A Novel Gene Underlies Bleomycin-Response Variation inCaenorhabditis elegans

Abstract

Bleomycin is a powerful chemotherapeutic drug used to treat a variety of cancers. However, individual patients vary in their responses to bleomycin. The identification of genetic differences that underlie this response variation could improve treatment outcomes by tailoring bleomycin dosages to each patient. We used the model organism Caenorhabditis elegans to identify genetic determinants of bleomycin-response differences by performing linkage mapping on recombinants derived from a cross between the laboratory strain ( N2 ) and a wild strain ( CB4856 ). This approach identified a small genomic region on chromosome V that underlies bleomycin-response variation. Using near-isogenic lines, and strains with CRISPR-Cas9 mediated deletions and allele replacements, we discovered that a novel nematode-specific gene ( scb-1 ) is required for bleomycin resistance. Although the mechanism by which this gene causes variation in bleomycin responses is unknown, we suggest that a rare variant present in the CB4856 strain might cause differences in the potential stress-response function of scb-1 between the N2 and CB4856 strains, thereby leading to differences in bleomycin resistance.

A single locus underlies variation inCaenorhabditis eleganschemotherapeutic responses

“…/ 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) .…”

“…A second set of 296 RIAILs generated previously by Andersen et al (Andersen et al 2015) (set 2 RIAILs) was used more extensively for drug phenotyping and linkage mapping. Near-isogenic lines (NILs) were generated by backcrossing a selected RIAIL for several generations (Brady et al 2019) , using PCR amplicons for insertion-deletion (indels) variants to track the introgressed region. NILs were whole-genome sequenced to verify clean introgressions.…”

“…NILs were whole-genome sequenced to verify clean introgressions. CRISPR-Cas9-mediated deletions of scb-1 were described in Brady et al (Brady et al 2019) . All strains are available upon request or from the C. elegans Natural Diversity Resource (Cook et al 2016) .…”

“…Animal length (median.TOF), optical density (median.norm.EXT), and brood size (norm.n) were quantified for each well using the COPAS BIOSORT. Phenotypic measurements collected by the BIOSORT were processed and analyzed using the R package easysorter (Shimko and Andersen 2014) as described previously (Brady et al 2019) .…”

“…A large panel of recombinant inbred advanced intercross lines (RIAILs) derived from two divergent strains, N2 and CB4856 (Rockman and Kruglyak 2009;Andersen et al 2015) , has been leveraged in several linkage mapping analyses (McGrath et al 2009;Lee et al 2017;Singh et al 2016;Zdraljevic et al 2019;Brady et al 2019;Zdraljevic et al 2017;Evans et al 2018;Andersen et al 2014;Viñuela et al 2010;Doroszuk et al 2009;Snoek et al 2014;Rodriguez et al 2012;Glater, Rockman, and Bargmann 2014;Rockman, Skrovanek, and Kruglyak 2010;Zamanian et al 2018a;Bendesky et al , 2012Schmid et al 2015;Balla et al 2015;Kammenga et al 2007;Gutteling, Doroszuk, et al 2007;Li et al 2006;Reddy et al 2009;Seidel et al 2011;Seidel, Rockman, and Kruglyak 2008) . Quantitative genetic analysis using these panels and a high-throughput phenotyping assay has facilitated the discovery of numerous QTL (Zamanian et al 2018b) , several quantitative trait genes (QTG) (Brady et al 2019) and quantitative trait nucleotides (QTN) (Zdraljevic et al 2019(Zdraljevic et al , 2017 underlying fitness-related traits in the nematode. Additionally, three pleiotropic genomic regions were recently found to influence responses to a diverse group of toxins (Evans et al 2018) .…”