Deep sequencing of small RNAs reveals the repertoire of miRNAs and piRNAs in Biomphalaria glabrata

Transcriptional landscape of small non-coding RNAs reveals diversity of categories and functions in molluscs

Small non-coding RNAs (sncRNAs) are non-coding RNA molecules that play various roles in metazoans. Among the sncRNAs, microRNAs (miRNAs) guide post-translational gene regulation during cellular development, proliferation, apoptosis, and differentiation, while PIWI-interacting RNAs (piRNAs) suppress transposon activity to safeguard the genome from detrimental insertion mutagenesis. While an increasing number of piRNAs are being identified in the soma and germlines of various organisms, they are scarcely reported in molluscs. To unravel the small RNA (sRNA) expression patterns and genomic function in molluscs, we generated a comprehensive sRNA dataset by sRNA sequencing (sRNA-seq) of eight mollusc species. Abundant miRNAs were identified and characterized in all investigated molluscs, and ubiquitous piRNAs were discovered in both somatic and gonadal tissues in six of the investigated molluscs, which are more closely associated with transposon silencing. Tens of piRNA clusters were also identified based on the genomic mapping results, which varied among different tissues and species. Our dataset serves as important reference data for future genomic and genetic studies on sRNAs in these molluscs and related species, especially in elucidating the ancestral state of piRNAs in bilaterians.

Exosome-derived small non-coding RNAs reveal immune response upon grafting transplantation in Pinctada fucata (Mollusca)

Exosomes, a subset of small extracellular vesicles, carry various nucleic acids, proteins, lipids, amino acids and metabolites. They function as a mode of intercellular communication and molecular transfer. Exosome cargo molecules, including small non-coding RNAs (sncRNAs), are involved in the immune response in various organisms. However, the role of exosome-derived sncRNAs in immune responses in molluscs remains unclear. Here, we aimed to reveal the sncRNAs involved in the immune response during grafting transplantation by the pearl oyster Pinctada fucata. Exosomes were successfully extracted from the P. fucata haemolymph during graft transplantation. Abundant microRNAs (miRNAs) and PIWI-interacting RNAs (piRNAs) were simultaneously discovered in P. fucata exosomes by small RNA sequencing. The expression patterns of the miRNAs and piRNAs at the grafting and initial stages were not substantially different, but varied significantly between the initial and later stages. Target prediction and functional analysis indicate that these miRNAs and piRNAs are related to immune response upon grafting transplantation, whereas piRNAs may also be associated with transposon silencing by targeting with genome transposon elements. This work provides the basis for a functional understanding of exosome-derived sncRNAs and helps to gain further insight into the PIWI/piRNA pathway function outside of germline cells in molluscs.

A Review of Discovery Profiling of PIWI-Interacting RNAs and Their Diverse Functions in Metazoans

PIWI-interacting RNAs (piRNAs) are a class of small non-coding RNAs (sncRNAs) that perform crucial biological functions in metazoans and defend against transposable elements (TEs) in germ lines. Recently, ubiquitously expressed piRNAs were discovered in soma and germ lines using small RNA sequencing (sRNA-seq) in humans and animals, providing new insights into the diverse functions of piRNAs. However, the role of piRNAs has not yet been fully elucidated, and sRNA-seq studies continue to reveal different piRNA activities in the genome. In this review, we summarize a set of simplified processes for piRNA analysis in order to provide a useful guide for researchers to perform piRNA research suitable for their study objectives. These processes can help expand the functional research on piRNAs from previously reported sRNA-seq results in metazoans. Ubiquitously expressed piRNAs have been discovered in the soma and germ lines in Annelida, Cnidaria, Echinodermata, Crustacea, Arthropoda, and Mollusca, but they are limited to germ lines in Chordata. The roles of piRNAs in TE silencing, gene expression regulation, epigenetic regulation, embryonic development, immune response, and associated diseases will continue to be discovered via sRNA-seq.

Mechanism of the Passage of Angiostrongylus cantonensis across the Final Host Blood-Brain Barrier Using the Next-Generation Sequencing

Background:

Multicellular parasites Angiostrogylus cantonensis larvae develop in the final host rat brain at the fourth stage (L4) and migrate to the lungs by the adult stage. The potential mechanism of its blood-brain barrier (BBB) passage remains unclear.

Methods:

By using Illumina Hiseq/Miseq sequencing, we obtained the transcriptomes of 3 groups of adult males and 3 groups of female of A. cantonensis to generate similarly expressed genes (SEGs) between 2 genders at the adult stage. Next 2 groups of L4 expressed genes were used to compared with SEGs to create differentially expressed genes (DEGs) between 2 life stages to unlock potential mechanism of BBB passage.

Results:

In total, we obtained 381 581 802 clean reads and 56 990 699 010 clean bases. Of these, 331 803 unigenes and 482 056 transcripts were successfully annotated. A total of 3 166 DEGs between L4 and adults SEGs were detected. Annotation of these DEGs showed 167 were down-regulated and 181 were up-regulated. Pathway analysis exhibited that calcium signaling pathway, the ECM−receptor interaction, focal adhesion, and cysteine and methionine metabolism were highly associated with DEGs. The function of these pathways might be related to BBB traversal, as well as neuro-regulation, interactions between parasite and host, environmental adaption.

Conclusion:

This study expanded the regulatory characteristics of the two important life stages of A. cantonensis. This information may provide a better appreciation of the biological features of the stages of the parasitic A. cantonensis.

PIWI silencing mechanism involving the retrotransposon nimbus orchestrates resistance to infection with Schistosoma mansoni in the snail vector, Biomphalaria glabrata

Background

Schistosomiasis remains widespread in many regions despite efforts at its elimination. By examining changes in the transcriptome at the host-pathogen interface in the snail Biomphalaria glabrata and the blood fluke Schistosoma mansoni, we previously demonstrated that an early stress response in juvenile snails, manifested by induction of heat shock protein 70 (Hsp 70) and Hsp 90 and of the reverse transcriptase (RT) domain of the B. glabrata non-LTR- retrotransposon, nimbus, were critical for B. glabrata susceptibility to S. mansoni. Subsequently, juvenile B. glabrata BS-90 snails, resistant to S. mansoni at 25°C become susceptible by the F2 generation when maintained at 32°C, indicating an epigenetic response.

Methodology/Principal findings

To better understand this plasticity in susceptibility of the BS-90 snail, mRNA sequences were examined from S. mansoni exposed juvenile BS-90 snails cultured either at 25°C (non-permissive temperature) or 32°C (permissive). Comparative analysis of transcriptomes from snails cultured at the non-permissive and permissive temperatures revealed that whereas stress related transcripts dominated the transcriptome of susceptible BS-90 juvenile snails at 32°C, transcripts encoding proteins with a role in epigenetics, such as PIWI (BgPiwi), chromobox protein homolog 1 (BgCBx1), histone acetyltransferase (BgHAT), histone deacetylase (BgHDAC) and metallotransferase (BgMT) were highly expressed in those cultured at 25°C. To identify robust candidate transcripts that will underscore the anti-schistosome phenotype in B. glabrata, further validation of the differential expression of the above transcripts was performed by using the resistant BS-90 (25°C) and the BBO2 susceptible snail stock whose genome has now been sequenced and represents an invaluable resource for molecular studies in B. glabrata. A role for BgPiwi in B. glabrata susceptibility to S. mansoni, was further examined by using siRNA corresponding to the BgPiwi encoding transcript to suppress expression of BgPiwi, rendering the resistant BS-90 juvenile snail susceptible to infection at 25°C. Given transposon silencing activity of PIWI as a facet of its role as guardian of the integrity of the genome, we examined the expression of the nimbus RT encoding transcript at 120 min after infection of resistant BS90 piwi-siRNA treated snails. We observed that nimbus RT was upregulated, indicating that modulation of the transcription of the nimbus RT was associated with susceptibility to S. mansoni in BgPiwi-siRNA treated BS-90 snails. Furthermore, treatment of susceptible BBO2 snails with the RT inhibitor lamivudine, before exposure to S. mansoni, blocked S. mansoni infection concurrent with downregulation of the nimbus RT transcript and upregulation of the BgPiwi encoding transcript in the lamivudine-treated, schistosome-exposed susceptible snails.

Conclusions and significance

These findings support a role for the interplay of BgPiwi and nimbus in the epigenetic modulation of plasticity of resistance/susceptibility in the snail-schistosome relationship.

Progress is being made to eliminate schistosomiasis, a tropical disease that remains endemic in the tropics and neotropics. In 2020, WHO proposed controlling the snail population as part of a strategy toward reducing schistosomiasis, a vector borne disease, by 2025. The life cycle of the causative parasite is, however, complex and in the absence of vaccines, new drugs, and access to clean water and sanitation, reduction of schistosomiasis will remain elusive. To break the parasite’s life cycle during the snail stage of its development, a better understanding of the molecular basis of how schistosomes survive, or not, in the snail is required. By examining changes in the transcriptome at the host-pathogen interface in the snail Biomphalaria glabrata and Schistosoma mansoni, we showed that early stress response, manifested by the induction of Heat Shock Proteins (Hsps) and the RT domain of the non-LTR retrotransposon, nimbus, were critical for snail susceptibility. Subsequently, juvenile B. glabrata BS-90 snails, resistant to S. mansoni at 25°C were observed to become susceptible by the F2 generation when maintained at 32°C, indicating an epigenetic response. This study confirms these earlier results and shows an interplay between PIWI and nimbus in the anti-schistosome response in the snail host.