Single-cell RNA-seq analyses show that long non-coding RNAs are conspicuously expressed in Schistosoma mansoni gamete and tegument progenitor cell populations

Abstract

Schistosoma mansoni is a flatworm that causes schistosomiasis, a neglected tropical disease that affects over 200 million people worldwide. New therapeutic targets are needed with only one drug available for treatment and no vaccine. Long non-coding RNAs (lncRNAs) are transcripts longer than 200 nucleotides with low or no protein-coding potential. In other organisms, they have been shown as involved with reproduction, stem cell maintenance and drug resistance, and they tend to exhibit tissue-specific expression patterns. S. mansoni expresses thousands of lncRNA genes; however, the cell type expression patterns of lncRNAs in the parasite remain uncharacterized. Here, we have re-analyzed publicly available single-cell RNA-sequencing (scRNA-seq) data obtained from adult S. mansoni to identify the lncRNAs signature of adult schistosome cell types. A total of 8023 lncRNAs (79% of all lncRNAs) were detected. Analyses of the lncRNAs expression profiles in the cells using statistically stringent criteria were performed to identify 74 lncRNA gene markers of cell clusters. Male gamete and tegument progenitor lineages clusters contained most of the cluster-specific lncRNA markers. We also identified lncRNA markers of specific neural clusters. Whole-mount in situ hybridization (WISH) and double fluorescence in situ hybridization were used to validate the cluster-specific expression of 13 out of 16 selected lncRNA genes (81%) in the male and female adult parasite tissues; for one of these 16 gene loci, probes for two different lncRNA isoforms were used, which showed differential isoform expression in testis and ovary. An atlas of the expression profiles across the cell clusters of all lncRNAs detected in our analysis is available as a public website resource (http://verjolab.usp.br:8081). The results presented here give strong support to a tissue-specific expression and to a regulated expression program of lncRNAs in S. mansoni. This will be the basis for further exploration of lncRNA genes as potential therapeutic targets.

Long non-coding RNAs are essential for Schistosoma mansoni pairing-dependent adult worm homeostasis and fertility

“…Results for ( A ) SmLINC101519, ( B ) SmLINC110998, and ( C ) SmLINC175062. For comparison purposes, single-cell RNA-Seq data from Morales-Vicente et al, 2022 [ 28 ] was retrieved from ( http://verjolab.usp.br:8081/ ). LincRNA expression patterns across the single-cell clusters are shown with UMAP plots, colored by gene expression levels (blue = low, red = high), and the scale represents log10(UMIs+1).…”

“…SmLINC101519 was expressed in the female uterus, vitellaria and around the female ovary, while in males, SmLINC101519 was present in testes, oesophagus and along the head and trunk ( Fig 8A , right). Single-cell RNA-Seq (scRNA-Seq) analysis of lincRNAs expression [ 28 ] showed that SmLINC101519 was detected in parenchyma, muscle and neuron cell clusters ( Fig 8A , left, cells clusters marked with 1, 2 and 3) . Combining the WISH localization (i.e.…”

“…On chr 1, two protein-coding genes are flanking the genomic region of SmLINC101519, namely T-box transcription factor TBX20 (Smp_003900) upstream, and High-affinity cGMP-specific 3’,5’-cyclic phosphodiesterase 9A (PDE9A) (Smp_342020) downstream of the SmLINC101519 locus ( see locus in the genome browser ). Inspection of the expression profiles of the two protein-coding genes and the SmLINC101519 in the adult worms scRNA-Seq data [ 28 ] (Fig G, panel A in S1 Text ) shows that both Smp_003900 and SmLINC101519 are expressed in the same cell clusters, namely muscle 1 and neuron 17 (Fig G, panel A in S1 Text ) ; one could raise the hypothesis that SmLINC101519 could be cis -acting to activate the expression of the neighbor TBX20 protein-coding gene, or that both TBX20 Smp_003900 and the SmLINC101519 are simultaneously co-regulated; however, further direct experimentation is needed to test this hypothesis. The major phenotypes observed upon SmLINC101519 silencing are in direct agreement with its expression profile and neighboring genes.…”

“…Recently, single-cell RNA-seq analyses showed that lncRNAs are conspicuously expressed in S . mansoni gamete and tegument progenitor cell populations [ 28 ]. In fact, lncRNAs have been associated with epigenetic drug treatment in S .…”

Chromatin structure around long non-coding RNA (lncRNA) genes inSchistosoma mansonigonads

“…Additionally, lncRNAs have been identified in different developmental stages of S. mansoni, suggesting their involvement in stage-specific gene expression and potential as biomarkers (Rocha et al, 2022). Furthermore, the expression patterns of lncRNAs in S. mansoni have been characterized at the singlecell level, revealing tissue-specific expression and regulated expression programs (Morales-Vicente et al, 2022). In Schistosoma japonicum infection, lncRNAs have been implicated in the formation of liver granulomas and the polarization of macrophages, providing a potential target for treatment (Zhao et al, 2023).…”