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Morris JP, Baslan T, Soltis DE, Soltis PS, Fox DT. Integrating the Study of Polyploidy Across Organisms, Tissues, and Disease. Annu Rev Genet 2024; 58:297-318. [PMID: 39227132 PMCID: PMC11590481 DOI: 10.1146/annurev-genet-111523-102124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2024]
Abstract
Polyploidy is a cellular state containing more than two complete chromosome sets. It has largely been studied as a discrete phenomenon in either organismal, tissue, or disease contexts. Increasingly, however, investigation of polyploidy across disciplines is coalescing around common principles. For example, the recent Polyploidy Across the Tree of Life meeting considered the contribution of polyploidy both in organismal evolution over millions of years and in tumorigenesis across much shorter timescales. Here, we build on this newfound integration with a unified discussion of polyploidy in organisms, cells, and disease. We highlight how common polyploidy is at multiple biological scales, thus eliminating the outdated mindset of its specialization. Additionally, we discuss rules that are likely common to all instances of polyploidy. With increasing appreciation that polyploidy is pervasive in nature and displays fascinating commonalities across diverse contexts, inquiry related to this important topic is rapidly becoming unified.
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Affiliation(s)
- John P Morris
- Department of Pharmacology and Lineberger Comprehensive Cancer Center, University of North Carolina School of Medicine, Chapel Hill, North Carolina, USA;
| | - Timour Baslan
- Center for Childhood Cancer Research, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Systems Pharmacology and Translational Therapeutics and Abramson Cancer Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Biomedical Sciences and Penn Vet Cancer Center, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Douglas E Soltis
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA;
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Polyploidy Integration and Innovation Institute
- Department of Biology, University of Florida, Gainesville, Florida, USA;
| | - Pamela S Soltis
- Biodiversity Institute, University of Florida, Gainesville, Florida, USA
- Florida Museum of Natural History, University of Florida, Gainesville, Florida, USA;
- Polyploidy Integration and Innovation Institute
| | - Donald T Fox
- Department of Pharmacology and Cancer Biology, Duke Regeneration Center, and Duke Cancer Institute, Duke University School of Medicine, Durham, North Carolina, USA;
- Polyploidy Integration and Innovation Institute
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Lin YH, Zhang S, Zhu M, Lu T, Chen K, Wen Z, Wang S, Xiao G, Luo D, Jia Y, Li L, MacConmara M, Hoshida Y, Singal A, Yopp A, Wang T, Zhu H. Mice With Increased Numbers of Polyploid Hepatocytes Maintain Regenerative Capacity But Develop Fewer Hepatocellular Carcinomas Following Chronic Liver Injury. Gastroenterology 2020; 158:1698-1712.e14. [PMID: 31972235 PMCID: PMC8902703 DOI: 10.1053/j.gastro.2020.01.026] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/24/2019] [Revised: 12/24/2019] [Accepted: 01/02/2020] [Indexed: 01/07/2023]
Abstract
BACKGROUND & AIMS Thirty to 90% of hepatocytes contain whole-genome duplications, but little is known about the fates or functions of these polyploid cells or how they affect development of liver disease. We investigated the effects of continuous proliferative pressure, observed in chronically damaged liver tissues, on polyploid cells. METHODS We studied Rosa-rtTa mice (controls) and Rosa-rtTa;TRE-short hairpin RNA mice, which have reversible knockdown of anillin, actin binding protein (ANLN). Transient administration of doxycycline increases the frequency and degree of hepatocyte polyploidy without permanently altering levels of ANLN. Mice were then given diethylnitrosamine and carbon tetrachloride (CCl4) to induce mutations, chronic liver damage, and carcinogenesis. We performed partial hepatectomies to test liver regeneration and then RNA-sequencing to identify changes in gene expression. Lineage tracing was used to rule out repopulation from non-hepatocyte sources. We imaged dividing hepatocytes to estimate the frequency of mitotic errors during regeneration. We also performed whole-exome sequencing of 54 liver nodules from patients with cirrhosis to quantify aneuploidy, a possible outcome of polyploid cell divisions. RESULTS Liver tissues from control mice given CCl4 had significant increases in ploidy compared with livers from uninjured mice. Mice with knockdown of ANLN had hepatocyte ploidy above physiologic levels and developed significantly fewer liver tumors after administration of diethylnitrosamine and CCl4 compared with control mice. Increased hepatocyte polyploidy was not associated with altered regenerative capacity or tissue fitness, changes in gene expression, or more mitotic errors. Based on lineage-tracing experiments, non-hepatocytes did not contribute to liver regeneration in mice with increased polyploidy. Despite an equivalent rate of mitosis in hepatocytes of differing ploidies, we found no lagging chromosomes or micronuclei in mitotic polyploid cells. In nodules of human cirrhotic liver tissue, there was no evidence of chromosome-level copy number variations. CONCLUSIONS Mice with increased polyploid hepatocytes develop fewer liver tumors following chronic liver damage. Remarkably, polyploid hepatocytes maintain the ability to regenerate liver tissues during chronic damage without generating mitotic errors, and aneuploidy is not commonly observed in cirrhotic livers. Strategies to increase numbers of polypoid hepatocytes might be effective in preventing liver cancer.
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Affiliation(s)
- Yu-Hsuan Lin
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Shuyuan Zhang
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Min Zhu
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Tianshi Lu
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine,Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Kenian Chen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Zhuoyu Wen
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Shidan Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Guanghua Xiao
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Danni Luo
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | - Yuemeng Jia
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | - Lin Li
- Children’s Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine
| | | | | | | | | | - Tao Wang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences,Kidney Cancer Program, Simmons Comprehensive Cancer Center,Center for the Genetics of Host Defense, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Hao Zhu
- Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, Texas.
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A direct comparison of interphase FISH versus low-coverage single cell sequencing to detect aneuploidy reveals respective strengths and weaknesses. Sci Rep 2019; 9:10508. [PMID: 31324840 PMCID: PMC6642082 DOI: 10.1038/s41598-019-46606-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2018] [Accepted: 06/21/2019] [Indexed: 01/09/2023] Open
Abstract
Aneuploidy has been reported to occur at remarkably high levels in normal somatic tissues using Fluorescence In Situ Hybridization (FISH). Recently, these reports were contradicted by single-cell low-coverage whole genome sequencing (scL-WGS) analyses, which showed aneuploidy frequencies at least an order of magnitude lower. To explain these seemingly contradictory findings, we used both techniques to analyze artificially generated mock aneuploid cells and cells with natural random aneuploidy. Our data indicate that while FISH tended to over-report aneuploidies, a modified 2-probe approach can accurately detect low levels of aneuploidy. Further, scL-WGS tends to underestimate aneuploidy levels, especially in a polyploid background.
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Abstract
Polyploid cells contain more than two homologous sets of chromosomes. The original observations of liver polyploidy date back to the 1940s, but functional roles for polyploid cells are still unclear. Liver polyploidy may influence regeneration, stress response, and cancer, although little evidence has established direct causal links between polyploidy and these biological phenotypes. In this review, we will introduce broad concepts about polyploidy including its distribution in nature and how polyploids form in normal and pathological situations. Then we will examine recent discoveries that have begun to clarify functionality and disease relevance of liver polyploidy. Finally, we will discuss implications and future directions of research about polyploidy in the liver.
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Affiliation(s)
- Shuyuan Zhang
- a Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine , University of Texas Southwestern Medical Center , Dallas , USA
| | - Yu-Hsuan Lin
- a Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine , University of Texas Southwestern Medical Center , Dallas , USA
| | - Branden Tarlow
- b Department of Internal Medicine , University of Texas Southwestern Medical Center , Dallas , TX , USA
| | - Hao Zhu
- a Children's Research Institute, Departments of Pediatrics and Internal Medicine, Center for Regenerative Science and Medicine , University of Texas Southwestern Medical Center , Dallas , USA
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Simonova VV, Vetchinova AS, Novosadova EV, Khaspekov LG, Illarioshkin SN. Genome Editing and the Problem of Tetraploidy in Cell Modeling of the Genetic Form of Parkinsonism. BIOCHEMISTRY (MOSCOW) 2018; 83:1040-1045. [PMID: 30472942 DOI: 10.1134/s0006297918090055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
The prevalent form of familial parkinsonism is caused by mutations in the LRRK2 gene encoding for the mitochondrial protein kinase. In the review, we discuss possible causes of appearance of tetraploid cells in neuronal precursors obtained from induced pluripotent stem cells from patients with the LRRK2-associated form of parkinsonism after genome editing procedure. As LRRK2 protein participates in cell proliferation and maintenance of the nuclear envelope, spindle fibers, and cytoskeleton, mutations in the LRRK2 gene can affect protein functions and lead, via various mechanisms, to the mitotic machinery disintegration and chromosomal aberration. These abnormalities can appear at different stages of fibroblast reprogramming; therefore, editing of the LRRK2 nucleotide sequence should be done during or before the reprogramming stage.
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Affiliation(s)
- V V Simonova
- Research Center of Neurology, Moscow, 125367, Russia
| | | | - E V Novosadova
- Institute of Molecular Genetics, Russian Academy of Sciences, Moscow, 123182, Russia.
| | - L G Khaspekov
- Research Center of Neurology, Moscow, 125367, Russia.
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Andriani GA, Vijg J, Montagna C. Mechanisms and consequences of aneuploidy and chromosome instability in the aging brain. Mech Ageing Dev 2017; 161:19-36. [PMID: 27013377 PMCID: PMC5490080 DOI: 10.1016/j.mad.2016.03.007] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2016] [Revised: 03/17/2016] [Accepted: 03/19/2016] [Indexed: 01/31/2023]
Abstract
Aneuploidy and polyploidy are a form of Genomic Instability (GIN) known as Chromosomal Instability (CIN) characterized by sporadic abnormalities in chromosome copy numbers. Aneuploidy is commonly linked to pathological states. It is a hallmark of spontaneous abortions and birth defects and it is observed virtually in every human tumor, therefore being generally regarded as detrimental for the development or the maturation of tissues under physiological conditions. Polyploidy however, occurs as part of normal physiological processes during maturation and differentiation of some mammalian cell types. Surprisingly, high levels of aneuploidy are present in the brain, and their frequency increases with age suggesting that the brain is able to maintain its functionality in the presence of high levels of mosaic aneuploidy. Because somatic aneuploidy with age can reach exceptionally high levels, it is likely to have long-term adverse effects in this organ. We describe the mechanisms accountable for an abnormal DNA content with a particular emphasis on the CNS where cell division is limited. Next, we briefly summarize the types of GIN known to date and discuss how they interconnect with CIN. Lastly we highlight how several forms of CIN may contribute to genetic variation, tissue degeneration and disease in the CNS.
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Affiliation(s)
- Grasiella A Andriani
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Jan Vijg
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department Ophthalmology and Visual Science, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Obstetrics & Gynecology and Women's Health, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA
| | - Cristina Montagna
- Department of Genetics, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA; Department of Pathology, Albert Einstein College of Medicine, Yeshiva University, Bronx, NY 10461, USA.
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Galan A, Dergham P, Escoll P, de-la-Hera A, D'Onofrio PM, Magharious MM, Koeberle PD, Frade JM, Saragovi HU. Neuronal injury external to the retina rapidly activates retinal glia, followed by elevation of markers for cell cycle re-entry and death in retinal ganglion cells. PLoS One 2014; 9:e101349. [PMID: 24983470 PMCID: PMC4077807 DOI: 10.1371/journal.pone.0101349] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Accepted: 06/05/2014] [Indexed: 11/22/2022] Open
Abstract
Retinal ganglion cells (RGCs) are neurons that relay visual signals from the retina to the brain. The RGC cell bodies reside in the retina and their fibers form the optic nerve. Full transection (axotomy) of the optic nerve is an extra-retinal injury model of RGC degeneration. Optic nerve transection permits time-kinetic studies of neurodegenerative mechanisms in neurons and resident glia of the retina, the early events of which are reported here. One day after injury, and before atrophy of RGC cell bodies was apparent, glia had increased levels of phospho-Akt, phospho-S6, and phospho-ERK1/2; however, these signals were not detected in injured RGCs. Three days after injury there were increased levels of phospho-Rb and cyclin A proteins detected in RGCs, whereas these signals were not detected in glia. DNA hyperploidy was also detected in RGCs, indicative of cell cycle re-entry by these post-mitotic neurons. These events culminated in RGC death, which is delayed by pharmacological inhibition of the MAPK/ERK pathway. Our data show that a remote injury to RGC axons rapidly conveys a signal that activates retinal glia, followed by RGC cell cycle re-entry, DNA hyperploidy, and neuronal death that is delayed by preventing glial MAPK/ERK activation. These results demonstrate that complex and variable neuro-glia interactions regulate healthy and injured states in the adult mammalian retina.
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Affiliation(s)
- Alba Galan
- Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
| | - Pauline Dergham
- Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
| | - Pedro Escoll
- Department of Medicine, Molecular Medicine Institute (IMMPA CSIC/UAH), School of Medicine, Alcalá University, Alcalá de Henares, Madrid, Spain
| | - Antonio de-la-Hera
- Department of Medicine, Molecular Medicine Institute (IMMPA CSIC/UAH), School of Medicine, Alcalá University, Alcalá de Henares, Madrid, Spain
| | - Philippe M. D'Onofrio
- Graduate Department of Rehabilitation Sciences, University of Toronto, Toronto, ON, Canada
| | - Mark M. Magharious
- Graduate Department of Rehabilitation Sciences, University of Toronto, Toronto, ON, Canada
| | | | - José María Frade
- Department of Molecular, Cellular and Developmental Neurobiology, Cajal Institute, CSIC, Madrid, Spain
| | - H. Uri Saragovi
- Lady Davis Institute-Jewish General Hospital, Montreal, Quebec, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, Quebec, Canada
- Department of Oncology and the Cancer Center, McGill University, Montreal, Quebec, Canada
- * E-mail:
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