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Herberts, Cameron

University of British Columbia

Life-prolonging targeted therapies exploiting genomic vulnerabilities are now standard-of-care in metastatic castration-resistant prostate cancer (mCRPC). However, consensus on optimal patient selection—including choice of molecular profiling—remains unestablished. Plasma cell-free DNA (cfDNA) is an established minimally-invasive tool for real-time profiling and may facilitate genomic stratification of mCRPC. In this thesis, next-generation sequencing was applied to cfDNA and tumour tissue to define the population frequencies and clinicogenomic properties of therapeutically-relevant mCRPC molecular subtypes: activating AKT1/PIK3CA mutations, mismatch-repair deficiency (MMRd), and DNA repair defects in BRCA2/CDK12/ATM. Targeted ctDNA sequencing detected AKT1/PIK3CA mutations in 6% of mCRPC. Clonal prevalence, consistent temporal redetection across serial cfDNA, and mutant-allele imbalance indicate PI3K pathway dependency in select patients. MMRd (4%) was identifiable in ctDNA via multiple correlated metrics of genome-scarring, and was associated with mutation-enabled oncogene activation, heightened subclonal diversity, and poor response to AR-targeted treatment. Defects in BRCA2/CDK12/ATM (15%) involved biallelic inactivation in most patients, suggesting driver etiology. Tumour suppressors were controlled via deleterious rearrangements in BRCA2-defective samples but via (negative-feedback) oncogene amplification in context of CDK12 defects. BRCA2/CDK12/ATM defects were re-detected across 94% of serial ctDNA and in all archival primary tissues, indicating origination prior to metastatic dissemination. BRCA2 and CDK12 (but not ATM) was associated with poor clinical outcomes. Optimized targeted cfDNA testing necessitates understanding of the dynamic clonal composition of bulk ctDNA. We performed deep whole-genome sequencing (WGS) of serial plasma and synchronous metastases, revealing ctDNA populational diversity involving variable whole-genome duplication and shifts in mutational processes. Although tissue and ctDNA harboured concordant clonally expanded driver alterations, most individual metastases contributed only a minor share of total ctDNA. By comparing serial ctDNA before and after progression on AR pathway inhibitors, we reveal population restructuring converging solely on AR augmentation as the dominant genomic driver of acquired treatment resistance. Finally we leverage ctDNA nucleosome footprints to infer metastatic tissue mRNA abundance, including treatment-induced changes in AR transcription factor signaling. In this context, my thesis informs future precision oncology clinical trial design and ctDNA testing strategies, and establishes serial ctDNA WGS as a discovery tool for understanding complex metastatic tumour biology.

Text

2024-03-21

Attribution-NonCommercial-NoDerivatives 4.0 International

http://hdl.handle.net/2429/87606

Genome Science and Technology

University of British Columbia

UBCV

http://creativecommons.org/licenses/by-nc-nd/4.0/