A single locus underlies variation inCaenorhabditis eleganschemotherapeutic responses

Abstract

Pleiotropy, the concept that a single gene controls multiple distinct traits, is prevalent in most organisms and has broad implications for medicine and agriculture. Identifying the molecular mechanisms underlying pleiotropy has the power to unveil previously unknown biological connections between seemingly unrelated traits. Additionally, the discovery of pleiotropic genes increases our understanding of both genetic and phenotypic complexity by characterizing novel gene functions. Quantitative trait locus (QTL) mapping has been used to identify several pleiotropic regions in many organisms. However, gene knockout studies are needed to eliminate the possibility of tightly linked, non-pleiotropic loci. Here, we use a panel of 296 recombinant inbred advanced intercross lines of Caenorhabditis elegans and a high-throughput fitness assay to identify a single large-effect QTL on the center of chromosome V associated with variation in responses to eight chemotherapeutics. We validate this QTL with near-isogenic lines and pair genome-wide gene expression data with drug response traits to perform mediation analysis, leading to the identification of a pleiotropic candidate gene, scb-1 . Using deletion strains created by genome editing, we show that scb-1 , which was previously implicated in response to bleomycin, also underlies responses to other double-strand DNA break-inducing chemotherapeutics. This finding provides new evidence for the role of scb-1 in the nematode drug response and highlights the power of mediation analysis to identify causal genes. : bioRxiv preprint / Here, we use linkage mapping to identify a single overlapping QTL on chromosome V that influences the responses to eight chemotherapeutic compounds. We show that these drug-response QTL also overlap with an expression QTL hotspot that contains the gene scb-1 , previously implicated in bleomycin response (Brady et al. 2019) . Although the exact mechanism of scb-1 is yet unknown, it is hypothesized to act in response to stress (Riedel et al. 2013) and has weak homology to a viral hydrolase (Zhang et al. 2018;Kelley et al. 2015) . Together, these data suggest that the importance of scb-1 expression might extend beyond bleomycin response. We validated the QTL using near-isogenic lines (NILs) and performed mediation analysis to predict that scb-1 expression explains the observed QTL for five of the eight drugs. Finally, we directly tested the effect of scb-1 loss of function on chemotherapeutic responses. We discovered that expression of scb-1 underlies differential responses to several chemotherapeutics that cause double-strand DNA breaks, not just bleomycin. This discovery of pleiotropy helps to further define the role of scb-1 by expanding its known functions and provides insights into the molecular mechanisms underlying the nematode drug response. MATERIALS AND METHODS StrainsAnimals were grown at 20°C on modified nematode growth media (NGMA) containing 1% agar and 0.7% agarose to prevent burrowing and fed OP50 (Ghosh et al. 2012) . The two parental str...