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Series GSE100412 Query DataSets for GSE100412
Status Public on May 23, 2019
Title Transcriptional signatures associated with in vivo growth of lung cancer cells
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary 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.
 
Overall design The following conditions were analyzed: (1)LLC In Vitro. RNA was extracted from LLC cells cultured in vitro. This condition has 5 independently cultured and harvested replicates.(2) LLC In Vivo. RNA was extracted from LLC cells that were injected into mice, formed a tumor, and cancer cells were isolated by flow cytometry. This condition has 5 independently injected and harvested replicates. Each replicate is a pool of 3-5 mice.(3) LLC Pass. A sample of LLC cells isolated from tumors was replated and further cultured in vitro. This condition has 5 independent replicates.(4) CMT In Vitro. RNA was extracted from CMT cells cultured in vitro. This condition has 3 independently cultured and harvested replicates.(5) CMT In Vivo. RNA was extracted from CMT cells that were injected into mice, formed a tumor, and cancer cells were isolated by flow cytometry. This condition has 3 independently injected and harvested replicates. Each replicate is a pool of 3-5 mice.(6) CMT Pass. A sample of LLC cells isolated from tumors was replated and further cultured in vitro. This condition has 3 independent replicates.
 
Contributor(s) Poczobutt JM, Li H, McSharry M, De S, Yadav VK, Kwak J, Bullock B, Sippel TR, Nguyen TT, Hanson D, Weiser-Evans MC, Nemenoff RA
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Submission date Jun 23, 2017
Last update date May 23, 2019
Contact name Joanna Poczobutt
E-mail joanna.poczobutt@UCDenver.edu
Organization name University of Colorado Denver
Department Medicine
Lab Nemenoff
Street address 12700 E. 19th Avenue, C281
City Aurora
ZIP/Postal code 80045
Country USA
 
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (24)
GSM2680500 LLC_InVitro_1
GSM2680501 LLC_InVitro_2
GSM2680502 LLC_InVitro_3
Relations
BioProject PRJNA391687
SRA SRP110258

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Supplementary file Size Download File type/resource
GSE100412_CMTandLLC_FPKM_table_V2.txt.gz 1.7 Mb (ftp)(http) TXT
SRA Run SelectorHelp
Raw data are available in SRA
Processed data is available on Series record

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