Pluto Bioinformatics

GSE100412: Transcriptional signatures associated with in vivo growth of lung cancer cells

Bulk RNA sequencing

Interactions between cancer cells and the host cells in the tumor microenvironment (TME) are critical for tumor growth and metastasis. While the host cells have been widely studied within the TME, cancer cell have been mostly studied in vitro. We hypothesized that the growth of cancer cells in vivo results in specific changes in cancer cells transcriptome that reflect specific interactions between cancer cell and the TME. To begin to define the changes in cancer cells growing in vivo, we performed RNA-seq transcriptome analysis of cancer cells isolated from murine tumors and compared them to transcriptomes of cells growing in vitro. In this study we used two murine lung cancer cell lines, both derived from a spontaneous lung adenocarcinoma in C57BL/6 mouse: (1) Lewis Lung carcinoma (LLC) and (2) CMT167(CMT). We first harvested RNA from these 2 cell lines cultured in vitro. To assess the transcriptome of cells growing in vivo, we employed an orthotopic immunocompetent model of lung adenocarcinoma in which murine lung cancer cells are directly implanted into the left lobe of syngeneic mice. LLC or CMT cells were injected into the lung of GFP-expressing mice of C57BL/6 strain. Resulting tumors were harvested, processed into single cell suspension, and cancer cells were isolated from host cells by flow cytometry, sorting for GFP-negative cells. RNA was extracted from freshly isolated cells. Furthermore, to assess if the changes associated with in vivo growth are permanent, we re-plated the cells isolated from mice, cultured them further in vitro, and extracted their RNA. Our RNA-seq analysis has shown that both cell lines undergo robust specific changes in transcriptional profile when growing in vivo as compared to cells cultured in vitro. Majority of these signatures were reversed in cells that were replated and further cultured in vitro after isolation from mice. SOURCE: Joanna Poczobutt ( - Nemenoff University of Colorado Denver

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