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Yuan F, Yang L, Hsiao SH, Herndon NL, Gaulke CA, Fang Y. A neonatal piglet model reveals interactions between nasal microbiota and influenza A virus pathogenesis. Virology 2024; 592:109996. [PMID: 38301448 DOI: 10.1016/j.virol.2024.109996] [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: 09/12/2023] [Revised: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 02/03/2024]
Abstract
While vaccination and therapeutics for prevention/treatment of influenza are available, new strategies are needed to combat influenza disease in susceptible populations, particularly young children and newborns. Host associated microbiota play an important role in modulating the virulence of numerous pathogens, including the influenza A virus. In this study, we examined microbiome-influenza interactions in a neonatal piglet model system. The nasal microbiome of newborn piglets was longitudinally sampled before and after intranasal infection with recombinant viruses expressing hemagglutinins (HAs) derived from distinct zoonotic H1 subtypes. We found that viruses expressing different parental HAs manifested unique patterns of pathogenicity, and varied impacts on microbial community diversity. Despite these virus specific differences, a consistent microbial signature of viral infection was detected. Our results indicate that influenza A virus infection associates with the restructuring of nasal microbiome and such shifts in microbial diversity may contribute to outcomes of viral infection in neonatal piglets.
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Affiliation(s)
- Fangfeng Yuan
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA
| | - Lufan Yang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA
| | - Shih-Hsuan Hsiao
- Veterinary Diagnostic Laboratory, Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Nicole L Herndon
- Department of Veterinary Clinical Medicine, College of Veterinary Medicine, University of Illinois at Urbana-Champaign, Urbana, IL, 61802, USA
| | - Christopher A Gaulke
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Personalized Nutrition Initiative, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Cancer Center at Illinois, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA.
| | - Ying Fang
- Department of Pathobiology, College of Veterinary Medicine, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA; Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana Champaign, Urbana, IL, 61802, USA.
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Hubert JN, Perret M, Riquet J, Demars J. Livestock species as emerging models for genomic imprinting. Front Cell Dev Biol 2024; 12:1348036. [PMID: 38500688 PMCID: PMC10945557 DOI: 10.3389/fcell.2024.1348036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Accepted: 01/19/2024] [Indexed: 03/20/2024] Open
Abstract
Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.
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Affiliation(s)
| | | | | | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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3
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De Windt S, Kourta D, Kanbar M, Wyns C. Optimized Recovery of Immature Germ Cells after Prepubertal Testicular Tissue Digestion and Multi-Step Differential Plating: A Step towards Fertility Restoration with Cancer-Cell-Contaminated Tissue. Int J Mol Sci 2023; 25:521. [PMID: 38203691 PMCID: PMC10779385 DOI: 10.3390/ijms25010521] [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: 10/25/2023] [Revised: 12/19/2023] [Accepted: 12/28/2023] [Indexed: 01/12/2024] Open
Abstract
Undifferentiated germ cells, including the spermatogonial stem cell subpopulation required for fertility restoration using human immature testicular tissue (ITT), are difficult to recover as they do not easily adhere to plastics. Due to the scarcity of human ITT for research, we used neonatal porcine ITT. Strategies for maximizing germ cell recovery, including a comparison of two enzymatic digestion protocols (P1 and P2) of ITT fragment sizes (4 mm3 and 8 mm3) and multi-step differential plating were explored. Cellular viability and yield, as well as numbers and proportions of DDX4+ germ cells, were assessed before incubating the cell suspensions overnight on uncoated plastics. Adherent cells were processed for immunocytochemistry (ICC) and floating cells were further incubated for three days on Poly-D-Lysine-coated plastics. Germ cell yield and cell types using ICC for SOX9, DDX4, ACTA2 and CYP19A1 were assessed at each step of the multi-step differential plating. Directly after digestion, cell suspensions contained >92% viable cells and 4.51% DDX4+ germ cells. Pooled results for fragment sizes revealed that the majority of DDX4+ cells adhere to uncoated plastics (P1; 82.36% vs. P2; 58.24%). Further incubation on Poly-D-Lysine-coated plastics increased germ cell recovery (4.80 ± 11.32 vs. 1.90 ± 2.07 DDX4+ germ cells/mm2, respectively for P1 and P2). The total proportion of DDX4+ germ cells after the complete multi-step differential plating was 3.12%. These results highlight a reduced proportion and number of germ cells lost when compared to data reported with other methods, suggesting that multi-step differential plating should be considered for optimization of immature germ cell recovery. While Poly-D-Lysine-coating increased the proportions of recovered germ cells by 16.18% (P1) and 28.98% (P2), future studies should now focus on less cell stress-inducing enzymatic digestion protocols to maximize the chances of fertility restoration with low amounts of cryo-banked human ITT.
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Affiliation(s)
- Sven De Windt
- Laboratoire d’andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (S.D.W.); (D.K.); (M.K.)
| | - Dhoha Kourta
- Laboratoire d’andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (S.D.W.); (D.K.); (M.K.)
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Marc Kanbar
- Laboratoire d’andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (S.D.W.); (D.K.); (M.K.)
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
| | - Christine Wyns
- Laboratoire d’andrologie, Pôle de Recherche en Physiologie de la Reproduction, Institut de Recherche Expérimentale et Clinique (IREC), Université Catholique de Louvain, 1200 Brussels, Belgium; (S.D.W.); (D.K.); (M.K.)
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium
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Nonneman DJ, Lents CA. Functional genomics of reproduction in pigs: Are we there yet? Mol Reprod Dev 2023; 90:436-444. [PMID: 35704517 DOI: 10.1002/mrd.23625] [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: 03/01/2022] [Revised: 05/26/2022] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
Reproductive failure is the main reason for culling females in swine herds and is both a financial and sustainability issue. Because reproductive traits are complex and lowly to moderately heritable, genomic selection within populations can achieve substantial genetic gain in reproductive efficiency. A better understanding of the physiological components affecting the expression of these traits will facilitate greater understanding of the genes affecting reproductive traits and is necessary to improve and optimize management strategies to maximize reproductive success of gilts and sows. Large-scale genotyping with single-nucleotide polymorphism (SNP) arrays are used for genome-wide association studies (GWAS) and have facilitated identification of positional candidate genes. Transcriptomic data can be used to weight SNP for GWAS and could lead to previously unidentified candidate genes. Resequencing and fine mapping of candidate genes are necessary to identify putative functional variants and some of these have been incorporated into new genotyping arrays. Sequence imputation and genotype by sequence are newer strategies that could reveal novel functional mutations. In this study, these approaches are discussed. Advantages and limitations are highlighted where additional research is needed.
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Affiliation(s)
- Dan J Nonneman
- United States Department of Agriculture, Agriculture Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
| | - Clay A Lents
- United States Department of Agriculture, Agriculture Research Service, U.S. Meat Animal Research Center, Clay Center, Nebraska, USA
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Wijesinghe P, Sastry A, Hui E, Cogan TA, Zheng B, Ho G, Kakal J, Nunez DA. Adult porcine (Sus scrofa) derived inner ear cells: Characteristics in in-vitro cultures. Anat Rec (Hoboken) 2023. [PMID: 36598271 DOI: 10.1002/ar.25149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 11/21/2022] [Accepted: 12/10/2022] [Indexed: 01/05/2023]
Abstract
There is a need for an animal model that closely parallels human cochlea gestational development. This study aims to document porcine inner ear anatomy, and in vitro porcine derived inner ear cell culture characteristics. Twenty-four temporal bone were harvested from 12 adult pigs (Sus scrofa). Six were formalin fixed and their maximal diameters were measured. The cochlea duct length was determined by the insertion length of a Nucleus 22 cochlear implant in two bones. Four formalin fixed bones were sectioned for histology. Cochlear and vestibular tissues were harvested from non-fixed bones, cultured and characterized at different passages (P). Gene and protein expression of multipotent stem/progenitor (Nestin and Sox2), inner ear hair (Myosin VIIa, Prestin) and supporting (Cytokeratin 18 and Vimentin) cell markers were determined. The porcine cochlea was a 3.5 turn spiral. There was a separate vestibular compartment. The cochlear mean maximal diameter and height was 7.99 and 3.77 mm, respectively. Sphere forming cells were identified on phase-contrast microscopy. The relative mRNA expression levels of KRT18, MYO7A and SLC26A5 were significantly positively correlated in cochlear cultures; and MYO7A and SLC26A5; SOX2 and KRT18; NES and SLC26A5 genes were positively correlated in vestibular cultures (p = .037, Spearman correlation [τ] = .900). Inner ear sensory and stem cell characteristics persist in passaged porcine inner ear cells. Further work is required to establish the usefulness of porcine inner ear cell cultures to the study of human inner ear disorders.
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Affiliation(s)
- Printha Wijesinghe
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Anand Sastry
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Elizabeth Hui
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Tristan A Cogan
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Boyuan Zheng
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Germain Ho
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Juzer Kakal
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
| | - Desmond A Nunez
- Division of Otolaryngology, Department of Surgery, University of British Columbia, Vancouver, British Columbia, Canada
- Vancouver Coastal Health Research Institute, Vancouver, British Columbia, Canada
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Lowe JWE. Humanising and dehumanising pigs in genomic and transplantation research. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:66. [PMID: 36417007 PMCID: PMC9684229 DOI: 10.1007/s40656-022-00545-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biologists who work on the pig (Sus scrofa) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to 'humanise' donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that 'humanise' the pig (or representations thereof) through using resources from human genomics, and the need to 'dehumanise' the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this.
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Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
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Bergmann T, Liu Y, Skov J, Mogus L, Lee J, Pfisterer U, Handfield LF, Asenjo-Martinez A, Lisa-Vargas I, Seemann SE, Lee JTH, Patikas N, Kornum BR, Denham M, Hyttel P, Witter MP, Gorodkin J, Pers TH, Hemberg M, Khodosevich K, Hall VJ. Production of human entorhinal stellate cell-like cells by forward programming shows an important role of Foxp1 in reprogramming. Front Cell Dev Biol 2022; 10:976549. [PMID: 36046338 PMCID: PMC9420913 DOI: 10.3389/fcell.2022.976549] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Stellate cells are principal neurons in the entorhinal cortex that contribute to spatial processing. They also play a role in the context of Alzheimer's disease as they accumulate Amyloid beta early in the disease. Producing human stellate cells from pluripotent stem cells would allow researchers to study early mechanisms of Alzheimer's disease, however, no protocols currently exist for producing such cells. In order to develop novel stem cell protocols, we characterize at high resolution the development of the porcine medial entorhinal cortex by tracing neuronal and glial subtypes from mid-gestation to the adult brain to identify the transcriptomic profile of progenitor and adult stellate cells. Importantly, we could confirm the robustness of our data by extracting developmental factors from the identified intermediate stellate cell cluster and implemented these factors to generate putative intermediate stellate cells from human induced pluripotent stem cells. Six transcription factors identified from the stellate cell cluster including RUNX1T1, SOX5, FOXP1, MEF2C, TCF4, EYA2 were overexpressed using a forward programming approach to produce neurons expressing a unique combination of RELN, SATB2, LEF1 and BCL11B observed in stellate cells. Further analyses of the individual transcription factors led to the discovery that FOXP1 is critical in the reprogramming process and omission of RUNX1T1 and EYA2 enhances neuron conversion. Our findings contribute not only to the profiling of cell types within the developing and adult brain's medial entorhinal cortex but also provides proof-of-concept for using scRNAseq data to produce entorhinal intermediate stellate cells from human pluripotent stem cells in-vitro.
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Affiliation(s)
- Tobias Bergmann
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Yong Liu
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jonathan Skov
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Leo Mogus
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Julie Lee
- Novo Nordisk Foundation Center for Stem Cell Research, DanStem University of Copenhagen, Copenhagen, Denmark
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Ulrich Pfisterer
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | | | - Andrea Asenjo-Martinez
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Irene Lisa-Vargas
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Stefan E. Seemann
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Jimmy Tsz Hang Lee
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Nikolaos Patikas
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Birgitte Rahbek Kornum
- Department of Neuroscience, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Mark Denham
- Danish Research Institute of Translational Neuroscience (DANDRITE), Nordic EMBL Partnership for Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Poul Hyttel
- Disease, Stem Cells and Embryology, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Menno P. Witter
- Kavli Institute for Systems Neuroscience, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Jan Gorodkin
- Center for non-coding RNA in Technology and Health, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
| | - Tune H. Pers
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Martin Hemberg
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, United Kingdom
| | - Konstantin Khodosevich
- Biotech Research and Innovation Centre (BRIC), Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Vanessa Jane Hall
- Group of Brain Development and Disease, Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg, Denmark
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Pang WK, Amjad S, Ryu DY, Adegoke EO, Rahman MS, Park YJ, Pang MG. Establishment of a male fertility prediction model with sperm RNA markers in pigs as a translational animal model. J Anim Sci Biotechnol 2022; 13:84. [PMID: 35794675 PMCID: PMC9261079 DOI: 10.1186/s40104-022-00729-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 05/08/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Male infertility is an important issue that causes low production in the animal industry. To solve the male fertility crisis in the animal industry, the prediction of sperm quality is the most important step. Sperm RNA is the potential marker for male fertility prediction. We hypothesized that the expression of functional genes related to fertilization will be the best target for male fertility prediction markers. To investigate optimum male fertility prediction marker, we compared target genes expression level and a wide range of field data acquired from artificial insemination of boar semen. RESULTS Among the genes related to acrosomal vesicle exocytosis and sperm-oocyte fusion, equatorin (EQTN), zona pellucida sperm-binding protein 4 (ZP4), and sperm acrosome membrane-associated protein 3 exhibited high accuracy (70%, 90%, and 70%, respectively) as markers to evaluate male fertility. Combinations of EQTN-ZP4, ZP4-protein unc-13 homolog B, and ZP4-regulating synaptic membrane exocytosis protein 1 (RIMS1) showed the highest prediction value, and all these markers are involved in the acrosome reaction. CONCLUSION The EQTN-ZP4 model was efficient in clustering the high-fertility group and may be useful for selection of animal that has superior fertility in the livestock industry. Compared to the EQTN-ZP4 model, the ZP4-RIMS1 model was more efficient in clustering the low-fertility group and may be useful in the diagnosis of male infertility in humans and other animals. The appointed translational animal model and established biomarker combination can be widely used in various scientific fields such as biomedical science.
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Affiliation(s)
- Won-Ki Pang
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Shehreen Amjad
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Do-Yeal Ryu
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Elikanah Olusayo Adegoke
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Md Saidur Rahman
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Yoo-Jin Park
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Myung-Geol Pang
- Department of Animal Science & Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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Gu W, Madrid DMC, Joyce S, Driver JP. A single-cell analysis of thymopoiesis and thymic iNKT cell development in pigs. Cell Rep 2022; 40:111050. [PMID: 35793622 PMCID: PMC9704770 DOI: 10.1016/j.celrep.2022.111050] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 04/26/2022] [Accepted: 06/13/2022] [Indexed: 12/13/2022] Open
Abstract
Many aspects of the porcine immune system remain poorly characterized, which poses a barrier to improving swine health and utilizing pigs as preclinical models. Here, we employ single-cell RNA sequencing (scRNA-seq) to create a cell atlas of the early-adolescent pig thymus. Our data show conserved features as well as species-specific differences in cell states and cell types compared with human thymocytes. We also describe several unconventional T cell types with gene expression profiles associated with innate effector functions. This includes a cell census of more than 11,000 differentiating invariant natural killer T (iNKT) cells, which reveals that the functional diversity of pig iNKT cells differs substantially from the iNKT0/1/2/17 subset differentiation paradigm established in mice. Our data characterize key differentiation events in porcine thymopoiesis and iNKT cell maturation and provide important insights into pig T cell development.
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Affiliation(s)
- Weihong Gu
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA
| | | | - Sebastian Joyce
- Department of Veterans Affairs, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN 37232, USA; Vanderbilt Institution for Infection, Immunology, and Inflammation, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - John P Driver
- Department of Animal Sciences, University of Florida, Gainesville, FL 32611, USA.
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Pang WK, Son JH, Ryu DY, Rahman MS, Park YJ, Pang MG. Heat shock protein family D member 1 in boar spermatozoa is strongly related to the litter size of inseminated sows. J Anim Sci Biotechnol 2022; 13:42. [PMID: 35422006 PMCID: PMC9012035 DOI: 10.1186/s40104-022-00689-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 02/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background Sperm quality evaluation is the logical first step in increasing field fertility. Spermatozoa contain cytoplasmic organelles and biomolecules known as sperm-intrinsic factors, which play key roles in sperm maturation, sperm-oocyte fusion, and embryo development. In particular, sperm membrane proteins [e.g., arginine vasopressin receptor 2, beta-actin, prohibitin, and heat shock protein family D member 1 (HSPD1)] and RNA could be used as functional indicators of male fertility. We sought to clarify the effects of differential mRNA expression of selected genes on several fertilisation parameters, including sperm motility, motion kinematics, capacitation, and litter size, in a porcine model. Results Our results demonstrated that HSPD1 expression was significantly correlated with male fertility, as measured by the litter size of inseminated sows. The expression of HSPD1 mRNA was linked to sperm motility and other motion kinematic characteristics. Furthermore, HSPD1 had a 66.7% overall accuracy in detecting male fertility, and the high-litter size group which was selected with the HSPD1 marker had a 1.34 greater litter size than the low-litter size group. Conclusions Our findings indicate that HSPD1 might be a helpful biomarker for superior boar selection for artificial insemination, which could boost field fertility. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00689-0.
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Gong Y, Zhang HY, Yuan Y, He Y, Zhang W, Han Y, Na R, Zeng Y, Luo J, Yang H, Huang Y, Zhao Y, Zhao Z, E GX. Genome-Wide Selection Sweep between Wild and Local Pigs from Europe for the Investigation of the Hereditary Characteristics of Domestication in Sus Scrofa. Animals (Basel) 2022; 12:ani12081037. [PMID: 35454283 PMCID: PMC9030587 DOI: 10.3390/ani12081037] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Revised: 02/23/2022] [Accepted: 04/12/2022] [Indexed: 11/16/2022] Open
Abstract
The phenotypic characteristics of existing domestic pigs (DPs) greatly differ from those of wild boar (WB) populations thousands of years ago. After thousands of years of human domestication, WB and DP have diverged greatly in terms of genetics. Theoretically, worldwide local pigs have independent contributions from their local WBs at the beginning of Sus scrofa domestication. The investigation of the vicissitude of the heredity material between domestic populations and their wild ancestors will help in further understanding the domestication history of domestic animals. In the present study, we performed a genome-wide association scan (GWSA) and phylogeny estimation with a total of 1098 public European Illumina 60K single nucleotide polymorphism data, which included 650 local DPs and 448 WBs. The results revealed that the phylogenetic relationship of WBs corresponds to their geographical distribution and carries large divergence with DPs, and all WB breeds (e.g., HRWB, SBWB, and TIWB) presents a closely linkage with the middle WB (e.g., HRWB, and PLWB). In addition, 64 selected candidate genes (e.g., IDH2, PIP5K1B, SMARCA2, KIF5C, and TJP2) were identified from GWSA. A total of 63 known multiple biological functional pathways were annotated by 22 genes, and ubiquinone and other terpenoid-quinone biosynthesis pathways that belong to the metabolism of cofactors and vitamins were significantly enriched (p < 0.05). The most frequent (28.57%) pathways were classified under metabolism. We confirmed that the middle European WB has made an important genetic contribution to the entire European WB populations. A series of selected genes discovered from this study provides the scientific community with a deeper understanding of the heredity performance of metabolism and emotion and the real purpose behind domestication.
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12
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Trott JF, Schennink A, Horigan KC, Lemay DG, Cohen JR, Famula TR, Dragon JA, Hovey RC. Unique Transcriptomic Changes Underlie Hormonal Interactions During Mammary Histomorphogenesis in Female Pigs. Endocrinology 2022; 163:bqab256. [PMID: 34918063 PMCID: PMC10409904 DOI: 10.1210/endocr/bqab256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Indexed: 11/19/2022]
Abstract
Successful lactation and the risk for developing breast cancer depend on growth and differentiation of the mammary gland (MG) epithelium that is regulated by ovarian steroids (17β-estradiol [E] and progesterone [P]) and pituitary-derived prolactin (PRL). Given that the MG of pigs share histomorphogenic features present in the normal human breast, we sought to define the transcriptional responses within the MG of pigs following exposure to all combinations of these hormones. Hormone-ablated female pigs were administered combinations of E, medroxyprogesterone 17-acetate (source of P), and either haloperidol (to induce PRL) or 2-bromo-α-ergocryptine. We subsequently monitored phenotypic changes in the MG including mitosis, receptors for E and P (ESR1 and PGR), level of phosphorylated STAT5 (pSTAT5), and the frequency of terminal ductal lobular unit (TDLU) subtypes; these changes were then associated with all transcriptomic changes. Estrogen altered the expression of approximately 20% of all genes that were mostly associated with mitosis, whereas PRL stimulated elements of fatty acid metabolism and an inflammatory response. Several outcomes, including increased pSTAT5, highlighted the ability of E to enhance PRL action. Regression of transcriptomic changes against several MG phenotypes revealed 1669 genes correlated with proliferation, among which 29 were E inducible. Additional gene expression signatures were associated with TDLU formation and the frequency of ESR1 or PGR. These data provide a link between the hormone-regulated genome and phenome of the MG in a species having a complex histoarchitecture like that in the human breast, and highlight an underexplored synergy between the actions of E and PRL during MG development.
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Affiliation(s)
- Josephine F Trott
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Anke Schennink
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Katherine C Horigan
- Department of Animal Science, University of Vermont, Burlington, Vermont 05405, USA
| | - Danielle G Lemay
- US Department of Agriculture ARS Western Human Nutrition Research Center, Davis, California 95616, USA
| | - Julia R Cohen
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Thomas R Famula
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
| | - Julie A Dragon
- Vermont Integrative Genomics Resource, University of Vermont, Burlington, Vermont 05405, USA
| | - Russell C Hovey
- Department of Animal Science, University of California, Davis, Davis, California 95616, USA
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13
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Archaeal and Bacterial Metagenome-Assembled Genome Sequences Derived from Pig Feces. Microbiol Resour Announc 2022; 11:e0114221. [PMID: 35049348 PMCID: PMC8772591 DOI: 10.1128/mra.01142-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
We report the recovery of metagenome-assembled genomes (MAGs) from fecal samples collected in 2018 from five healthy adult female pigs in southeast England. The resulting nonredundant catalog of 192 MAGs encompasses 102 metagenomic species, 41 of them novel, spanning 10 bacterial and 2 archaeal phyla.
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14
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Richert R, Ducret M, Alliot-Licht B, Bekhouche M, Gobert S, Farges JC. A critical analysis of research methods and experimental models to study pulpitis. Int Endod J 2022; 55 Suppl 1:14-36. [PMID: 35034368 DOI: 10.1111/iej.13683] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 01/10/2022] [Accepted: 01/11/2022] [Indexed: 11/29/2022]
Abstract
Pulpitis is the inflammatory response of the dental pulp to a tooth insult, whether it is microbial, chemical, or physical in origin. It is traditionally referred to as reversible or irreversible, a classification for therapeutic purposes that determines the capability of the pulp to heal. Recently, new knowledge about dental pulp physiopathology led to orientate therapeutics towards more frequent preservation of pulp vitality. However, full adoption of these vital pulp therapies by dental practitioners will be achieved only following better understanding of cell and tissue mechanisms involved in pulpitis. The current narrative review aimed to discuss the contribution of the most significant experimental models developed to study pulpitis. Traditionally, in vitro two(2D)- or three(3D)-dimensional cell cultures or in vivo animal models were used to analyse the pulp response to pulpitis inducers at cell, tissue or organ level. In vitro 2D cell cultures were mainly used to decipher the specific roles of key actors of pulp inflammation such as bacterial by-products, pro-inflammatory cytokines, odontoblasts or pulp stem cells. However, these simple models did not reproduce the 3D organisation of the pulp tissue and, with rare exceptions, did not consider interactions between resident cell types. In vitro tissue/organ-based models were developed to better reflect the complexity of the pulp structure. Their major disadvantage is that they did not allow the analysis of blood supply and innervation participation. On the contrary, in vivo models have allowed researchers to identify key immune, vascular and nervous actors of pulpitis and to understand their function and interplay in the inflamed pulp. However, inflammation was mainly induced by iatrogenic dentine drilling associated with simple pulp exposure to the oral environment or stimulation by individual bacterial by-products for short periods. Clearly, these models did not reflect the long and progressive development of dental caries. Lastly, the substantial diversity of the existing models makes experimental data extrapolation to the clinical situation complicated. Therefore, improvement in the design and standardization of future models, for example by using novel molecular biomarkers, databased models and artificial intelligence, will be an essential step in building an incremental knowledge of pulpitis in the future.
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Affiliation(s)
- Raphaël Richert
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Mécanique des Contacts et Structures, UMR 5259, Villeurbanne, France
| | - Maxime Ducret
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Brigitte Alliot-Licht
- Université de Nantes, Faculté d'Odontologie, Nantes, France.,CHU de Nantes, Odontologie Conservatrice et Pédiatrique, Service d, Nantes, France
| | - Mourad Bekhouche
- Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Stéphanie Gobert
- Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
| | - Jean-Christophe Farges
- Hospices Civils de Lyon, Service d'Odontologie, Lyon, France.,Université de Lyon, Université Claude Bernard Lyon 1, Faculté d'Odontologie, Lyon, France.,Laboratoire de Biologie Tissulaire et Ingénierie thérapeutique, UMR 5305, CNRS, Université, UMS, Claude Bernard Lyon 1, 3444 BioSciences Gerland-Lyon Sud, Lyon, France
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15
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Abayalath N, Malshani I, Ariyaratne R, Zhao S, Zhong G, Zhang G, Manipura A, Siribaddana A, Karunaratne P, Kodithuwakku SP. Characterization of airborne PAHs and metals associated with PM10 fractions collected from an urban area of Sri Lanka and the impact on airway epithelial cells. CHEMOSPHERE 2022; 286:131741. [PMID: 34358888 DOI: 10.1016/j.chemosphere.2021.131741] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 07/19/2021] [Accepted: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Airborne particulate matter (PM), polycyclic aromatic hydrocarbons (PAHs) and heavy metals (HMs) are significant contributors leading to many human health issues. Thus, this study was designed to perform chemical analysis and biological impact of airborne particulate matter 10 (PM10) in the World heritage City of Kandy City in Sri Lanka. 12 priority PAHs and 34 metals, including 10 highly toxic HMs were quantified. The biological effects of organic extracts were assayed using an in vitro primary porcine airway epithelial cell culture model. Cytotoxicity, DNA damage, and gene expressions of selected inflammatory and cancer-related genes were also assessed. Results showed that the total PAHs ranged from 3.062 to 36.887 ng/m3. The metals were dominated by Na > Ca > Mg > Al > K > Fe > Ti, while a few toxic HMs were much higher in the air than the existing ambient air quality standards. In the bioassays, a significant cytotoxicity (p < 0.05) was observed at 300 μg/mL treatment, and significant (p < 0.05) DNA damages were noted in all treatment groups. All genes assessed were found to be significantly up-regulated (p < 0.05) after 24 h of exposure and after 48 h, only TGF-β1 and p53 did not significantly up-regulate (p < 0.05). These findings confirm that the Kandy city air contains potential carcinogenic and mutagenic compounds and thus, exposure to Kandy air may increase the health risks and respiratory tract-related anomalies.
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Affiliation(s)
- Nirodha Abayalath
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Indeepa Malshani
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka; Department of Pharmacy, Faculty of Allied Health Sciences, University of Ruhuna, Galle, 80000, Sri Lanka
| | - Rajitha Ariyaratne
- Department of Chemical and Process Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Shizhen Zhao
- State Key Laboratory of Organic Geochemistry (SKLOG), Guangzhou Institute of Geochemistry (GIG), Chinese Academy of Sciences (CAS), Guangzhou, 510640, PR China
| | - Guangcai Zhong
- State Key Laboratory of Organic Geochemistry (SKLOG), Guangzhou Institute of Geochemistry (GIG), Chinese Academy of Sciences (CAS), Guangzhou, 510640, PR China
| | - Gan Zhang
- State Key Laboratory of Organic Geochemistry (SKLOG), Guangzhou Institute of Geochemistry (GIG), Chinese Academy of Sciences (CAS), Guangzhou, 510640, PR China
| | - Aruna Manipura
- Department of Chemical and Process Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | | | - Parakrama Karunaratne
- Department of Chemical and Process Engineering, Faculty of Engineering, University of Peradeniya, Peradeniya, 20400, Sri Lanka
| | - Suranga P Kodithuwakku
- Department of Animal Science, Faculty of Agriculture, University of Peradeniya, Peradeniya, 20400, Sri Lanka; Department of Obstetrics and Gynaecology, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, PR China.
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16
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Fourier Transform Infrared Microspectroscopy Combined with Principal Component Analysis and Artificial Neural Networks for the Study of the Effect of β-Hydroxy-β-Methylbutyrate (HMB) Supplementation on Articular Cartilage. Int J Mol Sci 2021; 22:ijms22179189. [PMID: 34502096 PMCID: PMC8430473 DOI: 10.3390/ijms22179189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/23/2021] [Accepted: 08/24/2021] [Indexed: 11/17/2022] Open
Abstract
The potential of Fourier Transform infrared microspectroscopy (FTIR microspectroscopy) and multivariate analyses were applied for the classification of the frequency ranges responsible for the distribution changes of the main components of articular cartilage (AC) that occur during dietary β-hydroxy-β-methyl butyrate (HMB) supplementation. The FTIR imaging analysis of histological AC sections originating from 35-day old male piglets showed the change in the collagen and proteoglycan contents of the HMB-supplemented group compared to the control. The relative amount of collagen content in the superficial zone increased by more than 23% and in the middle zone by about 17%, while no changes in the deep zone were observed compared to the control group. Considering proteoglycans content, a significant increase was registered in the middle and deep zones, respectively; 62% and 52% compared to the control. AFM nanoindentation measurements collected from animals administered with HMB displayed an increase in AC tissue stiffness by detecting a higher value of Young’s modulus in all investigated AC zones. We demonstrated that principal component analysis and artificial neural networks could be trained with spectral information to distinguish AC histological sections and the group under study accurately. This work may support the use and effectiveness of FTIR imaging combined with multivariate analyses as a quantitative alternative to traditional collagenous tissue-related histology.
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17
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Peroxiredoxin 4 directly affects the male fertility outcome in porcine. Theriogenology 2021; 171:85-93. [PMID: 34051589 DOI: 10.1016/j.theriogenology.2021.05.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 04/08/2021] [Accepted: 05/16/2021] [Indexed: 11/21/2022]
Abstract
Peroxiredoxins (Prdxs) are known to play a critical role in regulating male fertility as antioxidant enzymes. Although several studies have suggested a close association between Prdxs and male fertility, few studies have explored the efficacy of Prdxs to predict male fertility. Therefore, the current study was designed to discover the most efficient biomarkers among the Prdxs with six isoforms. Our study showed a significant positive correlation between the litter size and the levels of PRDX 4 among all isoforms in spermatozoa. Subsequently, a regression analysis using a combination of markers was conducted to increase efficacy for fertility prediction. Nevertheless, PRDX4 had the highest efficacy compared to other combination models to predict litter size. The prediction accuracy of male fertility was further evaluated through receiver operating characteristic curve analysis, which showed that PRDX 4 could predict the litter size with high overall accuracy of 95%. Moreover, litter size was increased by 1.55 piglets after predicting high litter size using PRDX 4. This is the first study to comprehensively elucidate the role of all isoforms of PRDXs on male fertility to the best of our knowledge. PRDX 4 was tested and evaluated up to a practical level. Data here reported suggesting PRDX 4 marker allowed the highest accuracy for male fertility prediction and diagnosis, leading to a measurable improvement in the male fertility outcome.
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18
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Aubeux D, Renard E, Pérez F, Tessier S, Geoffroy V, Gaudin A. Review of Animal Models to Study Pulp Inflammation. FRONTIERS IN DENTAL MEDICINE 2021. [DOI: 10.3389/fdmed.2021.673552] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Human dental pulp is a highly dynamic tissue equipped with a network of resident immunocompetent cells that play a major role in the defense against pathogens and during tissue injury. Animal studies are mandatory and complementary to in vitro experiments when studying the physiopathology of dental pulp, new diagnostic tools, or innovative therapeutic strategies. This animal approach makes it possible to define a benefit-risk ratio necessary to be subsequently tested in humans. Among the animal kingdom, rodents, rabbits, ferrets, swine, dogs, and non-human primates have been used to model human pulpitis. The diversity of animals found in studies indicate the difficulty of choosing the correct and most efficient model. Each animal model has its own characteristics that may be advantageous or limiting, according to the studied parameters. These elements have to be considered in preclinical studies. This article aims to provide a thorough understanding of the different animal models used to study pulp inflammation. This may help to find the most pertinent or appropriate animal model depending on the hypothesis investigated and the expected results.
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19
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Tiba MH, McCracken BM, Leander DC, Colmenero CI, Nemzek JA, Sjoding MW, Konopka KE, Flott TL, VanEpps JS, Daniels RC, Ward KR, Stringer KA, Dickson RP. A novel swine model of the acute respiratory distress syndrome using clinically relevant injury exposures. Physiol Rep 2021; 9:e14871. [PMID: 33991456 PMCID: PMC8123544 DOI: 10.14814/phy2.14871] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 04/17/2021] [Indexed: 12/18/2022] Open
Abstract
To date, existing animal models of the acute respiratory distress syndrome (ARDS) have failed to translate preclinical discoveries into effective pharmacotherapy or diagnostic biomarkers. To address this translational gap, we developed a high-fidelity swine model of ARDS utilizing clinically relevant lung injury exposures. Fourteen male swine were anesthetized, mechanically ventilated, and surgically instrumented for hemodynamic monitoring, blood, and tissue sampling. Animals were allocated to one of three groups: (1) Indirect lung injury only: animals were inoculated by direct injection of Escherichia coli into the kidney parenchyma, provoking systemic inflammation and distributive shock physiology; (2) Direct lung injury only: animals received volutrauma, hyperoxia, and bronchoscope-delivered gastric particles; (3) Combined indirect and direct lung injury: animals were administered both above-described indirect and direct lung injury exposures. Animals were monitored for up to 12 h, with serial collection of physiologic data, blood samples, and radiographic imaging. Lung tissue was acquired postmortem for pathological examination. In contrast to indirect lung injury only and direct lung injury only groups, animals in the combined indirect and direct lung injury group exhibited all of the physiological, radiographic, and histopathologic hallmarks of human ARDS: impaired gas exchange (mean PaO2 /FiO2 ratio 124.8 ± 63.8), diffuse bilateral opacities on chest radiographs, and extensive pathologic evidence of diffuse alveolar damage. Our novel porcine model of ARDS, built on clinically relevant lung injury exposures, faithfully recapitulates the physiologic, radiographic, and histopathologic features of human ARDS and fills a crucial gap in the translational study of human lung injury.
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Affiliation(s)
- Mohamad H. Tiba
- Department of Emergency MedicineUniversity of MichiganAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
| | - Brendan M. McCracken
- Department of Emergency MedicineUniversity of MichiganAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
| | - Danielle C. Leander
- Department of Emergency MedicineUniversity of MichiganAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
| | - Carmen I. Colmenero
- Department of Emergency MedicineUniversity of MichiganAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
| | - Jean A. Nemzek
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Unit of Laboratory Animal MedicineUniversity of MichiganAnn ArborMIUSA
| | - Michael W. Sjoding
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Division of Pulmonary and Critical Care MedicineDepartment of Internal MedicineUniversity of MichiganAnn ArborMIUSA
- Institute for Healthcare Policy and InnovationUniversity of MichiganAnn ArborMIUSA
- Department of Computational Medicine and BioinformaticsUniversity of MichiganAnn ArborMIUSA
| | - Kristine E. Konopka
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Department of PathologyUniversity of MichiganAnn ArborMIUSA
| | - Thomas L. Flott
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Department of Clinical PharmacyCollege of PharmacyUniversity of MichiganAnn ArborMIUSA
| | - J. Scott VanEpps
- Department of Emergency MedicineUniversity of MichiganAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMIUSA
- Biointerfaces InstituteUniversity of MichiganAnn ArborMIUSA
| | - Rodney C. Daniels
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMIUSA
- Department of PediatricsPediatric Critical Care MedicineUniversity of MichiganAnn ArborMIUSA
| | - Kevin R. Ward
- Department of Emergency MedicineUniversity of MichiganAnn ArborMIUSA
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Department of Biomedical EngineeringUniversity of MichiganAnn ArborMIUSA
| | - Kathleen A. Stringer
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Division of Pulmonary and Critical Care MedicineDepartment of Internal MedicineUniversity of MichiganAnn ArborMIUSA
- Department of Clinical PharmacyCollege of PharmacyUniversity of MichiganAnn ArborMIUSA
| | - Robert P. Dickson
- Michigan Center for Integrative Research in Critical CareUniversity of MichiganAnn ArborMIUSA
- Division of Pulmonary and Critical Care MedicineDepartment of Internal MedicineUniversity of MichiganAnn ArborMIUSA
- Department of Microbiology & ImmunologyUniversity of MichiganAnn ArborMIUSA
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20
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Fráguas-Eggenschwiler M, Eggenschwiler R, Söllner JH, Cortnumme L, Vondran FWR, Cantz T, Ott M, Niemann H. Direct conversion of porcine primary fibroblasts into hepatocyte-like cells. Sci Rep 2021; 11:9334. [PMID: 33927320 PMCID: PMC8085017 DOI: 10.1038/s41598-021-88727-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 04/12/2021] [Indexed: 01/01/2023] Open
Abstract
The pig is an important model organism for biomedical research, mainly due to its extensive genetic, physiological and anatomical similarities with humans. Until date, direct conversion of somatic cells into hepatocyte-like cells (iHeps) has only been achieved in rodents and human cells. Here, we employed lentiviral vectors to screen a panel of 12 hepatic transcription factors (TF) for their potential to convert porcine fibroblasts into hepatocyte-like cells. We demonstrate for the first time, hepatic conversion of porcine somatic cells by over-expression of CEBPα, FOXA1 and HNF4α2 (3TF-piHeps). Reprogrammed 3TF-piHeps display a hepatocyte-like morphology and show functional characteristics of hepatic cells, including albumin secretion, Dil-AcLDL uptake, storage of lipids and glycogen and activity of cytochrome P450 enzymes CYP1A2 and CYP2C33 (CYP2C9 in humans). Moreover, we show that markers of mature hepatocytes are highly expressed in 3TF-piHeps, while fibroblastic markers are reduced. We envision piHeps as useful cell sources for future studies on drug metabolism and toxicity as well as in vitro models for investigation of pig-to-human infectious diseases.
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Affiliation(s)
- Mariane Fráguas-Eggenschwiler
- Gastroenterology, Hepatology and Endocrinology Department, Hannover Medical School, Hannover, Germany. .,Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany.
| | - Reto Eggenschwiler
- Gastroenterology, Hepatology and Endocrinology Department, Hannover Medical School, Hannover, Germany.,Translational Hepatology and Stem Cell Biology, REBIRTH - Research Center for Translational Regenerative Medicine and Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Jenny-Helena Söllner
- Institute of Farm Animal Genetics, Friedrich-Loeffler-Institut (FLI), Mariensee, Neustadt, Germany
| | - Leon Cortnumme
- Translational Hepatology and Stem Cell Biology, REBIRTH - Research Center for Translational Regenerative Medicine and Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Florian W R Vondran
- Department of General, Visceral and Transplant Surgery, Hannover Medical School, Hannover, Germany.,German Centre for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Tübingen, Germany
| | - Tobias Cantz
- Gastroenterology, Hepatology and Endocrinology Department, Hannover Medical School, Hannover, Germany.,Translational Hepatology and Stem Cell Biology, REBIRTH - Research Center for Translational Regenerative Medicine and Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Michael Ott
- Gastroenterology, Hepatology and Endocrinology Department, Hannover Medical School, Hannover, Germany.,Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany
| | - Heiner Niemann
- Gastroenterology, Hepatology and Endocrinology Department, Hannover Medical School, Hannover, Germany. .,Twincore Centre for Experimental and Clinical Infection Research, Hannover, Germany.
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21
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Bertho N, Meurens F. The pig as a medical model for acquired respiratory diseases and dysfunctions: An immunological perspective. Mol Immunol 2021; 135:254-267. [PMID: 33933817 DOI: 10.1016/j.molimm.2021.03.014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 03/04/2021] [Accepted: 03/13/2021] [Indexed: 12/21/2022]
Abstract
By definition no model is perfect, and this also holds for biology and health sciences. In medicine, murine models are, and will be indispensable for long, thanks to their reasonable cost and huge choice of transgenic strains and molecular tools. On the other side, non-human primates remain the best animal models although their use is limited because of financial and obvious ethical reasons. In the field of respiratory diseases, specific clinical models such as sheep and cotton rat for bronchiolitis, or ferret and Syrian hamster for influenza and Covid-19, have been successfully developed, however, in these species, the toolbox for biological analysis remains scarce. In this view the porcine medical model is appearing as the third, intermediate, choice, between murine and primate. Herein we would like to present the pros and cons of pig as a model for acquired respiratory conditions, through an immunological point of view. Indeed, important progresses have been made in pig immunology during the last decade that allowed the precise description of immune molecules and cell phenotypes and functions. These progresses might allow the use of pig as clinical model of human respiratory diseases but also as a species of interest to perform basic research explorations.
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Affiliation(s)
| | - François Meurens
- Department of Veterinary Microbiology and Immunology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon S7N5E3, Canada
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22
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Donaldson B, Villagomez DAF, King WA. Classical, Molecular, and Genomic Cytogenetics of the Pig, a Clinical Perspective. Animals (Basel) 2021; 11:1257. [PMID: 33925534 PMCID: PMC8146943 DOI: 10.3390/ani11051257] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2021] [Revised: 04/16/2021] [Accepted: 04/23/2021] [Indexed: 02/06/2023] Open
Abstract
The chromosomes of the domestic pig (Sus scrofa domesticus) are known to be prone to reciprocal chromosome translocations and other balanced chromosome rearrangements with concomitant fertility impairment of carriers. In response to the remarkable prevalence of chromosome rearrangements in swine herds, clinical cytogenetics laboratories have been established in several countries in order to screen young boars for chromosome rearrangements prior to service. At present, clinical cytogenetics laboratories typically apply classical cytogenetics techniques such as giemsa-trypsin (GTG)-banding to produce high-quality karyotypes and reveal large-scale chromosome ectopic exchanges. Further refinements to clinical cytogenetics practices have led to the implementation of molecular cytogenetics techniques such as fluorescent in-situ hybridization (FISH), allowing for rearrangements to be visualized and breakpoints refined using fluorescently labelled painting probes. The next-generation of clinical cytogenetics include the implementation of DNA microarrays, and next-generation sequencing (NGS) technologies such as DNA sequencing to better explore tentative genome architecture changes. The implementation of these cytogenomics techniques allow the genomes of rearrangement carriers to be deciphered at the highest resolution, allowing rearrangements to be detected; breakpoints to be delineated; and, most importantly, potential gene implications of those chromosome rearrangements to be interrogated. Clinical cytogenetics has become an integral tool in the livestock industry, identifying rearrangements and allowing breeders to make informed breeding decisions.
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Affiliation(s)
- Brendan Donaldson
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
| | | | - W. Allan King
- Department of Biomedical Sciences, University of Guelph, Guelph, ON N1G 2W1, Canada;
- Karyotekk Inc., Box 363 OVC, University of Guelph, Guelph, ON N1G 2W1, Canada
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Basini G, Bussolati S, Grolli S, Ragionieri L, Di Lecce R, Grasselli F. Orexin B inhibits viability and differentiation of stromal cells from swine adipose tissue. Domest Anim Endocrinol 2021; 75:106594. [PMID: 33291037 DOI: 10.1016/j.domaniend.2020.106594] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Revised: 10/14/2020] [Accepted: 11/08/2020] [Indexed: 12/20/2022]
Abstract
Adipose tissue is recognized as a fundamental endocrine organ. Nowadays, we are also aware that it contains the highest number of stromal cells (ASCs) per unit of volume. These cells can differentiate between different phenotypes among which the adipocytes. The aim of this work was to verify whether orexin B, crucial mediator of the energy balance, modifies the differentiation of cultured ASCs. We used the pig as a model. Our data demonstrate that swine ASCs express prepro-orexin. Orexin B treatment inhibits ASCs proliferation (P < 0.05) and adipogenic differentiation (P < 0.05). Data collected could be interesting both in animal production field because consumers require lean meat, and in human medicine study about obesity because pig can be considered a valuable animal model for translational studies.
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Affiliation(s)
- G Basini
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio, 10, 43126 Parma, Italy.
| | - S Bussolati
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio, 10, 43126 Parma, Italy
| | - S Grolli
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio, 10, 43126 Parma, Italy
| | - L Ragionieri
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio, 10, 43126 Parma, Italy
| | - R Di Lecce
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio, 10, 43126 Parma, Italy
| | - F Grasselli
- Dipartimento di Scienze Medico-Veterinarie, Università degli Studi di Parma, Via del Taglio, 10, 43126 Parma, Italy
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24
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Marthey S, Estellé J, Blin A, Wahlberg P, Créchet F, Lecardonnel J, Tessiot F, Rogel-Gaillard C, Bourneuf E. Transcription from a gene desert in a melanoma porcine model. Mol Genet Genomics 2020; 295:1239-1252. [PMID: 32529263 DOI: 10.1007/s00438-020-01694-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 06/03/2020] [Indexed: 01/11/2023]
Abstract
The genetic mechanisms underlying cutaneous melanoma onset and progression need to be further understood to improve patients' care. Several studies have focused on the genetic determinism of melanoma development in the MeLiM pig, a biomedical model of cutaneous melanoma. The objective of this study was to better describe the influence of a particular genomic region on melanoma progression in the MeliM model. Indeed, a large region of the Sus scrofa chromosome 1 has been identified by linkage and association analyses, but the causal mechanisms have remained elusive. To deepen the analysis of this candidate region, a dedicated SNP panel was used to fine map the locus, downsizing the interval to less than 2 Mb, in a genomic region located within a large gene desert. Transcription from this locus was addressed using a tiling array strategy and further validated by RT-PCR in a large panel of tissues. Overall, the gene desert showed an extensive transcriptional landscape, notably dominated by repeated element transcription in tumor and fetal tissues. The transcription of LINE-1 and PERVs has been confirmed in skin and tumor samples from MeLiM pigs. In conclusion, although this study still does not identify a candidate mutation for melanoma occurrence or progression, it highlights a potential role of repeated element transcriptional activity in the MeLiM model.
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Affiliation(s)
- S Marthey
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Estellé
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - A Blin
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- Muséum national d'histoire naturelle, Centre national de la recherche scientifique, UMS 2700 2AD, CP51, 57 rue Cuvier, 75231, Paris Cedex 05, France
| | - P Wahlberg
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | - F Créchet
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
- LREG, IRCM, DRF, CEA, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - J Lecardonnel
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - F Tessiot
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - C Rogel-Gaillard
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - E Bourneuf
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
- LREG, IRCM, DRF, CEA, Université Paris-Saclay, 78350, Jouy-en-Josas, France.
- LCE, IRCM, DRF, CEA, Université Paris-Saclay, 92260, Fontenay-aux-Roses, France.
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25
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Ferreira-Lazarte A, Moreno FJ, Villamiel M. Bringing the digestibility of prebiotics into focus: update of carbohydrate digestion models. Crit Rev Food Sci Nutr 2020; 61:3267-3278. [PMID: 32744076 DOI: 10.1080/10408398.2020.1798344] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Oro-gastrointestinal digestion of dietary carbohydrates involves up to six different carbohydrases in a multistage process. Enzymes from the small intestinal brush border membrane play a major role in the digestibility of these substrates. However, to date, the inclusion of these small intestinal enzymes has been dismissed in most in vitro studies carried out, despite their importance in the degradation of carbohydrates. Several in vitro and in vivo studies have demonstrated the capability of brush border enzymes to degrade certain "non-digestible" carbohydrates to a different extent depending on their structural composition (monomeric composition, glycosidic linkage, etc.). In this sense, considering the available evidence, mucosal disaccharidases embedded in the small intestinal brush border membrane vesicles must be considered in addition to α-amylases; therefore, new approaches for the evaluation of the digestibility of carbohydrates have been recently reported. These new methods based on the utilization of the small intestinal enzymes present in the brush border membrane aim to fulfill the final and key step of the digestion of carbohydrates in the small intestine. Here, rat small intestinal extract enzymes as well as brush border membrane vesicles from pig have emerged as very reliable and useful tools to evaluate carbohydrate digestion. Thus, this review aims to go briefly through the most relevant digestion methods for carbohydrates that are currently available and to highlight the new improved methods, which include mammalian intestinal enzymes, and their current use in the evaluation of the digestibility of prebiotics.
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Affiliation(s)
| | - F Javier Moreno
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, Madrid, Spain
| | - Mar Villamiel
- Instituto de Investigación en Ciencias de la Alimentación (CIAL), CSIC-UAM, Madrid, Spain
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26
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Pang WK, Kang S, Ryu DY, Rahman MS, Park YJ, Pang MG. Optimization of sperm RNA processing for developmental research. Sci Rep 2020; 10:11606. [PMID: 32665575 PMCID: PMC7360572 DOI: 10.1038/s41598-020-68486-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 06/22/2020] [Indexed: 12/11/2022] Open
Abstract
Recent studies have demonstrated the significance of sperm RNA function as a transporter of important information directing the course of life. To determine the message contained in sperm RNA, it is necessary to optimize transcriptomic research tools. The current study was performed to optimize the processing of sperm RNA from sample storage to quantitative real-time PCR and assess the corresponding method with to evaluate male fertility and its representative markers, equatorin (EQTN) and peroxiredoxin (PRDX). Following successive steps of the Minimum Information for Publication of Quantitative Real-Time PCR Experiments guidelines, several options were compared using boar spermatozoa. To evaluate the optimized procedures, the relationship between mRNA expression of EQTN and PRDX in spermatozoa and the fertility (litter size) of 20 individual boars was assessed. Unexpectedly, DNase treatment during RNA isolation had the deleterious effect by decreasing the RNA concentration by 56% and eliminating the correlation between EQTN and PRDX4 mRNA expression and male fertility. Moreover, when sperm RNA was processed using the corresponding method, the results showed the highest exon sequence expression, male fertility prediction power, and consistency. This optimized protocol for predicting male fertility can be used to study the transport of messages directing the life course from spermatozoon to offspring.
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Affiliation(s)
- Won-Ki Pang
- Department of Animal Science and Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Saehan Kang
- Department of Animal Science and Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Do-Yeal Ryu
- Department of Animal Science and Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Md Saidur Rahman
- Department of Animal Science and Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Yoo-Jin Park
- Department of Animal Science and Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Myung-Geol Pang
- Department of Animal Science and Technology and BET Research Institute, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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27
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Warr A, Affara N, Aken B, Beiki H, Bickhart DM, Billis K, Chow W, Eory L, Finlayson HA, Flicek P, Girón CG, Griffin DK, Hall R, Hannum G, Hourlier T, Howe K, Hume DA, Izuogu O, Kim K, Koren S, Liu H, Manchanda N, Martin FJ, Nonneman DJ, O'Connor RE, Phillippy AM, Rohrer GA, Rosen BD, Rund LA, Sargent CA, Schook LB, Schroeder SG, Schwartz AS, Skinner BM, Talbot R, Tseng E, Tuggle CK, Watson M, Smith TPL, Archibald AL. An improved pig reference genome sequence to enable pig genetics and genomics research. Gigascience 2020; 9:5858065. [PMID: 32543654 PMCID: PMC7448572 DOI: 10.1093/gigascience/giaa051] [Citation(s) in RCA: 161] [Impact Index Per Article: 40.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/12/2020] [Accepted: 04/22/2020] [Indexed: 01/05/2023] Open
Abstract
Background The domestic pig (Sus scrofa) is important both as a food source and
as a biomedical model given its similarity in size, anatomy, physiology, metabolism,
pathology, and pharmacology to humans. The draft reference genome (Sscrofa10.2) of a
purebred Duroc female pig established using older clone-based sequencing methods was
incomplete, and unresolved redundancies, short-range order and orientation errors, and
associated misassembled genes limited its utility. Results We present 2 annotated highly contiguous chromosome-level genome assemblies created
with more recent long-read technologies and a whole-genome shotgun strategy, 1 for the
same Duroc female (Sscrofa11.1) and 1 for an outbred, composite-breed male (USMARCv1.0).
Both assemblies are of substantially higher (>90-fold) continuity and accuracy than
Sscrofa10.2. Conclusions These highly contiguous assemblies plus annotation of a further 11 short-read
assemblies provide an unprecedented view of the genetic make-up of this important
agricultural and biomedical model species. We propose that the improved Duroc assembly
(Sscrofa11.1) become the reference genome for genomic research in pigs.
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Affiliation(s)
- Amanda Warr
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Nabeel Affara
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Bronwen Aken
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Hamid Beiki
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Derek M Bickhart
- Dairy Forage Research Center, USDA-ARS, 1925 Linden Drive, Madison, WI 53706, USA
| | - Konstantinos Billis
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - William Chow
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - Lel Eory
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Heather A Finlayson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Carlos G Girón
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Darren K Griffin
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Richard Hall
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | | | - Thibaut Hourlier
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kerstin Howe
- Wellcome Sanger Institute, Wellcome Genome Campus, Cambridge CB10 1SA, UK
| | - David A Hume
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK.,Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane QLD 4104, Australia
| | - Osagie Izuogu
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Kristi Kim
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Haibou Liu
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA
| | - Nancy Manchanda
- Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Fergal J Martin
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton CB10 1SD, UK
| | - Dan J Nonneman
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Rebecca E O'Connor
- School of Biosciences, University of Kent, Giles Lane, Canterbury CT2 7NJ, UK
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, 9000 Rockville Pike, Bethesda, MD 20892, USA
| | - Gary A Rohrer
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | - Laurie A Rund
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Carole A Sargent
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Lawrence B Schook
- Department of Animal Sciences, University of Illinois, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | - Steven G Schroeder
- Animal Genomics and Improvement Laboratory, USDA-ARS, 10300 Baltimore Avenue, Beltsville, MD 20705-2350, USA
| | | | - Ben M Skinner
- Department of Pathology, University of Cambridge, Tennis Court Road, Cambridge CB2 1QP, UK
| | - Richard Talbot
- Edinburgh Genomics, University of Edinburgh, Charlotte Auerbach Road, Edinburgh EH9 3FL, UK
| | - Elizabeth Tseng
- Pacific Biosciences, 1305 O'Brien Drive, Menlo Park, CA 94025, USA
| | - Christopher K Tuggle
- Department of Animal Science, 2255 Kildee Hall, Iowa State University, Ames, IA 50011-3150, USA.,Bioinformatics and Computational Biology Program, Iowa State University, 2014 Molecular Biology Building, Ames, IA 50011, USA
| | - Mick Watson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
| | - Timothy P L Smith
- USDA-ARS U.S. Meat Animal Research Center, 844 Road 313, Clay Center, NE 68933, USA
| | - Alan L Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush Campus, Midlothian EH25 9RG, UK
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28
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Lim KRQ, Nguyen Q, Dzierlega K, Huang Y, Yokota T. CRISPR-Generated Animal Models of Duchenne Muscular Dystrophy. Genes (Basel) 2020; 11:genes11030342. [PMID: 32213923 PMCID: PMC7141101 DOI: 10.3390/genes11030342] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Revised: 03/21/2020] [Accepted: 03/23/2020] [Indexed: 02/07/2023] Open
Abstract
Duchenne muscular dystrophy (DMD) is a fatal X-linked recessive neuromuscular disorder most commonly caused by mutations disrupting the reading frame of the dystrophin (DMD) gene. DMD codes for dystrophin, which is critical for maintaining the integrity of muscle cell membranes. Without dystrophin, muscle cells receive heightened mechanical stress, becoming more susceptible to damage. An active body of research continues to explore therapeutic treatments for DMD as well as to further our understanding of the disease. These efforts rely on having reliable animal models that accurately recapitulate disease presentation in humans. While current animal models of DMD have served this purpose well to some extent, each has its own limitations. To help overcome this, clustered regularly interspaced short palindromic repeat (CRISPR)-based technology has been extremely useful in creating novel animal models for DMD. This review focuses on animal models developed for DMD that have been created using CRISPR, their advantages and disadvantages as well as their applications in the DMD field.
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Affiliation(s)
- Kenji Rowel Q. Lim
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (K.R.Q.L.); (Q.N.); (K.D.); (Y.H.)
| | - Quynh Nguyen
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (K.R.Q.L.); (Q.N.); (K.D.); (Y.H.)
| | - Kasia Dzierlega
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (K.R.Q.L.); (Q.N.); (K.D.); (Y.H.)
| | - Yiqing Huang
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (K.R.Q.L.); (Q.N.); (K.D.); (Y.H.)
| | - Toshifumi Yokota
- Department of Medical Genetics, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, AB T6G 2H7, Canada; (K.R.Q.L.); (Q.N.); (K.D.); (Y.H.)
- The Friends of Garrett Cumming Research & Muscular Dystrophy Canada, HM Toupin Neurological Science Research Chair, Edmonton, AB T6G 2H7, Canada
- Correspondence: ; Tel.: +1-780-492-1102
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29
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Baradaran-Rafii A, Sarvari M, Alavi-Moghadam S, Payab M, Goodarzi P, Aghayan HR, Larijani B, Rezaei-Tavirani M, Biglar M, Arjmand B. Cell-based approaches towards treating age-related macular degeneration. Cell Tissue Bank 2020; 21:339-347. [PMID: 32157501 DOI: 10.1007/s10561-020-09826-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 03/05/2020] [Indexed: 12/19/2022]
Abstract
Age-related macular degeneration as one of the most common causes of worldwide vision loss needs a proper approach for treatment. Therein, cell therapy and regenerative medicine can hold a great promise to be an effective approach. Accordingly, some preclinical and clinical studies were conducted to search around the therapeutic influence of stem cells in Age-related macular degeneration models and subjects. Hereupon, the purpose of the current review is to discuss the mechanisms of age-related macular degeneration, appropriate animal models along with suitable dosage and route of stem cell administration for its treatment.
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Affiliation(s)
- Alireza Baradaran-Rafii
- Ocular Tissue Engineering Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
- Ophthalmic Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Sarvari
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sepideh Alavi-Moghadam
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Moloud Payab
- Obesity and Eating Habits Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Parisa Goodarzi
- Brain and Spinal Cord Injury Research Center, Neuroscience Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Hamid Reza Aghayan
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Bagher Larijani
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Mahmood Biglar
- Endocrinology and Metabolism Research Center, Endocrinology and Metabolism Clinical Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Babak Arjmand
- Cell Therapy and Regenerative Medicine Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
- Metabolomics and Genomics Research Center, Endocrinology and Metabolism Molecular-Cellular Sciences Institute, Tehran University of Medical Sciences, Tehran, Iran.
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30
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Marfurt C, Anokwute MC, Fetcko K, Mahony-Perez E, Farooq H, Ross E, Baumanis MM, Weinberg RL, McCarron ME, Mankowski JL. Comparative Anatomy of the Mammalian Corneal Subbasal Nerve Plexus. Invest Ophthalmol Vis Sci 2019; 60:4972-4984. [PMID: 31790560 PMCID: PMC6886725 DOI: 10.1167/iovs.19-28519] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 10/24/2019] [Indexed: 12/20/2022] Open
Abstract
Purpose The subbasal nerve plexus (SNP) is the densest and most recognizable component of the mammalian corneal innervation; however, the anatomical configuration of the SNP in most animal models remains incompletely described. The purpose of the current study is to describe in detail the SNP architecture in eight different mammals, including several popular animal models used in cornea research. Methods Corneal nerves in mouse, rat, guinea pig, rabbit, dog, macaque, domestic pig, and cow eyes were stained immunohistochemically with antiserum directed against neurotubulin. SNP architecture was documented by digital photomicrography and large-scale reconstructions, that is, corneal nerve maps, using a drawing tube attached to a light microscope. Results Subbasal nerve fibers (SNFs) in mice, rats, guinea pigs, dogs, and macaques radiated centrally from the corneoscleral limbus toward the corneal apex in a whorl-like or spiraling pattern. SNFs in rabbit and bovine corneas swept horizontally across the ocular surface in a temporal-to-nasal direction and converged on the inferonasal limbus without forming a spiral. SNFs in the pig cornea radiated centrifugally in all directions, like a starburst, from a focal point located equidistant between the corneal apex and the superior pole. Conclusions The results of the present study have demonstrated for the first time substantial interspecies differences in the architectural organization of the mammalian SNP. The physiological significance of these different patterns and the mechanisms that regulate SNP pattern formation in the mammalian cornea remain incompletely understood and warrant additional investigation.
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Affiliation(s)
- Carl Marfurt
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Miracle C. Anokwute
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Kaleigh Fetcko
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Erin Mahony-Perez
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Hassan Farooq
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Emily Ross
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Maraya M. Baumanis
- Indiana University School of Medicine-Northwest-Gary, Gary, Indiana, United States
| | - Rachel L. Weinberg
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Megan E. McCarron
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
| | - Joseph L. Mankowski
- Johns Hopkins University School of Medicine, Baltimore, Maryland, United States
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31
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Vermeulen M, Del Vento F, Kanbar M, Pyr Dit Ruys S, Vertommen D, Poels J, Wyns C. Generation of Organized Porcine Testicular Organoids in Solubilized Hydrogels from Decellularized Extracellular Matrix. Int J Mol Sci 2019; 20:E5476. [PMID: 31684200 PMCID: PMC6862040 DOI: 10.3390/ijms20215476] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/30/2019] [Indexed: 01/15/2023] Open
Abstract
Cryopreservation of immature testicular tissue (ITT) prior to chemo/radiotherapy is now ethically accepted and is currently the only way to preserve fertility of prepubertal boys about to undergo cancer therapies. So far, three-dimensional culture of testicular cells isolated from prepubertal human testicular tissue was neither efficient nor reproducible to obtain mature spermatozoa, and ITT transplantation is not a safe option when there is a risk of cancer cell contamination of the testis. Hence, generation of testicular organoids (TOs) after cell selection is a novel strategy aimed at restoring fertility in these patients. Here, we created TOs using hydrogels developed from decellularized porcine ITT and compared cell numbers, organization and function to TOs generated in collagen only hydrogel. Organotypic culture of porcine ITT was used as a control. Rheological and mass spectrometry analyses of both hydrogels highlighted differences in terms of extracellular matrix stiffness and composition, respectively. Sertoli cells (SCs) and germ cells (GCs) assembled into seminiferous tubule-like structures delimited by a basement membrane while Leydig cells (LCs) and peritubular cells localized outside. TOs were maintained for 45 days in culture and secreted stem cell factor and testosterone demonstrating functionality of SCs and LCs, respectively. In both TOs GC numbers decreased and SC numbers increased. However, LC numbers decreased significantly in the collagen hydrogel TOs (p < 0.05) suggesting a better preservation of growth factors within TOs developed from decellularized ITT and thus a better potential to restore the reproductive capacity.
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Affiliation(s)
- Maxime Vermeulen
- Gynecology-Andrology Research Unit, Institut de Recherche Expérimentale et Clinique, Medical School, Université Catholique de Louvain, 1200 Brussels, Belgium.
| | - Federico Del Vento
- Gynecology-Andrology Research Unit, Institut de Recherche Expérimentale et Clinique, Medical School, Université Catholique de Louvain, 1200 Brussels, Belgium.
| | - Marc Kanbar
- Gynecology-Andrology Research Unit, Institut de Recherche Expérimentale et Clinique, Medical School, Université Catholique de Louvain, 1200 Brussels, Belgium.
| | - Sébastien Pyr Dit Ruys
- Phosphorylation - MassProt Unit, Institut de Duve, Université Catholique de Louvain, 1200 Brussels, Belgium.
| | - Didier Vertommen
- Phosphorylation - MassProt Unit, Institut de Duve, Université Catholique de Louvain, 1200 Brussels, Belgium.
| | - Jonathan Poels
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium.
| | - Christine Wyns
- Gynecology-Andrology Research Unit, Institut de Recherche Expérimentale et Clinique, Medical School, Université Catholique de Louvain, 1200 Brussels, Belgium.
- Department of Gynecology-Andrology, Cliniques Universitaires Saint-Luc, 1200 Brussels, Belgium.
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32
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Lindsay CD, Timperley CM. TRPA1 and issues relating to animal model selection for extrapolating toxicity data to humans. Hum Exp Toxicol 2019; 39:14-36. [PMID: 31578097 DOI: 10.1177/0960327119877460] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The transient receptor potential ankyrin 1 (TRPA1) ion channel is a sensor for irritant chemicals, has ancient lineage, and is distributed across animal species including humans, where it features in many organs. Its activation by a diverse panel of electrophilic molecules (TRPA1 agonists) through electrostatic binding and/or covalent attachment to the protein causes the sensation of pain. This article reviews the species differences between TRPA1 channels and their responses, to assess the suitability of different animals to model the effects of TRPA1-activating electrophiles in humans, referring to common TRPA1 activators (exogenous and endogenous) and possible mechanisms of action relating to their toxicology. It concludes that close matching of in vitro and in vivo models will help optimise the identification of relevant biochemical and physiological responses to benchmark the efficacy of potential therapeutic drugs, including TRPA1 antagonists, to counter the toxic effects of those electrophiles capable of harming humans. The analysis of the species issue provided should aid the development of medical treatments to counter poisoning by such chemicals.
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Affiliation(s)
- C D Lindsay
- Chemical, Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury, UK
| | - C M Timperley
- Chemical, Biological and Radiological (CBR) Division, Defence Science and Technology Laboratory (Dstl), Salisbury, UK
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33
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Affiliation(s)
- Debora L Hamernik
- Office of Research and Economic Development, University of Nebraska-Lincoln, Lincoln, NE
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34
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Beiki H, Liu H, Huang J, Manchanda N, Nonneman D, Smith TPL, Reecy JM, Tuggle CK. Improved annotation of the domestic pig genome through integration of Iso-Seq and RNA-seq data. BMC Genomics 2019; 20:344. [PMID: 31064321 PMCID: PMC6505119 DOI: 10.1186/s12864-019-5709-y] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 04/17/2019] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Our understanding of the pig transcriptome is limited. RNA transcript diversity among nine tissues was assessed using poly(A) selected single-molecule long-read isoform sequencing (Iso-seq) and Illumina RNA sequencing (RNA-seq) from a single White cross-bred pig. RESULTS Across tissues, a total of 67,746 unique transcripts were observed, including 60.5% predicted protein-coding, 36.2% long non-coding RNA and 3.3% nonsense-mediated decay transcripts. On average, 90% of the splice junctions were supported by RNA-seq within tissue. A large proportion (80%) represented novel transcripts, mostly produced by known protein-coding genes (70%), while 17% corresponded to novel genes. On average, four transcripts per known gene (tpg) were identified; an increase over current EBI (1.9 tpg) and NCBI (2.9 tpg) annotations and closer to the number reported in human genome (4.2 tpg). Our new pig genome annotation extended more than 6000 known gene borders (5' end extension, 3' end extension, or both) compared to EBI or NCBI annotations. We validated a large proportion of these extensions by independent pig poly(A) selected 3'-RNA-seq data, or human FANTOM5 Cap Analysis of Gene Expression data. Further, we detected 10,465 novel genes (81% non-coding) not reported in current pig genome annotations. More than 80% of these novel genes had transcripts detected in > 1 tissue. In addition, more than 80% of novel intergenic genes with at least one transcript detected in liver tissue had H3K4me3 or H3K36me3 peaks mapping to their promoter and gene body, respectively, in independent liver chromatin immunoprecipitation data. CONCLUSIONS These validated results show significant improvement over current pig genome annotations.
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Affiliation(s)
- H Beiki
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA
| | - H Liu
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA
| | - J Huang
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.,College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, Jiangxi, People's Republic of China
| | - N Manchanda
- Department of Ecology, Evolution, and Organismal Biology, Iowa State University, 819 Wallace Road, Ames, IA, 50011, USA
| | - D Nonneman
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - T P L Smith
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | - J M Reecy
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA
| | - C K Tuggle
- Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA, 50011, USA.
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35
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Caprate Modulates Intestinal Barrier Function in Porcine Peyer's Patch Follicle-Associated Epithelium. Int J Mol Sci 2019; 20:ijms20061418. [PMID: 30897851 PMCID: PMC6471651 DOI: 10.3390/ijms20061418] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Revised: 03/09/2019] [Accepted: 03/19/2019] [Indexed: 12/29/2022] Open
Abstract
Background: Many food components influence intestinal epithelial barrier properties and might therefore also affect susceptibility to the development of food allergies. Such allergies are triggered by increased antibody production initiated in Peyer’s patches (PP). Usually, the presentation of antigens in the lumen of the gut to the immune cells of the PP is strongly regulated by the follicle-associated epithelium (FAE) that covers the PP. As the food component caprate has been shown to impede barrier properties in villous epithelium, we hypothesized that caprate also affects the barrier function of the PP FAE, thereby possibly contributing a risk factor for the development of food allergies. Methods: In this study, we have focused on the effects of caprate on the barrier function of PP, employing in vitro and ex vivo experimental setups to investigate functional and molecular barrier properties. Incubation with caprate induced an increase of transepithelial resistance, and a marked increase of permeability for the paracellular marker fluorescein in porcine PP to 180% of control values. These effects are in accordance with changes in the expression levels of the barrier-forming tight junction proteins tricellulin and claudin-5. Conclusions: This barrier-affecting mechanism could be involved in the initial steps of a food allergy, since it might trigger unregulated contact of the gut lumen with antigens.
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36
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Wu KC, Chang YH, Liu HW, Ding DC. Transplanting human umbilical cord mesenchymal stem cells and hyaluronate hydrogel repairs cartilage of osteoarthritis in the minipig model. Tzu Chi Med J 2019; 31:11-19. [PMID: 30692826 PMCID: PMC6334562 DOI: 10.4103/tcmj.tcmj_87_18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
Abstract
Objectives: Osteoarthritis (OA) is a chronic disease of degenerative joints. Mesenchymal stem cells (MSCs) have been used for cartilage regeneration in OA. We investigated the therapeutic potential of human umbilical cord-derived MSCs (HUCMSCs) with hyaluronic acid (HA) hydrogel transplanted into a porcine OA preclinical model. Materials and Methods: The HUCMSCs were characterized with respect to morphology, surface markers, and differentiation capabilities. Quantitative reverse-transcriptase polymerase chain reaction (qRT-PCR) was used to examine gene expressions in a HUCMSC–HA coculture. Two healthy female minipigs weighing 30–40 kg and aged approximately 4 months were used in this large animal study. A full-thickness chondral injury was created in the trochlear groove of each of the pig's rear knees. After 3 weeks, a second osteochondral defect was created. Then, 1.5 mL of a HUCMSC (5 × 106 cells) and HA composite (4%) was transplanted into the chondral-injured area in the right knee of each pig. Using the same surgical process, an osteochondral defect (untreated) was created in the left knee as a control. The pigs were sacrificed 12 weeks after transplantation. Macroscopic and microscopic histologies, qRT-PCR, and immunostaining evaluated the degree of chondral degradation. Results: The HUCMSCs exhibited typical MSC characteristics, including spindle morphology, expression of surface markers (positive for CD29, CD4, CD73, CD90, and human leukocyte antigen [HLA]-ABC; negative for CD34, CD45, and HLA-DR), and multipotent differentiation (adipogenesis, osteogenesis, and chondrogenesis). More extensive proliferation of HUCMSCs was noted with 4% and 25% of HA than without HA. Expression of COL2A1 and aggrecan in the HUCMSC-derived chondrocytes was increased when HA was included. The treated knees showed significant gross and histological improvements in hyaline cartilage regeneration when compared to the control knees. The International Cartilage Repair Society histological score was higher for the treated knees than the control knees. Conclusion: Our findings suggest that cartilage regeneration using a mixture of HUCMSCs and HA in a large animal model may be an effective treatment for OA, and this study is a stepping stone toward the future clinical trials.
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Affiliation(s)
- Kun-Chi Wu
- Department of Orthopedics, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Yu-Hsun Chang
- Department of Pediatrics, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan
| | - Hwan-Wun Liu
- Department of Occupational Medicine, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan.,Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan
| | - Dah-Ching Ding
- Institute of Medical Sciences, Tzu Chi University, Hualien, Taiwan.,Department of Obstetrics and Gynecology, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation and Tzu Chi University, Hualien, Taiwan.,Department of Research, Stem Cell Laboratory, Hualien Tzu Chi Hospital, Buddhist Tzu Chi Medical Foundation, Hualien, Taiwan
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37
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Lowe JWE. Sequencing through thick and thin: Historiographical and philosophical implications. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2018; 72:10-27. [PMID: 30337139 DOI: 10.1016/j.shpsc.2018.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 07/11/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
DNA sequencing has been characterised by scholars and life scientists as an example of 'big', 'fast' and 'automated' science in biology. This paper argues, however, that these characterisations are a product of a particular interpretation of what sequencing is, what I call 'thin sequencing'. The 'thin sequencing' perspective focuses on the determination of the order of bases in a particular stretch of DNA. Based upon my research on the pig genome mapping and sequencing projects, I provide an alternative 'thick sequencing' perspective, which also includes a number of practices that enable the sequence to travel across and be used in wider communities. If we take sequencing in the thin manner to be an event demarcated by the determination of sequences in automated sequencing machines and computers, this has consequences for the historical analysis of sequencing projects, as it focuses attention on those parts of the work of sequencing that are more centralised, fast (and accelerating) and automated. I argue instead that sequencing can be interpreted as a more open-ended process including activities such as the generation of a minimum tile path or annotation, and detail the historiographical and philosophical consequences of this move.
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Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
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38
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Principe DR, Overgaard NH, Park AJ, Diaz AM, Torres C, McKinney R, Dorman MJ, Castellanos K, Schwind R, Dawson DW, Rana A, Maker A, Munshi HG, Rund LA, Grippo PJ, Schook LB. KRAS G12D and TP53 R167H Cooperate to Induce Pancreatic Ductal Adenocarcinoma in Sus scrofa Pigs. Sci Rep 2018; 8:12548. [PMID: 30135483 PMCID: PMC6105629 DOI: 10.1038/s41598-018-30916-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2018] [Accepted: 08/07/2018] [Indexed: 12/17/2022] Open
Abstract
Although survival has improved in recent years, the prognosis of patients with advanced pancreatic ductal adenocarcinoma (PDAC) remains poor. Despite substantial differences in anatomy, physiology, genetics, and metabolism, the overwhelming majority of preclinical testing relies on transgenic mice. Hence, while mice have allowed for tremendous advances in cancer biology, they have been a poor predictor of drug performance/toxicity in the clinic. Given the greater similarity of sus scrofa pigs to humans, we engineered transgenic sus scrofa expressing a LSL-KRASG12D-TP53R167H cassette. By applying Adeno-Cre to pancreatic duct cells in vitro, cells self-immortalized and established tumors in immunocompromised mice. When Adeno-Cre was administered to the main pancreatic duct in vivo, pigs developed extensive PDAC at the injection site hallmarked by excessive proliferation and desmoplastic stroma. This serves as the first large animal model of pancreatic carcinogenesis, and may allow for insight into new avenues of translational research not before possible in rodents.
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Affiliation(s)
- Daniel R Principe
- Medical Scientist Training Program, University of Illinois College of Medicine, Chicago, IL, USA
| | - Nana Haahr Overgaard
- Department of Immunology and Vaccinology, National Veterinary Institute, Technical University of Denmark Copenhagen, Copenhagen, Denmark
- University of Illinois Department of Animal Sciences, Urbana-Champaign, IL, USA
| | - Alex J Park
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Andrew M Diaz
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Carolina Torres
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Ronald McKinney
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Matthew J Dorman
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Karla Castellanos
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA
| | - Regina Schwind
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA
| | - David W Dawson
- Department of Pathology and Laboratory Medicine, Jonsson Comprehensive Cancer Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Ajay Rana
- Department of Surgery, University of Illinois at Chicago, Chicago, IL, USA
| | - Ajay Maker
- Department of Surgery, University of Illinois at Chicago, Chicago, IL, USA
| | | | - Lauretta A Rund
- University of Illinois Department of Animal Sciences, Urbana-Champaign, IL, USA
- Institute for Genomic Biology, University of Illinois, Urbana-Champaign, IL, USA
| | - Paul J Grippo
- Department of Medicine, University of Illinois at Chicago, Chicago, IL, USA.
| | - Lawrence B Schook
- University of Illinois Department of Animal Sciences, Urbana-Champaign, IL, USA.
- Department of Radiology, University of Illinois at Chicago, Chicago, IL, USA.
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39
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Ganesan S, Volodina O, Pearce SC, Gabler NK, Baumgard LH, Rhoads RP, Selsby JT. Acute heat stress activated inflammatory signaling in porcine oxidative skeletal muscle. Physiol Rep 2018; 5:5/16/e13397. [PMID: 28830980 PMCID: PMC5582270 DOI: 10.14814/phy2.13397] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2017] [Revised: 07/24/2017] [Accepted: 07/27/2017] [Indexed: 11/24/2022] Open
Abstract
Despite well-studied clinical manifestations, intracellular mechanisms of prolonged hyperthermic injury remain unclear, especially in skeletal muscle. Given muscle's large potential to impact systemic inflammation and metabolism, the response of muscle cells to heat-mediated injury warrants further investigation. We have previously reported increased activation of NF-κB signaling and increased NF-κB and AP-1-driven transcripts in oxidative skeletal muscle following 12 h of heat stress. The purpose of this investigation was to examine early heat stress-induced inflammatory signaling in skeletal muscle. We hypothesized that heat stress would increase NF-κB and AP-1 signaling in oxidative skeletal muscle. To address this hypothesis, 32 gilts were randomly assigned to one of four treatment groups (n = 8/group): control (0 h: 21°C) or exposed to heat stress conditions (37°C) for 2 h (n = 8), 4 h (n = 8), or 6 h (n = 8). Immediately following environmental exposure pigs were euthanized and the red portion of the semitendinosus muscle (STR) was harvested. We found evidence of NF-κB pathway activation as indicated by increased protein abundance of NF-κB activator IKK-α following 4 h and increased total NF-κB protein abundance following 6 h of heat stress. Heat stress also stimulated AP-1 signaling as AP-1 protein abundance was increased in nuclear fractions following 4 h of heat stress. Interleukin-6 protein abundance and activation of the JAK/STAT pathway were decreased in heat stressed muscle. These data indicate that heat stress activated inflammatory signaling in the porcine STR muscle via the AP-1 pathway and early activation of the NF-κB pathway.
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Affiliation(s)
- Shanthi Ganesan
- Department of Animal Science, Iowa State University, Ames, Iowa
| | - Olga Volodina
- Department of Animal Science, Iowa State University, Ames, Iowa
| | - Sarah C Pearce
- Department of Animal Science, Iowa State University, Ames, Iowa
| | | | | | - Robert P Rhoads
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, Virginia
| | - Joshua T Selsby
- Department of Animal Science, Iowa State University, Ames, Iowa
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40
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Ghosh M, Sharma N, Singh AK, Gera M, Pulicherla KK, Jeong DK. Transformation of animal genomics by next-generation sequencing technologies: a decade of challenges and their impact on genetic architecture. Crit Rev Biotechnol 2018; 38:1157-1175. [PMID: 29631431 DOI: 10.1080/07388551.2018.1451819] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
For more than a quarter of a century, sequencing technologies from Sanger's method to next-generation high-throughput techniques have provided fascinating opportunities in the life sciences. The continuing upward trajectory of sequencing technologies will improve livestock research and expedite the development of various new genomic and technological studies with farm animals. The use of high-throughput technologies in livestock research has increased interest in metagenomics, epigenetics, genome-wide association studies, and identification of single nucleotide polymorphisms and copy number variations. Such studies are beginning to provide revolutionary insights into biological and evolutionary processes. Farm animals, such as cattle, swine, and horses, have played a dual role as economically and agriculturally important animals as well as biomedical research models. The first part of this study explores the current state of sequencing methods, many of which are already used in animal genomic studies, and the second part summarizes the state of cattle, swine, horse, and chicken genome sequencing and illustrates its achievements during the last few years. Finally, we describe several high-throughput sequencing approaches for the improved detection of known, unknown, and emerging infectious agents, leading to better diagnosis of infectious diseases. The insights from viral metagenomics and the advancement of next-generation sequencing will strongly support specific and efficient vaccine development and provide strategies for controlling infectious disease transmission among animal populations and/or between animals and humans. However, prospective sequencing technologies will require further research and in-field testing before reaching the marketplace.
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Affiliation(s)
- Mrinmoy Ghosh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Neelesh Sharma
- b Department of Veterinary Science and Animal Husbandry , Sher-e-Kashmir University of Agricultural Sciences and Technology , R.S. Pura , India
| | - Amit Kumar Singh
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | - Meeta Gera
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
| | | | - Dong Kee Jeong
- a Department of Animal Biotechnology , Jeju National University , Jeju-Do , Republic of Korea
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41
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Arends D, Hesse D, Brockmann GA. Invited review: Genetic and genomic mouse models for livestock research. Arch Anim Breed 2018. [DOI: 10.5194/aab-61-87-2018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Abstract. Knowledge about the function and functioning of single or
multiple interacting genes is of the utmost significance for understanding the
organism as a whole and for accurate livestock improvement through genomic
selection. This includes, but is not limited to, understanding the
ontogenetic and environmentally driven regulation of gene action
contributing to simple and complex traits. Genetically modified mice, in
which
the functions of single genes are annotated; mice with reduced genetic
complexity; and simplified structured populations are tools to gain
fundamental knowledge of inheritance patterns and whole system genetics and
genomics. In this review, we briefly describe existing mouse resources and
discuss their value for fundamental and applied research in livestock.
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42
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Marx H, Hahne H, Ulbrich SE, Schnieke A, Rottmann O, Frishman D, Kuster B. Annotation of the Domestic Pig Genome by Quantitative Proteogenomics. J Proteome Res 2017. [PMID: 28625053 DOI: 10.1021/acs.jproteome.7b00184] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The pig is one of the earliest domesticated animals in the history of human civilization and represents one of the most important livestock animals. The recent sequencing of the Sus scrofa genome was a major step toward the comprehensive understanding of porcine biology, evolution, and its utility as a promising large animal model for biomedical and xenotransplantation research. However, the functional and structural annotation of the Sus scrofa genome is far from complete. Here, we present mass spectrometry-based quantitative proteomics data of nine juvenile organs and six embryonic stages between 18 and 39 days after gestation. We found that the data provide evidence for and improve the annotation of 8176 protein-coding genes including 588 novel and 321 refined gene models. The analysis of tissue-specific proteins and the temporal expression profiles of embryonic proteins provides an initial functional characterization of expressed protein interaction networks and modules including as yet uncharacterized proteins. Comparative transcript and protein expression analysis to human organs reveal a moderate conservation of protein translation across species. We anticipate that this resource will facilitate basic and applied research on Sus scrofa as well as its porcine relatives.
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Affiliation(s)
| | | | | | | | | | - Dmitrij Frishman
- Institute of Bioinformatics and Systems Biology , German Research Center for Environmental Health, Neuherberg, Germany.,St Petersburg State Polytechnical University , St Petersburg, Russia
| | - Bernhard Kuster
- Center for Integrated Protein Science Munich , Munich, Germany
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43
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Ventrella D, Dondi F, Barone F, Serafini F, Elmi A, Giunti M, Romagnoli N, Forni M, Bacci ML. The biomedical piglet: establishing reference intervals for haematology and clinical chemistry parameters of two age groups with and without iron supplementation. BMC Vet Res 2017; 13:23. [PMID: 28095847 PMCID: PMC5240404 DOI: 10.1186/s12917-017-0946-2] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Accepted: 01/11/2017] [Indexed: 11/21/2022] Open
Abstract
Background The similarities between swine and humans in physiological and genomic patterns, and the great correlation in size and anatomy, make pigs extremely useful in preclinical studies. New-born piglets can represent a model for congenital and genetic diseases in new-born children. It is known that piglets may have significant differences in clinicopathological results compared to adult pigs. Therefore, adult laboratory reference intervals cannot be applied to piglets. The aim of this study was to compare haematological and chemical variables in piglets of two ages and determinate age-related reference intervals for commercial hybrid young pigs. Blood samples were collected under general anaesthesia from 130 animals divided into five- (P5) and 30- (P30) day-old piglets. Only P30 animals were treated with parenteral iron after birth. Samples were analysed using automated haematology (ADVIA 2120) and chemistry analysers, and age-related reference intervals were calculated. Results Significant higher values of RBC, Hb and HCT were observed in P30 animals when compared to P5, with an opposite trend for MCV. These results were associated with a reduction of the RBC regeneration process and the thrombopoietic response. The TSAT and TIBC were significantly higher in P30 compared to P5; however, piglets remained iron deficient compared to adult reference intervals reported previously. Conclusions In conclusion, this paper emphasises the high variability occurring in clinicopathological variables between new-born and 30-day-old pigs, and between piglets and adult pigs. This study provides valuable reference data for piglets at precise ages and could be used in the future as historical control improving the Reduction in animal experiments, as suggested by the 3Rs principle. Electronic supplementary material The online version of this article (doi:10.1186/s12917-017-0946-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Domenico Ventrella
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Francesco Dondi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy.
| | - Francesca Barone
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Federica Serafini
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Alberto Elmi
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Massimo Giunti
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Noemi Romagnoli
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Monica Forni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
| | - Maria L Bacci
- Department of Veterinary Medical Sciences, Alma Mater Studiorum, University of Bologna, Via Tolara di Sopra 50, 40064, Ozzano dell'Emilia, BO, Italy
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Groenen MAM. A decade of pig genome sequencing: a window on pig domestication and evolution. Genet Sel Evol 2016; 48:23. [PMID: 27025270 PMCID: PMC4812630 DOI: 10.1186/s12711-016-0204-2] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2015] [Accepted: 03/16/2016] [Indexed: 12/02/2022] Open
Abstract
Insight into how genomes change and adapt due to selection addresses key questions in evolutionary biology and in domestication of animals and plants by humans. In that regard, the pig and its close relatives found in Africa and Eurasia represent an excellent group of species that enables studies of the effect of both natural and human-mediated selection on the genome. The recent completion of the draft genome sequence of a domestic pig and the development of next-generation sequencing technology during the past decade have created unprecedented possibilities to address these questions in great detail. In this paper, I review recent whole-genome sequencing studies in the pig and closely-related species that provide insight into the demography, admixture and selection of these species and, in particular, how domestication and subsequent selection of Sus scrofa have shaped the genomes of these animals.
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Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, Droevendaalsesteeg 1, 6708 PB, Wageningen, The Netherlands.
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Schook LB, Collares TV, Darfour-Oduro KA, De AK, Rund LA, Schachtschneider KM, Seixas FK. Unraveling the swine genome: implications for human health. Annu Rev Anim Biosci 2016; 3:219-44. [PMID: 25689318 DOI: 10.1146/annurev-animal-022114-110815] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The pig was first used in biomedical research in ancient Greece and over the past few decades has quickly grown into an important biomedical research tool. Pigs have genetic and physiological traits similar to humans, which make them one of the most useful and versatile animal models. Owing to these similarities, data generated from porcine models are more likely to lead to viable human treatments than those from murine work. In addition, the similarity in size and physiology to humans allows pigs to be used for many experimental approaches not feasible in mice. Research areas that employ pigs range from neonatal development to translational models for cancer therapy. Increasing numbers of porcine models are being developed since the release of the swine genome sequence, and the development of additional porcine genomic and epigenetic resources will further their use in biomedical research.
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Affiliation(s)
- Lawrence B Schook
- Department of Animal Sciences, University of Illinois, Urbana, Illinois 61801; , , , ,
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46
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Renukaradhya GJ, Narasimhan B, Mallapragada SK. Respiratory nanoparticle-based vaccines and challenges associated with animal models and translation. J Control Release 2015; 219:622-631. [PMID: 26410807 PMCID: PMC4760633 DOI: 10.1016/j.jconrel.2015.09.047] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 09/21/2015] [Accepted: 09/23/2015] [Indexed: 12/14/2022]
Abstract
Vaccine development has had a huge impact on human health. However, there is a significant need to develop efficacious vaccines for several existing as well as emerging respiratory infectious diseases. Several challenges need to be overcome to develop efficacious vaccines with translational potential. This review focuses on two aspects to overcome some barriers - 1) the development of nanoparticle-based vaccines, and 2) the choice of suitable animal models for respiratory infectious diseases that will allow for translation. Nanoparticle-based vaccines, including subunit vaccines involving synthetic and/or natural polymeric adjuvants and carriers, as well as those based on virus-like particles offer several key advantages to help overcome the barriers to effective vaccine development. These include the ability to deliver combinations of antigens, target the vaccine formulation to specific immune cells, enable cross-protection against divergent strains, act as adjuvants or immunomodulators, allow for sustained release of antigen, enable single dose delivery, and potentially obviate the cold chain. While mouse models have provided several important insights into the mechanisms of infectious diseases, they are often a limiting step in translation of new vaccines to the clinic. An overview of different animal models involved in vaccine research for respiratory infections, with advantages and disadvantages of each model, is discussed. Taken together, advances in nanotechnology, combined with the right animal models for evaluating vaccine efficacy, has the potential to revolutionize vaccine development for respiratory infections.
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Affiliation(s)
- Gourapura J Renukaradhya
- Food Animal Health Research Program, Ohio Agricultural Research and Development Center, The Ohio State University, Wooster, OH 44691, United States
| | - Balaji Narasimhan
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, United States
| | - Surya K Mallapragada
- Department of Chemical and Biological Engineering, Iowa State University, Ames, IA 50011, United States.
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Ha CW, Park YB, Chung JY, Park YG. Cartilage Repair Using Composites of Human Umbilical Cord Blood-Derived Mesenchymal Stem Cells and Hyaluronic Acid Hydrogel in a Minipig Model. Stem Cells Transl Med 2015; 4:1044-51. [PMID: 26240434 DOI: 10.5966/sctm.2014-0264] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 06/17/2015] [Indexed: 12/27/2022] Open
Abstract
UNLABELLED The cartilage regeneration potential of human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs) with a hyaluronic acid (HA) hydrogel composite has shown remarkable results in rat and rabbit models. The purpose of the present study was to confirm the consistent regenerative potential in a pig model using three different cell lines. A full-thickness chondral injury was intentionally created in the trochlear groove of each knee in 6 minipigs. Three weeks later, an osteochondral defect, 5 mm wide by 10 mm deep, was created, followed by an 8-mm-wide and 5-mm-deep reaming. A mixture (1.5 ml) of hUCB-MSCs (0.5×10(7) cells per milliliter) and 4% HA hydrogel composite was then transplanted into the defect on the right knee. Each cell line was used in two minipigs. The osteochondral defect created in the same manner on the left knee was untreated to act as the control. At 12 weeks postoperatively, the pigs were sacrificed, and the degree of subsequent cartilage regeneration was evaluated by gross and histological analysis. The transplanted knee resulted in superior and more complete hyaline cartilage regeneration compared with the control knee. The cellular characteristics (e.g., cellular proliferation and chondrogenic differentiation capacity) of the hUCB-MSCs influenced the degree of cartilage regeneration potential. This evidence of consistent cartilage regeneration using composites of hUCB-MSCs and HA hydrogel in a large animal model could be a stepping stone to a human clinical trial in the future. SIGNIFICANCE To date, several studies have investigated the chondrogenic potential of human umbilical cord blood-derived mesenchymal stem cells (hUCB-MSCs); however, the preclinical studies are still limited in numbers with various results. In parallel, in the past several years, the cartilage regeneration potential of hUCB-MSCs with a hyaluronic acid (HA) hydrogel composite have been investigated and remarkable results in rat and rabbit models have been attained. (These experimental results are currently in preparation for publication.) Before applying the cartilage regeneration technique in a human clinical trial, it seemed necessary to confirm the consistent result in a larger animal model. At 12 weeks postoperatively, the minipigs were sacrificed, and the degree of subsequent cartilage regeneration was evaluated by gross and histological analysis. The transplanted knee resulted in superior and more complete hyaline cartilage regeneration compared with the control knee. This evidence of consistent cartilage regeneration with composites of hUCB-MSCs and HA hydrogel in a large animal model could be a stepping stone to a human clinical trial in the future.
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Affiliation(s)
- Chul-Won Ha
- Department of Orthopedic Surgery, Stem Cell and Regenerative Medicine Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Ajou University Hospital, Ajou University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Jeju National University Hospital, Jeju National University School of Medicine, Jeju-do, Republic of Korea
| | - Yong-Beom Park
- Department of Orthopedic Surgery, Stem Cell and Regenerative Medicine Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Ajou University Hospital, Ajou University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Jeju National University Hospital, Jeju National University School of Medicine, Jeju-do, Republic of Korea
| | - Jun-Young Chung
- Department of Orthopedic Surgery, Stem Cell and Regenerative Medicine Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Ajou University Hospital, Ajou University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Jeju National University Hospital, Jeju National University School of Medicine, Jeju-do, Republic of Korea
| | - Yong-Geun Park
- Department of Orthopedic Surgery, Stem Cell and Regenerative Medicine Center, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Ajou University Hospital, Ajou University School of Medicine, Seoul, Republic of Korea; Department of Orthopedic Surgery, Jeju National University Hospital, Jeju National University School of Medicine, Jeju-do, Republic of Korea
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48
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Moderately increased maternal dietary energy intake delays foetal skeletal muscle differentiation and maturity in pigs. Eur J Nutr 2015; 55:1777-87. [PMID: 26179476 DOI: 10.1007/s00394-015-0996-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Accepted: 07/07/2015] [Indexed: 10/23/2022]
Abstract
OBJECTIVES This study aimed to evaluate the effects of moderately increased maternal dietary energy intake during gestation on foetal skeletal muscle development and metabolism with pig as a model. METHODS Twelve primiparous purebred Large White sows (initial body weight 135.5 ± 1.6 kg) were allocated to one of two energy intake treatments: normal-energy-intake group (Con, 30.96 MJ DE/day) as recommended by the National Research Council (NRC; 2012) and high-energy-intake group (HE, 34.15 MJ DE/day). The nutritional treatments were introduced from mating to day 90 of gestation. On day 90 of gestation, foetuses were examined by morphological, biochemical and molecular analysis of the longissimus muscle. Umbilical vein serum hormones were measured. RESULTS Sow body weight was increased in HE group compared with Con group (P < 0.05), whereas foetal myofibre density was decreased (P < 0.05). Meanwhile, protein concentration, creatine kinase and lactate dehydrogenase activities and umbilical vein serum triiodothyronine (T3) concentration were decreased in HE foetuses (P < 0.05). Maternal HE diets decreased the mRNA abundance of muscle growth-related genes, myosin heavy-chain (MYH/MyHC) genes (MYH2 and MYH1) and insulin-like growth factor 1 and insulin growth factor-binding protein 5 (P < 0.05). Furthermore, the protein expressions of myogenic differentiation factor 1, myogenin and fast-MyHC isoforms were reduced in HE foetuses (P < 0.05). CONCLUSION Our results suggest that moderately increased maternal dietary energy intake delays the differentiation and maturation in skeletal muscle of the foetus on day 90 of gestation.
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Porcine models of digestive disease: the future of large animal translational research. Transl Res 2015; 166:12-27. [PMID: 25655839 PMCID: PMC4458388 DOI: 10.1016/j.trsl.2015.01.004] [Citation(s) in RCA: 144] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/03/2014] [Revised: 01/03/2015] [Accepted: 01/07/2015] [Indexed: 12/14/2022]
Abstract
There is increasing interest in nonrodent translational models for the study of human disease. The pig, in particular, serves as a useful animal model for the study of pathophysiological conditions relevant to the human intestine. This review assesses currently used porcine models of gastrointestinal physiology and disease and provides a rationale for the use of these models for future translational studies. The pig has proven its utility for the study of fundamental disease conditions such as ischemia-reperfusion injury, stress-induced intestinal dysfunction, and short bowel syndrome. Pigs have also shown great promise for the study of intestinal barrier function, surgical tissue manipulation and intervention, as well as biomaterial implantation and tissue transplantation. Advantages of pig models highlighted by these studies include the physiological similarity to human intestine and mechanisms of human disease. Emerging future directions for porcine models of human disease include the fields of transgenics and stem cell biology, with exciting implications for regenerative medicine.
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Rajao DS, Vincent AL. Swine as a Model for Influenza A Virus Infection and Immunity. ILAR J 2015; 56:44-52. [DOI: 10.1093/ilar/ilv002] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
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