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Ruuskanen S. Early-life environmental effects on birds: epigenetics and microbiome as mechanisms underlying long-lasting phenotypic changes. J Exp Biol 2024; 227:jeb246024. [PMID: 38449325 DOI: 10.1242/jeb.246024] [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] [Indexed: 03/08/2024]
Abstract
Although the long-lasting effects of variation in early-life environment have been well documented across organisms, the underlying causal mechanisms are only recently starting to be unraveled. Yet understanding the underlying mechanisms of long-lasting effects can help us predict how organisms will respond to changing environments. Birds offer a great system in which to study developmental plasticity and its underlying mechanisms owing to the production of large external eggs and variation in developmental trajectories, combined with a long tradition of applied, physiological, ecological and evolutionary research. Epigenetic changes (such as DNA methylation) have been suggested to be a key mechanism mediating long-lasting effects of the early-life environment across taxa. More recently, changes in the early-life gut microbiome have been identified as another potential mediator of developmental plasticity. As a first step in understanding whether these mechanisms contribute to developmental plasticity in birds, this Review summarizes how changes in early-life environment (both prenatal and postnatal) influence epigenetic markers and the gut microbiome. The literature shows how both early-life biotic (such as resources and social environment) and abiotic (thermal environment and various anthropogenic stressors) factors modify epigenetic markers and the gut microbiome in birds, yet data concerning many other environmental factors are limited. The causal links of these modifications to lasting phenotypic changes are still scarce, but changes in the hypothalamic-pituitary-adrenal axis have been identified as one putative pathway. This Review identifies several knowledge gaps, including data on the long-term effects, stability of the molecular changes, and lack of diversity in the systems studied, and provides directions for future research.
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Affiliation(s)
- Suvi Ruuskanen
- Department of Biological and Environmental Science, University of Jyväskylä, Survontie 9C, 40500 Jyväskylä, Finland
- Department of Biology, University of Turku, Vesilinnankatu 5, 20500 Turku, Finland
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2
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Wang Y, Saelao P, Chanthavixay G, Gallardo RA, Wolc A, Fulton JE, Dekkers JM, Lamont SJ, Kelly TR, Zhou H. Genomic Regions and Candidate Genes Affecting Response to Heat Stress with Newcastle Virus Infection in Commercial Layer Chicks Using Chicken 600K Single Nucleotide Polymorphism Array. Int J Mol Sci 2024; 25:2640. [PMID: 38473888 DOI: 10.3390/ijms25052640] [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: 02/03/2024] [Revised: 02/19/2024] [Accepted: 02/22/2024] [Indexed: 03/14/2024] Open
Abstract
Heat stress results in significant economic losses to the poultry industry. Genetics plays an important role in chickens adapting to the warm environment. Physiological parameters such as hematochemical parameters change in response to heat stress in chickens. To explore the genetics of heat stress resilience in chickens, a genome-wide association study (GWAS) was conducted using Hy-Line Brown layer chicks subjected to either high ambient temperature or combined high temperature and Newcastle disease virus infection. Hematochemical parameters were measured during three treatment phases: acute heat stress, chronic heat stress, and chronic heat stress combined with NDV infection. Significant changes in blood parameters were recorded for 11 parameters (sodium (Na+, potassium (K+), ionized calcium (iCa2+), glucose (Glu), pH, carbon dioxide partial pressure (PCO2), oxygen partial pressure (PO2), total carbon dioxide (TCO2), bicarbonate (HCO3), base excess (BE), and oxygen saturation (sO2)) across the three treatments. The GWAS revealed 39 significant SNPs (p < 0.05) for seven parameters, located on Gallus gallus chromosomes (GGA) 1, 3, 4, 6, 11, and 12. The significant genomic regions were further investigated to examine if the genes within the regions were associated with the corresponding traits under heat stress. A candidate gene list including genes in the identified genomic regions that were also differentially expressed in chicken tissues under heat stress was generated. Understanding the correlation between genetic variants and resilience to heat stress is an important step towards improving heat tolerance in poultry.
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Affiliation(s)
- Ying Wang
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Perot Saelao
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
- Veterinary Pest Genetics Research Unit, United States Department of Agriculture U, Kerrville, TX 78006, USA
| | - Ganrea Chanthavixay
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
| | - Rodrigo A Gallardo
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Anna Wolc
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
- Hy-Line International, Dallas Center, IA 50063, USA
| | | | - Jack M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA 50011, USA
| | - Terra R Kelly
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- School of Veterinary Medicine, University of California, Davis, CA 95616, USA
| | - Huaijun Zhou
- Genomics to Improve Poultry Innovation Lab, University of California, Davis, CA 95616, USA
- Department of Animal Science, University of California, Davis, CA 95616, USA
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3
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Juiputta J, Chankitisakul V, Boonkum W. Appropriate Genetic Approaches for Heat Tolerance and Maintaining Good Productivity in Tropical Poultry Production: A Review. Vet Sci 2023; 10:591. [PMID: 37888543 PMCID: PMC10611393 DOI: 10.3390/vetsci10100591] [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: 08/14/2023] [Revised: 09/16/2023] [Accepted: 09/22/2023] [Indexed: 10/28/2023] Open
Abstract
Heat stress is a major environmental threat to poultry production systems, especially in tropical areas. The effects of heat stress have been discovered in several areas, including reduced growth rate, reduced egg production, low feed efficiency, impaired immunological responses, changes in intestinal microflora, metabolic changes, and deterioration of meat quality. Although several methods have been used to address the heat stress problem, it persists. The answer to this problem can be remedied sustainably if genetic improvement approaches are available. Therefore, the purpose of this review article was to present the application of different approaches to genetic improvement in poultry in the hope that users will find suitable solutions for their poultry population and be able to plan future poultry breeding programs.
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Affiliation(s)
- Jiraporn Juiputta
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (J.J.); (V.C.)
- Network Center for Animal Breeding and Omics Research, Khon Kaen University, Khon Kaen 40002, Thailand
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4
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Pan Z, Wang Y, Wang M, Wang Y, Zhu X, Gu S, Zhong C, An L, Shan M, Damas J, Halstead MM, Guan D, Trakooljul N, Wimmers K, Bi Y, Wu S, Delany ME, Bai X, Cheng HH, Sun C, Yang N, Hu X, Lewin HA, Fang L, Zhou H. An atlas of regulatory elements in chicken: A resource for chicken genetics and genomics. SCIENCE ADVANCES 2023; 9:eade1204. [PMID: 37134160 PMCID: PMC10156120 DOI: 10.1126/sciadv.ade1204] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
A comprehensive characterization of regulatory elements in the chicken genome across tissues will have substantial impacts on both fundamental and applied research. Here, we systematically identified and characterized regulatory elements in the chicken genome by integrating 377 genome-wide sequencing datasets from 23 adult tissues. In total, we annotated 1.57 million regulatory elements, representing 15 distinct chromatin states, and predicted about 1.2 million enhancer-gene pairs and 7662 super-enhancers. This functional annotation of the chicken genome should have wide utility on identifying regulatory elements accounting for gene regulation underlying domestication, selection, and complex trait regulation, which we explored. In short, this comprehensive atlas of regulatory elements provides the scientific community with a valuable resource for chicken genetics and genomics.
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Affiliation(s)
- Zhangyuan Pan
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mingshan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650000, China
| | - Yuzhe Wang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaoning Zhu
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100193, China
| | - Shenwen Gu
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Conghao Zhong
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Liqi An
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mingzhu Shan
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Joana Damas
- The Genome Center, University of California, Davis, CA 95616, USA
| | - Michelle M Halstead
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Dailu Guan
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Nares Trakooljul
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Klaus Wimmers
- Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
| | - Ye Bi
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Shang Wu
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Mary E Delany
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Xuechen Bai
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
| | - Hans H Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI 48823, USA
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, China Agricultural University, Beijing 100193, China
| | - Xiaoxiang Hu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650000, China
| | - Harris A Lewin
- The Genome Center, University of California, Davis, CA 95616, USA
- Department of Evolution and Ecology, University of California, Davis, CA 95616, USA
| | - Lingzhao Fang
- Center for Quantitative Genetics and Genomics, Aarhus University, Aarhus, 8000, DK
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, The University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis 95616, CA, USA
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Chu Z, Yang S, Li Q, Shang J, Ren Z, Ren F. The V protein in oncolytic Newcastle disease virus promotes HepG2 hepatoma cell proliferation at the single-cell level. BMC Cancer 2023; 23:346. [PMID: 37069523 PMCID: PMC10108501 DOI: 10.1186/s12885-023-10815-4] [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: 07/23/2022] [Accepted: 04/06/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND Newcastle disease virus (NDV) is an oncolytic virus that can inhibit cancer cell proliferation and kill cancer cells. The NDV nonstructural V protein can regulate viral replication; however, whether the V protein contributes to NDV oncolysis is unclear. RESULTS This study revealed that NDV inhibited tumor cell proliferation and that V protein expression promoted the proliferation of HepG2 cells, as determined at the single-cell level. In addition, to identify the regulatory mechanism of the V protein in HepG2 cells, transcriptome sequencing was performed and indicated that the expression/activation of multiple cell proliferation-related genes/signaling pathways were changed in cells overexpressing the V protein. Hence, the MAPK and WNT signaling pathways were selected for verification, and after blocking these two signaling pathways with inhibitors, the V protein promotion of cell proliferation was found to be attenuated. CONCLUSIONS The results showed that the V protein regulated the proliferation of cancer cells through multiple signaling pathways, providing valuable references for future studies on the mechanism by which the V protein regulates cancer cell proliferation.
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Affiliation(s)
- Zhili Chu
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China.
- Henan International Joint Laboratory of Immunity and Targeted Therapy for liver-intestinal Tumors, Xinxiang Medical University, Xinxiang, China.
| | - Sihui Yang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Qianru Li
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Jianing Shang
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Zilong Ren
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China
| | - Feng Ren
- Xinxiang Key Laboratory of Pathogenic Biology, Department of Pathogenic Biology, School of Basic Medical Sciences, Xinxiang Medical University, Xinxiang, China.
- Henan International Joint Laboratory of Immunity and Targeted Therapy for liver-intestinal Tumors, Xinxiang Medical University, Xinxiang, China.
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6
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Uyanga VA, Musa TH, Oke OE, Zhao J, Wang X, Jiao H, Onagbesan OM, Lin H. Global trends and research frontiers on heat stress in poultry from 2000 to 2021: A bibliometric analysis. Front Physiol 2023; 14:1123582. [PMID: 36824469 PMCID: PMC9941544 DOI: 10.3389/fphys.2023.1123582] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 01/23/2023] [Indexed: 02/09/2023] Open
Abstract
Background: Heat stress remains a major environmental factor affecting poultry production. With growing concerns surrounding climate change and its antecedent of global warming, research on heat stress in poultry has gradually gained increased attention. Therefore, this study aimed to examine the current status, identify the research frontiers, and highlight the research trends on heat stress in poultry research using bibliometric analysis. Methods: The literature search was performed on the Web of Science Core Collection database for documents published from 2000 to 2021. The documents retrieved were analyzed for their publication counts, countries, institutions, keywords, sources, funding, and citation records using the bibliometric app on R software. Network analysis for co-authorship, co-occurrence, citation, co-citation, and bibliographic coupling was visualized using the VOSviewer software. Results: A total of 468 publications were retrieved, and over the past two decades, there was a gradual increase in the annual number of publications (average growth rate: 4.56%). China had the highest contribution with respect to the number of publications, top contributing authors, collaborations, funding agencies, and institutions. Nanjing Agricultural University, China was the most prolific institution. Kazim Sahin from Firat University, Turkey contributed the highest number of publications and citations to heat stress in poultry research, and Poultry Science was the most productive and the most cited journal. The top 10 globally cited documents mainly focused on the effects of heat stress, alleviation of heat stress, and the association between heat stress and oxidative stress in poultry. All keywords were grouped into six clusters which included studies on "growth performance", "intestinal morphology", "heat stress", "immune response", "meat quality", and "oxidative stress" as current research hotspots. In addition, topics such as; "antioxidants", "microflora", "intestinal barrier", "rna-seq", "animal welfare", "gene expression", "probiotics", "feed restriction", and "inflammatory pathways" were identified for future research attention. Conclusion: This bibliometric study provides a detailed and comprehensive analysis of the global research trends on heat stress in poultry over the last two decades, and it is expected to serve as a useful reference for potential research that will help address the impacts of heat stress on poultry production globally.
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Affiliation(s)
- Victoria Anthony Uyanga
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China,*Correspondence: Victoria Anthony Uyanga, ; Hai Lin,
| | - Taha H. Musa
- Biomedical Research Institute, Darfur University College, Nyala, Sudan
| | - Oyegunle Emmanuel Oke
- Department of Animal Physiology, Federal University of Agriculture, Abeokuta, Nigeria
| | - Jingpeng Zhao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China
| | - Xiaojuan Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China
| | - Hongchao Jiao
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China
| | | | - Hai Lin
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Key Laboratory of Efficient Utilization of Non-Grain Feed Resources (Co-Construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Shandong Agricultural University, Tai’an, China,*Correspondence: Victoria Anthony Uyanga, ; Hai Lin,
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7
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Dehau T, Ducatelle R, Immerseel FV, Goossens E. Omics technologies in poultry health and productivity - part 1: current use in poultry research. Avian Pathol 2022; 51:407-417. [PMID: 35675291 DOI: 10.1080/03079457.2022.2086447] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
In biology, molecular terms with the suffix "-omics" refer to disciplines aiming at the collective characterization of pools of molecules derived from different layers (DNA, RNA, proteins, metabolites) of living organisms using high-throughput technologies. Such omics analyses have been widely implemented in poultry research in recent years. This first part of a bipartite review on omics technologies in poultry health and productivity examines the use of multiple omics and multi-omics techniques in poultry research. More specific present and future applications of omics technologies, not only for the identification of specific diagnostic biomarkers, but also for potential future integration in the daily monitoring of poultry production, are discussed in part 2. Approaches based on omics technologies are particularly used in poultry research in the hunt for genetic markers of economically important phenotypical traits in the host, and in the identification of key bacterial species or functions in the intestinal microbiome. Integrative multi-omics analyses, however, are still scarce. Host physiology is investigated via genomics together with transcriptomics, proteomics and metabolomics techniques, to understand more accurately complex production traits such as disease resistance and fertility. The gut microbiota, as a key player in chicken productivity and health, is also a main subject of such studies, investigating the association between its composition (16S rRNA gene sequencing) or function (metagenomics, metatranscriptomics, metaproteomics, metabolomics) and host phenotypes. Applications of these technologies in the study of other host-associated microbiota and other host characteristics are still in their infancy.
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Affiliation(s)
- Tessa Dehau
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Richard Ducatelle
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Filip Van Immerseel
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Evy Goossens
- Livestock Gut Health Team (LiGHT) Ghent, Department of Pathobiology, Pharmacology and Zoological Medicine, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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8
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Ibeagha-Awemu EM, Kiefer H, McKay S, Liu GE. Editorial: Epigenetic Variation Influences on Livestock Production and Disease Traits. Front Genet 2022; 13:942747. [PMID: 35783264 PMCID: PMC9241065 DOI: 10.3389/fgene.2022.942747] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/22/2022] Open
Affiliation(s)
- Eveline M. Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, QC, Canada
- *Correspondence: Eveline M. Ibeagha-Awemu,
| | - Hélène Kiefer
- Université Paris-Saclay, UVSQ, INRAE, BREED, Jouy-en-Josas, France
- Ecole Nationale Vétérinaire d’Alfort, BREED, Maisons-Alfort, France
| | - Stephanie McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, United States
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, United States Department of Agriculture, Beltsville, MD, United States
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9
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Gospel of malignant Glioma: Oncolytic virus therapy. Gene 2022; 818:146217. [PMID: 35093451 DOI: 10.1016/j.gene.2022.146217] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 12/09/2021] [Accepted: 01/13/2022] [Indexed: 12/12/2022]
Abstract
Glioma accounts for nearly 80% of all intracranial malignant tumors. It is a major challenge to society as it is causes to impaired brain function in many patients. Currently, gliomas are mainly treated with surgery, postoperative radiotherapy, and chemotherapy. However, the curative effects of these treatments are not satisfactory. Oncolytic virus (OV) is a novel treatment which works by activating the immune functions and inducing apoptosis of tumor cells. The OV propagates indefinitely in the host cell, eventually leading to the death of host cell. Subsequently, a large number of antigens and signal molecules are released which exert antitumor immunity. Several preclinical and clinical studies have shown that G207, DNX2401, Zika and other viruses have important roles in malignant tumors. For example, these viruses can reduce the growth of tumor cells without causing severe complications. However, the known OVs have not been clearly classified. Herein, we divided OVs into neurotropic and non-neurophilic OVs based on whether the OVs are naturally neurotropic or not. The therapeutic effects of each group were compared. Finally, challenges encountered in the clinical application of OVs in the treatment of malignant gliomas were summarized.
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10
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Dunislawska A, Pietrzak E, Wishna Kadawarage R, Beldowska A, Siwek M. Pre-hatching and post-hatching environmental factors related to epigenetic mechanisms in poultry. J Anim Sci 2021; 100:6473202. [PMID: 34932113 DOI: 10.1093/jas/skab370] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Epigenetic modifications are phenotypic changes unrelated to the modification of the DNA sequence. These modifications are essential for regulating cellular differentiation and organism development. In this case, epigenetics controls how the animal's genetic potential is used. The main epigenetic mechanisms are microRNA activity, DNA methylation and histone modification. The literature has repeatedly shown that environmental modulation has a significant influence on the regulation of epigenetic mechanisms in poultry. The aim of this review is to give an overview of the current state of the knowledge in poultry epigenetics in terms of issues relevant to overall poultry production and the improvement of the health status in chickens and other poultry species. One of the main differences between birds and mammals is the stage of embryonic development. The bird's embryo develops outside its mother, so an optimal environment of egg incubation before hatching is crucial for development. It is also the moment when many factors influence the activation of epigenetic mechanisms, i.e., incubation temperature, humidity, light, as well as in ovo treatments. Epigenome of the adult birds, might be modulated by: nutrition, supplementation and treatment, as well as modification of the intestinal microbiota. In addition, the activation of epigenetic mechanisms is influenced by pathogens (i.e., pathogenic bacteria, toxins, viruses and fungi) as well as, the maintenance conditions. Farm animal epigenetics is still a big challenge for scientists. This is a research area with many open questions. Modern methods of epigenetic analysis can serve both in the analysis of biological mechanisms and in the research and applied to production system, poultry health and welfare.
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Affiliation(s)
- A Dunislawska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - E Pietrzak
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - R Wishna Kadawarage
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - A Beldowska
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
| | - M Siwek
- Department of Animal Biotechnology and Genetics, Bydgoszcz University of Science and Technology, Mazowiecka , Bydgoszcz, Poland
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11
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Ibeagha-Awemu EM, Yu Y. Consequence of epigenetic processes on animal health and productivity: is additional level of regulation of relevance? Anim Front 2021; 11:7-18. [PMID: 34934525 PMCID: PMC8683131 DOI: 10.1093/af/vfab057] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec, Canada
| | - Ying Yu
- Department of Animal Breeding and Genetics, College of Animal Sciences and Technology, China Agricultural University, Beijing, China
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12
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MacPhillamy C, Pitchford WS, Alinejad-Rokny H, Low WY. Opportunity to improve livestock traits using 3D genomics. Anim Genet 2021; 52:785-798. [PMID: 34494283 DOI: 10.1111/age.13135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/24/2021] [Indexed: 11/30/2022]
Abstract
The advent of high-throughput chromosome conformation capture and sequencing (Hi-C) has enabled researchers to probe the 3D architecture of the mammalian genome in a genome-wide manner. Simultaneously, advances in epigenomic assays, such as chromatin immunoprecipitation and sequencing (ChIP-seq) and DNase-seq, have enabled researchers to study cis-regulatory interactions and chromatin accessibility across the same genome-wide scale. The use of these data has revealed many unique insights into gene regulation and disease pathomechanisms in several model organisms. With the advent of these high-throughput sequencing technologies, there has been an ever-increasing number of datasets available for study; however, this is often limited to model organisms. Livestock species play critical roles in the economies of developing and developed nations alike. Despite this, they are greatly underrepresented in the 3D genomics space; Hi-C and related technologies have the potential to revolutionise livestock breeding by enabling a more comprehensive understanding of how production traits are controlled. The growth in human and model organism Hi-C data has seen a surge in the availability of computational tools for use in 3D genomics, with some tools using machine learning techniques to predict features and improve dataset quality. In this review, we provide an overview of the 3D genome and discuss the status of 3D genomics in livestock before delving into advancing the field by drawing inspiration from research in human and mouse. We end by offering future directions for livestock research in the field of 3D genomics.
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Affiliation(s)
- C MacPhillamy
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - W S Pitchford
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
| | - H Alinejad-Rokny
- Biological & Medical Machine Learning Lab, The Graduate School of Biomedical Engineering, UNSW Sydney, Sydney, NSW, 2052, Australia.,School of Computer Science and Engineering, The University of New South Wales (UNSW Sydney), Sydney, NSW, 2052, Australia
| | - W Y Low
- Davies Livestock Research Centre, The University of Adelaide, Roseworthy Campus, Mudla Wirra Rd, Roseworthy, SA, 5371, Australia
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Wang M, Ibeagha-Awemu EM. Impacts of Epigenetic Processes on the Health and Productivity of Livestock. Front Genet 2021; 11:613636. [PMID: 33708235 PMCID: PMC7942785 DOI: 10.3389/fgene.2020.613636] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 12/21/2020] [Indexed: 12/23/2022] Open
Abstract
The dynamic changes in the epigenome resulting from the intricate interactions of genetic and environmental factors play crucial roles in individual growth and development. Numerous studies in plants, rodents, and humans have provided evidence of the regulatory roles of epigenetic processes in health and disease. There is increasing pressure to increase livestock production in light of increasing food needs of an expanding human population and environment challenges, but there is limited related epigenetic data on livestock to complement genomic information and support advances in improvement breeding and health management. This review examines the recent discoveries on epigenetic processes due to DNA methylation, histone modification, and chromatin remodeling and their impacts on health and production traits in farm animals, including bovine, swine, sheep, goat, and poultry species. Most of the reports focused on epigenome profiling at the genome-wide or specific genic regions in response to developmental processes, environmental stressors, nutrition, and disease pathogens. The bulk of available data mainly characterized the epigenetic markers in tissues/organs or in relation to traits and detection of epigenetic regulatory mechanisms underlying livestock phenotype diversity. However, available data is inadequate to support gainful exploitation of epigenetic processes for improved animal health and productivity management. Increased research effort, which is vital to elucidate how epigenetic mechanisms affect the health and productivity of livestock, is currently limited due to several factors including lack of adequate analytical tools. In this review, we (1) summarize available evidence of the impacts of epigenetic processes on livestock production and health traits, (2) discuss the application of epigenetics data in livestock production, and (3) present gaps in livestock epigenetics research. Knowledge of the epigenetic factors influencing livestock health and productivity is vital for the management and improvement of livestock productivity.
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Affiliation(s)
- Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
- Department of Animal Science, Laval University, Quebec, QC, Canada
| | - Eveline M. Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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