Identification of genes underlying nematode benzimidazole resistance using Caenorhabditis elegans statistical and population genetics
Final Report Abstract
Resistance of parasitic nematodes to anthelmintic drugs such as benzimidazoles (BZ) is a widespread problem in veterinary medicine and an increasing threat for human health worldwide. While main molecular targets for all major anthelmintic drug classes were well characterized using the "Caenorhabditis elegans" laboratory model, the molecular mechanisms contributing to anthelmintic resistance in natural nematode populations are mostly unclear. In the last decades, there is increasing evidence that anthelmintic resistance in nematode parasites is a complex trait which is influenced by multiple genetic factors. For the global control of this burden, a detailed understanding of these resistance mechanisms is urgently needed to facilitate drug-decision processes of mass drug administration programs but also to support the development of novel compounds with resistance-breaking properties. In the present project, we took advantage of the C. elegans natural genetic diversity to study the basis of resistance to six commonly used BZ in a natural nematode population. To this end, we tested 240 genetically distinct C. elegans wild isolates in a high-throughput assay and observed a broad variation in BZ sensitivity. In order to identify genomic regions underlying the observed BZ responses, we performed genome-wide association (GWA) mappings, and were able to identify multiple quantitative trait loci (QTL) that were significantly associated with BZ resistance in the assayed C. elegans wild isolates. Interestingly, some QTL were common to all BZ tested in the study, while other QTL appeared to be specific for individual chemical derivatives. These findings indicate that multiple resistance mechanisms exist within the tested C. elegans wild isolates. Furthermore, using a gene burden test to map resistance against one of the most commonly used BZ, albendazole (ABZ), we found a significant association between genetic variation at the ben-1 locus and reduced ABZ sensitivity. An in-depth survey of raw sequencing data revealed a large genetic heterogeneity at this locus including amino acid substitutions, alternative stop codons, but also structural variants like insertion and deletions. In total, we found 25 distinct ben-1 alleles which were in most cases not only postulated to be loss-of-function mutations but also highly associated with ABZ resistance. Finally, we used CRISPR/Cas9-mediated genome editing to validate that a ben-1 deletion as well as the most common parasitic nematode β-tubulin resistance allele, F200Y, confers high level of resistance in the otherwise ABZ-sensitive N2 strain.
Publications
- 2018. Extreme allelic heterogeneity at a Caenorhabditis elegans beta-tubulin locus explains natural resistance to benzimidazoles. PLoS Pathog. 2018 Oct 29;14(10):e1007226
Hahnel SR, Zdraljevic S, Rodriguez BC, Zhao Y, McGrath PT, Andersen EC
(See online at https://doi.org/10.1371/journal.ppat.1007226)
