Francisco J. Sánchez-Rivera, Ph.D. – VAI Seminar Series

Functional studies of genetic variation using precision genome editing

Speaker Information

Francisco J. Sánchez-Rivera, Ph.D.
Assistant Professor / HHMI Hanna H. Gray Fellow
Department of Biology at MIT
Koch Institute for Integrative Cancer Research at MIT

• Abstract/Bio: Cancer genomes typically harbor combinations of single nucleotide alterations and complex genomic rearrangements, and accumulating evidence suggests that tumor genotype can modulate cancer progression and responses to therapy. These observations have motivated efforts to treat cancers with genome-informed therapies — a paradigm often referred to as precision oncology. Still, the promise of precision oncology can only be met if we understand how different genetic variants precisely affect gene function and overall tumor phenotypes. Comprehensive variant-function maps that provide a mechanistic understanding of the biology driven by cancer-associated mutations are therefore needed to design these types of treatment strategies. Precision genome editing technologies like base editing (PMID: 27096365) and prime editing (PMID: 31634902) are uniquely suited to tackle this problem. Nevertheless, deploying these methods for systematic variant-function studies and disease modeling in vivo has not been straightforward due to lack of robust and scalable platforms capable of assessing editing efficiency and precision, particularly at endogenous loci. With this goal in mind, we previously developed and applied high-throughput base editing ‘sensor’ approaches that link endogenous genome editing outcomes with synthetic DNA-based readouts and cellular fitness measurements (PMID: 35165384). Using these approaches, we found that several previously uncharacterized mutant p53 alleles are bona fide drivers of cancer cell proliferation and in vivo tumor development. Building upon this work, we recently developed new prime editing guide RNA design tools and sensor-based approaches that similarly couple quantitative editing outcomes to cellular fitness, allowing us to significantly expand the breadth of cancer-associated mutations that can be interrogated using these precision genome editing technologies. I will describe ongoing work using base editing and prime editing sensor libraries to probe the function of thousands of cancer-associated variants, as well as for saturation mutagenesis studies of diverse cancer drivers, to map endogenous gene function with close to single base pair resolution. We anticipate that this generalizable precision genome editing framework will facilitate the functional interrogation of genetic variants across diverse biological contexts, providing much needed insight into cancer variant-function relationships that could be leveraged to develop more precise cancer therapies.
• Host: Bart Williams, Ph.D.