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Kuppa A, Alzamrooni A, Lopez R, Suhan T, Chaudhary R, Collins N, Van den Bergh F, Abouleisa R, Wang H, Mohamed T, Satin J, Lyssiotis C, Beard DA, Abdel-Latif A. Inherent Metabolic Adaptations in Adult Spiny Mouse ( Acomys ) Cardiomyocytes Facilitate Enhanced Cardiac Recovery Following Myocardial Infarction. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.22.595229. [PMID: 38826249 PMCID: PMC11142149 DOI: 10.1101/2024.05.22.595229] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The adult mammalian heart has limited regenerative capacity following injury, leading to progressive heart failure and mortality. Recent studies have identified the spiny mouse ( Acomys ) as a unique model for mammalian cardiac isch3emic resilience, exhibiting enhanced recovery after myocardial infarction (MI) compared to commonly used laboratory mouse strains. However, the underlying cellular and molecular mechanisms behind this unique response remain poorly understood. In this study, we comprehensively characterized the metabolic characteristics of cardiomyocytes in Acomys compared to the non-regenerative Mus musculus . We utilized single-nucleus RNA sequencing (snRNA-seq) in sham-operated animals and 1, 3, and 7 days post-myocardial infarction to investigate cardiomyocytes' transcriptomic and metabolomic profiles in response to myocardial infarction. Complementary targeted metabolomics, stable isotope-resolved metabolomics, and functional mitochondrial assays were performed on heart tissues from both species to validate the transcriptomic findings and elucidate the metabolic adaptations in cardiomyocytes following ischemic injury. Transcriptomic analysis revealed that Acomys cardiomyocytes inherently upregulate genes associated with glycolysis, the pentose phosphate pathway, and glutathione metabolism while downregulating genes involved in oxidative phosphorylation (OXPHOS). These metabolic characteristics are linked to decreased reactive oxygen species (ROS) production and increased antioxidant capacity. Our targeted metabolomic studies in heart tissue corroborated these findings, showing a shift from fatty acid oxidation to glycolysis and ancillary biosynthetic pathways in Acomys at baseline with adaptive changes post-MI. Functional mitochondrial studies indicated a higher reliance on glycolysis in Acomys compared to Mus , underscoring the unique metabolic phenotype of Acomys hearts. Stable isotope tracing experiments confirmed a shift in glucose utilization from oxidative phosphorylation in Acomys . In conclusion, our study identifies unique metabolic characteristics of Acomys cardiomyocytes that contribute to their enhanced ischemic resilience following myocardial infarction. These findings provide novel insights into the role of metabolism in regulating cardiac repair in adult mammals. Our work highlights the importance of inherent and adaptive metabolic flexibility in determining cardiomyocyte ischemic responses and establishes Acomys as a valuable model for studying cardiac ischemic resilience in adult mammals. Graphical abstract
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2
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Weinberger M, Riley PR. Animal models to study cardiac regeneration. Nat Rev Cardiol 2024; 21:89-105. [PMID: 37580429 DOI: 10.1038/s41569-023-00914-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 07/17/2023] [Indexed: 08/16/2023]
Abstract
Permanent fibrosis and chronic deterioration of heart function in patients after myocardial infarction present a major health-care burden worldwide. In contrast to the restricted potential for cellular and functional regeneration of the adult mammalian heart, a robust capacity for cardiac regeneration is seen during the neonatal period in mammals as well as in the adults of many fish and amphibian species. However, we lack a complete understanding as to why cardiac regeneration takes place more efficiently in some species than in others. The capacity of the heart to regenerate after injury is controlled by a complex network of cellular and molecular mechanisms that form a regulatory landscape, either permitting or restricting regeneration. In this Review, we provide an overview of the diverse array of vertebrates that have been studied for their cardiac regenerative potential and discuss differential heart regeneration outcomes in closely related species. Additionally, we summarize current knowledge about the core mechanisms that regulate cardiac regeneration across vertebrate species.
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Affiliation(s)
- Michael Weinberger
- Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford, UK
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Paul R Riley
- Institute of Developmental & Regenerative Medicine, University of Oxford, Oxford, UK.
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3
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Huang H, Huang GN, Payumo AY. Two decades of heart regeneration research: Cardiomyocyte proliferation and beyond. WIREs Mech Dis 2024; 16:e1629. [PMID: 37700522 PMCID: PMC10840678 DOI: 10.1002/wsbm.1629] [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: 05/15/2023] [Revised: 08/03/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023]
Abstract
Interest in vertebrate cardiac regeneration has exploded over the past two decades since the discovery that adult zebrafish are capable of complete heart regeneration, contrasting the limited regenerative potential typically observed in adult mammalian hearts. Undercovering the mechanisms that both support and limit cardiac regeneration across the animal kingdom may provide unique insights in how we may unlock this capacity in adult humans. In this review, we discuss key discoveries in the heart regeneration field over the last 20 years. Initially, seminal findings revealed that pre-existing cardiomyocytes are the major source of regenerated cardiac muscle, drawing interest into the intrinsic mechanisms regulating cardiomyocyte proliferation. Moreover, recent studies have identified the importance of intercellular interactions and physiological adaptations, which highlight the vast complexity of the cardiac regenerative process. Finally, we compare strategies that have been tested to increase the regenerative capacity of the adult mammalian heart. This article is categorized under: Cardiovascular Diseases > Stem Cells and Development.
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Affiliation(s)
- Herman Huang
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
| | - Guo N. Huang
- Cardiovascular Research Institute & Department of Physiology, University of California, San Francisco, San Francisco, CA, 94158, USA
- Eli and Edythe Broad Center for Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, 94158, USA
| | - Alexander Y. Payumo
- Department of Biological Sciences, San Jose State University, San Jose, CA 95192, USA
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4
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McCabe MC, Okamura DM, Erickson CB, Perry BW, Brewer CM, Nguyen ED, Saviola AJ, Majesky MW, Hansen KC. ECM-Focused Proteomic Analysis of Ear Punch Regeneration in Acomys Cahirinus. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.10.11.561940. [PMID: 37873317 PMCID: PMC10592745 DOI: 10.1101/2023.10.11.561940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2023]
Abstract
In mammals, significant injury is generally followed by the formation of a fibrotic scar which provides structural integrity but fails to functionally restore damaged tissue. Spiny mice of the genus Acomys represent the first example of full skin autotomy in mammals. Acomys cahirinus has evolved extremely weak skin as a strategy to avoid predation and is able to repeatedly regenerate healthy tissue without scar after severe skin injury or full-thickness ear punches. Extracellular matrix (ECM) composition is a critical regulator of wound repair and scar formation and previous studies have suggested that alterations in its expression may be responsible for the differences in regenerative capacity observed between Mus musculus and A. cahirinus , yet analysis of this critical tissue component has been limited in previous studies by its insolubility and resistance to extraction. Here, we utilize a 2-step ECM-optimized extraction to perform proteomic analysis of tissue composition during wound repair after full-thickness ear punches in A. cahirinus and M. musculus from weeks 1 to 4 post-injury. We observe changes in a wide range of ECM proteins which have been previously implicated in wound regeneration and scar formation, including collagens, coagulation and provisional matrix proteins, and matricryptic signaling peptides. We additionally report differences in crosslinking enzyme activity and ECM protein solubility between Mus and Acomys. Furthermore, we observed rapid and sustained increases in CD206, a marker of pro-regenerative M2 macrophages, in Acomys, whereas little or no increase in CD206 was detected in Mus. Together, these findings contribute to a comprehensive understanding of tissue cues which drive the regenerative capacity of Acomys and identify a number of potential targets for future pro-regenerative therapies.
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5
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Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE. Genome Report: chromosome-scale genome assembly of the African spiny mouse (Acomys cahirinus). G3 (BETHESDA, MD.) 2023; 13:jkad177. [PMID: 37552705 PMCID: PMC10542272 DOI: 10.1093/g3journal/jkad177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 04/03/2023] [Accepted: 06/23/2023] [Indexed: 08/10/2023]
Abstract
There is increasing interest in the African spiny mouse (Acomys cahirinus) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from 4 different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.
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Affiliation(s)
- Elizabeth Dong Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
| | - Vahid Nikoonejad Fard
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Bernard Y Kim
- Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Sarah Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Branden R Nelson
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Paul Wakenight
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Simone M Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Aaron McKenna
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH 03755, USA
| | - Theo K Bammler
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jim MacDonald
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA 98195, USA
| | - Daryl M Okamura
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA 98195, USA
- Howard Hughes Medical Institute, Seattle, WA 98195, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
| | - David R Beier
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Jan Marino Ramirez
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Department of Neurological Surgery, University of Washington, Seattle, WA 98195, USA
| | - Mark W Majesky
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, Seattle, WA 98101, USA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
| | - Kathleen J Millen
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Danny E Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA 98195, USA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA 98195, USA
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6
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van Beijnum H, Koopmans T, Tomasso A, Disela V, Te Lindert S, Bakkers J, Alemany A, Berezikov E, Bartscherer K. Spatial transcriptomics reveals asymmetric cellular responses to injury in the regenerating spiny mouse ( Acomys) ear. Genome Res 2023; 33:1424-1437. [PMID: 37726147 PMCID: PMC10547259 DOI: 10.1101/gr.277538.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Accepted: 07/19/2023] [Indexed: 09/21/2023]
Abstract
In contrast to other mammals, the spiny mouse (Acomys) regenerates skin and ear tissue, which includes hair follicles, glands, and cartilage, in a scar-free manner. Ear punch regeneration is asymmetric with only the proximal wound side participating in regeneration. Here, we show that cues originating from the proximal side are required for normal regeneration and use spatially resolved transcriptomics (tomo-seq) to understand the molecular and cellular events underlying this process. Analyzing gene expression across the ear and comparing expression modules between proximal and distal wound sides, we identify asymmetric gene expression patterns and pinpoint regenerative processes in space and time. Moreover, using a comparative approach with nonregenerative rodents (Mus, Meriones), we strengthen a hypothesis in which particularities in the injury-induced immune response may be one of the crucial determinants for why spiny mice regenerate whereas their relatives do not. Our data are available in SpinyMine, an easy-to-use and expandable web-based tool for exploring Acomys regeneration-associated gene expression.
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Affiliation(s)
- Henriëtte van Beijnum
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Tim Koopmans
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Antonio Tomasso
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Vanessa Disela
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
| | - Severin Te Lindert
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- Wageningen University, Wageningen, 6708WE, The Netherlands
| | - Jeroen Bakkers
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands
- University Medical Center Utrecht, 3584CX Utrecht, The Netherlands
| | - Anna Alemany
- Department of Anatomy and Embryology, Leiden University Medical Center, and the Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Leiden node, 2300RC Leiden, The Netherlands
| | - Eugene Berezikov
- European Research Institute for the Biology of Ageing, University of Groningen, University Medical Center Groningen, 9713 AV Groningen, The Netherlands
| | - Kerstin Bartscherer
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), 3584CT Utrecht, The Netherlands;
- Department of Biology/Chemistry, Osnabrück University, 49076 Osnabrück, Germany
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7
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Okamura DM, Nguyen ED, Collins SJ, Yoon K, Gere JB, Weiser-Evans MCM, Beier DR, Majesky MW. Mammalian organ regeneration in spiny mice. J Muscle Res Cell Motil 2023; 44:39-52. [PMID: 36131170 DOI: 10.1007/s10974-022-09631-3] [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: 04/07/2022] [Accepted: 08/30/2022] [Indexed: 11/26/2022]
Abstract
Fibrosis-driven solid organ failure is a major world-wide health burden with few therapeutic options. Spiny mice (genus: Acomys) are terrestrial mammals that regenerate severe skin wounds without fibrotic scars to evade predators. Recent studies have shown that spiny mice also regenerate acute ischemic and traumatic injuries to kidney, heart, spinal cord, and skeletal muscle. A common feature of this evolved wound healing response is a lack of formation of fibrotic scar tissue that degrades organ function, inhibits regeneration, and leads to organ failure. Complex tissue regeneration is an extremely rare property among mammalian species. In this article, we discuss the evidence that Acomys represents an emerging model organism that offers a unique opportunity for the biomedical community to investigate and clinically translate molecular mechanisms of scarless wound healing and regeneration of organ function in a mammalian species.
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Affiliation(s)
- Daryl M Okamura
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Elizabeth D Nguyen
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Sarah J Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Kevin Yoon
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Joshua B Gere
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
| | - Mary C M Weiser-Evans
- Department of Medicine, Division of Renal Diseases & Hypertension, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA
| | - David R Beier
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA
| | - Mark W Majesky
- Center for Developmental Biology & Regenerative Medicine, Seattle Children's Research Institute, 1900 Ninth Avenue, M/S C9S-5, Seattle, WA, 98101, USA.
- Department of Pediatrics, University of Washington, Seattle, WA, 98195, USA.
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA, 98195, USA.
- Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, 98195, USA.
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8
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Tomasso A, Koopmans T, Lijnzaad P, Bartscherer K, Seifert AW. An ERK-dependent molecular switch antagonizes fibrosis and promotes regeneration in spiny mice ( Acomys). SCIENCE ADVANCES 2023; 9:eadf2331. [PMID: 37126559 PMCID: PMC10132760 DOI: 10.1126/sciadv.adf2331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Although most mammals heal injured tissues and organs with scarring, spiny mice (Acomys) naturally regenerate skin and complex musculoskeletal tissues. Now, the core signaling pathways driving mammalian tissue regeneration are poorly characterized. Here, we show that, while immediate extracellular signal-regulated kinase (ERK) activation is a shared feature of scarring (Mus) and regenerating (Acomys) injuries, ERK activity is only sustained at high levels during complex tissue regeneration. Following ERK inhibition, ear punch regeneration in Acomys shifted toward fibrotic repair. Using single-cell RNA sequencing, we identified ERK-responsive cell types. Loss- and gain-of-function experiments prompted us to uncover fibroblast growth factor and ErbB signaling as upstream ERK regulators of regeneration. The ectopic activation of ERK in scar-prone injuries induced a pro-regenerative response, including cell proliferation, extracellular matrix remodeling, and hair follicle neogenesis. Our data detail an important distinction in ERK activity between regenerating and poorly regenerating adult mammals and open avenues to redirect fibrotic repair toward regenerative healing.
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Affiliation(s)
- Antonio Tomasso
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
- Cells in Motion Cluster of Excellence-International Max Planck Research School (CiM-IMPRS Graduate Program), Münster 48149, Germany
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, Utrecht 3584CT, Netherlands
- Department of Biology/Chemistry, Osnabrück University, Barbarastrasse 11, Osnabrück 49076, Germany
- Department of Biology, University of Kentucky, 101 T.H. Morgan Building, Lexington, KY 40506, USA
| | - Tim Koopmans
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, Utrecht 3584CT, Netherlands
- Department of Biology/Chemistry, Osnabrück University, Barbarastrasse 11, Osnabrück 49076, Germany
| | - Philip Lijnzaad
- Princess Máxima Center for Pediatric Oncology, Heidelberglaan 25, Utrecht 3584 CS, Netherlands
| | - Kerstin Bartscherer
- Max Planck Institute for Molecular Biomedicine, Röntgenstrasse 20, Münster 48149, Germany
- Cells in Motion Cluster of Excellence-International Max Planck Research School (CiM-IMPRS Graduate Program), Münster 48149, Germany
- Hubrecht Institute-KNAW (Royal Netherlands Academy of Arts and Sciences), Uppsalalaan 8, Utrecht 3584CT, Netherlands
- Department of Biology/Chemistry, Osnabrück University, Barbarastrasse 11, Osnabrück 49076, Germany
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, 101 T.H. Morgan Building, Lexington, KY 40506, USA
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9
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Nguyen ED, Fard VN, Kim BY, Collins S, Galey M, Nelson BR, Wakenight P, Gable SM, McKenna A, Bammler TK, MacDonald J, Okamura DM, Shendure J, Beier DR, Ramirez JM, Majesky MW, Millen KJ, Tollis M, Miller DE. GENOME REPORT: Chromosome-scale genome assembly of the African spiny mouse ( Acomys cahirinus ). BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.03.535372. [PMID: 37066261 PMCID: PMC10103962 DOI: 10.1101/2023.04.03.535372] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/19/2023]
Abstract
There is increasing interest in the African spiny mouse ( Acomys cahirinus ) as a model organism because of its ability for regeneration of tissue after injury in skin, muscle, and internal organs such as the kidneys. A high-quality reference genome is needed to better understand these regenerative properties at the molecular level. Here, we present an improved reference genome for A. cahirinus generated from long Nanopore sequencing reads. We confirm the quality of our annotations using RNA sequencing data from four different tissues. Our genome is of higher contiguity and quality than previously reported genomes from this species and will facilitate ongoing efforts to better understand the regenerative properties of this organism.
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Affiliation(s)
- Elizabeth Dong Nguyen
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
| | - Vahid Nikoonejad Fard
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | - Bernard Y. Kim
- Department of Biology, Stanford University, Stanford, CA
| | - Sarah Collins
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Miranda Galey
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA
| | - Branden R. Nelson
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
| | - Paul Wakenight
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
| | - Simone M. Gable
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | - Aaron McKenna
- Department of Molecular & Systems Biology, Dartmouth Geisel School of Medicine, Lebanon, NH
| | - Theo K. Bammler
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA
| | - Jim MacDonald
- Department of Environmental & Occupational Health Sciences, University of Washington, Seattle, WA
| | - Daryl M. Okamura
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Jay Shendure
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
- Department of Genome Sciences, University of Washington, Seattle, WA
- Allen Discovery Center for Cell Lineage Tracing, Seattle, WA
- Howard Hughes Medical Institute, Seattle, WA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA
| | - David R. Beier
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
| | - Jan Marino Ramirez
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
- Department of Neurological Surgery, University of Washington, Seattle WA
| | - Mark W. Majesky
- Department of Pediatrics, University of Washington, Seattle, WA
- Center for Developmental Biology & Regenerative Medicine, Seattle Children’s Research Institute, Seattle, WA
- Institute of Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
| | - Kathleen J. Millen
- Department of Pediatrics, University of Washington, Seattle, WA
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
- Center for Integrative Brain Research, Seattle Children’s Research Institute, Seattle, WA
| | - Marc Tollis
- School of Informatics, Computing, and Cyber Systems, Northern Arizona University, Flagstaff, AZ
| | - Danny E. Miller
- Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA
- Division of Genetic Medicine, Department of Pediatrics, University of Washington, Seattle, WA
- Department of Laboratory Medicine & Pathology, University of Washington, Seattle, WA
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10
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Rolland L, Jopling C. The multifaceted nature of endogenous cardiac regeneration. Front Cardiovasc Med 2023; 10:1138485. [PMID: 36998973 PMCID: PMC10043193 DOI: 10.3389/fcvm.2023.1138485] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Accepted: 02/09/2023] [Indexed: 03/15/2023] Open
Abstract
Since the first evidence of cardiac regeneration was observed, almost 50 years ago, more studies have highlighted the endogenous regenerative abilities of several models following cardiac injury. In particular, analysis of cardiac regeneration in zebrafish and neonatal mice has uncovered numerous mechanisms involved in the regenerative process. It is now apparent that cardiac regeneration is not simply achieved by inducing cardiomyocytes to proliferate but requires a multifaceted response involving numerous different cell types, signaling pathways and mechanisms which must all work in harmony in order for regeneration to occur. In this review we will endeavor to highlight a variety of processes that have been identifed as being essential for cardiac regeneration.
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11
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Powell JM, Inoue K, Wallace KJ, Seifert AW, Young LJ, Kelly AM. Distribution of vasopressin 1a and oxytocin receptor protein and mRNA in the basal forebrain and midbrain of the spiny mouse (Acomys cahirinus). Brain Struct Funct 2023; 228:413-431. [PMID: 36271259 PMCID: PMC9974677 DOI: 10.1007/s00429-022-02581-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2022] [Accepted: 10/07/2022] [Indexed: 01/25/2023]
Abstract
The nonapeptide system modulates numerous social behaviors through oxytocin and vasopressin activation of the oxytocin receptor (OXTR) and vasopressin receptor (AVPR1A) in the brain. OXTRs and AVPR1As are widely distributed throughout the brain and binding densities exhibit substantial variation within and across species. Although OXTR and AVPR1A binding distributions have been mapped for several rodents, this system has yet to be characterized in the spiny mouse (Acomys cahirinus). Here we conducted receptor autoradiography and in situ hybridization to map distributions of OXTR and AVPR1A binding and Oxtr and Avpr1a mRNA expression throughout the basal forebrain and midbrain of male and female spiny mice. We found that nonapeptide receptor mRNA is diffuse throughout the forebrain and midbrain and does not always align with OXTR and AVPR1A binding. Analyses of sex differences in brain regions involved in social behavior and reward revealed that males exhibit higher OXTR binding densities in the lateral septum, bed nucleus of the stria terminalis, and anterior hypothalamus. However, no association with gonadal sex was observed for AVPR1A binding. Hierarchical clustering analysis further revealed that co-expression patterns of OXTR and AVPR1A binding across brain regions involved in social behavior and reward differ between males and females. These findings provide mapping distributions and sex differences in nonapeptide receptors in spiny mice. Spiny mice are an excellent organism for studying grouping behaviors such as cooperation and prosociality, and the nonapeptide receptor mapping here can inform the study of nonapeptide-mediated behavior in a highly social, large group-living rodent.
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Affiliation(s)
- Jeanne M Powell
- Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Kiyoshi Inoue
- Center for Translational Social Neuroscience, Emory University, Atlanta, GA, 30329, USA
- Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
| | - Kelly J Wallace
- Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA
| | - Ashley W Seifert
- Department of Biology, University of Kentucky, 101 Morgan Building, Lexington, KY, 40506, USA
| | - Larry J Young
- Center for Translational Social Neuroscience, Emory University, Atlanta, GA, 30329, USA
- Emory National Primate Research Center, Emory University, Atlanta, GA, 30329, USA
- Department of Psychiatry and Behavioral Sciences, Emory University School of Medicine, Atlanta, GA, 30322, USA
| | - Aubrey M Kelly
- Department of Psychology, Emory University, 36 Eagle Row, Atlanta, GA, 30322, USA.
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Seifert AW, Temple-Smith P. A remarkable rodent: Regeneration and reproduction in spiny mice (Acomys). Curr Top Dev Biol 2022; 147:659-707. [PMID: 35337466 DOI: 10.1016/bs.ctdb.2021.12.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although certain organisms are chosen and employed to better understand a specific problem in biology (so-called model organisms), sometimes an animal model reveals its' biomedical importance by happenstance. In many ways, the advent of spiny mice (Acomys) as an emerging model to study regeneration and menstruation stands as a case study in scientific pseudoserendipity (Diaz de Chumaceiro, 1995). As we recount in this chapter, the discovery of these phenotypes, while not entirely accidental, was nonetheless unexpected. In addition to recounting how we uncovered these unusual mammalian traits, we outline recent work by our groups and others that has begun to outline the cellular and genetic mechanisms underlying bonafide mammalian tissue regeneration and a human-like mode of reproduction in spiny mice.
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Affiliation(s)
- Ashley W Seifert
- Department of Biology, University of Kentucky, Lexington, KY, United States; Department of Veterinary Anatomy and Physiology, University of Nairobi, Nairobi, Kenya.
| | - Peter Temple-Smith
- Department of Obstetrics & Gynecology, Monash University, Clayton, VIC, Australia
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13
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Okamura DM, Nguyen ED, Beier DR, Majesky MW. Wound healing and regeneration in spiny mice (Acomys cahirinus). Curr Top Dev Biol 2022; 148:139-164. [DOI: 10.1016/bs.ctdb.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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