In vivo shRNA screening in PDXs from 3 patients with melanoma.

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In vivo shRNA screening in PDXs from 3 patients with melanoma. In vivo shRNA screening in PDXs from 3 patients with melanoma. A, shRNA screening strategy: Surgical specimens of metastatic melanomas were dissociated and injected subcutaneously into NSG mice to obtain primary PDX1 tumors. PDX1 cells were infected with either the control (13K) or the epigenetic libraries and retransplanted (PDX2 tumors). Genomic DNAs extracted from PDX2 tumors and transduced PDX1 cells were subjected to PCR amplification and NGS to quantify the BCs. B and C, left, the scatter plots of BC frequency of the two replicate tumors (T1 and T2) arising from the transplantation of MM13-, MM16-, and MM27-transduced PDX1 cells expressing either the 13K library (B) or the epigenetic library (C). Gray dotted lines represent the axis bisectors. Pearson correlations (R) are reported. Right (B and C), the log2(ratio) distribution of the BC reads in the PDX2 tumors (mean of replicates) and in the transduced PDX1 cells. The gray dotted line in C represents the cutoff threshold (reported in gray on the x-axis) set to calculate the significantly depleted shRNAs (gray portion of the distribution curve). Medians are reported. D, Venn diagram reporting the number of genes scoring as depleted hits in the three PDXs. Daniela Bossi et al. Cancer Discov 2016;6:650-663 ©2016 by American Association for Cancer Research