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. Author manuscript; available in PMC: 2020 Jun 16.
Published in final edited form as: Nat Biotechnol. 2019 Dec 16;38(2):199–209. doi: 10.1038/s41587-019-0322-9

Figure 4: Proteasomal and peptidase shaping of the HLA-associated peptidome.

Figure 4:

a) Three types of primary tumor cell lines (melanoma [MEL], glioblastoma [GBM] and clear cell renal cell carcinoma [ccRCC]) used to identify HLA-associated peptidomes. b) Changes in relative protein abundance of proteasomal subunits and IFNγ inducible genes in patient-derived GBM cells with or without IFNγ-treatment based on MS proteome analysis. c) Schematic of cleavage signature analysis. d) Peptide processing signatures of HLA ligands presented by primary tumor and cancer cell lines at baseline (top, n=4 MEL, 3 GBM, 1 ccRCC, 1 Lung, biologically independent samples) and following IFNγ treatment (bottom, n=3 MEL, 3 GBM, 1 ccRCC, 1 Lung, biologically independent samples), showing overrepresented (red) or underrepresented (blue) amino acid residues upstream and downstream of the HLA peptide. The number in each cell denotes percent change over a background decoy set; color intensity indicates significance (see key, Chi-squared test, df=1). e) Heatmap of correlations between the processing preferences in untreated and IFNγ-treated samples at upstream and downstream positions. Signatures for peptides from the IFNγ treated cells correlate well with peptides eluted from untreated cells suggesting minimal to no difference between the two patterns (sample sizes as in 4d; Spearman’s rank correlation). See also Supplementary Figure 4.