Recurrent tumor cell–intrinsic transcriptomic, RTKinomic, and immune regulomic alterations in regressing melanoma on MAPKi therapy. Recurrent tumor cell–intrinsic.

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Recurrent tumor cell–intrinsic transcriptomic, RTKinomic, and immune regulomic alterations in regressing melanoma on MAPKi therapy. Recurrent tumor cell–intrinsic transcriptomic, RTKinomic, and immune regulomic alterations in regressing melanoma on MAPKi therapy. A, B, Pattern of differential expression of genes in the On-Tx tumor samples with recurrent (>50%) up-expression in any of the DTP, DTPP, Rr, or Ra set of samples (A, top 50 genes; B, RTK genes only; red and green, up-expression and down-expression). C, Immunofluorescence of PDGFRβ, EGFR, and c-MET using formalin-fixed, paraffin-embedded (FFPE) tumor tissues designated by letters (ruler, 100 μm); negative staining by gray circles. D, As in A and B except showing only top recurrently up-expressed immune regulomic genes. E and F, Expression ranges of immune genes in D among baseline versus On-Tx tumors (E) or P versus Rr or Ra lines (F). G (left), Correlation between FCs in PD-L2 mRNA expression and % methylation changes at the expression anticorrelated CpG site of PD-L2 across comparisons of DP versus baseline tumors and Rr versus P lines. Middle, correlation across all samples (from the left panel) and (right) all TCGA melanoma samples. R, Pearson correlation coefficient; P, Student t test. H, Methylation changes at all profiled CpG sites (green bubble, expression-correlated site; left) or absolute methylation levels at the expression-correlated CpG site (right) versus PD-L2 mRNA expression FC (left) or absolute levels (right). All changes relative to vehicle-treated M229. I, H3K27ac chromatin immunoprecipitation sequencing (ChIP-seq) peaks covering the PD-L2 expression–correlated CpG site in invasive versus proliferative melanoma cultures. PD-L2 mRNA levels also shown. J, Median fluorescence intensities (MFI) of PD-L1 and PD-L2 staining in P versus Rr or Ra lines. K, PD-L2 immunofluorescence using frozen tissues from patient #3 (100× scale bar, 50 μm; 400× scale bar, 20 μm). Several views shown for On-Tx tumor. Chunying Song et al. Cancer Discov 2017;7:1248-1265 ©2017 by American Association for Cancer Research