Figure S3.

Sequence and Location of the Five Most Common HLA-DR-SPs Presented by DR2a and DR2b on Peripheral Blood B Cells, Related to Figure 2

(A) Total number and location within the HLA-DR α/β-chain sequences of the HLA-DR-SPs presented by DR2a or DR2b on B cells. Colored amino acids within peptide sequences represent the core binding motif, analyzed by NetMHCII 2.3 server. The total number of each peptide is expressed as mean.

(B) Comparison of the binding affinities, analyzed by NetMHCII 2.3 server, of the HLA-DR-β-SPs to DR2a.

(C) Comparison of the binding affinities of the HLA-DR-SPs to DR2a and DR2b.

(D) Total number of the five most common HLA-DR-SPs presented by DR2a on B cells.

(E) Total number of the five most common HLA-DR-SPs presented by DR2b on B cells.

(F) Variability of α- and β-chains of HLA-DR molecules. The y axis shows the number of polymorphic residues identified at each position of the α- or β-chains. Sequences were obtained from the European Bioinformatics Institute (EMBL-EBI). Origins of HLA-DR-α-SPs and HLA-DR-β-SPs are highlighted.

(G) Analyses of the immunopeptidomes presented by HLA-II molecules from a broad range of tumor tissues, unaffected tissues around the tumor, and blood samples. The anti-HLA-DR antibody (L243) and the anti-HLA-DR/DP/DQ antibody (Tü39) were used together to analyze the immunopeptidomes. The proportion of samples that include the five most common unique HLA-DR-SPs in HLA-DR15⁻ samples (n = 497) and HLA-DR15⁺ samples (n = 108) was calculated.

Data are expressed as mean ± SEM, and p values were determined by unpaired t test.