Veterinary Biosciences - Research Publications

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    Proteomic analysis of Sarcoptes scabiei reveals that proteins differentially expressed between eggs and female adult stages are involved predominantly in genetic information processing, metabolism and/or host-parasite interactions
    Wang, T ; Gasser, RB ; Korhonen, PK ; Young, ND ; Ang, C-S ; Williamson, NA ; Ma, G ; Samarawickrama, GR ; Fernando, DD ; Fischer, K ; Taylan Ozkan, A (PUBLIC LIBRARY SCIENCE, 2022-12)
    Presently, there is a dearth of proteomic data for parasitic mites and their relationship with the host animals. Here, using a high throughput LC-MS/MS-based approach, we undertook the first comprehensive, large-scale proteomic investigation of egg and adult female stages of the scabies mite, Sarcoptes scabiei-one of the most important parasitic mites of humans and other animals worldwide. In total, 1,761 S. scabiei proteins were identified and quantified with high confidence. Bioinformatic analyses revealed differentially expressed proteins to be involved predominantly in biological pathways or processes including genetic information processing, energy (oxidative phosphorylation), nucleotide, amino acid, carbohydrate and/or lipid metabolism, and some adaptive processes. Selected, constitutively and highly expressed proteins, such as peptidases, scabies mite inactivated protease paralogues (SMIPPs) and muscle proteins (myosin and troponin), are proposed to be involved in key biological processes within S. scabiei, host-parasite interactions and/or the pathogenesis of scabies. These proteomic data will enable future molecular, biochemical and physiological investigations of early developmental stages of S. scabiei and the discovery of novel interventions, targeting the egg stage, given its non-susceptibility to acaricides currently approved for the treatment of scabies in humans.
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    Ubiquitination pathway model for the barber's pole worm - Haemonchus contortus
    Zheng, Y ; Ma, G ; Wang, T ; Hofmann, A ; Song, J ; Gasser, RB ; Young, ND (ELSEVIER SCI LTD, 2022-08)
    The ubiquitin-mediated pathway has been comprehensively explored in the free-living nematode Caenorhabditis elegans, but very little is known about this pathway in parasitic nematodes. Here, we inferred the ubiquitination pathway for an economically significant and pathogenic nematode - Haemonchus contortus - using abundant resources available for C. elegans. We identified 215 genes encoding ubiquitin (Ub; n = 3 genes), ubiquitin-activating enzyme (E1; one), -conjugating enzymes (E2s; 21), ligases (E3s; 157) and deubiquitinating enzymes (DUBs; 33). With reference to C. elegans, Ub, E1 and E2 were relatively conserved in sequence and structure, and E3s and DUBs were divergent, likely reflecting functional and biological uniqueness in H. contortus. Most genes encoding ubiquitination pathway components exhibit high transcription in the egg compared with other stages, indicating marked protein homeostasis in this early developmental stage. The ubiquitination pathway model constructed for H. contortus provides a foundation to explore the ubiquitin-proteasome system, crosstalk between autophagy and the proteasome system, and the parasite-host interactions. Selected E3 and DUB proteins which are very divergent in sequence and structure from host homologues or entirely unique to H. contortus and related parasitic nematodes may represent possible anthelmintic targets.
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    Thermal proteome profiling reveals Haemonchus orphan protein HCO_011565 as a target of the nematocidal small molecule UMW-868
    Taki, ACC ; Wang, T ; Nguyen, NNN ; Ang, C-S ; Leeming, MGG ; Nie, S ; Byrne, JJJ ; Young, NDD ; Zheng, Y ; Ma, G ; Korhonen, PKK ; Koehler, AVV ; Williamson, NAA ; Hofmann, A ; Chang, BCH ; Haeberli, C ; Keiser, J ; Jabbar, A ; Sleebs, BEE ; Gasser, RBB (FRONTIERS MEDIA SA, 2022-10-14)
    Parasitic roundworms (nematodes) cause destructive diseases, and immense suffering in humans and other animals around the world. The control of these parasites relies heavily on anthelmintic therapy, but treatment failures and resistance to these drugs are widespread. As efforts to develop vaccines against parasitic nematodes have been largely unsuccessful, there is an increased focus on discovering new anthelmintic entities to combat drug resistant worms. Here, we employed thermal proteome profiling (TPP) to explore hit pharmacology and to support optimisation of a hit compound (UMW-868), identified in a high-throughput whole-worm, phenotypic screen. Using advanced structural prediction and docking tools, we inferred an entirely novel, parasite-specific target (HCO_011565) of this anthelmintic small molecule in the highly pathogenic, blood-feeding barber's pole worm, and in other socioeconomically important parasitic nematodes. The "hit-to-target" workflow constructed here provides a unique prospect of accelerating the simultaneous discovery of novel anthelmintics and associated parasite-specific targets.
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    Evidence that Transcriptional Alterations in Sarcoptes scabiei Are under Tight Post-Transcriptional (microRNA) Control
    Korhonen, PK ; Wang, T ; Young, ND ; Samarawickrama, GR ; Fernando, DD ; Ma, G ; Gasser, RB ; Fischer, K (MDPI, 2022-09)
    Here, we explored transcriptomic differences among early egg (Ee), late egg (Le) and adult female (Af) stages of the scabies mite, Sarcoptes scabiei, using an integrative bioinformatic approach. We recorded a high, negative correlation between miRNAs and genes with decreased mRNA transcription between the developmental stages, indicating substantial post-transcriptional repression; we also showed a positive correlation between miRNAs and genes with increased mRNA transcription, suggesting indirect post-transcriptional regulation. The alterations in mRNA transcription between the egg and adult female stages of S. scabiei were inferred to be linked to metabolism (including carbohydrate and lipid degradation, amino acid and energy metabolism), environmental information processing (e.g., signal transduction and signalling molecules), genetic information processing (e.g., transcription and translation) and/or organismal systems. Taken together, these results provide insight into the transcription of this socioeconomically important parasitic mite, with a particular focus on the egg stage. This work encourages further, detailed laboratory studies of miRNA regulation across all developmental stages of S. scabiei and might assist in discovering new intervention targets in the egg stage of S. scabiei.
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    Repurposing of a human antibody-based microarray to explore conserved components of the signalome of the parasitic nematode Haemonchus contortus
    Adderley, J ; Wang, T ; Ma, G ; Zheng, Y ; Young, ND ; Doerig, C ; Gasser, RB (BMC, 2022-07-30)
    BACKGROUND: Gaining insight into molecular signalling pathways of socioeconomically important parasitic nematodes has implications for understanding their molecular biology and for developing novel anthelmintic interventions. METHODS: Here, we evaluated the use of a human antibody-based microarray to explore conserved elements of the signalome in the barber's pole worm Haemonchus contortus. To do this, we prepared extracts from mixed-sex (female and male) adult worms and third-stage larvae (L3s), incubated these extracts on the antibody microarray and then measured the amounts of antibody-bound proteins ('signal intensity'). RESULTS: In total, 878 signals were classified into two distinct categories: signals that were higher for adults than for larvae of H. contortus (n = 376), and signals that were higher for larvae than for adults of this species (n = 502). Following a data-filtering step, high confidence ('specific') signals were obtained for subsequent analyses. In total, 39 pan-specific signals (linked to antibodies that recognise target proteins irrespective of their phosphorylation status) and 65 phosphorylation-specific signals were higher in the adult stage, and 82 pan-specific signals and 183 phosphorylation-specific signals were higher in L3s. Thus, notably more signals were higher in L3s than in the adult worms. Using publicly available information, we then inferred H. contortus proteins that were detected (with high confidence) by specific antibodies directed against human homologues, and revealed relatively high structural conservation between the two species, with some variability for select proteins. We also in silico-matched 763 compound structures (listed in the DrugBank and Kinase SARfari public databases) to four H. contortus proteins (designated HCON_00005760, HCON_00079680, HCON_00013590 and HCON_00105100). CONCLUSIONS: We conclude that the present antibody-based microarray provides a useful tool for comparative analyses of signalling pathways between/among developmental stages and/or species, as well as opportunities to explore nematocidal target candidates in H. contortus and related parasites.
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    Chromosome-level genome of Schistosoma haematobium underpins genome-wide explorations of molecular variation
    Stroehlein, AJ ; Korhonen, PK ; Lee, VV ; Ralph, SA ; Mentink-Kane, M ; You, H ; McManus, DP ; Tchuente, L-AT ; Stothard, JR ; Kaur, P ; Dudchenko, O ; Aiden, EL ; Yang, B ; Yang, H ; Emery, AM ; Webster, BL ; Brindley, PJ ; Rollinson, D ; Chang, BCH ; Gasser, RB ; Young, ND ; Zamanian, M (PUBLIC LIBRARY SCIENCE, 2022-02)
    Urogenital schistosomiasis is caused by the blood fluke Schistosoma haematobium and is one of the most neglected tropical diseases worldwide, afflicting > 100 million people. It is characterised by granulomata, fibrosis and calcification in urogenital tissues, and can lead to increased susceptibility to HIV/AIDS and squamous cell carcinoma of the bladder. To complement available treatment programs and break the transmission of disease, sound knowledge and understanding of the biology and ecology of S. haematobium is required. Hybridisation/introgression events and molecular variation among members of the S. haematobium-group might effect important biological and/or disease traits as well as the morbidity of disease and the effectiveness of control programs including mass drug administration. Here we report the first chromosome-contiguous genome for a well-defined laboratory line of this blood fluke. An exploration of this genome using transcriptomic data for all key developmental stages allowed us to refine gene models (including non-coding elements) and annotations, discover 'new' genes and transcription profiles for these stages, likely linked to development and/or pathogenesis. Molecular variation within S. haematobium among some geographical locations in Africa revealed unique genomic 'signatures' that matched species other than S. haematobium, indicating the occurrence of introgression events. The present reference genome (designated Shae.V3) and the findings from this study solidly underpin future functional genomic and molecular investigations of S. haematobium and accelerate systematic, large-scale population genomics investigations, with a focus on improved and sustained control of urogenital schistosomiasis.
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    "Escalibur"-A practical pipeline for the de novo analysis of nucleotide variation in nonmodel eukaryotes
    Korhonen, PK ; Shaban, B ; Faux, NG ; Kinkar, L ; Chang, BCH ; Wang, D ; Yang, B ; Young, ND ; Gasser, RB (WILEY, 2022-07)
    The revolution in genomics has enabled large-scale population genetic investigations of a wide range of organisms, but there has been a relatively limited focus on improving analytical pipelines. To efficiently analyse large data sets, highly integrated and automated software pipelines, which are easy to use, efficient, reliable, reproducible and run in multiple computational environments, are required. A number of software workflows have been developed to handle and process such data sets for population genetic analyses, but effective, specialized pipelines for genetic and statistical analyses of nonmodel organisms are lacking. For most species, resources for variomes (sets of genetic variations found in populations of species) are not available, and/or genome assemblies are often incomplete and fragmented, complicating the selection of the most suitable reference genome when multiple assemblies are available. Additionally, the biological samples used often contain extraneous DNA from sources other than the species under investigation (e.g., microbial contamination), which needs to be removed prior to genetic analyses. For these reasons, we established a new pipeline, called Escalibur, which includes: functionalities, such as data trimming and mapping; selection of a suitable reference genome; removal of contaminating read data; recalibration of base calls; and variant-calling. Escalibur uses a proven gatk variant caller and workflow description language (WDL), and is, therefore, a highly efficient and scalable pipeline for the genome-wide identification of nucleotide variation in eukaryotes. This pipeline is available at https://gitlab.unimelb.edu.au/bioscience/escalibur (version 0.3-beta) and is essentially applicable to any prokaryote or eukaryote.
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    Mitochondrial genome of Bulinus truncatus (Gastropoda: Lymnaeoidea): Implications for snail systematics and schistosome epidemiology.
    Young, ND ; Kinkar, L ; Stroehlein, AJ ; Korhonen, PK ; Stothard, JR ; Rollinson, D ; Gasser, RB (Elsevier BV, 2021)
    Many freshwater snails of the genus Bulinus act as intermediate hosts in the life-cycles of schistosomes in Africa and adjacent regions. Currently, 37 species of Bulinus representing four groups are recognised. The mitochondrial cytochrome c oxidase subunit 1 (cox1) gene has shown utility for identifying and differentiating Bulinus species and groups, but taxonomic relationships based on genetic data are not entirely consistent with those inferred using morphological and biological features. To underpin future systematic studies of members of the genus, we characterised here the mitochondrial genome of Bulinus truncatus (from a defined laboratory strain) using a combined second- and third-generation sequencing and informatics approach, enabling taxonomic comparisons with other planorbid snails for which mitochondrial (mt) genomes were available. Analyses showed consistency in gene order and length among mitochondrial genomes of representative planorbid snails, with the lowest and highest nucleotide diversities being in the cytochrome c oxidase and nicotinamide dehydrogenase subunit genes, respectively. This first mt genome for a representative of the genus Bulinus should provide a useful resource for future investigations of the systematics, population genetics, epidemiology and/or ecology of Bulinus and related snails. The sequencing and informatic workflow employed here should find broad applicability to a range of other snail intermediate hosts of parasitic trematodes.
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    Nuclear genome of Bulinus truncatus, an intermediate host of the carcinogenic human blood fluke Schistosoma haematobium
    Young, ND ; Stroehlein, AJ ; Wang, T ; Korhonen, PK ; Mentink-Kane, M ; Stothard, JR ; Rollinson, D ; Gasser, RB (NATURE PORTFOLIO, 2022-02-21)
    Some snails act as intermediate hosts (vectors) for parasitic flatworms (flukes) that cause neglected tropical diseases, such as schistosomiases. Schistosoma haematobium is a blood fluke that causes urogenital schistosomiasis and induces bladder cancer and increased risk of HIV infection. Understanding the molecular biology of the snail and its relationship with the parasite could guide development of an intervention approach that interrupts transmission. Here, we define the genome for a key intermediate host of S. haematobium-called Bulinus truncatus-and explore protein groups inferred to play an integral role in the snail's biology and its relationship with the schistosome parasite. Bu. truncatus shared many orthologous protein groups with Biomphalaria glabrata-the key snail vector for S. mansoni which causes hepatointestinal schistosomiasis in people. Conspicuous were expansions in signalling and membrane trafficking proteins, peptidases and their inhibitors as well as gene families linked to immune response regulation, such as a large repertoire of lectin-like molecules. This work provides a sound basis for further studies of snail-parasite interactions in the search for targets to block schistosomiasis transmission.
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    Chromosome-scale Echinococcus granulosus (genotype G1) genome reveals the Eg95 gene family and conservation of the EG95-vaccine molecule
    Korhonen, PK ; Kinkar, L ; Young, ND ; Cai, H ; Lightowlers, MW ; Gauci, C ; Jabbar, A ; Chang, BCH ; Wang, T ; Hofmann, A ; Koehler, A ; Li, J ; Li, J ; Wang, D ; Yin, J ; Yang, H ; Jenkins, DJ ; Saarma, U ; Laurimae, T ; Rostami-Nejad, M ; Irshadullah, M ; Mirhendi, H ; Sharbatkhori, M ; Ponce-Gordo, F ; Simsek, S ; Casulli, A ; Zait, H ; Atoyan, H ; de la Rue, ML ; Romig, T ; Wassermann, M ; Aghayan, SA ; Gevorgyan, H ; Yang, B ; Gasser, RB (NATURE PORTFOLIO, 2022-03-03)
    Cystic echinococcosis is a socioeconomically important parasitic disease caused by the larval stage of the canid tapeworm Echinococcus granulosus, afflicting millions of humans and animals worldwide. The development of a vaccine (called EG95) has been the most notable translational advance in the fight against this disease in animals. However, almost nothing is known about the genomic organisation/location of the family of genes encoding EG95 and related molecules, the extent of their conservation or their functions. The lack of a complete reference genome for E. granulosus genotype G1 has been a major obstacle to addressing these areas. Here, we assembled a chromosomal-scale genome for this genotype by scaffolding to a high quality genome for the congener E. multilocularis, localised Eg95 gene family members in this genome, and evaluated the conservation of the EG95 vaccine molecule. These results have marked implications for future explorations of aspects such as developmentally-regulated gene transcription/expression (using replicate samples) for all E. granulosus stages; structural and functional roles of non-coding genome regions; molecular 'cross-talk' between oncosphere and the immune system; and defining the precise function(s) of EG95. Applied aspects should include developing improved tools for the diagnosis and chemotherapy of cystic echinococcosis of humans.