Overexpression screens identify conserved dosage chromosome instability genes in yeast and human cancer

Abstract

Somatic copy number amplification and gene overexpression are common features of many cancers. To determine the role of gene overexpression on chromosome instability (CIN), we performed genome-wide screens in the budding yeast for yeast genes that cause CIN when overexpressed, a phenotype we refer to as dosage CIN (dCIN), and identified 245 dCIN genes. This catalog of genes reveals human orthologs known to be recurrently overexpressed and/or amplified in tumors. We show that two genes, TDP1, a tyrosyl-DNA-phosphdiesterase, and TAF12, an RNA polymerase II TATA-box binding factor, cause CIN when overexpressed in human cells. Rhabdomyosarcoma lines with elevated human Tdp1 levels also exhibit CIN that can be partially rescued by siRNA-mediated knockdown of TDP1. Overexpression of dCIN genes represents a genetic vulnerability that could be leveraged for selective killing of cancer cells through targeting of an unlinked synthetic dosage lethal (SDL) partner. Using SDL screens in yeast, we identified a set of genes that when deleted specifically kill cells with high levels of Tdp1. One gene was the histone deacetylase RPD3, for which there are known inhibitors. Both HT1080 cells overexpressing hTDP1 and rhabdomyosarcoma cells with elevated levels of hTdp1 were more sensitive to histone deacetylase inhibitors valproic acid (VPA) and trichostatin A (TSA), recapitulating the SDL interaction in human cells and suggesting VPA and TSA as potential therapeutic agents for tumors with elevated levels of hTdp1. The catalog of dCIN genes presented here provides a candidate list to identify genes that cause CIN when overexpressed in cancer, which can then be leveraged through SDL to selectively target tumors.dosage chromosome instability | overexpression | synthetic dosage lethality | TDP1 | rhabdomyosarcoma

Dosage Mutator Genes in Saccharomyces cerevisiae: A Novel Mutator Mode-of-Action of the Mph1 DNA Helicase

“…Approximately half of the dmutator genes (18/37) function in biological pathways such as DNA damage repair, DNA replication, or transcription, processes well known to influence genome instability (Saccharomyces Genome Database). For 12 of the genes, overexpression also increases chromosome instability (Duffy et al 2016), highlighting the established considerable overlap between the mutator and chromosome instability phenotypes (Stirling et al 2011). …”

Hypermutation signature reveals a slippage and realignment model of translesion synthesis by Rev3 polymerase in cisplatin-treated yeast

“…The framework created here sought to establish the gene-drug relationships driving hypermutation in cells surviving genotoxin treatment beginning with canonical DNA repair pathways and drugs of clinical relevance. There remains a large space to be explored; in yeast, there are many hundreds of genes whose loss of function causes genome instability and hundreds of others whose increased dosage causes genome instability (8,41,42). The ways in which these will combine with each other and with various chemicals to permit mutagenesis remain incomplete.…”

Mapping a diversity of genetic interactions in yeast

“…Experimentally, dosage genetic interaction screens involve testing the effect of overexpression of a query gene within a genome-wide loss-of-function mutant collection, or, conversely, screening a loss-of-function query mutant with genome-wide plasmid libraries [20,24,25]. Both synthetic dosage lethality and dosage suppression screens have been performed systematically [19,26,27], and typically identify a few dozen interactions for each query mutant of interest.…”

“…2B). Synthetic dosage lethality can also occur between enzymes and their substrates, where overexpression of the substrate leads to a fitness defect in combination with reduced activity of the enzyme [25,27,28]. Indeed, synthetic dosage lethality screens using kinase mutants are able to capture many known kinase-substrate relationships, especially when the kinase is a negative regulator of a target protein [20,27].…”