Dana Farber Cancer Institute: Discovery of Novel Oncogenes

Widespread recurrent copy number alterations are observed across the majority of human cancers, yet the specific targets of such amplified or deleted regions remain undefined. Here, the CTD2 Center at the Dana Farber Cancer Institute took a systematic approach using cDNA overexpression screening to identify and validate oncogenes residing in such amplified regions. In representative examples, these experiments have identified the adaptor proteins CRKL, GAB2, FRS2 and the TLOC and SKIL proteins as novel amplified oncogenes.

A. Amplicon-Based Pooled in Vivo Transformation Screen

Amplified genes were systematically tested for their ability to promote tumor formation using an in vivo multiplexed transformation assay. One candidate, GAB2, was identified as a recurrently amplified gene that potently transforms immortalized ovarian and fallopian tube secretory epithelial cells.

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Experimental Approaches

Copy number data generated by TCGA was queried to identify 1,017 recurrently amplified genes resident in the 63 recurrently amplified regions in high-grade serous ovarian cancer (HGSOC). From this data an arrayed collection of 587 ORFs representing 455 amplified ovarian genes was created. 26 pools composed of ORF-expressing cell lines representing 16–24 ORFs was created and each group was implanted subcutaneously in six separate replicates in immunodeficient mice. 

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B. Identifying Cancer Driver Genes in the 3q26 Region

The CTD2 Center at the Dana Farber Cancer Institute functionally interrogated genes within the frequently amplified 3q26 region through gain- and loss-of-function studies.  These studies identified both TLOC1 and SKIL as driver genes at 3q26 and broadly suggest that cooperating genes may be co-amplified in other chromosomal regions.

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Experimental Approaches

Both gain- and loss-of-function approaches were applied to interrogate the 20 genes resident in the minimal common amplified region of 3q26 for effects on proliferation, anchorage-independent growth, and invasion. 

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C. Finding Both Amplified and Specifically Essential Ovarian Cancer Genes

50 genes that are recurrently amplified in HGSOC and essential for cancer proliferation and survival in ovarian cancer cell lines were interrogated.  One candidate, FRS2, was identified as an oncogene in a subset of HGSOC that harbor FRS2 amplifications.

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Experimental Approaches

By combining the output of ovarian cancer genome analysis with Project Achilles, 1,825 recurrently amplified genes in ovarian cancer were systematically interrogated to identify genes that are essential in ovarian cancer cell lines that harbor such amplifications. FRS2 was identified as an amplified and essential gene in HGSOC.

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If you cannot access the manuscript, or if you have additional questions, please email Barbara Weir.

Data

Access the CTD2 Data Portal.

Reference:

  1. Cheung et al. (2011). Systematic investigation of genetic vulnerabilities across cancer cell lines reveals lineage-specific dependencies in ovarian cancer. PNAS: 108(30):12372-7.(PMID: 21746896)
Last updated: June 07, 2016