1
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Schrade L, Mah N, Bandrowski A, Chen Y, Dewender J, Diecke S, Hiepen C, Lancaster MA, Marques-Bonet T, Martinez S, Mueller SC, Navara C, Prigione A, Seltmann S, Sochacki J, Sutcliffe MA, Zywitza V, Hildebrandt TB, Kurtz A. A Standardized Nomenclature Design for Systematic Referencing and Identification of Animal Cellular Material. Animals (Basel) 2024; 14:1541. [PMID: 38891588 PMCID: PMC11171381 DOI: 10.3390/ani14111541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024] Open
Abstract
The documentation, preservation and rescue of biological diversity increasingly uses living biological samples. Persistent associations between species, biosamples, such as tissues and cell lines, and the accompanying data are indispensable for using, exchanging and benefiting from these valuable materials. Explicit authentication of such biosamples by assigning unique and robust identifiers is therefore required to allow for unambiguous referencing, avoid identification conflicts and maintain reproducibility in research. A predefined nomenclature based on uniform rules would facilitate this process. However, such a nomenclature is currently lacking for animal biological material. We here present a first, standardized, human-readable nomenclature design, which is sufficient to generate unique and stable identifying names for animal cellular material with a focus on wildlife species. A species-specific human- and machine-readable syntax is included in the proposed standard naming scheme, allowing for the traceability of donated material and cultured cells, as well as data FAIRification. Only when it is consistently applied in the public domain, as publications and inter-institutional samples and data are exchanged, distributed and stored centrally, can the risks of misidentification and loss of traceability be mitigated. This innovative globally applicable identification system provides a standard for a sustainable structure for the long-term storage of animal bio-samples in cryobanks and hence facilitates current as well as future species conservation and biomedical research.
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Affiliation(s)
- Lisa Schrade
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany
| | - Nancy Mah
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Anita Bandrowski
- Department of Neuroscience, FAIR Data Informatics Lab, University of California San Diego, San Diego, CA 92093, USA
- SciCrunch Inc., San Diego, CA 92192, USA
| | - Ying Chen
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Johannes Dewender
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Sebastian Diecke
- Technology Platform Pluripotent Stem Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Christian Hiepen
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Madeline A. Lancaster
- MRC Laboratory of Molecular Biology, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
| | - Tomas Marques-Bonet
- Institute of Evolutionary Biology, Pompeu Fabra University—Spanish National Research Council, ICREA, 08003 Barcelona, Spain
- Catalan Institution for Research and Advanced Studies (ICREA), 08010 Barcelona, Spain
- Centro Nacional de Analisis Genomico (CNAG), 08028 Barcelona, Spain
- Catalan Institute of Palaeontology Miquel Crusafont, Universitat Autònoma de Barcelona, 08193 Barcelona, Spain
| | - Sira Martinez
- Institute of Evolutionary Biology, Pompeu Fabra University—Spanish National Research Council, ICREA, 08003 Barcelona, Spain
- European Molecular Biology Laboratory (EMBL) Barcelona, 08003 Barcelona, Spain
| | - Sabine C. Mueller
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Christopher Navara
- San Antonio Cellular Therapeutics Institute, University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Alessandro Prigione
- Department of General Pediatrics, Neonatology and Pediatric Cardiology, Duesseldorf University Hospital, Medical Faculty, Heinrich Heine University, 40225 Duesseldorf, Germany
| | - Stefanie Seltmann
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
| | - Jaroslaw Sochacki
- European Molecular Biology Laboratory (EMBL) Barcelona, 08003 Barcelona, Spain
| | | | - Vera Zywitza
- Technology Platform Pluripotent Stem Cells, Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Thomas B. Hildebrandt
- Department of Reproduction Management, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany
- Faculty of Veterinary Medicine, Free University of Berlin, 14163 Berlin, Germany
| | - Andreas Kurtz
- Fraunhofer Institute for Biomedical Engineering (IBMT), 66280 Sulzbach, Germany
- Berlin Institute of Health (BIH), Center for Regenerative Therapies (BCRT), 13353 Berlin, Germany
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2
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Simone R, Čižmár D, Holtze S, Michel G, Sporbert A, Okolo C, Hildebrandt TB. In vitro production of naked mole-rats' blastocysts from non-breeding females using in vitro maturation and intracytoplasmic sperm injection. Sci Rep 2023; 13:22355. [PMID: 38102304 PMCID: PMC10724253 DOI: 10.1038/s41598-023-49661-6] [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: 05/08/2023] [Accepted: 12/11/2023] [Indexed: 12/17/2023] Open
Abstract
The African naked mole-rat (Heterocephalus glaber) is an attractive model for cancer and aging research due to its peculiar biological traits, such as unusual long life span and resistance to cancer. The establishment of induced pluripotent stem cells (iPSCs) would be a useful tool for in vitro studies but, in this species, the reprogramming of somatic cells is problematic because of their stable epigenome. Therefore, an alternative approach is the derivation of embryonic stem cells from in vitro-produced embryos. In this study, immature oocytes, opportunistically retrieved from sexually inactive females, underwent first in vitro maturation (IVM) and then in vitro fertilization via piezo-intracytoplasmic sperm injection (ICSI). Injected oocytes were then cultivated with two different approaches: (i) in an in vitro culture and (ii) in an isolated mouse oviduct organ culture system. The second approach led to the development of blastocysts, which were fixed and stained for further analysis.
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Affiliation(s)
- Raffaella Simone
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin eV, Reproduction Management, Alfred-Kowalke-Straße, Berlin, Germany
- Freie Universitaet Berlin, Veterinary Medicine, Berlin, Germany
| | - Daniel Čižmár
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin eV, Reproduction Management, Alfred-Kowalke-Straße, Berlin, Germany.
| | - Susanne Holtze
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin eV, Reproduction Management, Alfred-Kowalke-Straße, Berlin, Germany
| | - Geert Michel
- FEM, Transgenic Technologies, Charité-Universitätsmedizin, Berlin, Germany
| | - Anje Sporbert
- Advanced Light Microscopy Technology Platform (Max Delbrück Center for Molecular Medicine), Campus Buch, Berlin, Germany
| | - Charlotte Okolo
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin eV, Reproduction Management, Alfred-Kowalke-Straße, Berlin, Germany
| | - Thomas B Hildebrandt
- Leibniz Institute for Zoo and Wildlife Research (IZW) in the Forschungsverbund Berlin eV, Reproduction Management, Alfred-Kowalke-Straße, Berlin, Germany
- Freie Universitaet Berlin, Veterinary Medicine, Berlin, Germany
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3
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Anwised P, Moorawong R, Samruan W, Somredngan S, Srisutush J, Laowtammathron C, Aksoy I, Parnpai R, Savatier P. An expedition in the jungle of pluripotent stem cells of non-human primates. Stem Cell Reports 2023; 18:2016-2037. [PMID: 37863046 PMCID: PMC10679654 DOI: 10.1016/j.stemcr.2023.09.013] [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: 06/16/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 10/22/2023] Open
Abstract
For nearly three decades, more than 80 embryonic stem cell lines and more than 100 induced pluripotent stem cell lines have been derived from New World monkeys, Old World monkeys, and great apes. In this comprehensive review, we examine these cell lines originating from marmoset, cynomolgus macaque, rhesus macaque, pig-tailed macaque, Japanese macaque, African green monkey, baboon, chimpanzee, bonobo, gorilla, and orangutan. We outline the methodologies implemented for their establishment, the culture protocols for their long-term maintenance, and their basic molecular characterization. Further, we spotlight any cell lines that express fluorescent reporters. Additionally, we compare these cell lines with human pluripotent stem cell lines, and we discuss cell lines reprogrammed into a pluripotent naive state, detailing the processes used to attain this. Last, we present the findings from the application of these cell lines in two emerging fields: intra- and interspecies embryonic chimeras and blastoids.
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Affiliation(s)
- Preeyanan Anwised
- University Lyon, University Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France; Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Ratree Moorawong
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Worawalan Samruan
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Sirilak Somredngan
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Jittanun Srisutush
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand
| | - Chuti Laowtammathron
- Siriraj Center of Excellence for Stem Cell Research, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Irene Aksoy
- University Lyon, University Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
| | - Rangsun Parnpai
- Embryo Technology and Stem Cell Research Center, School of Biotechnology, Institute of Agricultural Technology, Suranaree University of Technology, Nakhon Ratchasima 30000, Thailand.
| | - Pierre Savatier
- University Lyon, University Lyon 1, INSERM, Stem Cell and Brain Research Institute U1208, 69500 Bron, France.
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4
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Li S, Vazquez JM, Sudmant PH. The evolution of aging and lifespan. Trends Genet 2023; 39:830-843. [PMID: 37714733 PMCID: PMC11147682 DOI: 10.1016/j.tig.2023.08.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Revised: 08/18/2023] [Accepted: 08/21/2023] [Indexed: 09/17/2023]
Abstract
Aging is a nearly inescapable trait among organisms yet lifespan varies tremendously across different species and spans several orders of magnitude in vertebrates alone. This vast phenotypic diversity is driven by distinct evolutionary trajectories and tradeoffs that are reflected in patterns of diversification and constraint in organismal genomes. Age-specific impacts of selection also shape allele frequencies in populations, thus impacting disease susceptibility and environment-specific mortality risk. Further, the mutational processes that spawn this genetic diversity in both germline and somatic cells are strongly influenced by age and life history. We discuss recent advances in our understanding of the evolution of aging and lifespan at organismal, population, and cellular scales, and highlight outstanding questions that remain unanswered.
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Affiliation(s)
- Stacy Li
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA
| | - Juan Manuel Vazquez
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Peter H Sudmant
- Department of Integrative Biology, University of California, Berkeley, CA, USA; Center for Computational Biology, University of California, Berkeley, CA. USA.
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5
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Tyshkovskiy A, Ma S, Shindyapina AV, Tikhonov S, Lee SG, Bozaykut P, Castro JP, Seluanov A, Schork NJ, Gorbunova V, Dmitriev SE, Miller RA, Gladyshev VN. Distinct longevity mechanisms across and within species and their association with aging. Cell 2023; 186:2929-2949.e20. [PMID: 37269831 PMCID: PMC11192172 DOI: 10.1016/j.cell.2023.05.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Revised: 12/29/2022] [Accepted: 05/02/2023] [Indexed: 06/05/2023]
Abstract
Lifespan varies within and across species, but the general principles of its control remain unclear. Here, we conducted multi-tissue RNA-seq analyses across 41 mammalian species, identifying longevity signatures and examining their relationship with transcriptomic biomarkers of aging and established lifespan-extending interventions. An integrative analysis uncovered shared longevity mechanisms within and across species, including downregulated Igf1 and upregulated mitochondrial translation genes, and unique features, such as distinct regulation of the innate immune response and cellular respiration. Signatures of long-lived species were positively correlated with age-related changes and enriched for evolutionarily ancient essential genes, involved in proteolysis and PI3K-Akt signaling. Conversely, lifespan-extending interventions counteracted aging patterns and affected younger, mutable genes enriched for energy metabolism. The identified biomarkers revealed longevity interventions, including KU0063794, which extended mouse lifespan and healthspan. Overall, this study uncovers universal and distinct strategies of lifespan regulation within and across species and provides tools for discovering longevity interventions.
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Affiliation(s)
- Alexander Tyshkovskiy
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Siming Ma
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Anastasia V Shindyapina
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Stanislav Tikhonov
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Perinur Bozaykut
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Department of Molecular Biology and Genetics, Faculty of Engineering and Natural Sciences, Acibadem Mehmet Ali Aydinlar University, Istanbul 34752, Turkey
| | - José P Castro
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; i3S, Instituto de Investigação e Inovação em Saúde, Universidade do Porto, 4200-135 Porto, Portugal; Aging and Aneuploidy Laboratory, IBMC, Instituto de Biologia Molecular e Celular, Universidade do Porto, 4200-135 Porto, Portugal
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Nicholas J Schork
- Quantitative Medicine and Systems Biology Division, Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Sergey E Dmitriev
- Belozersky Institute of Physico-Chemical Biology, Moscow State University, Moscow 119234, Russia
| | - Richard A Miller
- Department of Pathology and Geriatrics Center, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Broad Institute, Cambridge, MA, USA.
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6
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Schraverus H, Larondelle Y, Page MM. Beyond the Lab: What We Can Learn about Cancer from Wild and Domestic Animals. Cancers (Basel) 2022; 14:cancers14246177. [PMID: 36551658 PMCID: PMC9776354 DOI: 10.3390/cancers14246177] [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: 11/03/2022] [Revised: 12/02/2022] [Accepted: 12/09/2022] [Indexed: 12/23/2022] Open
Abstract
Cancer research has benefited immensely from the use of animal models. Several genetic tools accessible in rodent models have provided valuable insight into cellular and molecular mechanisms linked to cancer development or metastasis and various lines are available. However, at the same time, it is important to accompany these findings with those from alternative or non-model animals to offer new perspectives into the understanding of tumor development, prevention, and treatment. In this review, we first discuss animals characterized by little or no tumor development. Cancer incidence in small animals, such as the naked mole rat, blind mole rat and bats have been reported as almost negligible and tumor development may be inhibited by increased defense and repair mechanisms, altered cell cycle signaling and reduced rates of cell migration to avoid tumor microenvironments. On the other end of the size spectrum, large animals such as elephants and whales also appear to have low overall cancer rates, possibly due to gene replicates that are involved in apoptosis and therefore can inhibit uncontrolled cell cycle progression. While it is important to determine the mechanisms that lead to cancer protection in these animals, we can also take advantage of other animals that are highly susceptible to cancer, especially those which develop tumors similar to humans, such as carnivores or poultry. The use of such animals does not require the transplantation of malignant cancer cells or use of oncogenic substances as they spontaneously develop tumors of similar presentation and pathophysiology to those found in humans. For example, some tumor suppressor genes are highly conserved between humans and domestic species, and various tumors develop in similar ways or because of a common environment. These animals are therefore of great interest for broadening perspectives and techniques and for gathering information on the tumor mechanisms of certain types of cancer. Here we present a detailed review of alternative and/or non-model vertebrates, that can be used at different levels of cancer research to open new perspectives and fields of action.
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Yamamura Y, Kawamura Y, Oka K, Miura K. Carcinogenesis resistance in the longest-lived rodent, the naked mole-rat. Cancer Sci 2022; 113:4030-4036. [PMID: 36083242 DOI: 10.1111/cas.15570] [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: 07/01/2022] [Revised: 08/24/2022] [Accepted: 09/01/2022] [Indexed: 12/15/2022] Open
Abstract
Certain mammalian species are resistant to cancer, and a better understanding of how this cancer resistance arises could provide valuable insights for basic cancer research. Recent technological innovations in molecular biology have allowed the study of cancer-resistant mammals, despite the fact that they are not the classical model animals, which are easily studied using genetic approaches. Naked mole-rats (NMRs; Heterocephalus glaber) are the longest-lived rodent, with a maximum lifespan of more than 37 years, and almost never show spontaneous carcinogenesis. NMRs are currently attracting much attention from aging and cancer researchers, and published studies on NMR have continued to increase over the past decade. Cancer development occurs via multiple steps and involves many biological processes. Recent research on the NMR as a model for cancer resistance suggests that they possess various unique carcinogenesis-resistance mechanisms, including efficient DNA repair pathways, cell-autonomous resistance to transformation, and dampened inflammatory response. Here, we summarize the molecular mechanisms of carcinogenesis resistance in NMR, which have been uncovered over the past two decades, and discuss future perspectives.
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Affiliation(s)
- Yuki Yamamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Yoshimi Kawamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kaori Oka
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan
| | - Kyoko Miura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, Japan
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8
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Sandoval AGW, Maden M, Bates LE, Silva JC. Tumor suppressors inhibit reprogramming of African spiny mouse ( Acomys) fibroblasts to induced pluripotent stem cells. Wellcome Open Res 2022; 7:215. [PMID: 36060301 PMCID: PMC9437536 DOI: 10.12688/wellcomeopenres.18034.1] [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] [Accepted: 08/04/2022] [Indexed: 12/15/2022] Open
Abstract
Background: The African spiny mouse ( Acomys) is an emerging mammalian model for scar-free regeneration, and further study of Acomys could advance the field of regenerative medicine. Isolation of pluripotent stem cells from Acomys would allow for development of transgenic or chimeric animals and in vitro study of regeneration; however, the reproductive biology of Acomys is not well characterized, complicating efforts to derive embryonic stem cells. Thus, we sought to generate Acomys induced pluripotent stem cells (iPSCs) by reprogramming somatic cells back to pluripotency. Methods: To generate Acomys iPSCs, we attempted to adapt established protocols developed in Mus. We utilized a PiggyBac transposon system to genetically modify Acomys fibroblasts to overexpress the Yamanaka reprogramming factors as well as mOrange fluorescent protein under the control of a doxycycline-inducible TetON operon system. Results: Reprogramming factor overexpression caused Acomys fibroblasts to undergo apoptosis or senescence. When SV40 Large T antigen (SV40 LT) was added to the reprogramming cocktail, Acomys cells were able to dedifferentiate into pre-iPSCs. Although use of 2iL culture conditions induced formation of colonies resembling Mus PSCs, these Acomys iPS-like cells lacked pluripotency marker expression and failed to form embryoid bodies. An EOS-GiP system was unsuccessful in selecting for bona fide Acomys iPSCs; however, inclusion of Nanog in the reprogramming cocktail along with 5-azacytidine in the culture medium allowed for generation of Acomys iPSC-like cells with increased expression of several naïve pluripotency markers. Conclusions: There are significant roadblocks to reprogramming Acomys cells, necessitating future studies to determine Acomys-specific reprogramming factor and/or culture condition requirements. The requirement for SV40 LT during Acomys dedifferentiation may suggest that tumor suppressor pathways play an important role in Acomys regeneration and that Acomys may possess unreported cancer resistance.
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Affiliation(s)
- Aaron Gabriel W. Sandoval
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Department of Biology & UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Malcolm Maden
- Department of Biology & UF Genetics Institute, University of Florida, Gainesville, FL, USA
| | - Lawrence E. Bates
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU, UK
| | - Jose C.R. Silva
- Wellcome-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge, CB2 0AW, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1GA, UK
- Guangzhou Laboratory, Guangzhou International Bio Island, Guangzhou 510005, Guangdong Province, China
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Bolton RL, Mooney A, Pettit MT, Bolton AE, Morgan L, Drake GJ, Appeltant R, Walker SL, Gillis JD, Hvilsom C. Resurrecting biodiversity: advanced assisted reproductive technologies and biobanking. REPRODUCTION AND FERTILITY 2022; 3:R121-R146. [PMID: 35928671 PMCID: PMC9346332 DOI: 10.1530/raf-22-0005] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 06/30/2022] [Indexed: 11/21/2022] Open
Abstract
Biodiversity is defined as the presence of a variety of living organisms on the Earth that is essential for human survival. However, anthropogenic activities are causing the sixth mass extinction, threatening even our own species. For many animals, dwindling numbers are becoming fragmented populations with low genetic diversity, threatening long-term species viability. With extinction rates 1000–10,000 times greater than natural, ex situ and in situ conservation programmes need additional support to save species. The indefinite storage of cryopreserved (−196°C) viable cells and tissues (cryobanking), followed by assisted or advanced assisted reproductive technology (ART: utilisation of oocytes and spermatozoa to generate offspring; aART: utilisation of somatic cell genetic material to generate offspring), may be the only hope for species’ long-term survival. As such, cryobanking should be considered a necessity for all future conservation strategies. Following cryopreservation, ART/aART can be used to reinstate lost genetics back into a population, resurrecting biodiversity. However, for this to be successful, species-specific protocol optimisation and increased knowledge of basic biology for many taxa are required. Current ART/aART is primarily focused on mammalian taxa; however, this needs to be extended to all, including to some of the most endangered species: amphibians. Gamete, reproductive tissue and somatic cell cryobanking can fill the gap between losing genetic diversity today and future technological developments. This review explores species prioritisation for cryobanking and the successes and challenges of cryopreservation and multiple ARTs/aARTs. We here discuss the value of cryobanking before more species are lost and the potential of advanced reproductive technologies not only to halt but also to reverse biodiversity loss.
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Affiliation(s)
- Rhiannon L Bolton
- Nature’s SAFE, Chapel Field Stud, Ash Lane, Whitchurch, Shropshire, UK
| | | | - Matt T Pettit
- Nature’s SAFE, Chapel Field Stud, Ash Lane, Whitchurch, Shropshire, UK
- IMT International Limited, Tattenhall, Chester, UK
| | - Anthony E Bolton
- Nature’s SAFE, Chapel Field Stud, Ash Lane, Whitchurch, Shropshire, UK
| | - Lucy Morgan
- Gemini Genetics, Chapel Field Stud, Ash Lane, Whitchurch, UK
| | | | - Ruth Appeltant
- Nuffield Department of Women’s and Reproductive Health, University of Oxford, Women’s Centre, Level 3, John Radcliffe Hospital, Oxford, UK
| | - Susan L Walker
- Nature’s SAFE, Chapel Field Stud, Ash Lane, Whitchurch, Shropshire, UK
- Chester Zoo, Upton-by-Chester, UK
| | - James D Gillis
- South-East Zoo Alliance for Reproduction & Conservation, Yulee, Florida, USA
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10
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Horvath S, Haghani A, Macoretta N, Ablaeva J, Zoller JA, Li CZ, Zhang J, Takasugi M, Zhao Y, Rydkina E, Zhang Z, Emmrich S, Raj K, Seluanov A, Faulkes CG, Gorbunova V. DNA methylation clocks tick in naked mole rats but queens age more slowly than nonbreeders. NATURE AGING 2022; 2:46-59. [PMID: 35368774 PMCID: PMC8975251 DOI: 10.1038/s43587-021-00152-1] [Citation(s) in RCA: 35] [Impact Index Per Article: 17.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/15/2023]
Abstract
Naked mole rats (NMRs) live an exceptionally long life, appear not to exhibit age-related decline in physiological capacity and are resistant to age-related diseases. However, it has been unknown whether NMRs also evade aging according to a primary hallmark of aging: epigenetic changes. To address this question, we profiled n = 385 samples from 11 tissue types at loci that are highly conserved between mammalian species using a custom array (HorvathMammalMethylChip40). We observed strong epigenetic aging effects and developed seven highly accurate epigenetic clocks for several tissues (pan-tissue, blood, kidney, liver, skin clocks) and two dual-species (human-NMR) clocks. The skin clock correctly estimated induced pluripotent stem cells derived from NMR fibroblasts to be of prenatal age. The NMR epigenetic clocks revealed that breeding NMR queens age more slowly than nonbreeders, a feature that is also observed in some eusocial insects. Our results show that despite a phenotype of negligible senescence, the NMR ages epigenetically.
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Affiliation(s)
- Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
- Altos Labs, San Diego, CA, USA
- These authors contributed equally: Steve Horvath, Amin Haghani
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
- These authors contributed equally: Steve Horvath, Amin Haghani
| | - Nicholas Macoretta
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Julia Ablaeva
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Joseph A. Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Caesar Z. Li
- Department of Biostatistics, Fielding School of Public Health, University of California, Los Angeles, Los Angeles, CA, USA
| | - Joshua Zhang
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Masaki Takasugi
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Yang Zhao
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Elena Rydkina
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Zhihui Zhang
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Stephan Emmrich
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
| | - Ken Raj
- Radiation Effects Department, Centre for Radiation, Chemical and Environmental Hazards, Public Health England, Chilton, Didcot, UK
| | - Andrei Seluanov
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
- These authors jointly supervised this work: Andrei Seluanov, Chris G. Faulkes, Vera Gorbunova
| | - Chris G. Faulkes
- School of Biological and Chemical Sciences, Queen Mary University of London, London, UK
- These authors jointly supervised this work: Andrei Seluanov, Chris G. Faulkes, Vera Gorbunova
| | - Vera Gorbunova
- Departments of Biology and Medicine, University of Rochester, Rochester, NY, USA
- These authors jointly supervised this work: Andrei Seluanov, Chris G. Faulkes, Vera Gorbunova
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11
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Small molecules for cell reprogramming: a systems biology analysis. Aging (Albany NY) 2021; 13:25739-25762. [PMID: 34919532 PMCID: PMC8751603 DOI: 10.18632/aging.203791] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 11/24/2021] [Indexed: 12/22/2022]
Abstract
If somatic stem cells would be able to maintain their regenerative capacity over time, this might, to a great extent, resolve rejuvenation issues. Unfortunately, the pool of somatic stem cells is limited, and they undergo cell aging with a consequent loss of functionality. During the last decade, low molecular weight compounds that are able to induce or enhance cell reprogramming have been reported. They were named “Small Molecules” (SMs) and might present definite advantages compared to the exogenous introduction of stemness-related transcription factors (e.g. Yamanaka’s factors). Here, we undertook a systemic analysis of SMs and their potential gene targets. Data mining and curation lead to the identification of 92 SMs. The SM targets fall into three major functional categories: epigenetics, cell signaling, and metabolic “switchers”. All these categories appear to be required in each SM cocktail to induce cell reprogramming. Remarkably, many enriched pathways of SM targets are related to aging, longevity, and age-related diseases, thus connecting them with cell reprogramming. The network analysis indicates that SM targets are highly interconnected and form protein-protein networks of a scale-free topology. The extremely high contribution of hubs to network connectivity suggests that (i) cell reprogramming may require SM targets to act cooperatively, and (ii) their network organization might ensure robustness by resistance to random failures. All in all, further investigation of SMs and their relationship with longevity regulators will be helpful for developing optimal SM cocktails for cell reprogramming with a perspective for rejuvenation and life span extension.
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12
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Zhao Y, Seluanov A, Gorbunova V. Revelations About Aging and Disease from Unconventional Vertebrate Model Organisms. Annu Rev Genet 2021; 55:135-159. [PMID: 34416119 DOI: 10.1146/annurev-genet-071719-021009] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Aging is a major risk factor for multiple diseases. Understanding the underlying mechanisms of aging would help to delay and prevent age-associated diseases. Short-lived model organisms have been extensively used to study the mechanisms of aging. However, these short-lived species may be missing the longevity mechanisms that are needed to extend the lifespan of an already long-lived species such as humans. Unconventional long-lived animal species are an excellent resource to uncover novel mechanisms of longevity and disease resistance. Here, we review mechanisms that evolved in nonmodel vertebrate species to counteract age-associated diseases. Some antiaging mechanisms are conserved across species; however, various nonmodel species also evolved unique mechanisms to delay aging and prevent disease. This variety of antiaging mechanisms has evolved due to the remarkably diverse habitats and behaviors of these species. We propose that exploring a wider range of unconventional vertebrates will provide important resources to study antiaging mechanisms that are potentially applicable to humans.
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Affiliation(s)
- Yang Zhao
- Department of Biology, University of Rochester, Rochester, New York 14627, USA; ,
| | - Andrei Seluanov
- Department of Biology, University of Rochester, Rochester, New York 14627, USA; ,
| | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, New York 14627, USA; ,
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13
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Yamamura Y, Kawamura Y, Oiwa Y, Oka K, Onishi N, Saya H, Miura K. Isolation and characterization of neural stem/progenitor cells in the subventricular zone of the naked mole-rat brain. Inflamm Regen 2021; 41:31. [PMID: 34719407 PMCID: PMC8559411 DOI: 10.1186/s41232-021-00182-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 09/18/2021] [Indexed: 12/11/2022] Open
Abstract
Background The naked mole-rat (NMR) is the longest-lived rodent with a maximum lifespan of more than 37 years and shows a negligible senescence phenotype, suggesting that tissue stem cells of NMRs are highly capable of maintaining homeostasis. However, the properties of NMR tissue stem cells, including neural stem cells (NSCs), are largely unclear. Methods Neural stem/progenitor cells (NS/PCs) were isolated from the subventricular zone of the neonate NMR brain (NMR-NS/PCs) and cultured in neurosphere and adherent culture conditions. Expression of NSC markers and markers of neurons, astrocytes, and oligodendrocytes was analyzed by immunocytochemistry. In adherent culture conditions, the proliferation rate and cell cycle of NMR-NS/PCs were assessed and compared with those of NS/PCs from mice (mouse-NS/PCs). The DNA damage response to γ-irradiation was analyzed by immunocytochemistry and reverse transcription-quantitative PCR. Results NMR-NS/PCs expressed several NSC markers and differentiated into neurons, astrocytes, and oligodendrocytes. NMR-NS/PCs proliferated markedly slower than mouse-NS/PCs, and a higher percentage of NMR-NS/PCs than mouse-NS/PCs was in G0/G1 phase. Notably, upon γ-irradiation, NMR-NS/PCs exhibited a faster initiation of the DNA damage response and were less prone to dying than mouse-NS/PCs. Conclusions NMR-NS/PCs were successfully isolated and cultured. The slow proliferation of NMR-NS/PCs and their resistance to DNA damage may help to prevent stem cell exhaustion in the brain during the long lifespan of NMRs. Our findings provide novel insights into the mechanism underlying delayed aging of NMRs. Further analysis of NMR tissue stem cells may lead to the development of new strategies that can prevent aging in humans. Supplementary Information The online version contains supplementary material available at 10.1186/s41232-021-00182-7.
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Affiliation(s)
- Yuki Yamamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yoshimi Kawamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Yuki Oiwa
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Kaori Oka
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-0811, Japan
| | - Nobuyuki Onishi
- Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-0016, Japan
| | - Hideyuki Saya
- Division of Gene Regulation, Institute for Advanced Medical Research, Keio University School of Medicine, Tokyo, 160-0016, Japan
| | - Kyoko Miura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, 860-0811, Japan. .,Center for Metabolic Regulation of Healthy Aging, Kumamoto University, Kumamoto, 860-8556, Japan.
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14
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Augereau A, Mariotti M, Pousse M, Filipponi D, Libert F, Beck B, Gorbunova V, Gilson E, Gladyshev VN. Naked mole rat TRF1 safeguards glycolytic capacity and telomere replication under low oxygen. SCIENCE ADVANCES 2021; 7:eabe0174. [PMID: 33608273 PMCID: PMC7895426 DOI: 10.1126/sciadv.abe0174] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Accepted: 01/06/2021] [Indexed: 05/31/2023]
Abstract
The naked mole rat (NMR), a long-lived and cancer-resistant rodent, is highly resistant to hypoxia. Here, using robust cellular models wherein the mouse telomeric protein TRF1 is substituted by NMR TRF1 or its mutant forms, we show that TRF1 supports maximal glycolytic capacity under low oxygen, shows increased nuclear localization and association with telomeres, and protects telomeres from replicative stress. We pinpoint this evolutionary gain of metabolic function to specific amino acid changes in the homodimerization domain of this protein. We further find that NMR TRF1 accelerates telomere shortening. These findings reveal an evolutionary strategy to adapt telomere biology for metabolic control under an extreme environment.
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Affiliation(s)
- Adeline Augereau
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | - Marco Mariotti
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Mélanie Pousse
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Doria Filipponi
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
| | - Frédérick Libert
- Institut de Recherche Interdisciplinaire en Biologie Humaine et Moléculaire (IRIBHM), Université Libre de Bruxelles (ULB), 1070 Brussels, Belgium
| | | | - Vera Gorbunova
- Department of Biology, University of Rochester, Rochester, NY 14627, USA
| | - Eric Gilson
- Université Côte d'Azur, CNRS, Inserm, Institute for Research on Cancer and Aging, Nice (IRCAN), 06107 Nice, France
- Department of Medical Genetics, Archet 2 Hospital, CHU of Nice, FHU Oncoage, 06107 Nice, France
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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15
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Miura K, Oiwa Y, Kawamura Y. Induced Pluripotent Stem Cells from Cancer-Resistant Naked Mole-Rats. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1319:329-339. [PMID: 34424523 DOI: 10.1007/978-3-030-65943-1_13] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Stem cells play essential roles in the development and tissue homeostasis of animals and are closely associated with carcinogenesis and aging. Also, the somatic cell reprogramming process to induced pluripotent stem (iPS) cells shares several characteristics with carcinogenesis. In this chapter, we focus on iPS cells and the reprogramming process of somatic cells in the naked mole-rat (NMR), the longest-living rodent with remarkable cancer resistance capabilities. NMR somatic cells show resistance to reprogramming induction, and generated NMR-iPS cells have a unique tumor-resistant phenotype. This phenotype is regulated by expressional activation of the tumor suppressor ARF gene and loss-of-function mutation in oncogene ERAS. Notably, it was also found that NMR somatic cells undergo senescence when ARF is suppressed during reprogramming, which would contribute to the resistance to both reprogramming and cancer in NMR somatic cells. Further studies on reprogramming resistance in NMR somatic cells and their concomitant tumor resistance in NMR-iPS cells would contribute to a better understanding of both cancer resistance and delayed aging in NMRs. In addition, NMR-iPS cells can be used as a new and important cell source for advancing research concerning several extraordinary physiological characteristics of NMR. Furthermore, study of NMR-iPS cells could lead to the development of safer regenerative therapies in the future.
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Affiliation(s)
- Kyoko Miura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan. .,Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan.
| | - Yuki Oiwa
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
| | - Yoshimi Kawamura
- Department of Aging and Longevity Research, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan.,Biomedical Animal Research Laboratory, Institute for Genetic Medicine, Hokkaido University, Sapporo, Japan
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16
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Endo Y, Kamei KI, Inoue-Murayama M. Genetic Signatures of Evolution of the Pluripotency Gene Regulating Network across Mammals. Genome Biol Evol 2020; 12:1806-1818. [PMID: 32780791 PMCID: PMC7643368 DOI: 10.1093/gbe/evaa169] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2020] [Indexed: 01/01/2023] Open
Abstract
Mammalian pluripotent stem cells (PSCs) have distinct molecular and biological characteristics among species, but to date we lack a comprehensive understanding of regulatory network evolution in mammals. Here, we carried out a comparative genetic analysis of 134 genes constituting the pluripotency gene regulatory network across 48 mammalian species covering all the major taxonomic groups. We report that mammalian genes in the pluripotency regulatory network show a remarkably high degree of evolutionary stasis, suggesting the conservation of fundamental biological process of mammalian PSCs across species. Nevertheless, despite the overall conservation of the regulatory network, we discovered rapid evolution of the downstream targets of the core regulatory elements and specific amino acid residues that have undergone positive selection. Our data indicate development of lineage-specific pluripotency regulating networks that may explain observed variations in some characteristics of mammalian PSCs. We further revealed that positively selected genes could be associated with species' unique adaptive characteristics that were not dedicated to regulation of PSCs. These results provide important insight into the evolution of the pluripotency gene regulatory network underlying variations in characteristics of mammalian PSCs.
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Affiliation(s)
| | - Ken-ichiro Kamei
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Japan
| | - Miho Inoue-Murayama
- Wildlife Research Center, Kyoto University, Japan
- Institute for Integrated Cell-Material Sciences (WPI-iCeMS), Kyoto University, Japan
- Wildlife Genome Collaborative Research Group, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan
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17
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Lam EK, Allen KN, Torres-Velarde JM, Vázquez-Medina JP. Functional Studies with Primary Cells Provide a System for Genome-to-Phenome Investigations in Marine Mammals. Integr Comp Biol 2020; 60:348-360. [PMID: 32516367 DOI: 10.1093/icb/icaa065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Marine mammals exhibit some of the most dramatic physiological adaptations in their clade and offer unparalleled insights into the mechanisms driving convergent evolution on relatively short time scales. Some of these adaptations, such as extreme tolerance to hypoxia and prolonged food deprivation, are uncommon among most terrestrial mammals and challenge established metabolic principles of supply and demand balance. Non-targeted omics studies are starting to uncover the genetic foundations of such adaptations, but tools for testing functional significance in these animals are currently lacking. Cellular modeling with primary cells represents a powerful approach for elucidating the molecular etiology of physiological adaptation, a critical step in accelerating genome-to-phenome studies in organisms in which transgenesis is impossible (e.g., large-bodied, long-lived, fully aquatic, federally protected species). Gene perturbation studies in primary cells can directly evaluate whether specific mutations, gene loss, or duplication confer functional advantages such as hypoxia or stress tolerance in marine mammals. Here, we summarize how genetic and pharmacological manipulation approaches in primary cells have advanced mechanistic investigations in other non-traditional mammalian species, and highlight the need for such investigations in marine mammals. We also provide key considerations for isolating, culturing, and conducting experiments with marine mammal cells under conditions that mimic in vivo states. We propose that primary cell culture is a critical tool for conducting functional mechanistic studies (e.g., gene knockdown, over-expression, or editing) that can provide the missing link between genome- and organismal-level understanding of physiological adaptations in marine mammals.
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Affiliation(s)
- Emily K Lam
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Kaitlin N Allen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, CA 94720, USA
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18
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Shepard A, Kissil JL. The use of non-traditional models in the study of cancer resistance-the case of the naked mole rat. Oncogene 2020; 39:5083-5097. [PMID: 32535616 DOI: 10.1038/s41388-020-1355-8] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 05/15/2020] [Accepted: 06/03/2020] [Indexed: 12/16/2022]
Abstract
Non-traditional model organisms are typically defined as any model the deviates from the typical laboratory animals, such as mouse, rat, and worm. These models are becoming increasingly important in human disease research, such as cancer, as they often display unusual biological features. Naked mole rats (NMRs) are currently one of the most popular non-traditional model, particularly in the longevity and cancer research fields. NMRs display an exceptionally long lifespan (~30 years), yet have been observed to display a low incidence of cancer, making them excellent candidates for understanding endogenous cancer resistance mechanisms. Over the past decade, many potential resistance mechanisms have been characterized. These include unique biological mechanisms involved in genome stability, protein stability, oxidative metabolism, and other cellular mechanisms such as cell cycle regulation and senescence. This review aims to summarize the many identified cancer resistance mechanisms to understand some of the main hypotheses that have thus far been generated. Many of these proposed mechanisms remain to be fully characterized or confirmed in vivo, giving the field a direction to grow and further understand the complex biology displayed by the NMR.
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Affiliation(s)
- Alyssa Shepard
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA
| | - Joseph L Kissil
- Department of Molecular Medicine, The Scripps Research Institute, Jupiter, FL, 33458, USA.
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19
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Tombline G, Gigas J, Macoretta N, Zacher M, Emmrich S, Zhao Y, Seluanov A, Gorbunova V. Proteomics of Long-Lived Mammals. Proteomics 2020; 20:e1800416. [PMID: 31737995 PMCID: PMC7117992 DOI: 10.1002/pmic.201800416] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Revised: 10/25/2019] [Indexed: 12/29/2022]
Abstract
Mammalian species differ up to 100-fold in their aging rates and maximum lifespans. Long-lived mammals appear to possess traits that extend lifespan and healthspan. Genomic analyses have not revealed a single pro-longevity function that would account for all longevity effects. In contrast, it appears that pro-longevity mechanisms may be complex traits afforded by connections between metabolism and protein functions that are impossible to predict by genomic approaches alone. Thus, metabolomics and proteomics studies will be required to understand the mechanisms of longevity. Several examples are reviewed that demonstrate the naked mole rat (NMR) shows unique proteomic signatures that contribute to longevity by overcoming several hallmarks of aging. SIRT6 is also discussed as an example of a protein that evolves enhanced enzymatic function in long-lived species. Finally, it is shown that several longevity-related proteins such as Cip1/p21, FOXO3, TOP2A, AKT1, RICTOR, INSR, and SIRT6 harbor posttranslational modification (PTM) sites that preferentially appear in either short- or long-lived species and provide examples of crosstalk between PTM sites. Prospects of enhancing lifespan and healthspan of humans by altering metabolism and proteoforms with drugs that mimic changes observed in long-lived species are discussed.
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Affiliation(s)
- Gregory Tombline
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Jonathan Gigas
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Nicholas Macoretta
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Max Zacher
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Stephan Emmrich
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Yang Zhao
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Andrei Seluanov
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
| | - Vera Gorbunova
- University of Rochester, Department of Biology, Rochester,
New York 14627, USA
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20
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Abstract
Human pluripotent stem (PS) cells can be isolated from preimplantation embryos or by reprogramming of somatic cells or germline progenitors. Human PS cells are considered the "holy grail" of regenerative medicine because they have the potential to form all cell types of the adult body. Because of their similarity to humans, nonhuman primate (NHP) PS cells are also important models for studying human biology and disease, as well as for developing therapeutic strategies and test bed for cell replacement therapy. This chapter describes adjusted methods for cultivation of PS cells from different primate species, including African green monkey, rhesus monkey, chimpanzee, and human. Supplementation of E8 medium and inhibitors of the Tankyrase and GSK3 kinases to various primate PS cell media reduce line-dependent predisposition for spontaneous differentiation in conventional PS cell cultures. We provide methods for basic characterization of primate PS cell lines, which include immunostaining for pluripotency markers such as OCT4 and TRA-1-60, as well as in vivo teratoma formation assay. We provide methods for generating alternative PS cells including region-selective primed PS cells, two different versions of naïve-like cells, and recently reported extended pluripotent stem (EPS) cells. These derivations are achieved by acclimation of conventional PS cells to target media, episomal reprogramming of somatic cells, or resetting conventional PS cells to a naïve-like state by overexpression of KLF2 and NANOG. We also provide methods for isolation of PS cells from human blastocysts. We describe how to generate interspecies primate-mouse chimeras at the blastocyst and postimplantation embryo stages. Systematic evaluation of the chimeric competency of human and primate PS cells will aid in efforts to overcome species barriers and achieve higher grade chimerism in postimplantation conceptuses that could enable organ-specific enrichment of human xenogeneic PS cell derivatives in large animals such as pigs and sheep.
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Affiliation(s)
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX, USA.
- Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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21
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Abstract
Cancer researchers have traditionally used the mouse and the rat as staple model organisms. These animals are very short-lived, reproduce rapidly and are highly prone to cancer. They have been very useful for modelling some human cancer types and testing experimental treatments; however, these cancer-prone species offer little for understanding the mechanisms of cancer resistance. Recent technological advances have expanded bestiary research to non-standard model organisms that possess unique traits of very high value to humans, such as cancer resistance and longevity. In recent years, several discoveries have been made in non-standard mammalian species, providing new insights on the natural mechanisms of cancer resistance. These include mechanisms of cancer resistance in the naked mole rat, blind mole rat and elephant. In each of these species, evolution took a different path, leading to novel mechanisms. Many other long-lived mammalian species display cancer resistance, including whales, grey squirrels, microbats, cows and horses. Understanding the molecular mechanisms of cancer resistance in all these species is important and timely, as, ultimately, these mechanisms could be harnessed for the development of human cancer therapies.
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Affiliation(s)
- Andrei Seluanov
- University of Rochester, Department of Biology, Rochester, NY, USA
| | - Vadim N Gladyshev
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Vera Gorbunova
- University of Rochester, Department of Biology, Rochester, NY, USA.
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22
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Lee SG, Mikhalchenko AE, Yim SH, Gladyshev VN. A naked mole rat iPSC line expressing drug-inducible mouse pluripotency factors developed from embryonic fibroblasts. Stem Cell Res 2018; 31:197-200. [PMID: 30107334 DOI: 10.1016/j.scr.2018.06.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 05/17/2018] [Accepted: 06/19/2018] [Indexed: 12/30/2022] Open
Abstract
Naked mole rats (NMRs, Heterocephalus glaber) are long-lived, cancer-resistant rodents. Here, we report the development of an induced pluripotent stem cell (iPSC) line generated from immortalized NMR embryonic fibroblasts transduced with a doxycycline-inducible mouse OSKM polycistronic vector. This iPSC line was shown to express pluripotency-associated markers, form embryoid bodies, differentiate in vitro to the derivatives of three germ layers, and exhibit normal karyotype. The ability of iPSCs to differentiate in vivo was supported by the contribution to interspecific chimera upon injection into mouse blastocysts. This NMR iPSC line may be a useful tool in cancer and aging research.
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Affiliation(s)
- Sang-Goo Lee
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Aleksei E Mikhalchenko
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA; Center for Data-Intensive Biomedicine and Biotechnology, Skolkovo Institute of Science and Technology, Moscow 143028, Russia
| | - Sun Hee Yim
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
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23
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Interspecies chimeras. Curr Opin Genet Dev 2018; 52:36-41. [PMID: 29859382 DOI: 10.1016/j.gde.2018.05.007] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 05/18/2018] [Accepted: 05/19/2018] [Indexed: 12/18/2022]
Abstract
By probing early embryogenesis and regeneration, interspecies chimeras provide a unique platform for discovery and clinical use. Although efficient generation of human:animal chimeric embryos remains elusive, recent advancements attempt to overcome incompatibilities in xenogeneic development and transplantation.
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24
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Naked Mole Rat Cells Have a Stable Epigenome that Resists iPSC Reprogramming. Stem Cell Reports 2017; 9:1721-1734. [PMID: 29107597 PMCID: PMC5831052 DOI: 10.1016/j.stemcr.2017.10.001] [Citation(s) in RCA: 59] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2016] [Revised: 09/29/2017] [Accepted: 10/02/2017] [Indexed: 12/15/2022] Open
Abstract
Naked mole rat (NMR) is a valuable model for aging and cancer research due to its exceptional longevity and cancer resistance. We observed that the reprogramming efficiency of NMR fibroblasts in response to OSKM was drastically lower than that of mouse fibroblasts. Expression of SV40 LargeT antigen (LT) dramatically improved reprogramming of NMR fibroblasts. Inactivation of Rb alone, but not p53, was sufficient to improve reprogramming efficiency, suggesting that NMR chromatin may be refractory to reprogramming. Analysis of the global histone landscape revealed that NMR had higher levels of repressive H3K27 methylation marks and lower levels of activating H3K27 acetylation marks than mouse. ATAC-seq revealed that in NMR, promoters of reprogramming genes were more closed than mouse promoters, while expression of LT led to massive opening of the NMR promoters. These results suggest that NMR displays a more stable epigenome that resists de-differentiation, contributing to the cancer resistance and longevity of this species. Naked mole rat (NMR) fibroblasts are resistant to OSKM reprogramming Inactivation of Rb facilitates reprogramming of NMR cells NMR cells have higher levels of repressive H3K27 methylation relative to the mouse NMR cells have more closed chromatin in promoters relative to the mouse
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