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Series GSE118942 Query DataSets for GSE118942
Status Public on Mar 01, 2019
Title Separation of breast cancer and organ microenvironment transcriptomes in metastases
Organisms Homo sapiens; Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary The seed-and-soil hypothesis was described over a century ago to describe why cancer cells (seeds) grow in certain organs (soil). Since then, the genetic properties that define the cancer cells have been heavily investigated, however, the genetic mediators within the organ microenvironment that mediate successful metastatic growth are less understood. In these studies, a set of human breast cancer patient-derived xenograft (PDX) metastasis models were utilized. Mammary tumors and metastases to the liver, lung, and brain were RNA-sequenced with the goal of identifying complementary cancer and organ-specific genetic properties that mediate metastatic growth. During metastatic growth of PDXs, the genetic changes that occurred in the liver and lung microenvironment were more consistent and higher in magnitude than the cancer cell transcriptomes . Integration of the liver microenvironment gene signature into genetic data from liver metastasis autopsy samples or fine-needle aspirates revealed the contribution of the microenvironment to the metastatic transcriptome. These insights identify cancer and organ-specific genetic drivers  of metastasis.
 
Overall design Mammary tumors and metastases to the liver, lung, and brain were RNA-sequenced with the goal of identifying complementary cancer and organ-specific genetic properties that mediate metastatic growth.
 
Contributor(s) Alzubi MA, Turner TH, Olex AL, Sohal SS, Tobin NP, Bergh J, Hatschek T, Parker J, Sartorius CA, Perou CM, Dozmorov MG, Harrell JC
Citation(s) 30841919, 32001757
Submission date Aug 22, 2018
Last update date Feb 10, 2020
Contact name Wright Center for Clinical and Translational Research Bioinformatics Core
E-mail(s) [email protected]
Phone 804-828-1621
Organization name Virginia Commonwealth University
Street address 203 E Cary St
City Richmond
State/province VA
ZIP/Postal code 23298
Country USA
 
Platforms (2)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
GPL22245 Illumina HiSeq 2500 (Homo sapiens; Mus musculus)
Samples (128)
GSM3351491 HCI01 Liver Metastasis from mouse 100672
GSM3351492 HCI01 Liver Metastasis from mouse 100757
GSM3351493 HCI01 Liver Metastasis from mouse 100794
Relations
BioProject PRJNA487493
SRA SRP158730

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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE118942_RAW.tar 487.1 Mb (http)(custom) TAR (of TXT)
GSE118942_TPM_human_AllGenes_AllPDX.txt.gz 14.5 Mb (ftp)(http) TXT
GSE118942_TPM_mouse_AllGenes_AllPDX.txt.gz 12.8 Mb (ftp)(http) TXT
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Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record
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