Exposure to hycanthone alters chromatin structure around specific gene functions and specific repeats in Schistosoma mansoni

Abstract

Schistosoma mansoni is a parasitic plathyhelminth responsible for intestinal schistosomiasis (or bilharzia), a disease affecting 67 million people worldwide and causing an important economic burden. The schistosomicides hycanthone, and its later proxy oxamniquine, were widely used for treatments in endemic areas during the twentieth century. Recently, the mechanism of action, as well as the genetic origin of a stably and Mendelian inherited resistance for both drugs was elucidated in two strains. However, several observations suggested early on that alternative mechanisms might exist, by which resistance could be induced for these two drugs in sensitive lines of schistosomes. This induced resistance appeared rapidly, within the first generation, but was metastable (not stably inherited). Epigenetic inheritance could explain such a phenomenon and we therefore re-analyzed the historical data with our current knowledge of epigenetics. In addition, we performed new experiments such as ChIP-seq on hycanthone treated worms. We found distinct chromatin structure changes between sensitive worms and induced resistant worms from the same strain. No specific pathway was discovered, but genes in which chromatin structure modifications were observed are mostly associated with transport and catabolism, which makes sense in the context of the elimination of the drug. Specific differences were observed in the repetitive compartment of the genome. We finally describe what types of experiments are needed to understand the complexity of heritability that can be based on genetic and/or epigenetic mechanisms for drug resistance in schistosomes.

Frequency and mitotic heritability of epimutations in Schistosoma mansoni

“…We had shown before that S. mansoni worms exposed transiently to hycanthone, an anthelmintic drug, possess 57 days later a characteristic chromatin profile different from unexposed worms (Roquis et al . ). At that time, we were not able to tell if the drug directly induced the different profiles, or if it acted as a selection agent, killing most of the parasites in the population, except those with a pre‐existing distinct chromatin structure.…”

Histone deacetylase inhibition modulates histone acetylation at gene promoter regions and affects genome-wide gene transcription in Schistosoma mansoni

“…As a qPCR normalizer control we used the gene promoter region for the Sm Val19 gene (Smp_123090), which was not expressed either in the HDACi- or the vehicle-treated schistosomula assays, and has no histone acetylation and methylation marks at its promoter region, as seen in the public ChIP-Seq datasets from [37] available at the Schistosoma genome browser (http://schistosoma.usp.br). …”

Schistosoma mansoni Egg, Adult Male and Female Comparative Gene Expression Analysis and Identification of Novel Genes by RNA-Seq

“…To assess further evidence for the transcription start site (TSS) of S . mansoni genes, we downloaded the Chromatin Immunoprecipitation Sequencing (ChIP-Seq) dataset of adult worm Histone H3K4me3 (SRR1107840) [ 9 ], and we used the HOMER pipeline [ 35 ] to map the ChIP-Seq sequences to the genome and to find the genomic coordinates of H3K4me3 enriched peaks. HOMER found enriched peaks by calculating the density of the reads at the peaks that should be at least 4-fold higher than the peaks in the surrounding 10 kb region [ 35 ].…”

“…Our gene models (Trinity-assembled contigs) and all the histone mark data [ 9 ] mapped to the genome are accessible through a local installation of the UCSC Genome Browser in a Box (GBiB) [ 36 ] at http://schistosoma.usp.br/ .…”

“…mansoni sequence predictions [ 4 ]. We then cross-referenced the new genomic coordinates of these transcript start sites (TSSs) with the genomic coordinates of the publicly available dataset of promoter-associated H3K4me3 histone marks obtained by ChIP-Seq [ 9 ], and the coincident coordinates for the TSS and the H3K4me3 provided genome-wide evidence of a possible involvement of this histone modification in the transcriptional regulation of these genes. Moreover, an in silico analysis of the de novo- assembled transcriptome revealed new protein coding genes with conserved domains not previously predicted in the parasite genome.…”