Compartmentalization of functions and predicted miRNA regulation among contiguous regions of the nematode intestine

Abstract

The intestine of parasitic nematodes has proven an important target for therapies aimed at prevention and treatment of diseases caused by these pathogens in humans, animals and plants. We have developed a unique research model with the intestine of Ascaris suum, the large round worm of swine and humans, that will enhance biological research on this tissue. To expand utility of this model, we quantitatively compared expression of 15,382 coding RNAs and 277 noncoding, micro RNAs (miRNAs) among 3 contiguous regions of the adult A. suum intestine. Differentially expressed transcripts were identified among regions, with the largest number expressed at significantly higher levels in the anterior region, identifying this region as the most functionally unique compared to middle and posterior regions. We further identified 64 exon splice variants (from 47 genes) that are differentially expressed among these regions. A total of 2,063 intestinal mRNA transcripts were predicted to be targeted by intestinal miRNA, and negative correlation coefficients for miRNA:mRNA abundances predicted 22 likely influential miRNAs and 503 likely associated miRNA:mRNA pairs. A. suum intestinal miRNAs were identified that are conserved with intestinal miRNAs from C. elegans (10 mature sequences and 13 seed sequences conserved), and prospective intestinal miRNAs from the murine gastrointestinal nematode, Heligmosomoides polygyrus (5 mature and 11 seeds). Most of the conserved intestinal miRNAs were also high abundance miRNAs. The data provide the most comprehensive compilation of constitutively and differentially expressed genes along the length of the intestine for any nematode species. The information will guide prospective development of many hypotheses on nematode intestinal functions encoded by mRNAs, miRNAs and interactions between these RNA populations.

Direct experimental manipulation of intestinal cells in Ascaris suum , with minor influences on the global transcriptome

“…RISC; Khan et al, 2009), which could stabilize target transcripts that are normally downregulated by intestinal miRNAs. We previously identified predicted intestinal miRNA target transcripts in A. suum intestinal cells (Gao et al, 2016), but found no general upregulation of these intestinal transcripts. Thus, we have no ready explanation for the effects on other cellular transcripts documented here.…”

“…One upregulated gene (GS_19094) was associated with RNA processing (“RNA-binding protein 5/10”, K13094, related to intron splicing), and the seven other genes have a variety of functions with no obvious theme, including a dopamine receptor (GS_19561), a sulfate permease (GS_00322), and an aconitate hydratase (GS_09209), while the most significantly upregulated gene in the set (GS_11054) has no functional annotation assigned. The four genes downregulated by hsiRNA treatments in both the anterior and posterior intestine included: (i) GS_04133, which has no functional annotation, but was previously predicted to be a target for endogenous miRNA silencing in the A. suum intestine (Gao et al, 2016); (ii) GS_13545, an RNA polymerase II for which the C. elegans ortholog ( rpb-12 ) was used as a non-variable control gene in other studies (Ventura et al, 2009; Darom et al, 2010); (iii) GS_21168, a C-type lectin, and (iv) GS_05428, which has no informative functional information.…”

“…The small size, biological complexity, and experimentally intractable nature of most parasitic nematodes hinder research aimed at elucidating essential functions in these pathogens. However, recently developed ‘omics’ resources (Jex et al, 2011; Jasmer et al, 2014; Rosa et al, 2014, 2015; Wang et al, 2015; Gao et al, 2016) and experimental capabilities (Chen et al, 2011; Jasmer et al, 2014; McCoy et al, 2015) established for the large round worm of swine and humans, Ascaris suum , continue to build on this global pathogen’s importance as a facile model system to conduct research on essential cellular functions in parasitic nematodes.…”

“…Nevertheless, limitations to knowledge and experimental methods have impeded research on this and other tissues of parasitic nematodes. Multiomics databases have been established for the intestine and other tissues of A. suum (Jasmer et al, 2014; Rosa et al, 2014; Gao et al, 2016), including proteomics distinguishing multiple intestinal cell compartments (Rosa et al, 2015) and pan-Nematoda intestinal transcriptome comparisons (Wang et al, 2015). This knowledge base helps to guide experimental design and interpret results from studies using the model organism A. suum .…”

De novo identification of toxicants that cause irreparable damage to parasitic nematode intestinal cells

“…To better understand the basic intestinal cell and tissue functions of this critical organ in parasitic nematodes and facilitate improved methods of therapy, we have established a foundational model of the STH intestinal system using Ascaris suum . With this model, we have identified 1) genes, proteins and predicted functions characterizing 10 different adult A. suum tissues (including the intestine) using microarrays [18] and RNA-seq [19], 2) transcripts, proteins and functions that are preferentially or constitutively expressed among three contiguous regions of the intestine [20], and 3) intestinal proteins that differentially localize to several intestinal cellular compartments by LC-MS/MS [21, 22]. This information was integrated with pan-Nematoda intestinal protein family databases [23] developed for the purpose of broad application of intestinal research to many different nematode pathogens.…”