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GEO help: Mouse over screen elements for information. |
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| 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
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| 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.
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| 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.
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| 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 |
| Citation(s) |
31133614, 36686777 |
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| Submission date |
Jun 23, 2017 |
| Last update date |
Feb 06, 2023 |
| Contact name |
Joanna Poczobutt |
| E-mail(s) |
joanna.poczobutt@UCDenver.edu
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| Organization name |
University of Colorado Denver
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| Department |
Medicine
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| Lab |
Nemenoff
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| Street address |
12700 E. 19th Avenue, C281
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| City |
Aurora |
| ZIP/Postal code |
80045 |
| Country |
USA |
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| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
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| Samples (24)
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| Relations |
| BioProject |
PRJNA391687 |
| SRA |
SRP110258 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE100412_CMTandLLC_FPKM_table_V2.txt.gz |
1.7 Mb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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