Systematic analysis of the cancer-stroma interactome of a diverse collection of patient-derived xenografts

Transcriptomes of the cancer (human) and stroma (mouse) of 70 PDX samples consisted of 9 distinctive tumor types were analyzed in this study to investigate to the tumor micro-environment (TME). PDX models recapitulated the features of the original tumors, including tumor-purity, stromal cell composition, and putative signaling. An integrated analysis was conducted to identify the upstream paracrine effectors that govern the stromal transcriptome in KIRC PDXs, which were confirmed by using the complementary cancer transcriptome based on the hypothesis that cancer-derived effectors which play key roles in the formation of the cancer-stroma communication should be upregulated in cancer cells. 70 PDX samples consisted of 9 distinctive tumor types were established. Whole transcriptome sequencing of the samples and subsequent read assignment to human/mouse taxonomies yeilded cancer or stroma transcriptome data of each PDX sample. ----------------------------------------------------------- Authors state " Unfortunately, I am not allowed to make raw sequencing data (in fastq or BAM formats) to be available publicly due to the restriction of our Institutional Review Board and Ethic Committee because of patient privacy concerns."