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Fig. 1 | Journal for ImmunoTherapy of Cancer

Fig. 1

From: Immunopeptidomics of colorectal cancer organoids reveals a sparse HLA class I neoantigen landscape and no increase in neoantigens with interferon or MEK-inhibitor treatment

Fig. 1

HLA-I immunopeptidome in five PDOs. a Number of unique peptides detected per PDO. b Number of source proteins to which peptides from A uniquely mapped. c Correlation of HLA-I molecules per cell (assessed by flow cytometry) against the number of unique peptides for all five PDOs. The Pearson correlation coefficient is shown. d RNA expression of genes involved in antigen processing and presentation on HLA-I. e DNA copy number data generated from exome sequencing of PDO CRC-05. f Venn diagrams showing the concordance and discordance of all peptides between pairs of PDOs which share the indicated HLA-I allele. Venn diagrams were re-scaled so the area represents the peptide numbers in each segment. g Comparison of the normalized peptide intensity of PDOs that share HLA-I alleles. h Violin plot of percentile ranks predicted by NetMHCpan4.0 for all MS identified peptides from panel A to the autologous HLA molecules per PDO. Dashed lines show the median for each PDO (red) and the overall median (black). i Number of MS detected peptides expressed at or below the indicated RNA expression value

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