Date of Graduation

5-2015

Document Type

Dissertation (PhD)

Program Affiliation

Human and Molecular Genetics

Degree Name

Doctor of Philosophy (PhD)

Advisor/Committee Chair

Dr. Ann Killary

Committee Member

Dr. Timothy McDonald

Committee Member

Dr. Subrata Sen

Committee Member

Dr. Khandan Keyomarsi

Committee Member

Dr. Swathi Arur

Committee Member

Dr. Steven Lott

Abstract

Ductal carcinoma in situ (DCIS) is thought to be one of the earliest pre-invasive form of and non-obligate precursor to invasive ductal carcinoma (IDC). There is an urgent need to identify predictive and prognostic biomarkers for breast cancers with a heightened risk of progression from DCIS to IDC. Our laboratory has previously discovered a novel TRIM family member, DEAR1 (Ductal Epithelium Associated Ring Chromosome 1, annotated as TRIM62) within chromosome 1p35.1, that is mutated and homozygously deleted in breast cancer and whose expression is downregulated/lost in DCIS. Previous work has shown that DEAR1 is a novel tumor suppressor that acts as a dominant regulator of polarity, tissue architecture, and TGFβ-driven epithelial-mesenchymal transition (EMT)1,2. Herein, I have shown by pan-cancer database analysis that chromosomal loss of DEAR1 is a moderately frequent event in multiple epithelial cancers and that targeted deletion of Dear1 in the mouse recapitulates the tumor spectrum of human tumor types undergoing DEAR1 copy number losses, including mammary tumors. Therefore, these results indicate the relevance of the Dear1 mouse model to human disease and suggest that genomic alteration of DEAR1 could play a role in the etiology of multiple cancers, including breast cancer. Because DEAR1 is downregulated in DCIS and regulates polarity and EMT, I hypothesized that DEAR1 mutations might be driver events in the progression of DCIS to IDC. Therefore, targeted ultra-deep sequencing of DEAR1 was completed in FFPE samples of 17 Pure DCIS and 17 DCIS samples associated with invasive lesions. Deep sequencing of DCIS indicate DEAR1 is mutated in 71% of DCIS. Within these samples, multiple mutations within DEAR1, including exonic variants previously discovered in IDC and novel nonsense mutations were discovered and validated. Interestingly, variants in samples of DCIS associated with an invasive component indicate few variants shared between the two components, possibly supporting an independent yet parallel evolution between DCIS and IDC. Further, functional screens were performed on a subset of mutations identified and demonstrated that mutations effect DEAR1’s regulation of tissue architecture and TGFβ signaling. Altogether, this data suggests that genomic alteration of DEAR1 is an important mechanism for its loss of function and may be of significance for future targeted therapies aimed at the pathways regulated by DEAR1.

Keywords

ultra-deep targeted sequencing, DEAR1, TRIM62, DCIS, Invasive breast cancer

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