title: Saccharomyces cerevisiae genetics predicts candidate therapeutic genetic interactions at the mammalian replication fork.
abstract: The concept of synthetic lethality has gained popularity as a rational guide for predicting chemotherapeutic targets based on negative genetic interactions between tumor-specific somatic mutations and a second-site target gene. One hallmark of most cancers that can be exploited by chemotherapies is chromosome instability (CIN). Because chromosome replication, maintenance, and segregation represent conserved and cell-essential processes, they can be modeled effectively in simpler eukaryotes such as Saccharomyces cerevisiae. Here we analyze and extend genetic networks of CIN cancer gene orthologs in yeast, focusing on essential genes. This identifies hub genes and processes that are candidate targets for synthetic lethal killing of cancer cells with defined somatic mutations. One hub process in these networks is DNA replication. A nonessential, fork-associated scaffold, CTF4, is among the most highly connected genes. As Ctf4 lacks enzymatic activity, potentially limiting its development as a therapeutic target, we exploited its function as a physical interaction hub to rationally predict synthetic lethal interactions between essential Ctf4-binding proteins and CIN cancer gene orthologs. We then validated a subset of predicted genetic interactions in a human colorectal cancer cell line, showing that siRNA-mediated knockdown of MRE11A sensitizes cells to depletion of various replication fork-associated proteins. Overall, this work describes methods to identify, predict, and validate in cancer cells candidate therapeutic targets for tumors with known somatic mutations in CIN genes using data from yeast. We affirm not only replication stress but also the targeting of DNA replication fork proteins themselves as potential targets for anticancer therapeutic development.
authors: Michael Smith Laboratories, University of British Columbia, Vancouver, British Columbia, Canada.
authors: Derek M
authors: DM
authors: van Pel
authors: Peter C
authors: PC
authors: Stirling
authors: Sean W
authors: SW
authors: Minaker
authors: Payal
authors: P
authors: Sipahimalani
authors: Philip
authors: P
authors: Hieter
mesh_terms: D043171:Chromosomal Instability / Q000187:drug effects / Q000235:genetics*; D015179:Colorectal Neoplasms / Q000235:genetics / Q000378:metabolism; D004261:DNA Replication; D004268:DNA-Binding Proteins / Q000037:antagonists & inhibitors / Q000235:genetics / Q000378:metabolism; D053263:Gene Regulatory Networks; D020043:Genes, Essential; D016681:Genome, Fungal; D045325:HCT116 Cells; D006801:Humans; D000076228:MRE11 Homologue Protein; D009153:Mutagens / Q000633:toxicity; D009154:Mutation; D034622:RNA Interference; D034741:RNA, Small Interfering / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000187:drug effects / Q000235:genetics*; D029701:Saccharomyces cerevisiae Proteins / Q000235:genetics
chemical_list: C078338:CTF4 protein, S cerevisiae; D004268:DNA-Binding Proteins; C121766:MRE11 protein, human; D009153:Mutagens; D034741:RNA, Small Interfering; D029701:Saccharomyces cerevisiae Proteins; D000076228:MRE11 Homologue Protein
keywords: DNA replication; cancer therapy; chromosome instability; synthetic lethality; yeast genomics
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