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Fig. 4 | Journal for ImmunoTherapy of Cancer

Fig. 4

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. 4

Changes of the immunopeptidome through IFNγ treatment (600 ng/ml for 48 h) in four PDOs. a Flow cytometric quantification of HLA-I molecules per cell with and without IFNγ treatment. b Number of unique peptides detected per PDO with and without IFNγ treatment. c Change in peptide diversity and HLA-I abundance with and without IFNγ treatment. d Venn diagram comparing the specific peptides detected in untreated and IFNγ-treated PDOs. Venn diagrams were re-scaled so the area represents the peptide numbers in each segment. e Volcano plots showing the fold change of normalized peptide abundance with IFNγ treatment. Known IFNγ-inducible genes which show a statistically significant (q < 0.05) fold change above +/− 2 are drawn in red. f MS intensities of neoantigens between untreated and IFNγ-treated conditions. g Number of unique peptides detected by MS on HLA-II molecules with and without IFNγ treatment. h Flow cytometric quantification of HLA-II molecules per cell with and without IFNγ treatment

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