Biology subjects

McVeigh, P.

Publications and source records attributed to McVeigh, P..

10 recordsLinked to original sources

bioRxiv2026

Conserved core RNAi machinery in trematode-vectoring snails indicates gene silencing potential in the absence of classical systemic and amplification effectors

RNA interference (RNAi) is a widely exploited reverse-genetics tool with potential uses for disease control. Successful RNAi has been reported in trematode-vectoring snails, but the composition of RNAi effector-encoding gene complements, a key driver for RNAi efficiency, remain unstudied in these species. Using bioinformatics and comparative genomics, we searched for orthologues of 115 RNAi effector sequences in genomes or transcriptomes of four snail vectors: Biomphalaria glabrata, B. pfeifferi, Bulinus truncatus, and Lymnaea staginalis. Gene expression patterns of selected RNAi effectors were then examined across developmental stages and tissues of the model B. glabrata snail. At least 74 RNAi-related proteins were conserved across all four species, including core components known to be essential for gene silencing. Classical systemic RNAi-deficient (SID) genes that facilitate systemic RNAi in other systems were absent, suggesting that alternative pathways may compensate for dsRNA uptake and transport. Core effectors of secondary RNAi amplification and heritable RNAi were not detected. Expressions of Dicer-1, Argonaute-2, and the exonuclease Eri-1 did not vary significantly with snail size. A putative RNAi-inhibiting Staufen orthologue showed elevated expression in the ovotestis, while another putative cholesterol-interacting gene was overexpressed in the trunk tissue and may partly contribute to RNAi import. Altogether, our results present the most comprehensive overview of RNAi pathway effectors in major intermediate snail hosts for trematodes. The findings underscore the likely broad potential for RNAi use in trematode intermediate hosts as an experimental tool and potential control method.

evolutionary biology↗

bioRxiv2025

Dietary variations drive divergent phenotypic, transcriptomic, and metatranscriptomic profiles in Biomphalaria glabrata, a schistosomiasis vector snail

BackgroundThe freshwater snail Biomphalaria glabrata is an important natural vector for the human parasitic trematode Schistosoma mansoni, which causes schistosomiasis. In the laboratory, B. glabrata are routinely maintained on simple lettuce diets. We aimed to explore and compare the impact of alternative diets on snail performance, global gene expression, and microbiome. MethodsSnails were raised in groups on fresh lettuce (FL), fish food (FF) and artificial snail gel (SG) diet for eight weeks, while measuring dietary impacts on growth, survival, and fecundity. RNA sequencing (RNA-Seq) was performed to correlate dietary phenotypes with changes in the snail transcriptome and associated microbial metatranscriptome. ResultsRelative to FL, FF and SG diets markedly enhanced growth, survival, and fecundity, with FF generating the highest fecundity rate. RNA-Seq identified 21,887 nutritionally modulated genes in the snail transcriptome. Fish food (FF) and SG diets drove upregulation of genes associated with antimicrobial immunity, growth, and reproduction, while elevated expression of genes linked to xenobiotic metabolism and oxidative stress was observed in FL-fed snails. Metatranscriptomic analysis identified 104 microbial classes, with a total of twenty-three classes significantly enriched in FF and SG snails, including short-chain fatty acid-producing and nutrient-cycling bacteria. Significant correlation (r = 0.63, p = 0.001) linked differentially expressed genes with enriched microbial taxa, highlighting the impact of diet on key snail health and performance metrics. ConclusionsThis work is the first nutritranscriptomic analysis of laboratory-bred B. glabrata. We describe key insights into the diet-phenotype-transcriptome-microbiome axis, which will inform dietary precision and optimisation for laboratory culture of B. glabrata. These data also highlight fundamental aspects of snail biology which could be exploited for molecular snail control approaches.

genomics↗

bioRxiv2025

Polo-like kinase 1 regulates growth in juvenile Fasciola hepatica

Fasciola sp. (liver fluke) are parasitic flatworms that impose a significant burden on the agri-food industry and human health. Immature worms can cause severe damage to the liver as they migrate towards the bile ducts, and yet there is only a single drug to treat this pathogenic life stage, driving the need to identify targets for novel flukicides. Given their crucial role in the growth/development of immature Fasciola hepatica, neoblast-like stem cells are an attractive source of new flukicide targets. Kinases are a hugely diverse group of phosphorylating enzymes with key roles in almost all cellular processes. Kinase dysregulation can result in the development of cancerous cells/tissues, linking many to cell cycle-associated proliferation and growth. Here, we annotate the F. hepatica kinome, identifying 271 putative protein kinases, representing around 1.6% of predicted F. hepatica protein-coding genes with family proportions similar to those of other parasitic flatworms. Many of these kinases, such as polo-like kinase 1 (fhplk1), are upregulated in immature worms undergoing rapid growth and development, a process underpinned by the proliferation of neoblast-like stem cells. RNA interference (RNAi)-mediated silencing of fhplk1 in juvenile liver fluke reduced growth and cell proliferation, suggesting a conserved role within the cell-cycle; the cessation of stem cell proliferation persisted for at least a week following fhplk1-RNAi. A PLK inhibitor (BI 2536) was shown to phenocopy the fhplk1-RNAi phenotype in a dose-dependent manner, supporting the feasibility of targeting F. hepatica neoblast-like cells through kinase inhibitors. Transcriptomic analysis of fhplk1-RNAi juveniles revealed 946 downregulated genes, principally associated with the cell cycle or ribosomes. Over 80 of these downregulated genes were also downregulated following juvenile F. hepatica irradiation, supporting roles for these kinases in neoblast-like stem cells, and marking them as putative targets for control. Among the 1244 upregulated genes in fhplk1-RNAi juvenile worms were many neurotransmitters, receptors and ion channels, exposing the apparent upregulation of diverse inter-cellular signalling systems. While many neurotransmitter pathways promote proliferation in mammalian systems the interaction between neoblast-like stem cells and neuronal signalling in parasitic flatworms remains elusive. Here, the transcriptomic response of fhplk1-RNAi juveniles supports a link between neoblast-like stem cell driven growth/development and neuronal signalling. Author SummaryThe liver fluke is a parasitic flatworm which causes disease in livestock and humans around the world. While establishing the infection, immature liver fluke migrate through the host liver causing significant damage. Unfortunately, only one drug is currently recommended for treatment of these immature worms, though resistance to this drug is now widespread and exposes the pressing need to develop novel drugs. As worms migrate through the liver, they undergo growth and development which is facilitated by proliferating stem cells. These neoblast-like cells are akin to stem cells seen in other organisms, and as such are responsible for new tissue growth. Many stem cells express kinases, a large family of enzymes that control many cellular processes. In this study we identified all the potential kinases in the liver fluke, including those that may function in neoblast-like stem cells. One of these kinases, polo-like kinase 1 (PLK1), has been linked to cancer development in humans. We used reverse genetics to silence this gene, allowing us to understand its function. Silencing PLK1 reduced worm growth and stopped neoblast-like cell proliferation, confirming that it has an important role in growth and cell division. Also, we showed that a PLK1 inhibitor, developed for cancer treatments, reduced growth and neoblast-like cell activity, illustrating the potential for targeting liver fluke kinases associated with neoblast-like cells with drugs, providing new routes to drug development. We then carried out RNA sequencing of worms after PLK1 was silenced to show the effects of neoblast-like cell loss on the expression of other genes. We found a decrease in the expression of genes that regulate cell division, but an increase in the expression of genes related to inter-cell signalling, including neuronal genes. This supports evidence for interactions between the nervous system and neoblast-like cells which could be exploited in future drug discovery.

molecular biology↗

bioRxiv2023

Neoblast-like Stem Cells of Fasciola hepatica

The common liver fluke (Fasciola hepatica) causes the disease fasciolosis, which results in considerable losses within the global agri-food industry. There is a shortfall in the drugs that are effective against both the adult and juvenile life stages within the mammalian host, such that new drug targets are needed. Over the last decade the stem cells of parasitic flatworms have emerged as reservoirs of putative novel targets due to their role in development and homeostasis, including at host-parasite interfaces. Here, we investigate and characterise the proliferating cells that underpin development in F. hepatica. We provide evidence that these cells are capable of self-renewal, differentiation, and are sensitive to ionising radiation - all attributes of neoblasts in other flatworms. Changes in cell proliferation were also noted during the early stages of in vitro juvenile growth/development (around four to seven days post excystment), which coincided with a marked reduction in the nuclear area of proliferating cells. Furthermore, we generated transcriptomes from worms following irradiation-based ablation of neoblasts, identifying 124 significantly downregulated transcripts, including known stem cell markers such as fgfrA and plk1. Sixty-eight of these had homologues associated with neoblast-like cells in Schistosoma mansoni. Finally, RNA interference mediated knockdown of histone h2b (a marker of proliferating cells), ablated neoblast-like cells and impaired worm development in vitro. In summary, this work demonstrates that the proliferating cells of F. hepatica are equivalent to neoblasts of other flatworm species and demonstrate that they may serve as attractive targets for novel anthelmintics. Author SummaryLiver fluke are parasitic worms that infect both livestock and humans worldwide, threatening food security and human health. Treatments against this disease-causing parasite are limited, and growing resistance to drugs is undermining the effectiveness of control strategies. Since drugs represent the only viable control option, it is crucial that new drugs are discovered through the identification and validation of new drug targets. Stem cells play important roles in the normal growth and repair processes of many organisms, but when these cells become dysregulated through mutation, they can drive the development of cancers. Stem cells of liver fluke may be attractive novel drug targets as disruption would affect worm survival and/or development within their host. In this research we describe the characteristics of liver fluke stem cells, such as their sensitivity to radiation and their ability to develop into new cell types (key stem cell features). We used radiation in combination with RNA sequencing to identify genes associated with the liver fluke stem cells. Finally, we used reverse genetics to reduce the expression of a gene associated with stem cells, which led to the loss of stem cells and reduced worm growth/development. These data provide evidence to support the exploitation of stem cells as a source of novel drug targets for liver fluke control.

molecular biology↗

bioRxiv2023

Discovery of long non-coding RNAs in the liver fluke, Fasciola hepatica

Long non-coding (lnc)RNAs are a class of eukaryotic RNA that do not code for protein and are linked with transcriptional regulation, amongst a myriad of other functions. Using a custom in silico pipeline we have identified 6,436 putative lncRNA transcripts in the liver fluke parasite, Fasciola hepatica; none of which are conserved with those previously described from Schistosoma mansoni. F. hepatica lncRNAs were distinct from F. hepatica mRNAs in transcript length, coding probability, exon/intron composition, expression patterns, and genome distribution. RNA-Seq and digital droplet PCR measurements demonstrated developmentally regulated expression of lncRNAs between intra-mammalian life stages; a similar proportion of lncRNAs (14.2 %) and mRNAs (12.8 %) were differentially expressed (p<0.001), supporting a functional role for lncRNAs in F. hepatica life stages. While most lncRNAs (81%) were intergenic, we identified some that overlapped protein coding loci in antisense (13%) or intronic (6%) configurations. We found no unequivocal evidence for correlated developmental expression within positionally correlated lncRNA:mRNA pairs, but global co-expression analysis identified five lncRNA that were inversely co-regulated with 89 mRNAs, including a large number of functionally essential proteases. The presence of micro (mi)RNA binding sites in 3135 lncRNAs indicates the potential for miRNA-based post-transcriptional regulation of lncRNA, and/or their function as competing endogenous (ce)RNAs. This first description of lncRNAs in F. hepatica provides an avenue to future functional and comparative genomics studies that will provide a new perspective on a poorly understood aspect of parasite biology.

genomics↗

bioRxiv2022

Pan-phylum In Silico Analyses of Nematode Endocannabinoid Signalling Systems Highlight Novel Opportunities for Parasite Drug Target Discovery

The endocannabinoid signalling (ECS) system is a complex lipid signalling pathway that modulates diverse physiological processes in both vertebrate and invertebrate systems. In nematodes, knowledge of endocannabinoid (EC) biology is derived primarily from the free-living model species Caenorhabditis elegans, where ECS has been linked to key aspects of nematode biology. The conservation and complexity of nematode ECS beyond C. elegans is largely uncharacterised, undermining the understanding of ECS biology in nematodes including species with key importance to human, veterinary and plant health. In this study we exploited publicly available omics datasets, in silico bioinformatics and phylogenetic analyses to examine the presence, conservation and life-stage expression profiles of EC-effectors across phylum Nematoda. Our data demonstrate that: (i) ECS is broadly conserved across phylum Nematoda, including in therapeutically and agriculturally relevant species; (ii) EC-effectors appear to display clade and lifestyle-specific conservation patterns; (iii) filarial species possess a reduced EC-effector complement; (iv) there are key differences between nematode and vertebrate EC-effectors; (v) life stage-, tissue- and sex-specific EC-effector expression profiles suggest a role for ECS in therapeutically relevant parasitic nematodes. These data also highlight putative novel targets for anthelmintic therapies. To our knowledge, this study represents the most comprehensive characterisation of ECS pathways in phylum Nematoda and inform our understanding of nematode ECS complexity. Fundamental knowledge of nematode ECS systems will seed follow-on functional studies in key nematode parasites to underpin novel drug target discovery efforts. CONTRIBUTION TO THE FIELDThis manuscript reports the in silico characterisation of endocannabinoid (EC) signalling pathways across the nematode phylum. The physiological relevance and therapeutic potential of EC signalling in higher organisms has received significant attention. In contrast much of our knowledge on EC signalling in nematodes has been derived from the free-living nematode Caenorhabditis elegans where the EC signalling system appears to play key roles in nematode biology and features GPCRs distinct from vertebrate cannabinoid receptors. Unfortunately, the configuration and broader biological significance of EC signalling pathways across the nematode phylum, including in parasites of agricultural, veterinary and medical significance, remains unknown. The in silico exploration of the nematode EC signalling system reported here will provide baseline data on novel neuronal signalling pathways to seed future drug target discovery pipelines for parasites.

neuroscience↗

bioRxiv2022

Transcriptomic analysis reveals a role for the nervous system in regulating growth and development of Fasciola hepatica juveniles

Fasciola spp. liver fluke have significant impacts in veterinary and human medicine. The absence of a vaccine and increasing anthelmintic resistance threaten sustainable control and underscore the need for novel flukicides. Functional genomic approaches underpinned by in vitro culture of juvenile Fasciola hepatica facilitate control target validation in the most pathogenic life stage. Comparative transcriptomics of in vitro and in vivo maintained 21 day old F. hepatica finds that 86% of genes are expressed at similar levels across maintenance treatments suggesting commonality in core biological functioning within these juveniles. Phenotypic comparisons revealed higher cell proliferation and growth rates in the in vivo juveniles compared to their in vitro counterparts. These phenotypic differences were consistent with the upregulation of neoblast-like stem cell and cell-cycle associated genes in in vivo maintained worms. The more rapid growth/development of in vivo juveniles was further evidenced by a switch in cathepsin protease expression profiles, dominated by cathepsin B in in vitro juveniles and then by cathepsin L in in vivo juveniles. Coincident with more rapid growth/development was the marked downregulation of both classical and peptidergic neuronal signalling components in in vivo maintained juveniles, supporting a role for the nervous system in regulating liver fluke growth and development. Differences in the miRNA complements of in vivo and in vitro juveniles identified 31 differentially expressed miRNAs, notably fhe-let-7a-5p, fhe-mir-124-3p and, miRNAs predicted to target Wnt-signalling, supporting a key role for miRNAs in driving the growth/developmental differences in the in vitro and in vivo maintained juvenile liver fluke. Widespread differences in the expression of neuronal genes in juvenile fluke grown in vitro and in vivo expose significant interplay between neuronal signalling and the rate of growth/development, encouraging consideration of neuronal targets in efforts to dysregulate growth/development for parasite control. Author SummaryParasitic worms are notoriously difficult to study outside of a host organism. However, recent developments in culture methods for Fasciola hepatica liver fluke juveniles support growth and development of these parasites in the laboratory (in vitro) towards adult parasites. Having the ability to grow pathogenic juvenile stages in vitro enables functional studies to validate potential drug and vaccine targets. However, comparison of in vitro grown juveniles to juveniles retrieved from infected hosts (in vivo) shows considerable size differences suggesting at least some differences in biology that could undermine the relevance of data generated from in vitro maintained parasites. This study examines gene expression differences between in vitro and in vivo maintained F. hepatica juveniles via transcriptomic analysis to identify similarities and differences in their biology which may help explain differences in the rate of growth and development. 86% of genes were shown to be expressed at similar levels across treatment groups suggesting a high level of biological similarity between in vitro and in vivo juveniles. However, the genes that are expressed differently between these juveniles will help improve current culture methods and provide a new group of potential drug targets that impact on juvenile growth and development.

molecular biology↗

bioRxiv2021

Developmental regulation and functional prediction of microRNAs in an expanded Fasciola hepatica miRNome

1The liver fluke, Fasciola hepatica, is a global burden on the wellbeing and productivity of farmed ruminants, and a zoonotic threat to human health. Despite the clear need for accelerated discovery of new drug and vaccine treatments for this pathogen, we still have a relatively limited understanding of liver fluke biology and host interactions. Noncoding RNAs, including micro (mi)RNAs, are key to transcriptional regulation in all eukaryotes, such that an understanding of miRNA biology can shed light on organismal function at a systems level. Four previous publications have reported up to 89 mature miRNA sequences from F. hepatica, but our data show that this does not represent a full account of this species miRNome. We have expanded on previous studies by sequencing, for the first time, miRNAs from multiple life stages (adult, newly excysted juvenile (NEJ), metacercariae and adult-derived extracellular vesicles (EVs)). These experiments detected an additional 61 high-confidence miRNAs, most of which have not been described in any other species, expanding the F. hepatica miRNome to 150 mature sequences. We used quantitative (q)PCR assays to provide the first developmental profile of miRNA expression across metacercariae, NEJ, adult and adult-derived Evs. The majority of miRNAs were expressed most highly in metacercariae, with at least six distinct expression clusters apparent across life stages. Intracellular miRNAs were functionally analysed to identify target mRNAs with inversely correlated expression in F. hepatica tissue transcriptomes, highlighting regulatory interactions with key virulence transcripts including cathepsin proteases, and neuromuscular genes that control parasite growth, development and motility. We also linked 28 adult-derived EV miRNAs with downregulation of 397 host genes in F. hepatica-infected transcriptomes from ruminant lymph node, peripheral blood mononuclear cell (PBMC) and liver tissue transcriptomes. These included genes involved in signal transduction, immune and metabolic pathways, adding to the evidence for miRNA-based immunosuppression during fasciolosis. These data expand our understanding of the F. hepatica miRNome, provide the first data on developmental miRNA regulation in this species, and provide a set of testable hypotheses for functional genomics interrogations of liver fluke miRNA biology. CONTRIBUTION TO THE FIELDPrevious studies identified 89 micro (mi)RNAs (non-coding RNAs responsible for regulating gene expression) in the trematode parasite, Fasciola hepatica, and attached functional annotations to the miRNAs that are secreted by liver fluke in vitro. This study expands the known miRNA complement of F. hepatica by 40%, adding an additional 61 miRNAs, many of which appear Fasciola-specific. We used this expanded dataset to perform the first analysis of developmental miRNA expression across intra-mammalian parasites, showing clear developmentally regulated expression profiles across infectious metacercariae, juvenile and adult parasites, and extracellular vesicles secreted by adult parasites. We performed rigorous functional annotation of cellular miRNAs, correlating their expression with mRNA transcriptomes to identify potential roles for specific miRNAs in regulating expression of important proteases and nerve/muscle transcripts, all of which are important for parasite virulence. We also functionally analysed miRNAs secreted by adult parasites in terms of interactions with host transcripts; for the first time this analysis was supported by host transcriptome data, linking secreted miRNAs with mRNAs that are downregulated by fluke infection in sheep and cattle. This work contributes new data, insights and analyses to the field, providing a rich source of hypotheses for future experimental validation.

molecular biology↗

bioRxiv2020

RNA interference dynamics in juvenile Fasciola hepatica are altered during in vitro growth and development

For over a decade RNA interference (RNAi) has been an important molecular tool for functional genomics studies in parasitic flatworms. Despite this, our understanding of RNAi dynamics in many flatworm parasites, such as the temperate liver fluke (Fasciola hepatica), remains rudimentary. The ability to maintain developing juvenile fluke in vitro provides the opportunity to perform functional studies during development of the key pathogenic life stage. Here, we investigate the RNAi competence of developing juvenile liver fluke. Firstly, all life stages examined possess, and express, core candidate RNAi effectors encouraging the hypothesis that all life stages of F. hepatica are RNAi competent. RNAi effector analyses supported growing evidence that parasitic flatworms have evolved a separate clade of RNAi effectors with unknown function. Secondly, we assessed the impact of growth / development during in vitro culture on RNAi in F. hepatica juveniles and found that during the first week post-excystment liver fluke juveniles exhibit quantitatively lower RNAi mediated transcript knockdown when maintained in growth inducing media. This did not appear to occur in older in vitro juveniles, suggesting that rapidly shifting transcript dynamics over the first week following excystment alters RNAi efficacy after a single 24 hour exposure to double stranded (ds)RNA. Finally, RNAi efficiency was found to be improved through use of a repeated dsRNA exposure methodology that has facilitated silencing of genes in a range of tissues, thereby increasing the utility of RNAi as a functional genomics tool in F. hepatica.

molecular biology↗

bioRxiv2017

Profiling G protein-coupled receptors of Fasciola hepatica identifies orphan rhodopsins unique to phylum Platyhelminthes

G protein-coupled receptors (GPCRs) are established drug targets. Despite their considerable appeal as targets for next-generation anthelmintics, poor understanding of their diversity and function in parasitic helminths has thwarted progress towards GPCR-targeted anti-parasite drugs. This study facilitates GPCR research in the liver fluke, Fasciola hepatica, by generating the first profile of GPCRs from the F. hepatica genome. Our dataset describes 146 high confidence GPCRs, representing the largest cohort of GPCRs, and the most complete set of in silico ligand-receptor predictions, yet reported in any parasitic helminth. All GPCRs fall within the established GRAFS nomenclature; comprising three glutamate, 135 rhodopsin, two adhesion, five frizzled and one smoothened GPCR. Stringent annotation pipelines identified 18 highly diverged rhodopsins in F. hepatica that maintained core rhodopsin signatures, but lacked significant similarity with non-flatworm sequences, providing a new sub-group of potential flukicide targets. These facilitated identification of a larger cohort of 76 related sequences from available flatworm genomes, representing new members of existing groups of flatworm-specific rhodopsins. These receptors imply flatworm specific GPCR functions, and/or co-evolution with unique flatworm ligands, and could facilitate development of exquisitely selective anthelminthics. Ligand binding domain sequence conservation relative to deorphanised rhodopsins enabled high confidence ligand-receptor matching of seventeen receptors activated by acetylcholine, neuropeptide F/Y, octopamine or serotonin. RNA-Seq analyses showed expression of 101 GPCRs across various developmental stages, with the majority expressed most highly in the pathogenic intra-mammalian juvenile parasites. These data identify a broad complement of GPCRs in F. hepatica, including rhodopsins likely to have key functions in neuromuscular control and sensory perception, as well as frizzled and adhesion families implicated, in other species, in growth, development and reproduction. This catalogue of liver fluke GPCRs provides a platform for new avenues into our understanding of flatworm biology and anthelmintic discovery.\n\nAuthor SummaryFasciola spp. liver fluke are important veterinary pathogens with impacts on human and animal health, and food security, around the world. Liver fluke have developed resistance to most of the drugs used to treat them (flukicides). Since no vaccines exist, we need to develop new flukicides as a matter of urgency. Most anthelmintic drugs used to treat parasitic worm infections operate by impeding the functioning of their nerve and muscle. In flatworms, most nervous signals are received by a type of receptor called a G protein-coupled receptor (GPCR). Since GPCRs control important parasite functions (e.g. movement, egg-laying, feeding), they represent appealing targets for new flukicides, but have not yet been targeted as such. This work exploited the F. hepatica genome to determine the quantity and diversity of GPCRs in liver fluke. We found more GPCRs in the Fasciola genome than have been reported in any other parasitic worm. These findings provide a foundation that for researchers to determine the functions of these receptors, and which molecules/ligands they are activated by. These data will pave the way to exploring the potential of F. hepatica GPCRs as targets for new flukicides.

bioinformatics↗