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theses

RET is a receptor tyrosine kinase that is crucial for normal tissue development and maintenance, but deregulation of its activity is a known contributor to oncogenesis in several cancers. Gain-of-function alterations in thyroid and lung cancers, causally-associated mutations in hereditary forms of endocrine disorders combined with the observed tumor responses to tyrosine kinase inhibitors with anti-RET activity underscore the potential use of RET as a therapeutic target in breast cancer. In breast cancer, correlations of RET overexpression with endocrine resistance and reduced expression with improved overall survival in estrogen receptor positive cases are driving clinical investigations of using RET-targeting kinase inhibitors for treatment of this disease. In efforts to identify clinically relevant biomarkers that may help direct individualized patient treatment, our initial finding of RET gene rearrangements in two independent breast cancers initiated our inquiry into the frequency and therapeutic relevance of RET gene alterations in breast cancer. Upon analyzing ~9,700 breast cancers that were deep-sequenced using a targeted, hybrid capture assay, which includes relevant intronic details of RET, we discovered a spectrum of RET structural alterations in 121 cases (1.25%), of which, a majority were triple negative breast cancers that are known to have poorer prognosis and limited targeted treatment options. RET alterations were also identified in a subset of HER2-amplified breast cancers, primarily as RET amplification. We further characterized the functional consequence of RET amplification, the most frequent alteration, and the two initially identified RET rearrangements, NCOA4-RET and RASGEF1A-RET, by generating cell line and xenograft models. Comparison with an inactive RET kinase mutant and a known active RET kinase mutant by ectopic expression revealed constitutive kinase activation and downstream signaling of oncogenic pathways by both RET amplification and rearrangements. Results revealed that RET rearrangements induce transformation of non-tumorigenic cells, support xenograft tumor formation, and render cells carrying these alterations sensitive to RET inhibition in vitro and in vivo. Moreover, detection of the NCOA4-RET fusion in an index case of metastatic breast cancer that progressed on HER2-targeted therapy led to subsequent patient treatment with the RET inhibitor, cabozantinib, resulting in a rapid clinical and radiographic response. In another index case of advanced breast cancer, a RET amplification was detected and noted to be acquired in the setting of resistance to HER2-targeted therapy. RET expression was confirmed in a patient-derived cell line and xenograft model generated from this resistant tumor. Our xenograft model revealed tumor growth inhibition with cabozantinib and tested the applicability of its combination with HER2-targeting agents. Overall, this work presents a comprehensive, mutational analysis of RET in breast cancer and by using cell line models, patient-derived models, and index case reports, signifies the functional role of RET alterations as well as the therapeutic relevance of targeting RET in this selected subset of breast cancers.

ETD_9357

Ph.D.

Includes bibliographical references

by Bhavna S. Paratala

doi:10.7282/t3-rsdk-av61

ETD doctoral

The author owns the copyright to this work.