My lab is using functional genomics, molecular biology, biochemistry, and advanced imaging in both the yeast model and cultured human cells to study fundamental mechanisms of genome maintenance and stability. Failure to maintain genome integrity leads to mutations that can promote tumour formation. Normal genome maintenance mechanisms can be overwhelmed by carcinogen exposure, or the presence of germline or somatic variants that induce genomic instability. Our work is aimed at determining the causes of genomic instability as an enabling characteristic of tumour formation, and exploring the potential of these early events to suggest novel therapeutic targets. Currently we are working on several projects, briefly outlined below.

Roles of RNA processing in genome maintenance

Functional genomic screening of the yeast model, Saccharomyces cerevisiae, and of mammalian cells has revealed that most steps in RNA metabolism (including transcription, processing, and decay) can cause genome instability when disrupted. In some cases it is clear that mutations in RNA processing factors lead to transcription-coupled DNA:RNA hybrids that form R-loops. R-loop structures expose damage-prone single-stranded DNA, and can also impede DNA replication fork progression, causing breaks. Importantly, not all genome destabilizing RNA processing mutants create R-loops, and we are also interested in defining these alternative mechanisms.

RNA processing mutations are now recognized to occur in various tumours. These include widely distributed and frequent mutations of the spliceosome (e.g. SF3B1 in hematopoietic malignancies), mutations in the RNA degrading exosome (e.g. DIS3), and mRNA processing genes (e.g. FIP1L1). The importance of these cancer-associated mutations for genome maintenance and the potential for R-loop formation to contribute to cancer cell phenotypes is also under investigation. Finally, some yeast RNA processing mutants exhibit synthetic lethality with cancer-associated genome maintenance genes, and therefore represent candidate therapeutic targets. We are exploring the conservation of such interactions and the potential for inhibiting aspects of RNA metabolism for therapeutic benefit.

DNA repair: mutation signatures and transcription-replication conflicts

Mutational processes leave a characteristic pattern of mutations on tumour genomes based on the underlying biology that is disrupted or the causative environmental agent. While elegant computational methods can extract such mutation ‘signatures’ from tumour genomes, the mechanisms are usually unknown. We have established a yeast model for linking specific genetic changes in conserved genome integrity pathways, and their interactions with genotoxic drugs, to patterns of accumulated mutations using whole genome sequencing. Yeast provides a clean and tractable genetic system whose genome can be sequenced in an efficient, cost-effective manner. These signatures have led to new insights to biochemical mechanisms of DNA repair (e.g. slippage and realignment in DNA translesion synthesis polymerases: bioRxiv 086512, doi: https://doi.org/10.1101/086512) and to an appreciation that defects in DNA repair can increase transcription-replication conflicts.

Our observation that some DNA repair defects increase transcription-replication conflicts, likely due to R-loops impairing DNA replication, connects to a growing body of literature which links genome maintenance factors (e.g. BRCA2, XPF/XPG, the Fanconi Anemia pathway and p53) to the suppression of R-loop-mediated genome instability. Our group is actively pursuing various DNA repair proteins that can suppress R-loop formation in yeast and human cells. We are developing tools to directly probe the molecular mechanisms of these effects and screen for conditions which enhance R-loop formation genetically or chemically.

The global cellular response to genotoxic stress

We have a long-standing interest in how cells respond to environmental stress dating back to Dr. Stirling’s earliest research on molecular chaperones (c. 2002-2008). Currently, this work is focused on the ways in which RNA and protein quality control machinery respond to genotoxic chemicals. These pathways may  serve as chemoresistance mechanisms in the face of genotoxic cancer therapies. Using the yeast model, we have found that transcriptome changes following genotoxic stress directly regulate the constituents of protein aggregate structures. We believe that factors  ejected from chromatin due to the transcriptional upheaval of a stress response are captured by protein quality control machinery in order to promote adaptation and recovery. The interplay between transcriptome dynamics, protein quality control, and RNA quality control (i.e. through P-bodies and Stress Granules) is an active area of interest in the lab.

Affiliations

Associate Professor, Medical Genetics, University of British Columbia

Credentials

With the exception of valuable training in California, Dr. Stirling is a life-long British Columbian. He grew up in Port Alberni, British Columbia and now resides in East Vancouver. He has a long-standing interest in the natural world and has been pursuing a career in the basic sciences for decades. Dr. Stirling is a CIHR New Investigator and a Michael Smith Foundation for Health Research Scholar. Details of his training are listed below.

Education:

• PhD (Molecular Biology and Biochemistry), Simon Fraser University, 2007

• BSc (Biochemistry), University of Victoria, 2002

Post-Graduate Training:

• Postdoctoral Research Fellow (Supervisor: Dr. Philip Hieter)
Michael Smith Laboratories, University of British Columbia (UBC), 2009 – 2013

• Postdoctoral Research Fellow (Supervisor: Dr. David Drubin)
Molecular and Cell Biology, University of California, 2007 – 2008

Professional Experience:

• Scientist, Terry Fox Laboratory, BC Cancer Agency (BCCA), Jan 2014 –

• Assistant Professor, Medical Genetics, UBC, Jan 2014 – June 2019

• Associate Professor, Medical Genetics, UBC, July 2019 –

Expertise:

• Biochemistry

• Genetics

• Cell biology

• Functional genomics

• Molecular mechanism

• Translational and therapeutic anti-cancer application

• Budding yeast

• Synthetic lethality

Selected Publications

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