Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments

Bulk RNA-Seq: Gene expression analysis of stromal and tumor fractions of primary and metastatic lesions of polyclonal and monoclonal origin. Primary tumor control samples consist of monoclonal Thy1.1 (no replicates), monoclonal parental (no replicates), monoclonal IL11 (duplicate), monoclonal FIGF (duplicate), and monoclonal CFP (duplicate). Primary polyclonal tumor samples consist of separated Thy 1.1 (duplicate), CFP (no replicates), IL11 (triplicate), and FIGF (triplicate). Metastatic tumor samples consist of monoclonal CFP (duplicate), monoclonal IL11 (quadruplicate), monoclonal FIGF (quadruplicate), monoclonal Thy1.1 (duplicate), and polyclonal samples (duplicate). Metastatic stromal fractions consist of monoclonal CFP (duplicate), monoclonal FIGF (quadruplicate), monoclonal IL11 (quadruplicate), monoclonal parental (duplicate), monoclonal Thy1.1 (duplicate), and polyclonal samples (triplicate). Primary stromal samples consist of monoclonal CFP (duplicate), monoclonal FIGF (duplicate), monoclonal IL11 (duplicate), monoclonal parental (no replicates), monoclonal Thy1.1 (duplicate), and polyclonal samples (triplicate). Further stromal controls consisted of a single fatpad sample and lung sample. Single cell RNA-Seq: Blood, tumors and lungs were isolated from test groups (DOX+ and DOX-) and tumor-naïve animals. Samples were pooled across 3 animals per group, and CD45+populations were FACS-sorted. Two thousand single cells were targeted for each sample. Overall design: Gene expression analysis of IL11RA and PLXDC sorted fractions from lungs of tumor-bearing mice. Tumor cells were induced to overexpress IL11/FIGF with DOX diet given to the animals.