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
    LINEYWVLTAAHVVEGC1s1614C1s complement
    SPMYSIITPNILRLESKC33815C3 complement
    VSGTLVLLQGARGFAB,KCD141320CD14 monocyte differentiation antigen
    SNVDMDFEVENAVLGKDFKF13A1201Coagulation factor XIII A1
    ESDTSYVSLKAPLTKPLKCRP149C-reactive protein
    SPERPFLAILGGAKVADKKPGK173Phosphoglycerate kinase 1
  • 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.