Research Interests: we want to understand how parasitic nematodes infect their host at a molecular and genetic level.  Our research investigates the protein-coding genes and the small RNAs that have a role in nematode parasitism. We use the parasitic nematode Strongyloides ratti, a gastrointestinal of rodents, as a model to understand nematode parasitism. 

 

Research questions we are interested in include:

- which protein-coding genes and gene families have a role in nematode parasitism?

- how are 'parasitism genes' regulated by small RNA pathways?

- what proteins and non-coding RNAs are parasitic nematodes secreting into their host during infection, and how do they manipulate the host environment? 

- how have small RNA pathways diversified among nematode taxa, particularly in relation to parasitism, but also in free-living nematodes?

I. Protein-coding genes with a role in  Strongyloides parasitsm

We have sequenced the genomes of four Strongyloides species (S. ratti, S. venezuelensis - parasites of rodents, S. stercoralis - a parasite of humans and dogs, and S. papillosus - a parasite of sheep) and two closely related species, Parastrongyloides trichosuri - a parasite of possums, and Rhabditophanes - a free-living nematode. Using  genomic, genetic, transcriptomic and proteomic comparative analyses we have identified gene and protein families with a putative role in parasitism. Several of these families have expanded in the IVa clade of nematodes (which includes Strongyloides species), coinciding with the evolution of parasitism in this clade.  Phylogenies of some of the key gene families associated with the parasitic adult stage of Strongyloides nematodes are shown below. Many of the proteins coding for by these genes are secreted by the parasitic (cf. genetically identical free-living) life cycle stage of Strongyloides and are therefore likely to have a role in modulating the host environment, for example, aspects of the host immune response. 

a                                                  b

The gene families coding for Astacin metallopeptidases (a) and SCPTAPS CAP domain-containing proteins (b) have massively expanded in Strongyloides (blue) compared to most other nematode species. Gene families have expanded from a single gene copy. The SCPTAPS gene family has also expanded independently in the hookworm Necator americanus. Astacins and SCP/TAPS are associated with roles in parasitism including tissue degradation and immunomodulation. 

Hunt et al (2016) Nature Genetics 48 299-307. 

The acetylcholinesterase gene family has expanded in parasitic species of clade IVa nematodes - Strongyloides spp. (red) and P. trichosuri (orange) - but not in the free living species Rhabditophanes (pink). Acetylcholine is associated with the regulation of peristalsis and mucin production in the gut which are important host responses involved in the explosion of gut parasites such as Strongyloides. The acetylcholinesterase expansion in Strongyloides could therefore represent an adaptive strategy to counteract acetylcholine-dependent host responses.

Hunt et al (2017) Parasitology 144 (3): 343-358. 

The speckle-type POZ-like gene family has expanded in the S. venezuelensis (red)-S. papillosus (blue) subclade of Strongyloides nematodes, and in both of these species these genes are highly upregulated in the parasite (cf. free-living) adult transcriptome suggesting they have an important role in parasitism. Each point represents a gene; one-two copies of these genes are found in a range of nematode species (black, and green background 'A'); genes unregulated in the parasitic stage transcriptome are highlighted with a pink background (e.g. the 'B' cluster).

Hunt et al (2018) Scientific Reports 8: 5192.  

II. small RNAs with a role in nematode parasitsm

There are two possible roles of small RNAs in nematode parasitism and parasitism more generally:

(i) small RNAs may regulate the expression of endogenous genes with a role in parasitism (e.g. astacins, SCP/TAPS, acetylcholinesterase, speckle-type POZ-like coding genes - see above). 

(ii) small RNAs may be secreted by the parasite into the host to target and modulate host gene expression e.g. genes involved in the host immune response.  

The expression of miRNAs in parasitic, compared with free-living, adult female S. ratti. ​ Several miRNAs are specifically upregulated in the parasitic stage (red) or free-living stage (blue). Each data point represents a miRNA; logFC = log fold change of expression, logCPM = log counts per million reads. In preparation for publication.    

We are investigating the role of small RNA pathways in parasitism by Strongyloides nematodes including projects on:

microRNAs with a role in parasitism: Comparison of small RNA expression in S. ratti parasitic and free-living life cycle stages, has identified microRNAs that are specifically upregulated in the parasitic life cycle stage, suggesting these miRNAs have a role in parasitism. We are also interested in which endogenous nematode genes these miRNAs are regulating. 

Worm-specific Argonaute (WAGO) proteins:  We have identified a subset of WAGOs that are specifically upregulated in the transcriptome of the parasitic (cf. free-living) adult life cycle stage of Strongyloides nematodes. These WAGOs may represent a small RNA pathway with a role in parasitism. Hunt et al (2018) Scientific Reports 8: 5192. 

Secreted exosome-like vesicles (ELVs): Strongyloides secrete ELVs into their host, presumably to target and module the host environment e.g. host immune response. We have identified a cocktail of proteases in these ELVs, and we are now beginning to investigate other contents e.g. non-coding RNA that may be transported into the host in ELVs.  

III. Diversity of small RNA pathways in nematodes

The orthologue of ergo-1 is absent from the C. inopinata genome.  The ergo-1 region of the genome is highly conserved in C. .elegans and C. briggsae but has undergone rearrangement in C. inopinata, likely the result of higher levels of transposase activity in the C. inopinata genome. Orthologous genes are highlighted in the same colour. Kanzaki et al (2018). Nature Communications 9:3216

Orthologues of C. elegans genes involved in small RNA pathways are largely conserved in C. inopinata and C. briggsae, however, three orthologues (ergo-1, eri-6 and eri-9) are missing in the C. inopinata genome.  All three of these genes are involved in the ERGO-1 pathway.  This pathway is particularly active in the female germline and has been associated with roles in targeting and suppressing the expression of newly duplicated genes, particularly of viral origin, and potentially deleterious non-coding regions of the genome. 

We are currently investigating small RNA pathways in C. inopinata and we are interested in the diversity of small RNA pathways more generally across nematodes.