Fig. 5: Altered antigenic landscape mediated by HLA LOH and APPM defects.
a, Inferred HLA allele-specific CN and their expression level in participant MEL-2, represented as bars and connected dots above, respectively. b, HLA allele distribution of all unique MS-identified antigen sequences (left, n = 27,910) and of HC-TSAs (right, n = 37) from participant MEL-2. c, mIF staining of a tumor tissue sample derived from participant MEL-2 (n = 1 slide). d, mIF quantification of HLA-ABC and HLA-DR on cancer cells (Sox10+) from participant MEL-2 (n = 352 tiles). e, Genome-wide CNVs in samples MEL-3-A (top), MEL-3-B (center) and MEL-3-C (bottom). Chromosomal segments are displayed along the x axis and their estimated minor and major CNs are displayed along the y axis. The color map represents the CCF of the B2M p.Glu67fs mutation across samples. f, Inferred HLA allele-specific CNs and their expression level in participant MEL-3, represented as bars and connected dots above, respectively. g, Expression levels of B2M in healthy sun-exposed skin (GTEx, n = 701), MEL samples (TCGA, n = 468) and MEL-3 samples, correlated with B2M CCF. The box plot center lines represent the median. The bounds of the box represent the 25th and 75th percentiles (IQR). The whiskers extend to the 5th and 95th percentiles. h, mIF staining of a tumor tissue sample derived from participant MEL-3 (n = 1 slide). i, mIF quantification of HLA-ABC and HLA-DR on cancer cells (Sox10+) from participant MEL-3 (n = 605 tiles).
