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Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments

ABSTRACT: Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments

PROVIDER: PRJNA430336 | ENA |

REPOSITORIES: ENA

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Subclonal cooperation drives metastasis by modulating local and systemic immune microenvironments.

Project description: Not available

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Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments

Project description: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-naÃ¯ve animals. Samples were pooled across 3 animals per group, and CD45+populations were FACS-sorted. Two thousand single cells were targeted for each sample.

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Project description:Interaction of hematopoietic progenitors with the thymic stromal microenvironment induces them to proliferate, adopt the T cell fate, and asymmetrically diverge into multiple T lineages. Progenitors at various developmental stages are stratified among different regions of the thymus, implying that the corresponding microenvironments differ from one another, and provide unique sets of signals to progenitors migrating between them. The nature of these differences remains undefined. Here we use novel physical and computational approaches to characterize these stromal subregions, distinguishing gene expression in microdissected tissues from that of their lymphoid constituents. Using this approach, we comprehensively map gene expression in functionally distinct stromal microenvironments, and identify clusters of genes that define each region. Quite unexpectedly, we find that the central cortex lacks distinctive features of its own, and instead appears to function by sequestering unique microenvironments found at the cortical extremities, and modulating the relative proximity of progenitors moving between them. 4 to 6 weeks old male C57bl6/J were used for microdissection of 3 thymic cortical subregions and thymic medulla or for sorting cortical and medullary thymocytes. These samples were used for subsequent RNA purification, labeling and hybridization to Affymetrix arrays

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