre-mRNA processing factor 19 | [SwissProt:PRP19_HUMAN] |
α-enolaseb | [SwissProt:ENOA_HUMAN] |
Poly(rC)-binding protein 1 | [SwissProt:PCBP1_HUMAN] |
Protein ID on gel | HEp-2 cell protein | SwissProt accession number | MW th/es | pHi th/es | Number of unique identified peptides# | Total ion score | Best ion score | Sequence coverage (%) |
---|---|---|---|---|---|---|---|---|
550 | Far upstream element-binding protein 2 (N) | [SwissProt:FUBP2_HUMAN] | 73/80 | 6.8/7.1 | 10/17 | 554 | 108 | 37 |
553 | Far upstream element-binding protein 2 (N) | [SwissProt:FUBP2_HUMAN] | 73/79 | 6.8/7.3 | 11/17 | 864 | 153 | 32 |
554 | Far upstream element-binding protein 2 (N) | [SwissProt:FUBP2_HUMAN] | 73/79 | 6.8/7.5 | 10/17 | 598 | 105 | 34 |
617 | Lamin A/C (N) | [SwissProt:LMNA_HUMAN] | 74/73 | 6.6/7.0 | 11/29 | 680 | 127 | 50 |
762 | RNA-binding protein FUS (N) | [SwissProt:FUS_HUMAN] | 53/61 | 9.4/7.8 | 2/5 | 64 | 45 | 17 |
771 | Ras GTPase-activating protein-binding protein 1 (N) | [SwissProt:G3BP1_HUMAN] | 52/61 | 5.4/6.0 | 5/12 | 381 | 131 | 39 |
913 | Lamin A/C (T) | [SwissProt:LMNA_HUMAN] | 74/77 | 6.6/7.0 | 5/14 | 120 | 39 | 28 |
914 | Lamin A/C (T) | [SwissProt:LMNA_HUMAN] | 74/77 | 6.6/6.8 | 7/23 | 121 | 38 | 42 |
921 | RuvB-like 1 (N) | [SwissProt:RUVB1_HUMAN] | 50/50 | 6.0/6.8 | 8/16 | 591 | 131 | 50 |
Protein DEK (N) | [SwissProt:DEK_HUMAN] | 43/50 | 8.7/6.8 | 2/4 | 162 | 92 | 12 | |
924 | Heterogeneous nuclear ribonucleoprotein H (N) | [SwissProt:HNRH1_HUMAN] | 49/49 | 5.9/6.4 | 8/15 | 440 | 80 | 53 |
1132 | 60-kDa heat shock protein, mitochondrial precursor (T) | [SwissProt:CH60_HUMAN] | 61/61 | 5.7/5.5 | 7/15 | 176 | 36 | 28 |
1191 | Serine/threonine protein phosphatase PP1-β catalytic subunit (N) | [SwissProt:PP1B_HUMAN] | 37/34 | 5.8/6.1 | 2/10 | 62 | 41 | 35 |
1629 | Annexin A1 (T) | [SwissProt:ANXA1_HUMAN] | 39/38 | 6.6/6.7 | 6/13 | 233 | 73 | 50 |
2212 | Stathmin (T) | [SwissProt:STMN1_HUMAN] | 17/18 | 5.8/6.2 | 2/6 | 82 | 51 | 32 |
2039 | Histone-binding protein RBBP4 (N) | [SwissProt:RBBP4_HUMAN] | 48/48 | 4.7/5.1 | 7/10 | 414 | 103 | 27 |
Comparison of IgG reactivities in sera from HCs and SSc patients
Subset-specific IgG reactivities in sera from patients with unidentified ANAs
Subset of patients | Protein ID on gel | HEp-2 cell protein | SwissProt accession number | MW th/es | pHi th/es | Number of unique identified peptides# | Total ion score | Best ion score | Sequence coverage (%) |
---|---|---|---|---|---|---|---|---|---|
dcSSc/SRC | 1100 | Calreticulin precursor (T) | [SwissProt:CALR_HUMAN] | 48/63 | 4.3/4.4 | 5/16 | 136 | 36 | 25 |
1420 | Pre-mRNA splicing factor SPF27 (N) | [SwissProt:SPF27_HUMAN] | 26/25 | 5.5/5.9 | 6/10 | 377 | 115 | 47 | |
1636 | Eukaryotic translation initiation factor 5A-1 (N) | [SwissProt:IF5A1_HUMAN] | 17/16 | 5.1/5.7 | 3/3 | 163 | 101 | 33 | |
2249 | Eukaryotic translation initiation factor 5A-1 (T) | [SwissProt:IF5A1_HUMAN] | 17/17 | 5.1/5.6 | 2/5 | 80 | 69 | 22 | |
dcSSc/PAH | - | - | - | - | - | ||||
dcSSc/ILD | 589 | Probable ATP-dependent RNA helicase DDX17 (N) | [SwissProt:DDX17_HUMAN] | 72/76 | 8.8/8.0 | 8/20 | 207 | 35 | 36 |
1101 | Poly(rC)-binding protein 2 (N) | [SwissProt:PCBP2_HUMAN] | 39/39 | 6.3/6.9 | 5/10 | 132 | 56 | 41 | |
1151 | Serine/threonine protein phosphatase PP1-α catalytic subunit (N) | [SwissProt:PP1A_HUMAN] | 37/35 | 5.9/6.5 | 10/17 | 476 | 114 | 61 | |
dcSSc* | 1417 | DNA-directed RNA polymerases I, II and III, subunit RPABC1 (N) | [SwissProt:RPAB1_HUMAN] | 25/25 | 5.7/6.3 | 2/4 | 150 | 117 | 21 |
2163 | Cofilin 1 (T) | [SwissProt:COF1_HUMAN] | 19/19 | 8.2/9.5 | 3/7 | 134 | 72 | 54 | |
lcSSc/DU | 2317 | Histone H2A type 1-J (T) | [SwissProt:H2A1J_HUMAN] | 14/16 | 10.9/6.1 | 2/3 | 37 | 20 | 27 |
lcSSc/PAH | 882 | Telomeric repeat binding factor 2-interacting protein 1 (N) | [SwissProt:TE2IP_HUMAN] | 44/52 | 4.6/4.9 | 9/15 | 286 | 71 | 48 |
1119 | Heterogeneous nuclear ribonucleoprotein A/B (N) | [SwissProt:ROAA_HUMAN] | 36/38 | 8.2/6.5 | 3/5 | 55 | 27 | 15 | |
2079 | Peroxiredoxin 2 (T) | [SwissProt:PRDX2_HUMAN] | 22/23 | 5.7/6.0 | 5/7 | 143 | 40 | 26 | |
lcSSc/ILD | 901 | 78-kDa glucose-regulated protein precursor (T) | [SwissProt:GRP78_HUMAN] | 72/76 | 5.1/5.4 | 13/29 | 711 | 121 | 28 |
2063 | ATP-dependent DNA helicase 2, subunit 1 (N) | [SwissProt:KU70_HUMAN] | 70/70 | 6.2/6.9 | 3/14 | 89 | 45 | 29 | |
lcSSc* | 820 | U4/U6 small nuclear ribonucleoprotein Prp31 (N) | [SwissProt:PRP31_HUMAN] | 55/57 | 5.6/6.4 | 3/7 | 112 | 64 | 16 |
1478 | Calumenin precursor (T) | [SwissProt:CALU_HUMAN] | 37/44 | 4.5/4.6 | 3/7 | 82 | 39 | 29 | |
1895 | Tumour protein D54 (T) | [SwissProt:TPD54_HUMAN] | 22/29 | 5.3/5.6 | 1/3 | 47 | 47 | 23 |