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Zheng Y, Young ND, Wang T, Chang BCH, Song J, Gasser RB. Systems biology of Haemonchus contortus - Advancing biotechnology for parasitic nematode control. Biotechnol Adv 2025; 81:108567. [PMID: 40127743 DOI: 10.1016/j.biotechadv.2025.108567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2025] [Revised: 03/19/2025] [Accepted: 03/21/2025] [Indexed: 03/26/2025]
Abstract
Parasitic nematodes represent a substantial global burden, impacting animal health, agriculture and economies worldwide. Of these worms, Haemonchus contortus - a blood-feeding nematode of ruminants - is a major pathogen and a model for molecular and applied parasitology research. This review synthesises some key advances in understanding the molecular biology, genetic diversity and host-parasite interactions of H. contortus, highlighting its value for comparative studies with the free-living nematode Caenorhabditis elegans. Key themes include recent developments in genomic, transcriptomic and proteomic technologies and resources, which are illuminating critical molecular pathways, including the ubiquitination pathway, protease/protease inhibitor systems and the secretome of H. contortus. Some of these insights are providing a foundation for identifying essential genes and exploring their potential as targets for novel anthelmintics or vaccines, particularly in the face of widespread anthelmintic resistance. Advanced bioinformatic tools, such as machine learning (ML) algorithms and artificial intelligence (AI)-driven protein structure prediction, are enhancing annotation capabilities, facilitating and accelerating analyses of gene functions, and biological pathways and processes. This review also discusses the integration of these tools with cutting-edge single-cell sequencing and spatial transcriptomics to dissect host-parasite interactions at the cellular level. The discussion emphasises the importance of curated databases, improved culture systems and functional genomics platforms to translate molecular discoveries into practical outcomes, such as novel interventions. New research findings and resources not only advance research on H. contortus and related nematodes but may also pave the way for innovative solutions to the global challenges with anthelmintic resistance.
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Affiliation(s)
- Yuanting Zheng
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Tao Wang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Bill C H Chang
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jiangning Song
- Faculty of IT, Department of Data Science and AI, Monash University, Victoria, Australia; Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Victoria, Australia; Monash Data Futures Institute, Monash University, Victoria, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, Victoria 3010, Australia.
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Shi Y, Li X, Liang K, Lu T, Chen Y, Lai Y, Li Y, Wei S, He S, Tang L, Liu D, Li Y. Characteristics and immunoprotective functions of three cysteine proteases from Clonorchis sinensis. Front Immunol 2025; 16:1550775. [PMID: 40248698 PMCID: PMC12003271 DOI: 10.3389/fimmu.2025.1550775] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2024] [Accepted: 03/18/2025] [Indexed: 04/19/2025] Open
Abstract
Introduction Cysteine proteases from Clonorchis sinensis, including various proteins, are essential for its pathogenicity and serve as potential vaccine candidates. This study assesses the protective effects of three C. sinensis cysteine proteases (CsCP1-3). Methods Mice immunized with recombinant CsCP1-3 and adjuvants were subsequently infected with C. sinensis metacercariae after three immunization rounds. Liver damage was evaluated through hematoxylin and eosin (H&E), Masson's trichrome, and immunohistochemical analyses. The levels of IgG1, IgG2a antibodies, and cytokines (IFN-g, IL-2, IL-4, and IL-10) were quantified by enzyme-linked immunosorbent assay (ELISA). Results RT-qPCR revealed that CsCP1-2 exhibited the highest expression in newly encysted larvae (NEL), while CsCP3 was predominantly expressed in adult stages. Immunohistochemical localization confirmed that CsCP1-3 are present in the eggshells, syncytial layers of metacercariae, NEL cuticle, and adult intestines. Histological and immunohistochemical analysis demonstrated that the rCsCP1-3-immunized group displayed reduced liver inflammation and biliary fibrosis compared to the control group. The rCsCP1-3 induced a progressive increase in specific IgG1 and IgG2a antibody titers by the second week post-immunization. In the CsCP1-2 group, cytokines IFN-g, IL-2, IL-4, and IL-10 were elevated relative to the control, with particularly high levels of IFN-g and IL-10 in CsCP1, indicating a strong mixed Th1/Th2 immune response. In contrast, the CsCP3 immunization group exhibited a transient increase in cytokines (IFN-g, IL-2, IL-4, and IL-10) three days postinfection, which subsided after one to two weeks. Discussion These findings suggest that CsCP1-3 elicit robust antibody and cellular immune responses, mitigating liver damage caused by C. sinensis infection. CsCP1, in particular, induces a potent mixed Th1/Th2 response, positioning it as a promising vaccine candidate.
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Affiliation(s)
- Yunliang Shi
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Xiaoqin Li
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Department of Medical Laboratory, Shenzhen Longgang District Eighth People’s Hospital, Shenzhen, China
| | - Kai Liang
- Gastroenterology Department, Guangxi Zhuang Autonomous Region People’s Hospital, Nanning, China
| | - Ting Lu
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yu Chen
- Department of Schistosomiasis Prevention and Control, Disease Prevention and Control Center of Hengzhou City, Hengzhou, China
| | - Yashi Lai
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Yaoting Li
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Shuai Wei
- Department of Medical Laboratory, Hechi People’s Hospital, Hechi, China
| | - Shanshan He
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Lili Tang
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
| | - Dengyu Liu
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
| | - Yanwen Li
- Parasitology Department, School of Basic Medical Sciences, Guangxi Medical University, Nanning, China
- Key Laboratory of Basic Research on Regional Diseases (Guangxi Medical University), Education Department of Guangxi Zhuang Autonomous Region, Nanning, China
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Boschiero C, Beshah E, Bakshi M, Miramontes E, Hebert D, Thompson PC, Li CJ, Zhu X, Zarlenga D, Liu GE, Tuo W. Transcriptional Profiling of Abomasal Mucosa from Young Calves Experimentally Infected with Ostertagia ostertagi. Int J Mol Sci 2025; 26:2264. [PMID: 40076885 PMCID: PMC11900041 DOI: 10.3390/ijms26052264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2025] [Revised: 02/21/2025] [Accepted: 02/24/2025] [Indexed: 03/14/2025] Open
Abstract
Ostertagia ostertagi, also known as the brown stomach worm, causes significant pathology in the abomasum, resulting in production and nutritional losses in cattle. Alternative control measures, such as vaccination, are urgently needed because of rapidly growing anthelmintic drug resistance. There is a need to understand host responses to the infection, especially immune responses, to advance vaccine discovery and design. Therefore, the present study investigated comprehensive changes in gene transcription in the abomasal mucosa of cattle infected with O. ostertagi at 0, 3-5, 7-9, 10, and 21 days post-infection (dpi) using RNA sequencing (RNA-seq). Compared to uninfected controls, infected animals exhibited significant increases in differentially expressed genes (DEGs) throughout the infection period. Infection induced more upregulated than downregulated genes in the abomasal fundic mucosa (FUN) when compared to the abomasal pyloric mucosa (PYL). The largest transcriptional changes occurred between 7-9 and 10 dpi during the final development of the L4 and their emergence from the gastric glands. Most DEGs are associated with host immunity, cellular reorganization, cell migration, and proliferation. Tuft/epithelial cell response to the infection was atypical, lacking an anticipated increase in key alarmin cytokine genes. Numerous genes associated with T helper (Th) 1, Th2, and Th17 responses and T cell exhaustion were upregulated, suggesting altered immune regulation. The data collectively indicate that O. ostertagi infection elicits massive host responses, particularly immune responses, which are intertwined with the parasite's disruption of abomasal function, which likely impairs the nutrient utilization of the host. The infection is characterized by the absence of a dominant Th response and displaying a mixed activation of Th1, Th2, and Th17 pathways. Elevated expression of T cell exhaustion genes and lack of increase in epithelial alarmin cytokine genes suggest a downregulation of, or a deficiency in initiating, effective host immunity to the infection. Understanding mechanisms of parasite-mediated immune evasion and their nutritional consequences will facilitate the rational design of protective vaccines against infections of complex nematode parasites.
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Affiliation(s)
- Clarissa Boschiero
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Ethiopia Beshah
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Mariam Bakshi
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Eliseo Miramontes
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Deborah Hebert
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Peter C. Thompson
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Xiaoping Zhu
- Department of Veterinary Medicine, University of Maryland, College Park, MD 20742, USA
| | - Dante Zarlenga
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
| | - Wenbin Tuo
- Animal Parasitic Diseases Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD 20705, USA
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Li X, Liu Y, Zou Y, Zhang J, Wang Y, Ding Y, Shi Z, Guo X, Zhang S, Yin H, Guo A, Wang S. Echinococcus multilocularis serpin regulates macrophage polarization and reduces gut dysbiosis in colitis. Infect Immun 2024; 92:e0023224. [PMID: 39037247 PMCID: PMC11320943 DOI: 10.1128/iai.00232-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2024] [Accepted: 07/01/2024] [Indexed: 07/23/2024] Open
Abstract
Helminths serve as principal regulators in modulating host immune responses, and their excretory-secretory proteins are recognized as potential therapeutic agents for inflammatory bowel disease. Nevertheless, our comprehension of the mechanisms underlying immunoregulation remains restricted. This investigation delves into the immunomodulatory role of a secretory protein serpin (Emu-serpin), within the larval stage of Echinococcus multilocularis. Our observations indicate that Emu-serpin effectively alleviates dextran sulfate sodium-induced colitis, yielding a substantial reduction in immunopathology and an augmentation of anti-inflammatory cytokines. Furthermore, this suppressive regulatory effect is concomitant with the reduction of gut microbiota dysbiosis linked to colitis, as evidenced by a marked impediment to the expansion of the pathobiont taxa Enterobacteriaceae. In vivo experiments demonstrate that Emu-serpin facilitates the expansion of M2 phenotype macrophages while concurrently diminishing M1 phenotype macrophages, alongside an elevation in anti-inflammatory cytokine levels. Subsequent in vitro investigations involving RAW264.7 and bone marrow macrophages reveal that Emu-serpin induces a conversion of M2 macrophage populations from a pro-inflammatory to an anti-inflammatory phenotype through direct inhibition. Adoptive transfer experiments reveal the peritoneal macrophages induced by Emu-serpin alleviate colitis and gut microbiota dysbiosis. In summary, these findings propose that Emu-serpin holds the potential to regulate macrophage polarization and maintain gut microbiota homeostasis in colitis, establishing it as a promising candidate for developing helminth therapy for preventing inflammatory diseases.
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Affiliation(s)
- Xiaolu Li
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Yihui Liu
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Yang Zou
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Jiayun Zhang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Yugui Wang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Yingying Ding
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Zhiqi Shi
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Xiaola Guo
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Shaohua Zhang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
| | - Hong Yin
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Aijiang Guo
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
| | - Shuai Wang
- State Key Laboratory of Animal Disease Control and Prevention, College of Veterinary Medicine, Lanzhou University, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
- Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou, Gansu, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, Jiangsu, China
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Hasan MW, Ehsan M, Wang Q, Haseeb M, Lakho SA, Haider A, Lu M, Xu L, Song X, Yan R, Li X. PLGA-Encapsulated Haemonchus contortus Antigen ES-15 Augments Immune Responses in a Murine Model. Vaccines (Basel) 2023; 11:1794. [PMID: 38140198 PMCID: PMC10748113 DOI: 10.3390/vaccines11121794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 11/25/2023] [Accepted: 11/27/2023] [Indexed: 12/24/2023] Open
Abstract
Haemonchus contortus is a gastrointestinal parasite that adversely impacts small ruminants, resulting in a notable reduction in animal productivity. In the current investigation, we developed a nanovaccine by encapsulating the recombinant protein rHcES-15, sourced from the excretory/secretory products of H. contortus, within biodegradable poly (D, L-lactide-co-glycolide) (PLGA) nanoparticles (NPs). The development of this nanovaccine involved the formulation of PLGA NPs using a modified double emulsion solvent evaporation technique. Scanning electron microscopy (SEM)verified the successful encapsulation of rHcES-15 within PLGA NPs, exhibiting a size range of 350-400 nm. The encapsulation efficiency (EE) of the antigen in the nanovaccine was determined to be 72%. A total of forty experimental mice were allocated into five groups, with the nanovaccine administered on day 0 and the mice euthanized at the end of the 14-day trial. The stimulation index (SI) from the mice subjected to the nanovaccine indicated heightened lymphocyte proliferation (*** p < 0.001) and a noteworthy increase in anti-inflammatory cytokines (IL-4, IL-10, and IL-17). Additionally, the percentages of T-cells (CD4+, CD8+) and dendritic cell phenotypes (CD83+, CD86+) were significantly elevated (** p < 0.01, *** p < 0.001) in mice inoculated with the nanovaccine compared to control groups and the rHcES-15 group. Correspondingly, higher levels of antigen-specific serum immunoglobulins (IgG1, IgG2a, IgM) were observed in response to the nanovaccine in comparison to both the antigenic (rHcES-15) and control groups (* p < 0.05, ** p < 0.01). In conclusion, the data strongly supports the proposal that the encapsulation of rHcES-15 within PLGA NPs effectively triggers immune cells in vivo, ultimately enhancing the antigen-specific adaptive immune responses against H. contortus. This finding underscores the promising potential of the nanovaccine, justifying further investigations to definitively ascertain its efficacy.
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Affiliation(s)
- Muhammad Waqqas Hasan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Muhammad Ehsan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
- Department of Parasitology, Faculty of Veterinary and Animal Sciences, The Islamia University of Bahawalpur, Punjab 63100, Pakistan
| | - Qiangqiang Wang
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Muhammad Haseeb
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Shakeel Ahmed Lakho
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Ali Haider
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Mingmin Lu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Lixin Xu
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Xiaokai Song
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Ruofeng Yan
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
| | - Xiangrui Li
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210095, China; (M.W.H.); (M.E.); (Q.W.); (M.H.); (S.A.L.); (A.H.); (M.L.); (L.X.); (X.S.)
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Zheng Y, Young ND, Song J, Gasser RB. Genome-Wide Analysis of Haemonchus contortus Proteases and Protease Inhibitors Using Advanced Informatics Provides Insights into Parasite Biology and Host-Parasite Interactions. Int J Mol Sci 2023; 24:12320. [PMID: 37569696 PMCID: PMC10418638 DOI: 10.3390/ijms241512320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/24/2023] [Accepted: 07/24/2023] [Indexed: 08/13/2023] Open
Abstract
Biodiversity within the animal kingdom is associated with extensive molecular diversity. The expansion of genomic, transcriptomic and proteomic data sets for invertebrate groups and species with unique biological traits necessitates reliable in silico tools for the accurate identification and annotation of molecules and molecular groups. However, conventional tools are inadequate for lesser-known organismal groups, such as eukaryotic pathogens (parasites), so that improved approaches are urgently needed. Here, we established a combined sequence- and structure-based workflow system to harness well-curated publicly available data sets and resources to identify, classify and annotate proteases and protease inhibitors of a highly pathogenic parasitic roundworm (nematode) of global relevance, called Haemonchus contortus (barber's pole worm). This workflow performed markedly better than conventional, sequence-based classification and annotation alone and allowed the first genome-wide characterisation of protease and protease inhibitor genes and gene products in this worm. In total, we identified 790 genes encoding 860 proteases and protease inhibitors representing 83 gene families. The proteins inferred included 280 metallo-, 145 cysteine, 142 serine, 121 aspartic and 81 "mixed" proteases as well as 91 protease inhibitors, all of which had marked physicochemical diversity and inferred involvements in >400 biological processes or pathways. A detailed investigation revealed a remarkable expansion of some protease or inhibitor gene families, which are likely linked to parasitism (e.g., host-parasite interactions, immunomodulation and blood-feeding) and exhibit stage- or sex-specific transcription profiles. This investigation provides a solid foundation for detailed explorations of the structures and functions of proteases and protease inhibitors of H. contortus and related nematodes, and it could assist in the discovery of new drug or vaccine targets against infections or diseases.
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Affiliation(s)
- Yuanting Zheng
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Neil D. Young
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
| | - Jiangning Song
- Department of Data Science and AI, Faculty of IT, Monash University, Melbourne, VIC 3800, Australia;
- Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, Melbourne, VIC 3800, Australia
- Monash Data Futures Institute, Monash University, Melbourne, VIC 3800, Australia
| | - Robin B. Gasser
- Melbourne Veterinary School, Faculty of Science, The University of Melbourne, Parkville, VIC 3010, Australia;
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