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Desire S, Johnsson M, Ros-Freixedes R, Chen CY, Holl JW, Herring WO, Gorjanc G, Mellanby RJ, Hickey JM, Jungnickel MK. A genome-wide association study for loin depth and muscle pH in pigs from intensely selected purebred lines. Genet Sel Evol 2023; 55:42. [PMID: 37322449 DOI: 10.1186/s12711-023-00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 05/26/2023] [Indexed: 06/17/2023] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) aim at identifying genomic regions involved in phenotype expression, but identifying causative variants is difficult. Pig Combined Annotation Dependent Depletion (pCADD) scores provide a measure of the predicted consequences of genetic variants. Incorporating pCADD into the GWAS pipeline may help their identification. Our objective was to identify genomic regions associated with loin depth and muscle pH, and identify regions of interest for fine-mapping and further experimental work. Genotypes for ~ 40,000 single nucleotide morphisms (SNPs) were used to perform GWAS for these two traits, using de-regressed breeding values (dEBV) for 329,964 pigs from four commercial lines. Imputed sequence data was used to identify SNPs in strong ([Formula: see text] 0.80) linkage disequilibrium with lead GWAS SNPs with the highest pCADD scores. RESULTS Fifteen distinct regions were associated with loin depth and one with loin pH at genome-wide significance. Regions on chromosomes 1, 2, 5, 7, and 16, explained between 0.06 and 3.55% of the additive genetic variance and were strongly associated with loin depth. Only a small part of the additive genetic variance in muscle pH was attributed to SNPs. The results of our pCADD analysis suggests that high-scoring pCADD variants are enriched for missense mutations. Two close but distinct regions on SSC1 were associated with loin depth, and pCADD identified the previously identified missense variant within the MC4R gene for one of the lines. For loin pH, pCADD identified a synonymous variant in the RNF25 gene (SSC15) as the most likely candidate for the muscle pH association. The missense mutation in the PRKAG3 gene known to affect glycogen content was not prioritised by pCADD for loin pH. CONCLUSIONS For loin depth, we identified several strong candidate regions for further statistical fine-mapping that are supported in the literature, and two novel regions. For loin muscle pH, we identified one previously identified associated region. We found mixed evidence for the utility of pCADD as an extension of heuristic fine-mapping. The next step is to perform more sophisticated fine-mapping and expression quantitative trait loci (eQTL) analysis, and then interrogate candidate variants in vitro by perturbation-CRISPR assays.
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Affiliation(s)
- Suzanne Desire
- The Roslin Institute, The University of Edinburgh, Midlothian, UK.
| | - Martin Johnsson
- Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida-Agrotecnio-CERCA Center, Lleida, Spain
| | - Ching-Yi Chen
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | - Justin W Holl
- The Pig Improvement Company, Genus Plc, Hendersonville, TN, USA
| | | | - Gregor Gorjanc
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
| | - Richard J Mellanby
- The Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Midlothian, UK
| | - John M Hickey
- The Roslin Institute, The University of Edinburgh, Midlothian, UK
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Nottle MB, Hawthorne WJ, Cowan PJ. The birth of Dolly and xenotransplantation 25 years on. Xenotransplantation 2023; 30:e12782. [PMID: 36413478 DOI: 10.1111/xen.12782] [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: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/23/2022]
Abstract
A number of reviews have been written recently celebrating the 25th anniversary of the birth of Dolly the cloned sheep and the effect this breakthrough has had on various fields of research. However, arguably the biggest impact Dolly has had is on the field of xenotransplantation, described here based on our own experience and that of others.
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Affiliation(s)
- Mark B Nottle
- School of Biomedicine and Robinson Research Institute, University of Adelaide, Adelaide, South Australia, Australia
| | - Wayne J Hawthorne
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, New South Wales, Australia.,Department of Surgery, Westmead Hospital, School of Medical Sciences, University of Sydney, Westmead, New South Wales, Australia
| | - Peter J Cowan
- Immunology Research Centre, St. Vincent's Hospital, Melbourne, Victoria, Australia.,Department of Medicine, University of Melbourne, Melbourne, Victoria, Australia
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Hawthorne WJ, Salvaris EJ, Chew YV, Burns H, Hawkes J, Barlow H, Hu M, Lew AM, Nottle MB, O’Connell PJ, Cowan PJ. Xenotransplantation of Genetically Modified Neonatal Pig Islets Cures Diabetes in Baboons. Front Immunol 2022; 13:898948. [PMID: 35784286 PMCID: PMC9243461 DOI: 10.3389/fimmu.2022.898948] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Accepted: 05/12/2022] [Indexed: 11/13/2022] Open
Abstract
Xenotransplantation using porcine donors is rapidly approaching clinical applicability as an alternative therapy for treatment of many end-stage diseases including type 1 diabetes. Porcine neonatal islet cell clusters (NICC) have normalised blood sugar levels for relatively short periods in the preclinical diabetic rhesus model but have met with limited success in the stringent baboon model. Here we report that NICC from genetically modified (GM) pigs deleted for αGal and expressing the human complement regulators CD55 and CD59 can cure diabetes long-term in immunosuppressed baboons, with maximum graft survival exceeding 22 months. Five diabetic baboons were transplanted intraportally with 9,673 – 56,913 islet equivalents (IEQ) per kg recipient weight. Immunosuppression consisted of T cell depletion with an anti-CD2 mAb, tacrolimus for the first 4 months, and maintenance with belatacept and anti-CD154; no anti-inflammatory treatment or cytomegalovirus (CMV) prophylaxis/treatment was given. This protocol was well tolerated, with all recipients maintaining or gaining weight. Recipients became insulin-independent at a mean of 87 ± 43 days post-transplant and remained insulin-independent for 397 ± 174 days. Maximum graft survival was 675 days. Liver biopsies showed functional islets staining for all islet endocrine components, with no evidence of the inflammatory blood-mediated inflammatory reaction (IBMIR) and minimal leukocytic infiltration. The costimulation blockade-based immunosuppressive protocol prevented an anti-pig antibody response in all recipients. In conclusion, we demonstrate that genetic modification of the donor pig enables attenuation of early islet xenograft injury, and in conjunction with judicious immunosuppression provides excellent long-term function and graft survival in the diabetic baboon model.
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Affiliation(s)
- Wayne J. Hawthorne
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Department of Surgery, Westmead Hospital, School of Medical Sciences, University of Sydney, Westmead, NSW, Australia
- *Correspondence: Wayne J. Hawthorne,
| | - Evelyn J. Salvaris
- Immunology Research Centre, St. Vincent’s Hospital, Melbourne, VIC, Australia
| | - Yi Vee Chew
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Heather Burns
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Joanne Hawkes
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Helen Barlow
- Immunology Research Centre, St. Vincent’s Hospital, Melbourne, VIC, Australia
| | - Min Hu
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Andrew M. Lew
- Division of Immunology, Walter and Eliza Hall Institute, Melbourne, VIC, Australia
| | - Mark B. Nottle
- Department of Obstetrics and Gynaecology, University of Adelaide, Adelaide, SA, Australia
| | - Philip J. O’Connell
- The Centre for Transplant & Renal Research, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Peter J. Cowan
- Immunology Research Centre, St. Vincent’s Hospital, Melbourne, VIC, Australia
- Department of Medicine, University of Melbourne, Melbourne, VIC, Australia
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CRISPR FokI Dead Cas9 System: Principles and Applications in Genome Engineering. Cells 2020; 9:cells9112518. [PMID: 33233344 PMCID: PMC7700487 DOI: 10.3390/cells9112518] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/05/2020] [Accepted: 11/19/2020] [Indexed: 12/18/2022] Open
Abstract
The identification of the robust clustered regularly interspersed short palindromic repeats (CRISPR) associated endonuclease (Cas9) system gene-editing tool has opened up a wide range of potential therapeutic applications that were restricted by more complex tools, including zinc finger nucleases (ZFNs) and transcription activator-like effector nucleases (TALENs). Nevertheless, the high frequency of CRISPR system off-target activity still limits its applications, and, thus, advanced strategies for highly specific CRISPR/Cas9-mediated genome editing are continuously under development including CRISPR–FokI dead Cas9 (fdCas9). fdCas9 system is derived from linking a FokI endonuclease catalytic domain to an inactive Cas9 protein and requires a pair of guide sgRNAs that bind to the sense and antisense strands of the DNA in a protospacer adjacent motif (PAM)-out orientation, with a defined spacer sequence range around the target site. The dimerization of FokI domains generates DNA double-strand breaks, which activates the DNA repair machinery and results in genomic edit. So far, all the engineered fdCas9 variants have shown promising gene-editing activities in human cells when compared to other platforms. Herein, we review the advantages of all published variants of fdCas9 and their current applications in genome engineering.
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Kalsi R, Messner F, Brandacher G. Skin xenotransplantation: technological advances and future directions. Curr Opin Organ Transplant 2020; 25:464-476. [PMID: 32773504 DOI: 10.1097/mot.0000000000000798] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW To summarize the evolution of skin xenotransplantation and contextualize technological advances and the status of clinically applicable large animal research as well as prospects for translation of this work as a viable future treatment option. RECENT FINDINGS Porcine xenografts at the start of the millennium were merely biologic dressings subject to rapid rejection. Since then, numerous important advances in swine to nonhuman primate models have yielded xenotransplant products at the point of clinical translation. Critical genetic modifications in swine from a designated pathogen-free donor herd have allowed xenograft survival reaching 30 days without preconditioning or maintenance immunosuppression. Further, xenograft coverage appears not to sensitize the recipient to subsequent allograft placement and vice versa, allowing for temporary coverage times to be doubled using both xeno and allografts. SUMMARY Studies in large animal models have led to significant progress in the creation of living, functional skin xenotransplants with clinically relevant shelf-lives to improve the management of patients with extensive burns.
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Affiliation(s)
- Richa Kalsi
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation (VCA) Laboratory, Johns Hopkins University School of Medicine.,Department of General Surgery, University of Maryland Medical Center, Baltimore, Maryland, USA
| | - Franka Messner
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation (VCA) Laboratory, Johns Hopkins University School of Medicine.,Department of Visceral, Transplant and Thoracic Surgery, Center of Operative Medicine, Medical University of Innsbruck, Innsbruck, Austria
| | - Gerald Brandacher
- Department of Plastic and Reconstructive Surgery, Vascularized Composite Allotransplantation (VCA) Laboratory, Johns Hopkins University School of Medicine
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Kemter E, Schnieke A, Fischer K, Cowan PJ, Wolf E. Xeno-organ donor pigs with multiple genetic modifications - the more the better? Curr Opin Genet Dev 2020; 64:60-65. [PMID: 32619817 DOI: 10.1016/j.gde.2020.05.034] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Accepted: 05/25/2020] [Indexed: 01/05/2023]
Abstract
The number of donated human organs and tissues for patients with terminal organ failure falls far short of the need. Alternative sources, such as organs and tissues from animals, are therefore urgently required. During the past few years, major progress has been made in the development of genetically multi-modified donor pigs, and their organs have been shown to be safe and efficacious in life-supporting transplantation models into non-human primates, paving the way to clinical xenotransplantation studies. Here, we summarize recent developments in pig genome engineering and discuss efforts to develop the optimum donor pig for xenotransplantation. In addition, we speculate on how many genetic modifications may be required for initial xenotransplantation clinical trials.
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Affiliation(s)
- Elisabeth Kemter
- Chair of Molecular Animal Breeding and Biotechnology, and Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany
| | - Angelika Schnieke
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, 85350 Freising, Germany
| | - Konrad Fischer
- Chair of Livestock Biotechnology, School of Life Sciences Weihenstephan, Technische Universität München, 85350 Freising, Germany
| | - Peter J Cowan
- Immunology Research Centre, St. Vincent's Hospital Melbourne, and Department of Medicine, University of Melbourne, Victoria, Australia
| | - Eckhard Wolf
- Chair of Molecular Animal Breeding and Biotechnology, and Laboratory for Functional Genome Analysis (LAFUGA), Gene Center, LMU Munich, 81377 Munich, Germany; Center for Innovative Medical Models (CiMM), Department of Veterinary Sciences, LMU Munich, 85764 Oberschleißheim, Germany.
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7
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Chen AM, Burlak C. Xenotransplantation literature update, January/February 2020. Xenotransplantation 2020; 27:e12589. [PMID: 32170808 DOI: 10.1111/xen.12589] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 02/25/2020] [Indexed: 11/30/2022]
Affiliation(s)
- Angela M Chen
- Division of Transplant Surgery, Department of Surgery, Indiana University School of Medicine, Indianapolis, Indiana
| | - Christopher Burlak
- Department of Surgery, Schulze Diabetes Institute, University of Minnesota Medical School, Minneapolis, Minnesota
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