Table III

Disease-specific and promiscuous epitopes, their predicted binding to 25 HLA-DR molecules and their source proteins

Epitopes in commonaGene symbolNo. IDbNo. of DR molecules the peptide is predicted to bindcSource proteins
Only the two RA patients
    SRLPIIDVAPLDVGAPDTCOL1A1119Collagen, type I, α-1
    NLDFLKAVDTNRASVGQDSPEPRKPLXDC296Plexin domain-containing protein 2
    DGKRIQYQLVDISQDNSH3BGRL339TNF-inhibitory protein
Only the two LA patients
    KDKTYSYLNKLPVKSKNPC2611Epididymal secretory protein E1
    GPRPEEYEFLTPVEEAPKARHGDIB34Rho GDP dissociation inhibitor 1β
Identified in three or more patients' samples
    SGKPQYMVLVPSLLHTETA2M7224α2-Macroglobulin
    LINEYWVLTAAHVVEGC1s1614C1s complement
    SPMYSIITPNILRLESKC33815C3 complement
    VSGTLVLLQGARGFAB,KCD141320CD14 monocyte differentiation antigen
    SNVDMDFEVENAVLGKDFKF13A1201Coagulation factor XIII A1
    ESDTSYVSLKAPLTKPLKCRP149C-reactive protein
    TGDAYVILKTVQLRNGNLKGSN3225Gelsolin
    TGAQELLRVLRAQPVQVAGSN1213Gelsolin
    SPERPFLAILGGAKVADKKPGK173Phosphoglycerate kinase 1
    LFEQLGEYKFQNALLVRYTKKB,TALB908Serum albumin
  • a Amino acid sequence of HLA-DR bound epitopes. Because the peptide flanking regions varied, the longest identified peptide is shown. Peptides followed by a capitalized superscripted letter indicate that these HLA-DR-bound peptides were identified in other tissues: “T” for thyroid (21), “B” for bronchoalveolar lavage cells (20), and “K” for kidney (19). Tandem MS/MS spectra obtained for the listed peptides are presented in supplemental material pages 3–17.

  • b Number of times a peptide sequence was identified in the patients' samples.

  • c Of the 25 HLA-DR molecules modeled in TEPITOPE, the number of molecules predicted to present the peptide at a threshold setting of ≤3.