Eric Wong - Doctoral Exam

“Prediction and Characterization of Protein-Protein Interfaces that Bind Intrinsically Disordered Protein Regions”, by Eric Wong, doctoral candidate, Gsponer Lab.

Thursday, November 28, 2019 12:30-3:30 pm, Room 203, Graduate Student Centre, 6371 Crescent Road.

Abstract:

Protein–protein interactions mediated by intrinsically disordered regions (IDRs) are differentiated from classical interactions between folded domains in terms of structure and function. Therefore, we developed a computational method specifically for the prediction of IDR-binding sites on the structures of folded domains. I will also discuss characteristics of IDR interactions, including localization patterns of disease and benign mutations that highlight the functional importance of IDR interactions.

“Human-yeast cross-species complementation of chromosome instability genes”, by Akil Hamza, doctoral candidate, Hieter Lab.

Monday, September 30, 2019 at 2:30 in LSC#3

Abstract

Humanized yeast offer a valuable resource with which to model and study human biology. Using cross-species complementation, model organisms like the budding yeast, Saccharomyces cerevisiae, can be utilized to measure the impact of tumor-specific mutations and screen for genetic vulnerabilities of genes overexpressed in cancer. To this end, we performed three parallel screens, one-to-one complementation screens for essential and nonessential yeast genes implicated in chromosome instability (CIN) and a pool-to-pool screen that queried all possible essential yeast genes for rescue of lethality by all possible human homologs. Our work identified 65 human cDNAs that can replace the null allele of essential yeast genes, including the nonorthologous pair yRFT1/hSEC61A1. For the nonessential yeast genes, 20 human-yeast complementation pairs were determined to be replaceable in 44 assays that test rescue of chemical sensitivity and/or CIN defects. For five human-yeast complementation pairs expressing human cDNAs encoding hLIG1, hSSRP1, hPPP1CA, hPPP1CC and hPPP2R1A, we introduced 45 tumor-specific missense mutations and assayed for growth defects and sensitivity to DNA-damaging agents in yeast. This set of human-yeast gene complementation pairs allows human genetic variants to be readily characterized in yeast, generating a prioritized list of somatic mutations that could contribute to chromosome instability in human tumors. We also selected a human-yeast pair expressing hFEN1, which is frequently overexpressed in cancer and is an anti-cancer therapeutic target, to perform synthetic dosage lethal (SDL) screens using ectopic overexpression of wild-type and catalytically inactive hFEN1 in yeast. The SDL screens identified homologous recombination (HR) repair mutants as synthetic lethal with overexpression of catalytically-inactive hFen1. The SDL interactions were dependent on binding of hFen1 to DNA suggesting that toxicity was a result of catalytically inactive hFen1 becoming trapped on DNA and resulting in DNA damage. Our study establishes the utility of using cross-species complementation and ectopic overexpression to generate human-yeast genetic interaction networks and to model protein-inhibitor interactions using genetic approaches. Overall, these data establish the utility of this cross-species experimental approach.

“New approaches for addressing the effect of genetic variation at scale,” by Douglas M. Fowler, Associate Professor, Department of Gnome Sciences, University of Washington, School of Medicine.

How does a protein’s sequence encode its fold and function?  How do changes in sequence influence disease risk, prognosis and treatment? How do gene expression patterns combine with protein activity to define cellular processes like growth, migration and communication? The Fowler lab is interested in developing new ways to probe the relationship between genotype and phenotype, enabling us to better answer these questions. In particular, we have applied large-scale mutagenesis to reveal a new mechanism of kinase regulation, to better understand the meaning of variants in human genomes, and to better predict the impact of mutations.

Monday, October 7, 1019, at 2:30 pm, LSC #3

Hosted: by Christian Kastrup