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Lee E, Orton K, Langton M, Irving J, Evans K. Clinical validation of an abbreviated karyotype analysis protocol for fertility evaluation. Pathology 2024:S0031-3025(24)00169-7. [PMID: 39060196 DOI: 10.1016/j.pathol.2024.04.010] [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: 10/12/2023] [Revised: 03/20/2024] [Accepted: 04/24/2024] [Indexed: 07/28/2024]
Abstract
Conventional G-banded karyotype is an essential tool for detecting chromosomal variants in patients undergoing fertility evaluation. In Australia, 15 cells are traditionally analysed or counted, to enhance detection of mosaic chromosomal variants. However, this protocol is not backed by clinical evidence. This study aims to assess the test performance of an abbreviated 5-cell karyotype analysis protocol in adult patients undergoing fertility evaluation. A retrospective review of 53,293 blood karyotype tests, performed between 2019 and 2023, was conducted on a patient cohort primarily referred by reproductive endocrinology specialists. There were 513 variants reported in this cohort. Low level mosaic variants, where the variant was observed in less than 40% of cells, were reported in 13 cases, or one in 4,100 patients. Due to reduced sensitivity for low level mosaic variants, a 5-cell protocol is estimated to have a test sensitivity of 97.3% and a negative predictive value of 99.97%. A decision-making flowchart is proposed and we show that additional chromosome analysis and/or counts would be triggered in fewer than one in 10 cases using a 5-cell protocol, whilst remaining appropriate for detecting clinically significant mosaicism. A 5-cell karyotype analysis protocol therefore maintains analytical and clinical validity in adult patients undergoing fertility-related blood karyotyping. Future research is recommended to validate these findings across laboratories and to explore their application to other clinical contexts.
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Affiliation(s)
- Eric Lee
- Cytogenetics Department, Virtus Diagnostics, Milton, QLD, Australia; Molecular Genetics Department, Virtus Diagnostics, Revesby, NSW, Australia.
| | - Kaylee Orton
- Molecular Genetics Department, Virtus Diagnostics, Revesby, NSW, Australia
| | - Meg Langton
- Cytogenetics Department, Virtus Diagnostics, Milton, QLD, Australia
| | - Jodi Irving
- Cytogenetics Department, Virtus Diagnostics, Milton, QLD, Australia
| | - Ken Evans
- Cytogenetics Department, Virtus Diagnostics, Milton, QLD, Australia
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2
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Dirican CD, Nelson PS. Y Chromosome Loss and Implications for Oncology. Mol Cancer Res 2024; 22:603-612. [PMID: 38647375 PMCID: PMC11217729 DOI: 10.1158/1541-7786.mcr-24-0105] [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: 01/24/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
The Y chromosome has recognized functions in promoting male sex determination and regulating aspects of fertility. However, recent work has demonstrated important roles for the Y chromosome and Y-encoded genes in multiple domains of male health, including cancer. It is well established that males experience shorter lifespans than females, and this sex bias on overall mortality is accentuated in populations with longer life expectancy, in part related to elevated rates of cancer. The majority of human malignancies exhibit a sex bias with elevated frequencies in males. For many of these cancer types, the disparity has not been explained by environmental risk factors such as tobacco use. Notably, loss of the Y chromosome (LOY) detected in blood cells, termed mosaic LOY, is a common event that is related to advancing age and is associated with a shortened lifespan. Mosaic LOY is linked to increased incidence and mortality across a range of malignancies. Furthermore, tumors arising in different anatomic sites exhibit different frequencies of partial or complete Y chromosome loss. Causal oncogenic or tumor-suppressive roles have been documented for several Y-encoded genes, such as lysine-specific demethylase 5 D, that exert pleiotropic effects on cellular functions by virtue of genome-wide regulation of gene activity. In this review, we discuss aspects of the Y chromosome relevant to oncology. The recent completion of the entire human Y-chromosome sequence provides a reference map of Y-encoded genes and regulatory elements to enable causal molecular studies that may explain and exploit the marked disparity in male cancer risk and mortality.
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Affiliation(s)
- Canan D. Dirican
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington.
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington.
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3
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Vinson AJ, Zhang X, Dahhou M, Süsal C, Döhler B, Melk A, Sapir-Pichhadze R, Cardinal H, Wong G, Francis A, Pilmore H, Grinspan LT, Foster BJ. Differences in excess mortality by recipient sex after heart transplant: An individual patient data meta-analysis. J Heart Lung Transplant 2024; 43:1162-1173. [PMID: 38522764 DOI: 10.1016/j.healun.2024.03.016] [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: 10/11/2023] [Revised: 03/07/2024] [Accepted: 03/20/2024] [Indexed: 03/26/2024] Open
Abstract
BACKGROUND Identification of differences in mortality risk between female and male heart transplant recipients may prompt sex-specific management strategies. Because worldwide, males of all ages have higher absolute mortality rates than females, we aimed to compare the excess risk of mortality (risk above the general population) in female vs male heart transplant recipients. METHODS We used relative survival models conducted separately in SRTR and CTS cohorts from 1988-2019, and subsequently combined using 2-stage individual patient data meta-analysis, to compare the excess risk of mortality in female vs male first heart transplant recipients, accounting for the modifying effects of donor sex and recipient current age. RESULTS We analyzed 108,918 patients. When the donor was male, female recipients 0-12 years (Relative excess risk (RER) 1.13, 95% CI 1.00-1.26), 13-44 years (RER 1.17, 95% CI 1.10-1.25), and ≥45 years (RER 1.14, 95% CI 1.02-1.27) showed higher excess mortality risks than male recipients of the same age. When the donor was female, only female recipients 13-44 years showed higher excess risks of mortality than males (RER 1.09, 95% CI 1.00-1.20), though not significantly (p = 0.05). CONCLUSIONS In the setting of a male donor, female recipients of all ages had significantly higher excess mortality than males. When the donor was female, female recipients of reproductive age had higher excess risks of mortality than male recipients of the same age, though this was not statistically significant. Further investigation is required to determine the reasons underlying these differences.
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Affiliation(s)
- Amanda J Vinson
- Department of Medicine, Nephrology Division, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Xun Zhang
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Mourad Dahhou
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada
| | - Caner Süsal
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany; Transplant Immunology Research Center of Excellence, Koç University, Istanbul, Turkey
| | - Bernd Döhler
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anette Melk
- Children's Hospital, Hannover Medical School, Hannover, Germany
| | - Ruth Sapir-Pichhadze
- Department of Medicine, Division of Nephrology, McGill University, Montreal, Quebec, Canada
| | - Heloise Cardinal
- Department of Medicine, Division of Nephrology, Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Germaine Wong
- School of Public Health, University of Sydney, Sydney, New South Wales, Australia
| | - Anna Francis
- School of Clinical Medicine, University of Queensland, Brisbane, Australia; Department of Nephrology, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Helen Pilmore
- Department of Renal Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Lauren T Grinspan
- Recanati/Miller Transplantation Institute, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Bethany J Foster
- Research Institute of the McGill University Health Centre, Montréal, Quebec, Canada; Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montreal, Quebec, Canada; Department of Pediatrics, Division of Nephrology, McGill University Faculty of Medicine, Montreal, Quebec, Canada
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4
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Gutiérrez-Hurtado IA, Sánchez-Méndez AD, Becerra-Loaiza DS, Rangel-Villalobos H, Torres-Carrillo N, Gallegos-Arreola MP, Aguilar-Velázquez JA. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health. Int J Mol Sci 2024; 25:4230. [PMID: 38673816 PMCID: PMC11050192 DOI: 10.3390/ijms25084230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.
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Affiliation(s)
- Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47820, Jalisco, Mexico
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
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5
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Wang Y, Sano S. Why Y matters? The implication of loss of Y chromosome in blood and cancer. Cancer Sci 2024; 115:706-714. [PMID: 38258457 PMCID: PMC10921008 DOI: 10.1111/cas.16072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/23/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Hematopoietic mosaic loss of Y chromosome (mLOY) has emerged as a potential male-specific accelerator of biological aging, increasing the risk of various age-related diseases, including cancer. Importantly, mLOY is not confined to hematopoietic cells; its presence has also been observed in nonhematological cancer cells, with the impact of this presence previously unknown. Recent studies have revealed that, whether occurring in leukocytes or cancer cells, mLOY plays a role in promoting the development of an immunosuppressive tumor microenvironment. This occurs through the modulation of tumor-infiltrating immune cells, ultimately enabling cancer cells to evade the vigilant immune system. In this review, we illuminate recent progress concerning the effects of hematopoietic mLOY and cancer mLOY on cancer progression. Examining cancer progression from the perspective of LOY adds a new layer to our understanding of cancer immunity, promising insights that hold the potential to identify innovative and potent immunotherapy targets for cancer.
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Affiliation(s)
- Ying Wang
- Department of CardiologyThe Second Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Soichi Sano
- Laboratory of Cardiovascular MosaicismNational Cerebral and Cardiovascular CenterOsakaJapan
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6
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Sundi D, Collier KA, Yang Y, Diaz DA, Pohar KS, Singer EA, Gupta S, Carson WE, Clinton SK, Li Z, Messing EM. Roles of Androgen Receptor Signaling in Urothelial Carcinoma. Cancers (Basel) 2024; 16:746. [PMID: 38398136 PMCID: PMC10886823 DOI: 10.3390/cancers16040746] [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: 01/15/2024] [Revised: 01/31/2024] [Accepted: 02/07/2024] [Indexed: 02/25/2024] Open
Abstract
Preclinical and clinical data suggest that androgen receptor signaling strongly contributes to bladder cancer development. The roles of the androgen receptor in bladder carcinogenesis have obvious implications for understanding the strong male sex bias in this disease and for potential therapeutic strategies as well. In this review, we summarize what is known about androgen receptor signaling in urothelial carcinoma as well as in tumor-infiltrating immune cells, reviewing preclinical and clinical data. We also highlight clinical trial efforts in this area.
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Affiliation(s)
- Debasish Sundi
- Department of Urology, Division of Urologic Oncology, Pelotonia Institute for Immuno-Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Katharine A. Collier
- Department of Internal Medicine, Division of Medical Oncology, Pelotonia Institute for Immuno-Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Yuanquan Yang
- Department of Internal Medicine, Division of Medical Oncology, Pelotonia Institute for Immuno-Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Dayssy Alexandra Diaz
- Department of Radiation Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Kamal S. Pohar
- Department of Urology, Division of Urologic Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA (E.A.S.)
| | - Eric A. Singer
- Department of Urology, Division of Urologic Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA (E.A.S.)
| | - Sanjay Gupta
- Department of Urology, Case Western Reserve University School of Medicine, The Urology Institute, University Hospitals Cleveland Medical Center, Cleveland, OH 44106, USA;
| | - William E. Carson
- Department of Surgery, Division of Surgical Oncology, Pelotonia Institute for Immuno-Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Steven K. Clinton
- Department of Internal Medicine, Division of Medical Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Zihai Li
- Department of Internal Medicine, Division of Medical Oncology, Pelotonia Institute for Immuno-Oncology, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Edward M. Messing
- Departments of Urology, Oncology, and Pathology, University of Rochester Medical Center, Rochester, NY 14642, USA
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7
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Wilson PC, Verma A, Yoshimura Y, Muto Y, Li H, Malvin NP, Dixon EE, Humphreys BD. Mosaic loss of Y chromosome is associated with aging and epithelial injury in chronic kidney disease. Genome Biol 2024; 25:36. [PMID: 38287344 PMCID: PMC10823641 DOI: 10.1186/s13059-024-03173-2] [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: 06/12/2023] [Accepted: 01/12/2024] [Indexed: 01/31/2024] Open
Abstract
BACKGROUND Mosaic loss of Y chromosome (LOY) is the most common chromosomal alteration in aging men. Here, we use single-cell RNA and ATAC sequencing to show that LOY is present in the kidney and increases with age and chronic kidney disease. RESULTS The likelihood of a cell having LOY varies depending on its location in the nephron. Cortical epithelial cell types have a greater proportion of LOY than medullary or glomerular cell types, which may reflect their proliferative history. Proximal tubule cells are the most abundant cell type in the cortex and are susceptible to hypoxic injury. A subset of these cells acquires a pro-inflammatory transcription and chromatin accessibility profile associated with expression of HAVCR1, VCAM1, and PROM1. These injured epithelial cells have the greatest proportion of LOY and their presence predicts future kidney function decline. Moreover, proximal tubule cells with LOY are more likely to harbor additional large chromosomal gains and express pro-survival pathways. Spatial transcriptomics localizes injured proximal tubule cells to a pro-fibrotic microenvironment where they adopt a secretory phenotype and likely communicate with infiltrating immune cells. CONCLUSIONS We hypothesize that LOY is an indicator of increased DNA damage and potential marker of cellular senescence that can be applied to single-cell datasets in other tissues.
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Affiliation(s)
- Parker C Wilson
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA.
| | - Amit Verma
- Division of Diagnostic Innovation, Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yasuhiro Yoshimura
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Yoshiharu Muto
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Haikuo Li
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Nicole P Malvin
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Eryn E Dixon
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
| | - Benjamin D Humphreys
- Division of Nephrology, Department of Medicine, Washington University in St. Louis, St. Louis, MO, USA
- Department of Developmental Biology, Washington University in St. Louis, St. Louis, MO, USA
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8
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. CELL GENOMICS 2024; 4:100462. [PMID: 38190107 PMCID: PMC10794785 DOI: 10.1016/j.xgen.2023.100462] [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: 06/01/2023] [Revised: 08/15/2023] [Accepted: 11/14/2023] [Indexed: 01/09/2024]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors-ZFX and ZFY-encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Alexander K Godfrey
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Neha V Bokil
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | | | | | - Shanlee M Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA; Developmental Pediatrics, eXtraOrdinarY Kids Program, Children's Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA; Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA.
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9
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Chang VC, Zhou W, Berndt SI, Andreotti G, Yeager M, Parks CG, Sandler DP, Rothman N, Beane Freeman LE, Machiela MJ, Hofmann JN. Glyphosate Use and Mosaic Loss of Chromosome Y among Male Farmers in the Agricultural Health Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:127006. [PMID: 38055050 PMCID: PMC10699410 DOI: 10.1289/ehp12834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Glyphosate is the most commonly used herbicide worldwide and has been implicated in the development of certain hematologic cancers. Although mechanistic studies in human cells and animals support the genotoxic effects of glyphosate, evidence in human populations is scarce. OBJECTIVES We evaluated the association between lifetime occupational glyphosate use and mosaic loss of chromosome Y (mLOY) as a marker of genotoxicity among male farmers. METHODS We analyzed blood-derived DNA from 1,606 farmers ≥ 50 years of age in the Biomarkers of Exposure and Effect in Agriculture study, a subcohort of the Agricultural Health Study. mLOY was detected using genotyping array intensity data in the pseudoautosomal region of the sex chromosomes. Cumulative lifetime glyphosate use was assessed using self-reported pesticide exposure histories. Using multivariable logistic regression, we estimated odds ratios (ORs) and 95% confidence intervals (CIs) for the associations between glyphosate use and any detectable mLOY (overall mLOY) or mLOY affecting ≥ 10 % of cells (expanded mLOY). RESULTS Overall, mLOY was detected in 21.4% of farmers, and 9.8% of all farmers had expanded mLOY. Increasing total lifetime days of glyphosate use was associated with expanded mLOY [highest vs. lowest quartile; OR = 1.75 (95% CI: 1.00, 3.07), p trend = 0.03 ] but not with overall mLOY; the associations with expanded mLOY were most apparent among older (≥ 70 years of age) men [OR = 2.30 (95% CI: 1.13, 4.67), p trend = 0.01 ], never smokers [OR = 2.32 (95% CI: 1.04, 5.21), p trend = 0.04 ], and nonobese men [OR = 2.04 (95% CI: 0.99, 4.19), p trend = 0.03 ]. Similar patterns of associations were observed for intensity-weighted lifetime days of glyphosate use. DISCUSSION High lifetime glyphosate use could be associated with mLOY affecting a larger fraction of cells, suggesting glyphosate could confer genotoxic or selective effects relevant for clonal expansion. As the first study to investigate this association, our findings contribute novel evidence regarding the carcinogenic potential of glyphosate and require replication in future studies. https://doi.org/10.1289/EHP12834.
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Affiliation(s)
- Vicky C. Chang
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, USA
| | - Sonja I. Berndt
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Gabriella Andreotti
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, USA
| | - Christine G. Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, North Carolina, USA
| | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, North Carolina, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Laura E. Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Mitchell J. Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, USA
| | - Jonathan N. Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
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10
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Thierry AR, Sanchez C, Colinge J, Pisareva E. Circulating DNA reveals a specific and higher fragmentation of the Y chromosome. Hum Genet 2023; 142:1603-1609. [PMID: 37743368 DOI: 10.1007/s00439-023-02600-x] [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: 06/21/2023] [Accepted: 09/11/2023] [Indexed: 09/26/2023]
Abstract
Chromosome stability is a key point in genome evolution, particularly that of the Y chromosome. The Y chromosome loss in blood and tumor cells is well established. Through processes that are common to other chromosomes too, the Y chromosome undergoes degradation and fragmentation in the blood stream before elimination. This process gives rise to circulating DNA (cirDNA) fragments, whose examination may provide potential insight into the role of DNA fragmentation in blood for the Y chromosome elimination. In this study, we employed shallow whole genome sequencing (sWGS) to comprehensively assess the total cirDNA and the individual chromosome fragment size profiles in the plasma of healthy male individuals. Here, we show that (i) the fragment size profiles of total circulating DNA (cirDNA) and DNA fragments originating from autosomes and the X chromosome in blood plasma are homogeneous, and have a remarkably low variability (mean CV = 7%) among healthy individuals, (ii) the Y chromosome has a distinct fragment size profile with the accumulation of the fragment < 145 bp and depletion of the dinucleosome-associated fragments (290-390 bp), and its fragment fraction in blood decreases with age. These results indicate a higher fragmentation of the Y chromosome compared to other chromosomes and this in turn might be due to its increased susceptibility to degradation. Our findings pave the way for an elucidation of the impact of chromosomal origin on DNA degradation and the Y chromosome biology.
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Affiliation(s)
- Alain R Thierry
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
- ICM, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France.
| | - Cynthia Sanchez
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
- ICM, Institut Régional du Cancer de Montpellier, 34298, Montpellier, France
| | - Jacques Colinge
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France
| | - Ekaterina Pisareva
- IRCM, Institut de Recherche en Cancérologie de Montpellier, INSERM U1194, Université de Montpellier, Montpellier, France.
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11
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Doshi B, Athans SR, Woloszynska A. Biological differences underlying sex and gender disparities in bladder cancer: current synopsis and future directions. Oncogenesis 2023; 12:44. [PMID: 37666817 PMCID: PMC10477245 DOI: 10.1038/s41389-023-00489-9] [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: 05/08/2023] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 09/06/2023] Open
Abstract
Sex and gender disparities in bladder cancer have long been a subject of interest to the cancer research community, wherein men have a 4 times higher incidence rate than women, and female patients often present with higher-grade disease and experience worse outcomes. Despite the known differences in disease incidence and clinical outcomes between male and female bladder cancer patients, clinical management remains the same. In this review, we critically analyze studies that report on the biological differences between men and women and evaluate how these differences contribute to sex and gender disparities in bladder cancer. Distinct characteristics of the male and female immune systems, differences in circulating hormone levels and hormone receptor expression, and different genetic and epigenetic alterations are major biological factors that all likely contribute to disparate incidence rates and outcomes for male and female bladder cancer patients. Future preclinical and clinical studies in this area should employ experimental approaches that account for and consider sex and gender disparities in bladder cancer, thereby facilitating the development of precision medicine for the effective treatment of bladder cancer in all patients.
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Affiliation(s)
- Bhavisha Doshi
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Sarah R Athans
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA
| | - Anna Woloszynska
- Department of Pharmacology and Therapeutics, Roswell Park Comprehensive Cancer Center, Buffalo, NY, 14203, USA.
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12
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Kuroki Y, Fukami M. Y Chromosome Genomic Variations and Biological Significance in Human Diseases and Health. Cytogenet Genome Res 2023; 163:5-13. [PMID: 37562362 DOI: 10.1159/000531933] [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: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023] Open
Abstract
The Y chromosome is a haploid genome unique to males with no genes essential for life. It is easily transmitted to the next generation without being repaired by recombination, even if a major genomic structural alteration occurs. On the other hand, the Y chromosome genome is basically a region transmitted only from father to son, reflecting a male-specific inheritance between generations. The Y chromosome exhibits genomic structural differences among different ethnic groups and individuals. The Y chromosome was previously thought to affect only male-specific phenotypes, but recent studies have revealed associations between the Y chromosomes and phenotypes common to both males and females, such as certain types of cancer and neuropsychiatric disorders. This evidence was discovered with the finding of the mosaic loss of the Y chromosome in somatic cells. This phenomenon is also affected by environmental factors, such as smoking and aging. In the past, functional analysis of the Y chromosome has been elucidated by assessing the function of Y chromosome-specific genes and the association between Y chromosome haplogroups and human phenotypes. These studies are currently being conducted intensively. Additionally, the recent advance of large-scale genome cohort studies has increased the amount of Y chromosome genomic information available for analysis, making it possible to conduct more precise studies of the relationship between genome structures and phenotypes. In this review, we will introduce recent analyses using large-scale genome cohort data and previously reported association studies between Y chromosome haplogroups and human phenotypes, such as male infertility, cancer, cardiovascular system traits, and neuropsychiatric disorders. The function and biological role of the Y chromosome in human phenotypes will also be discussed.
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Affiliation(s)
- Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Center for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Center for Child Health and Development, Tokyo, Japan
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13
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Demanelis K, Delgado DA, Tong L, Jasmine F, Ahmed A, Islam T, Parvez F, Kibriya MG, Graziano JH, Ahsan H, Pierce BL. Somatic loss of the Y chromosome is associated with arsenic exposure among Bangladeshi men. Int J Epidemiol 2023; 52:1035-1046. [PMID: 36130227 PMCID: PMC10695470 DOI: 10.1093/ije/dyac176] [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: 12/02/2021] [Accepted: 09/01/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Arsenic exposure increases the risk of several cancers in humans and contributes to genomic instability. Somatic loss of the Y chromosome (LoY) is a potential biomarker of genomic instability and cancer risk. Smoking is associated with LoY, but few other carcinogens have been investigated. We tested the cross-sectional association between arsenic exposure and LoY in leukocytes among genotyped Bangladeshi men (age 20-70 years) from the Health Effects of Arsenic Longitudinal Study. METHODS We extracted the median of logR-ratios from probes on the Y chromosome (mLRR-chrY) from genotyping arrays (n = 1364) and estimated the percentage of cells with LoY (% LoY) from mLRR-chrY. We evaluated the association between arsenic exposure (measured in drinking water and urine) and LoY using multivariable linear and logistic regression models. The association between LoY and incident arsenic-induced skin lesions was also examined. RESULTS Ten percent of genotyped men had LoY in at least 5% of cells and % LoY increased with age. Among men randomly selected for genotyping (n = 778), higher arsenic in drinking water, arsenic consumed and urinary arsenic were associated with increased % LoY (P = 0.006, P = 0.06 and P = 0.13, respectively). LoY was associated with increased risk of incident skin lesions (P = 0.008). CONCLUSION Arsenic exposure was associated with increased LoY, providing additional evidence that arsenic contributes to genomic instability. LoY was associated with developing skin lesions, a risk factor for cancer, suggesting that LoY may be a biomarker of susceptibility in arsenic-exposed populations. The effect of arsenic on somatic events should be further explored in cancer-prone tissue types.
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Affiliation(s)
- Kathryn Demanelis
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Dayana A Delgado
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | | | | | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
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14
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Jiang L, Song M, Song F, Zhou Y, Yao H, Li G, Luo H. Characterization of loss of chromosome Y in peripheral blood cells in male Han Chinese patients with schizophrenia. BMC Psychiatry 2023; 23:469. [PMID: 37370034 DOI: 10.1186/s12888-023-04929-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Schizophrenia (SCZ) has a global prevalence of 1% and increases the risk of mortality, reducing life expectancy. There is growing evidence that the risk of this disorder is higher in males than in females and it tends to develop in early adulthood. The Y chromosome is thought to be involved in biological processes other than sex determination and spermatogenesis. Studies have shown that loss of chromosome Y (LOY) in peripheral blood cells is associated with a variety of diseases (including cancer) and increased all-cause mortality. An analysis of the relationship between LOY and schizophrenia is warranted. METHODS A total of 442 Chinese males (271 patients with schizophrenia vs. 171 controls) were included in this study. The copy numbers of the Y and X chromosomes were detected by positive droplets targeting the amelogenin gene (AMEL) on the Y chromosome and X chromosome (AMELY and AMELX, respectively), using droplet digital PCR (ddPCR). The LOY percentage was defined as the difference between the concentration of AMELX and the concentration of AMELY divided by the concentration of AMELX, denoted as (X - Y)/X. RESULTS In the Han Chinese population, the LOY percentage was higher in the schizophrenia group than in the control group (p < 0.05), although there was no significant difference in the presence of LOY between the two groups. A strong correlation was found between the average of the disease duration and the average of the LOY percentage (R2 = 0.506, p = 0.032). The logistic regression analysis implied that the risk of LOY increases by 0.058 and 0.057 per year according to age at onset and duration of disease, respectively (ponset = 0.013, pduration = 0.017). CONCLUSIONS In the Han Chinese population, the LOY percentage of the disease group was significantly different from that of the control group. The age of onset and duration of schizophrenia might be risk factors for LOY in peripheral blood cells. A larger sample size and expanded clinical information are needed for more in-depth and specific analyses.
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Affiliation(s)
- Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Gangqin Li
- Department of Forensic Psychiatry, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China.
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15
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Qi M, Pang J, Mitsiades I, Lane AA, Rheinbay E. Loss of chromosome Y in primary tumors. Cell 2023; 186:S0092-8674(23)00646-3. [PMID: 37385248 DOI: 10.1016/j.cell.2023.06.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 01/17/2023] [Accepted: 06/08/2023] [Indexed: 07/01/2023]
Abstract
Certain cancer types afflict female and male patients disproportionately. The reasons include differences in male/female physiology, effect of sex hormones, risk behavior, environmental exposures, and genetics of the sex chromosomes X and Y. Loss of Y (LOY) is common in peripheral blood cells in aging men, and this phenomenon is associated with several diseases. However, the frequency and role of LOY in tumors is little understood. Here, we present a comprehensive catalog of LOY in >5,000 primary tumors from male patients in the TCGA. We show that LOY rates vary by tumor type and provide evidence for LOY being either a passenger or driver event depending on context. LOY in uveal melanoma specifically is associated with age and survival and is an independent predictor of poor outcome. LOY creates common dependencies on DDX3X and EIF1AX in male cell lines, suggesting that LOY generates unique vulnerabilities that could be therapeutically exploited.
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Affiliation(s)
- Meifang Qi
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Jiali Pang
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Irene Mitsiades
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Andrew A Lane
- Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA 02215, USA
| | - Esther Rheinbay
- Massachusetts General Hospital Center for Cancer Research, Charlestown, MA 02129, USA; Harvard Medical School, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Massachusetts General Hospital Department of Pathology, Boston, MA 02114, USA.
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16
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Allen JB, Ludtka C, James BD. Sex as a Biological Variable in Tissue Engineering and Regenerative Medicine. Annu Rev Biomed Eng 2023; 25:311-331. [PMID: 37104652 PMCID: PMC10312304 DOI: 10.1146/annurev-bioeng-092222-030857] [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: 04/29/2023]
Abstract
Although sex differences have been noted in cellular function and behavior, therapy efficacy, and disease incidence and outcomes, the adoption of sex as a biological variable in tissue engineering and regenerative medicine remains limited. Furthering the development of personalized, precision medicine requires considering biological sex at the bench and in the clinic. This review provides the basis for considering biological sex when designing tissue-engineered constructs and regenerative therapies by contextualizing sex as a biological variable within the tissue engineering triad of cells, matrices, and signals. To achieve equity in biological sex within medicine requires a cultural shift in science and engineering research, with active engagement by researchers, clinicians, companies, policymakers, and funding agencies.
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Affiliation(s)
- Josephine B Allen
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida, USA;
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA;
| | - Christopher Ludtka
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA;
| | - Bryan D James
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA;
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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17
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San Roman AK, Skaletsky H, Godfrey AK, Bokil NV, Teitz L, Singh I, Blanton LV, Bellott DW, Pyntikova T, Lange J, Koutseva N, Hughes JF, Brown L, Phou S, Buscetta A, Kruszka P, Banks N, Dutra A, Pak E, Lasutschinkow PC, Keen C, Davis SM, Lin AE, Tartaglia NR, Samango-Sprouse C, Muenke M, Page DC. The human Y and inactive X chromosomes similarly modulate autosomal gene expression. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.05.543763. [PMID: 37333288 PMCID: PMC10274745 DOI: 10.1101/2023.06.05.543763] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/20/2023]
Abstract
Somatic cells of human males and females have 45 chromosomes in common, including the "active" X chromosome. In males the 46th chromosome is a Y; in females it is an "inactive" X (Xi). Through linear modeling of autosomal gene expression in cells from individuals with zero to three Xi and zero to four Y chromosomes, we found that Xi and Y impact autosomal expression broadly and with remarkably similar effects. Studying sex-chromosome structural anomalies, promoters of Xi- and Y-responsive genes, and CRISPR inhibition, we traced part of this shared effect to homologous transcription factors - ZFX and ZFY - encoded by Chr X and Y. This demonstrates sex-shared mechanisms by which Xi and Y modulate autosomal expression. Combined with earlier analyses of sex-linked gene expression, our studies show that 21% of all genes expressed in lymphoblastoid cells or fibroblasts change expression significantly in response to Xi or Y chromosomes.
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Affiliation(s)
| | - Helen Skaletsky
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Alexander K. Godfrey
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Neha V. Bokil
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Levi Teitz
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | - Isani Singh
- Whitehead Institute; Cambridge, MA 02142, USA
- Harvard Medical School, Boston, MA 02115, USA
| | | | | | | | - Julian Lange
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
| | | | | | - Laura Brown
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Sidaly Phou
- Whitehead Institute; Cambridge, MA 02142, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health; Bethesda, MD 20892 USA
| | - Amalia Dutra
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | - Evgenia Pak
- Cytogenetics and Microscopy Core, National Human Genome Research Institute, National Institutes of Health; Bethesda, MD 20892 USA
| | | | | | - Shanlee M. Davis
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
| | - Angela E. Lin
- Medical Genetics, Massachusetts General for Children, Boston, MA 02114, USA; Department of Pediatrics, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole R. Tartaglia
- Department of Pediatrics, University of Colorado School of Medicine, Aurora, CO 80045, USA
- Developmental Pediatrics, eXtraOrdinarY Kids Program, Children’s Hospital Colorado, Aurora, CO 80011, USA
| | - Carole Samango-Sprouse
- Focus Foundation, Davidsonville, MD 21035, USA
- Department of Pediatrics, George Washington University, Washington, DC 20052, USA; Department of Human and Molecular Genetics, Florida International University, Miami, FL 33199, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda; MD 20892, USA
| | - David C. Page
- Whitehead Institute; Cambridge, MA 02142, USA
- Department of Biology, Massachusetts Institute of Technology; Cambridge, MA 02139, USA
- Howard Hughes Medical Institute, Whitehead Institute; Cambridge, MA 02142, USA
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18
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Vinson AJ, Zhang X, Dahhou M, Süsal C, Döhler B, Melk A, Sapir-Pichhadze R, Cardinal H, Wong G, Francis A, Pilmore H, Foster BJ. A multinational cohort study uncovered sex differences in excess mortality after kidney transplant. Kidney Int 2023; 103:1131-1143. [PMID: 36805451 DOI: 10.1016/j.kint.2023.01.022] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Revised: 01/14/2023] [Accepted: 01/19/2023] [Indexed: 02/21/2023]
Abstract
Worldwide and at all ages, males have a higher mortality risk than females. This mortality bias should be preserved in kidney transplant recipients unless there are sex differences in the effects of transplantation. Here we compared the excess risk of mortality (risk above the general population) in female versus male recipients of all ages recorded in three large transplant databases. This included first deceased donor kidney transplant recipients and accounted for the modifying effects of donor sex and recipient age. After harmonization of variables across cohorts, relative survival models were fitted in each cohort separately and results were combined using individual patient data meta-analysis among 466,892 individuals (1988-2019). When the donor was male, female recipients 0-12 years (Relative Excess Risk 1.54, 95% Confidence Interval 1.20-1.99), 13-24 years (1.17, 1.01-1.34), 25-44 years (1.11, 1.05-1.18) and 60 years and older (1.05, 1.02-1.08) showed higher excess mortality risks than male recipients of the same age. When the donor was female, the Relative Excess Risk for those over 12 years were similar to those when the donor was male. There is a higher excess mortality risk in female than male recipients with differences larger at younger than older ages and only statistically significant when the donor was male. While these findings may be partly explained by the known sex differences in graft loss risks, sex differences in the risks of death with graft function may also contribute. Thus, higher risks in females than males suggest that management needs to be modified to optimize transplant outcomes among females.
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Affiliation(s)
- Amanda J Vinson
- Department of Medicine, Nephrology Division, Dalhousie University, Halifax, Nova Scotia, Canada.
| | - Xun Zhang
- Research Institute of the McGill University Health Centre, Centre for Outcomes Research and Evaluation, Montréal, Québec, Canada
| | - Mourad Dahhou
- Research Institute of the McGill University Health Centre, Centre for Outcomes Research and Evaluation, Montréal, Québec, Canada
| | - Caner Süsal
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany; Transplant Immunology Research Center of Excellence, Koç University, Istanbul, Turkey
| | - Bernd Döhler
- Institute of Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Anette Melk
- Children's Hospital, Hannover Medical School, Hannover, Germany
| | - Ruth Sapir-Pichhadze
- Research Institute of the McGill University Health Centre, Centre for Outcomes Research and Evaluation, Montréal, Québec, Canada; Department of Medicine, Division of Nephrology, McGill University, Montréal, Québec, Canada; Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada
| | - Heloise Cardinal
- Department of Medicine, Division of Nephrology, Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Germaine Wong
- School of Public Health, University of Sydney, Sydney, New South Wales, Australia
| | - Anna Francis
- School of Clinical Medicine, University of Queensland, Brisbane, Queensland, Australia; Department of Nephrology, Queensland Children's Hospital, Brisbane, Queensland, Australia
| | - Helen Pilmore
- Department of Renal Medicine, Auckland City Hospital, Auckland, New Zealand
| | - Bethany J Foster
- Research Institute of the McGill University Health Centre, Centre for Outcomes Research and Evaluation, Montréal, Québec, Canada; Department of Epidemiology, Biostatistics, and Occupational Health, McGill University, Montréal, Québec, Canada; Department of Pediatrics, Division of Nephrology, McGill University Faculty of Medicine, Montréal, Québec, Canada.
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19
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Suarez LM, Diaz-Del Cerro E, Felix J, Gonzalez-Sanchez M, Ceprian N, Guerra-Perez N, G Novelle M, Martinez de Toda I, De la Fuente M. Sex differences in neuroimmunoendocrine communication. Involvement on longevity. Mech Ageing Dev 2023; 211:111798. [PMID: 36907251 DOI: 10.1016/j.mad.2023.111798] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 03/07/2023] [Accepted: 03/07/2023] [Indexed: 03/13/2023]
Abstract
Endocrine, nervous, and immune systems work coordinately to maintain the global homeostasis of the organism. They show sex differences in their functions that, in turn, contribute to sex differences beyond reproductive function. Females display a better control of the energetic metabolism and improved neuroprotection and have more antioxidant defenses and a better inflammatory status than males, which is associated with a more robust immune response than that of males. These differences are present from the early stages of life, being more relevant in adulthood and influencing the aging trajectory in each sex and may contribute to the different life lifespan between sexes.
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Affiliation(s)
- Luz M Suarez
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain.
| | - Estefania Diaz-Del Cerro
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Judith Felix
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Monica Gonzalez-Sanchez
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Noemi Ceprian
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Natalia Guerra-Perez
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Marta G Novelle
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain
| | - Irene Martinez de Toda
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain
| | - Monica De la Fuente
- Department of Genetics, Physiology, and Microbiology (Unit of Animal Physiology), Faculty of Biology, Complutense University, Madrid, Spain; Institute of Investigation Hospital 12 Octubre (imas12), Madrid, Spain.
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20
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Iannuzzi V, Bacalini MG, Franceschi C, Giuliani C. The role of genetics and epigenetics in sex differences in human survival. GENUS 2023. [DOI: 10.1186/s41118-023-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AbstractSex differences in human survival have been extensively investigated in many studies that have in part uncovered the biological determinants that promote a longer life in females with respect to males. Moreover, researches performed in the past years have prompted increased awareness about the biological effects of environmental factors that can modulate the magnitude of the sex gap in survival. Besides the genetic background, epigenetic modifications like DNA methylation, that can modulate cell function, have been particularly studied in this framework. In this review, we aim to summarize the role of the genetic and epigenetic mechanisms in promoting female advantage from the early in life (“INNATE” features), and in influencing the magnitude of the gap in sex differences in survival and ageing (“VARIABLE” features). After briefly discussing the biological bases of sex determination in humans, we will provide much evidence showing that (i) “innate” mechanisms common to all males and to all females (both genetic and epigenetic) play a major role in sex differences in lifespan; (ii) “variable” genetic and epigenetic patterns, that vary according to context, populations and exposures to different environments, can affect the magnitude of the gap in sex differences in survival. Then we will describe recent findings in the use of epigenetic clocks to uncover sex differences in biological age and thus potentially in mortality. In conclusion, we will discuss how environmental factors cannot be kept apart from the biological factors providing evidence from the field of human ecology.
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21
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Mendelian Randomisation Confirms the Role of Y-Chromosome Loss in Alzheimer's Disease Aetiopathogenesis in Men. Int J Mol Sci 2023; 24:ijms24020898. [PMID: 36674414 PMCID: PMC9863537 DOI: 10.3390/ijms24020898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2022] [Revised: 12/21/2022] [Accepted: 12/31/2022] [Indexed: 01/06/2023] Open
Abstract
Mosaic loss of chromosome Y (mLOY) is a common ageing-related somatic event and has been previously associated with Alzheimer's disease (AD). However, mLOY estimation from genotype microarray data only reflects the mLOY degree of subjects at the moment of DNA sampling. Therefore, mLOY phenotype associations with AD can be severely age-confounded in the context of genome-wide association studies. Here, we applied Mendelian randomisation to construct an age-independent mLOY polygenic risk score (mloy-PRS) using 114 autosomal variants. The mloy-PRS instrument was associated with an 80% increase in mLOY risk per standard deviation unit (p = 4.22 × 10-20) and was orthogonal with age. We found that a higher genetic risk for mLOY was associated with faster progression to AD in men with mild cognitive impairment (hazard ratio (HR) = 1.23, p = 0.01). Importantly, mloy-PRS had no effect on AD conversion or risk in the female group, suggesting that these associations are caused by the inherent loss of the Y chromosome. Additionally, the blood mLOY phenotype in men was associated with increased cerebrospinal fluid levels of total tau and phosphorylated tau181 in subjects with mild cognitive impairment and dementia. Our results strongly suggest that mLOY is involved in AD pathogenesis.
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22
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Müller P, Velazquez Camacho O, Yazbeck AM, Wölwer C, Zhai W, Schumacher J, Heider D, Buettner R, Quaas A, Hillmer AM. Why loss of Y? A pan-cancer genome analysis of tumors with loss of Y chromosome. Comput Struct Biotechnol J 2023; 21:1573-1583. [PMID: 36874157 PMCID: PMC9978323 DOI: 10.1016/j.csbj.2023.02.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 02/17/2023] Open
Abstract
Loss of the Y chromosome (LoY) is frequently observed in somatic cells of elderly men. However, LoY is highly increased in tumor tissue and correlates with an overall worse prognosis. The underlying causes and downstream effects of LoY are widely unknown. Therefore, we analyzed genomic and transcriptomic data of 13 cancer types (2375 patients) and classified tumors of male patients according to loss or retain of the Y chromosome (LoY or RoY, average LoY fraction: 0.46). The frequencies of LoY ranged from almost absence (glioblastoma, glioma, thyroid carcinoma) to 77% (kidney renal papillary cell carcinoma). Genomic instability, aneuploidy, and mutation burden were enriched in LoY tumors. In addition, we found more frequently in LoY tumors the gate keeping tumor suppressor gene TP53 mutated in three cancer types (colon adenocarcinoma, head and neck squamous carcinoma, lung adenocarcinoma) and oncogenes MET, CDK6, KRAS, and EGFR amplified in multiple cancer types. On the transcriptomic level, we observed MMP13, known to be involved in invasion, to be up-regulated in LoY of three adenocarcinomas and down-regulation of the tumor suppressor gene GPC5 in LoY of three cancer types. Furthermore, we found enrichment of a smoking-related mutation signature in LoY tumors of head and neck and lung cancer. Strikingly, we observed a correlation between cancer type-specific sex bias in incidence rates and frequencies of LoY, in line with the hypothesis that LoY increases cancer risk in males. Overall, LoY is a frequent phenomenon in cancer that is enriched in genomically unstable tumors. It correlates with genomic features beyond the Y chromosome and might contribute to higher incidence rates in males.
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Affiliation(s)
- Philipp Müller
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Oscar Velazquez Camacho
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Ali M Yazbeck
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Christina Wölwer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Weiwei Zhai
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing, China
| | - Johannes Schumacher
- Institute of Human Genetics, University Hospital of Marburg, Marburg, Germany
| | - Dominik Heider
- Department of Data Science in Biomedicine, Faculty of Mathematics and Computer Science, Philipps-University of Marburg, Germany
| | - Reinhard Buettner
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany
| | - Alexander Quaas
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany.,Cologne Group of Sex-specific Oncobiology (CGSO), Germany
| | - Axel M Hillmer
- University of Cologne, Faculty of Medicine and University Hospital Cologne, Institute of Pathology, Cologne, Germany.,Cologne Group of Sex-specific Oncobiology (CGSO), Germany.,University of Cologne, Center for Molecular Medicine Cologne, Cologne, Germany
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23
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Evans MA, Walsh K. Clonal hematopoiesis, somatic mosaicism, and age-associated disease. Physiol Rev 2023; 103:649-716. [PMID: 36049115 PMCID: PMC9639777 DOI: 10.1152/physrev.00004.2022] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022] Open
Abstract
Somatic mosaicism, the occurrence of multiple genetically distinct cell clones within the same tissue, is an evitable consequence of human aging. The hematopoietic system is no exception to this, where studies have revealed the presence of expanded blood cell clones carrying mutations in preleukemic driver genes and/or genetic alterations in chromosomes. This phenomenon is referred to as clonal hematopoiesis and is remarkably prevalent in elderly individuals. While clonal hematopoiesis represents an early step toward a hematological malignancy, most individuals will never develop blood cancer. Somewhat unexpectedly, epidemiological studies have found that clonal hematopoiesis is associated with an increase in the risk of all-cause mortality and age-related disease, particularly in the cardiovascular system. Studies using murine models of clonal hematopoiesis have begun to shed light on this relationship, suggesting that driver mutations in mature blood cells can causally contribute to aging and disease by augmenting inflammatory processes. Here we provide an up-to-date review of clonal hematopoiesis within the context of somatic mosaicism and aging and describe recent epidemiological studies that have reported associations with age-related disease. We will also discuss the experimental studies that have provided important mechanistic insight into how driver mutations promote age-related disease and how this knowledge could be leveraged to treat individuals with clonal hematopoiesis.
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Affiliation(s)
- Megan A Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
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24
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Vermeersch G, Delforge M, Havelange V, Graux C, Michaux L, Devos T. Case report: Chronic neutrophilic leukemia associated with monoclonal gammopathies. A case series and review of genetic characteristics and practical management. Front Oncol 2022; 12:1014671. [PMID: 36568246 PMCID: PMC9768602 DOI: 10.3389/fonc.2022.1014671] [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: 08/10/2022] [Accepted: 11/04/2022] [Indexed: 12/12/2022] Open
Abstract
Chronic neutrophilic leukemia (CNL) is a rare but potentially aggressive BCR::ABL1 negative myeloproliferative neoplasm, characterized by sustained mature, neutrophilic leukocytosis. The discovery of key driver mutations in the colony-stimulating-factor-3 receptor (CSF3R) gene resulted in the updated World Health Organization (WHO) diagnostic criteria in 2016. A significant number of CNL cases have been associated with plasma cell dyscrasias, predominantly multiple myeloma (MM) and monoclonal gammopathy of unknown significance (MGUS). Compared to pure CNL, mutated CSF3R is infrequently reported in CNL cases associated with monoclonal gammopathies (MG). Until now it remains unclear whether CNL and occurring plasma cell neoplasms are clonally related or CNL is developing secondary to the underlying dyscrasia. Owing to its rarity, currently no standard of care management exists for CNL and MG-associated CNL. In this case series we report the multi-center experience of five MG-associated CNL cases with a median age of diagnosis of 69 years. Three patients (66%) showed predominance of lambda light chain expression. Four (80%) eventually evolved to MM, and one CNL-MGUS patient developed secondary acute myeloid leukemia (AML). Mutated CSF3R was present in the patient who developed AML but was absent in other cases. To assess possible associated genetic aberrations we performed recurrent analysis with next-generation sequencing (NGS). Two patients (40%) deceased with a median time of survival of 8 years after CNL diagnosis. Three (60%) are currently in follow-up with no reoccurring leukocytosis. This case series, followed by a short review, provides a long-term clinical and genetic overview of five CNL cases associated with MG.
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Affiliation(s)
- Gaël Vermeersch
- Department of Hematology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Michel Delforge
- Department of Hematology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
| | - Violaine Havelange
- Department of Hematology, Université Catholique de Louvain Saint-Luc, Woluwe-Saint-Lambert, Belgium
| | - Carlos Graux
- Department of Hematology, Université Catholique de Louvain, CHU UCL Namur - site Godinne, Yvoir, Belgium
| | | | - Timothy Devos
- Department of Hematology, University Hospitals Leuven, KU Leuven, Leuven, Belgium
- Department of Microbiology and Immunology, Laboratory of Molecular Immunology (Rega Institute), KU Leuven, Leuven, Belgium
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25
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Argouarch AR, Schultz N, Yang AC, Jang Y, Garcia K, Cosme CG, Corrales CI, Nana AL, Karydas AM, Spina S, Grinberg LT, Miller B, Wyss-Coray T, Abyzov A, Goodarzi H, Seeley WW, Kao AW. Postmortem Human Dura Mater Cells Exhibit Phenotypic, Transcriptomic and Genetic Abnormalities that Impact their Use for Disease Modeling. Stem Cell Rev Rep 2022; 18:3050-3065. [PMID: 35809166 PMCID: PMC9622518 DOI: 10.1007/s12015-022-10416-x] [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] [Accepted: 06/19/2022] [Indexed: 11/24/2022]
Abstract
Patient-derived cells hold great promise for precision medicine approaches in human health. Human dermal fibroblasts have been a major source of cells for reprogramming and differentiating into specific cell types for disease modeling. Postmortem human dura mater has been suggested as a primary source of fibroblasts for in vitro modeling of neurodegenerative diseases. Although fibroblast-like cells from human and mouse dura mater have been previously described, their utility for reprogramming and direct differentiation protocols has not been fully established. In this study, cells derived from postmortem dura mater are directly compared to those from dermal biopsies of living subjects. In two instances, we have isolated and compared dermal and dural cell lines from the same subject. Notably, striking differences were observed between cells of dermal and dural origin. Compared to dermal fibroblasts, postmortem dura mater-derived cells demonstrated different morphology, slower growth rates, and a higher rate of karyotype abnormality. Dura mater-derived cells also failed to express fibroblast protein markers. When dermal fibroblasts and dura mater-derived cells from the same subject were compared, they exhibited highly divergent gene expression profiles that suggest dura mater cells originated from a mixed mural lineage. Given their postmortem origin, somatic mutation signatures of dura mater-derived cells were assessed and suggest defective DNA damage repair. This study argues for rigorous karyotyping of postmortem derived cell lines and highlights limitations of postmortem human dura mater-derived cells for modeling normal biology or disease-associated pathobiology.
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Affiliation(s)
- Andrea R. Argouarch
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Nina Schultz
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Andrew C. Yang
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, Stanford, CA 94304 USA
| | - Yeongjun Jang
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Kristle Garcia
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Celica G. Cosme
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Christian I. Corrales
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Alissa L. Nana
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Anna M. Karydas
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Salvatore Spina
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Lea T. Grinberg
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Pathology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Bruce Miller
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Tony Wyss-Coray
- Department of Neurology and Neurological Sciences, School of Medicine, Stanford University, Stanford, CA 94304 USA
| | - Alexej Abyzov
- Department of Quantitative Health Sciences, Center for Individualized Medicine, Mayo Clinic, Rochester, MN 55905 USA
| | - Hani Goodarzi
- Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Urology, University of California San Francisco, San Francisco, CA 94158 USA
| | - William W. Seeley
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
- Department of Pathology, University of California San Francisco, San Francisco, CA 94158 USA
| | - Aimee W. Kao
- Memory and Aging Center, Weill Institute for Neurosciences, Department of Neurology, University of California San Francisco, San Francisco, CA 94158 USA
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26
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Alcedo PE, Gutierrez-Rodrigues F, Patel BA. Somatic mutations in VEXAS Syndrome and Erdheim-Chester Disease: Inflammatory Myeloid Diseases. Semin Hematol 2022; 59:156-166. [DOI: 10.1053/j.seminhematol.2022.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 07/12/2022] [Accepted: 07/28/2022] [Indexed: 12/27/2022]
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27
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Li G, Wang C, Guan X, Bai Y, Feng Y, Wei W, Meng H, Fu M, He M, Zhang X, Lu Y, Lin Y, Guo H. Age-related DNA methylation on Y chromosome and their associations with total mortality among Chinese males. Aging Cell 2022; 21:e13563. [PMID: 35120273 PMCID: PMC8920452 DOI: 10.1111/acel.13563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
In view of the sex differences in aging‐related diseases, sex chromosomes may play a critical role during aging process. This study aimed to identify age‐related DNA methylation changes on Y chromosome (ChrY). A two‐stage study design was conducted in this study. The discovery stage contained 419 Chinese males, including 205 from the Wuhan‐Zhuhai cohort panel, 107 from the coke oven workers panel, and 107 from the Shiyan panel. The validation stage contained 587 Chinese males from the Dongfeng‐Tongji sub‐cohort. We used the Illumina HumanMethylation BeadChip to determine genome‐wide DNA methylation in peripheral blood of the study participants. The associations between age and methylation levels of ChrY CpGs were investigated by using linear regression models with adjustment for potential confounders. Further, associations of age‐related ChrY CpGs with all‐cause mortality were tested in the validation stage. We identified the significant associations of 41 ChrY CpGs with age at false discovery rate (FDR) <0.05 in the discovery stage, and 18 of them were validated in the validation stage (p < 0.05). Meta‐analysis of both stages confirmed the robust positive associations of 14 CpGs and negative associations of 4 CpGs with age (FDR<0.05). Among them, cg03441493 and cg17816615 were significantly associated with all‐cause mortality risk [HR(95% CI) = 1.37 (1.04, 1.79) and 0.70 (0.54, 0.93), respectively]. Our results highlighted the importance of ChrY CpGs on male aging.
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Affiliation(s)
- Guyanan Li
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
- Department of Clinical Laboratory Medicine Shanghai Fifth People's Hospital Fudan University Shanghai China
| | - Chenming Wang
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xin Guan
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yansen Bai
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yue Feng
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Wei Wei
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Hua Meng
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Ming Fu
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Meian He
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yanjun Lu
- Department of Laboratory Medicine Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yong Lin
- Department of Clinical Laboratory Medicine Shanghai Fifth People's Hospital Fudan University Shanghai China
- Department of Laboratory Medicine Huashan Hospital Fudan University Shanghai China
- National Clinical Research Center for Aging and Medicine Huashan Hospital Fudan University Shanghai China
| | - Huan Guo
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology Wuhan China
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28
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Trujillo N, Martínez-Pacheco M, Soldatini C, Ancona S, Young RC, Albores-Barajas YV, Orta AH, Rodríguez C, Székely T, Drummond H, Urrutia AO, Cortez D. Lack of age-related mosaic loss of W chromosome in long-lived birds. Biol Lett 2022; 18:20210553. [PMID: 35193370 PMCID: PMC8864339 DOI: 10.1098/rsbl.2021.0553] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Females and males often exhibit different survival in nature, and it has been hypothesized that sex chromosomes may play a role in driving differential survival rates. For instance, the Y chromosome in mammals and the W chromosome in birds are often degenerated, with reduced numbers of genes, and loss of the Y chromosome in old men is associated with shorter life expectancy. However, mosaic loss of sex chromosomes has not been investigated in any non-human species. Here, we tested whether mosaic loss of the W chromosome (LOW) occurs with ageing in wild birds as a natural consequence of cellular senescence. Using loci-specific PCR and a target sequencing approach we estimated LOW in both young and adult individuals of two long-lived bird species and showed that the copy number of W chromosomes remains constant across age groups. Our results suggest that LOW is not a consequence of cellular ageing in birds. We concluded that the inheritance of the W chromosome in birds, unlike the Y chromosome in mammals, is more stable.
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Affiliation(s)
- Nancy Trujillo
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México
| | - Mónica Martínez-Pacheco
- Laboratorio de Biología Celular y Molecular, Facultad de Ciencias Naturales, Universidad Autónoma de Querétaro, CP76010, Querétaro, México
| | - Cecilia Soldatini
- Centro de Investigación Científica y Educación Superior de Ensenada - Unidad La Paz, Calle Miraflores 334, CP23050, La Paz, Baja California Sur, México
| | - Sergio Ancona
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Rebecca C Young
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Yuri V Albores-Barajas
- CONACYT. Consejo Nacional de Ciencia y Tecnología, Av. Insurgentes Sur 1582, Col. Crédito Constructor. Alcaldía Benito Juárez, CP03940, Ciudad de México, México.,Universidad Autónoma de Baja California Sur., Km. 5.5 Carr. 1. La Paz, Baja California Sur, México
| | - Alberto H Orta
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México
| | - Cristina Rodríguez
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Tamas Székely
- Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK.,Department of Evolutionary Zoology and Human Biology, University of Debrecen, Debrecen H-4032, Hungary
| | - Hugh Drummond
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México
| | - Araxi O Urrutia
- Instituto de Ecología, UNAM, Ciudad Universitaria, CP04510, Ciudad de México, México.,Milner Centre for Evolution, Department of Biology and Biochemistry, University of Bath, Bath BA2 7AY, UK
| | - Diego Cortez
- Centro de Ciencias Genómicas, UNAM, CP62210, Cuernavaca, México
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29
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Fukami M, Miyado M. Mosaic loss of the Y chromosome and men's health. Reprod Med Biol 2022; 21:e12445. [PMID: 35386373 PMCID: PMC8967293 DOI: 10.1002/rmb2.12445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
- Maki Fukami
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
| | - Mami Miyado
- Department of Molecular Endocrinology National Research Institute for Child Health and Development Tokyo Japan
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30
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Kirsch-Volders M, Fenech M. Aneuploidy, inflammation and diseases. Mutat Res 2022; 824:111777. [PMID: 35358789 DOI: 10.1016/j.mrfmmm.2022.111777] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 02/22/2022] [Accepted: 03/15/2022] [Indexed: 05/23/2023]
Abstract
This review discusses how numerical aneuploidy may trigger inflammation in somatic cells and its consequences. Therefore we: i) summarized current knowledge on the cellular and molecular pathological effects of aneuploidy; ii) considered which of these aspects are able to trigger inflammation; iii) determined the genetic and environmental factors which may modulate the link between aneuploidy and inflammation; iv) explored the rôle of diet in prevention of aneuploidy and inflammation; v) examined whether aneuploidy and inflammation are causes and/or consequences of diseases; vi) identified the knowledge gaps and research needed to translate these observations into improved health care and disease prevention. The relationships between aneuploidy, inflammation and diseases are complex, because they depend on which chromosomes are involved, the proportion of cells affected and which organs are aneuploid in the case of mosaic aneuploidy. Therefore, a systemic approach is recommended to understand the emergence of aneuploidy-driven diseases and to take preventive measures to protect individuals from exposure to aneugenic conditions.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA 5048, Australia; Clinical and Health Sciences, University of South Australia, SA 5000, Australia.
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31
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Abstract
Mosaic loss of the Y chromosome (LOY) is the most frequent chromosomal aberration in aging men and is strongly correlated with mortality and disease. To date, studies of LOY have only been performed in humans, and so it is unclear whether LOY is a natural consequence of our relatively long lifespan or due to exposure to human-specific external stressors. Here, we explored whether LOY could be detected in rats. We applied a locus-specific PCR and target sequencing approach that we used as a proxy to estimate LOY in 339 samples covering eleven tissues from young and old individuals. We detected LOY in four tissues of older rats. To confirm the results from the PCR screening, we re-sequenced 60 full genomes from old rats, which revealed that the Y chromosome is the sole chromosome with low copy numbers. Finally, our results suggest that LOY is associated with other structural aberrations on the Y chromosome and possibly linked to the mosaic loss of the X chromosome. This is the first report, to our knowledge, demonstrating that the patterns of LOY observed in aging men are also present in a rodent, and conclude that LOY may be a natural process in placental mammals.
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Riaz M, Mattisson J, Polekhina G, Bakshi A, Halvardson J, Danielsson M, Ameur A, McNeil J, Forsberg LA, Lacaze P. A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells. Cell Biosci 2021; 11:205. [PMID: 34895331 PMCID: PMC8667399 DOI: 10.1186/s13578-021-00716-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Mosaic loss of Y chromosome (LOY) is the most common somatic change that occurs in circulating white blood cells of older men. LOY in leukocytes is associated with increased risk for all-cause mortality and a range of common disease such as hematological and non-hematological cancer, Alzheimer’s disease, and cardiovascular events. Recent genome-wide association studies identified up to 156 germline variants associated with risk of LOY. The objective of this study was to use these variants to calculate a novel polygenic risk score (PRS) for LOY, and to assess the predictive performance of this score in a large independent population of older men. Results We calculated a PRS for LOY in 5131 men aged 70 years and older. Levels of LOY were estimated using microarrays and validated by whole genome sequencing. After adjusting for covariates, the PRS was a significant predictor of LOY (odds ratio [OR] = 1.74 per standard deviation of the PRS, 95% confidence intervals [CI] 1.62–1.86, p < 0.001). Men in the highest quintile of the PRS distribution had > fivefold higher risk of LOY than the lowest (OR = 5.05, 95% CI 4.05–6.32, p < 0.001). Adding the PRS to a LOY prediction model comprised of age, smoking and alcohol consumption significantly improved prediction (AUC = 0.628 [CI 0.61–0.64] to 0.695 [CI 0.67–0.71], p < 0.001). Conclusions Our results suggest that a PRS for LOY could become a useful tool for risk prediction and targeted intervention for common disease in men. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00716-z.
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Affiliation(s)
- Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Galina Polekhina
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Andrew Bakshi
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia.
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Guo X, Li J, Xue J, Fenech M, Wang X. Loss of Y chromosome: An emerging next-generation biomarker for disease prediction and early detection? MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108389. [PMID: 34893154 DOI: 10.1016/j.mrrev.2021.108389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022]
Abstract
As human life expectancy increases substantially and aging is the primary risk factor for most chronic diseases, there is an urgent need for advancing the development of post-genomic era biomarkers that can be used for disease prediction and early detection (DPED). Mosaic loss of Y chromosome (LOY) is the state of nullisomy Y in sub-groups of somatic cells acquired from different post-zygotic development stages and onwards throughout the lifespan. Multiple large-cohort based epidemiology studies have found that LOY in blood cells is a significant risk factor for future mortality and various diseases in males. Many features intrinsic to LOY analysis may be leveraged to enhance its use as a non-invasive, sensitive, reliable, high throughput-biomarker for DPED. Here, we review the emerging literatures in LOY studies and highlight ten strengths for using LOY as a novel biomarker for genomics-driven DPED diagnostics. Meanwhile, the current limitations in this area are also discussed. We conclude by identifying some important knowledge gaps regarding the consequences of malsegregation of the Y chromosome and propose further steps that are required before clinical implementation of LOY. Taken together, we think that LOY has substantial potential as a biomarker for DPED, despite some hurdles that still need to be addressed before its integration into healthcare becomes acceptable.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China; Yunnan Environmental Mutagen Society, Kunming, Yunnan, 650500, China.
| | - Jianfei Li
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA, 5048, Australia; University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, SA, 5000, Australia; Centre of Healthy Ageing and Wellness, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Xu Wang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China; Yunnan Environmental Mutagen Society, Kunming, Yunnan, 650500, China.
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Johansson M, Pedersen A, Cole JW, Lagging C, Lindgren A, Maguire JM, Rost NS, Söderholm M, Worrall BB, Stanne TM, Jern C. Genetic Predisposition to Mosaic Chromosomal Loss Is Associated With Functional Outcome After Ischemic Stroke. NEUROLOGY-GENETICS 2021; 7:e634. [PMID: 34786478 PMCID: PMC8589264 DOI: 10.1212/nxg.0000000000000634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 09/15/2021] [Indexed: 11/27/2022]
Abstract
Background and Objectives To test the hypothesis that a predisposition to acquired genetic alterations is associated with ischemic stroke outcome by investigating the association between a polygenic risk score (PRS) for mosaic loss of chromosome Y (mLOY) and outcome in a large international data set. Methods We used data from the genome-wide association study performed within the Genetics of Ischemic Stroke Functional Outcome network, which included 6,165 patients (3,497 men and 2,668 women) with acute ischemic stroke of mainly European ancestry. We assessed a weighted PRS for mLOY and examined possible associations with the modified Rankin Scale (mRS) score 3 months poststroke in logistic regression models. We investigated the whole study sample as well as men and women separately. Results Increasing PRS for mLOY was associated with poor functional outcome (mRS score >2) with an odds ratio (OR) of 1.11 (95% confidence interval [CI] 1.03–1.19) per 1 SD increase in the PRS after adjustment for age, sex, ancestry, stroke severity (NIH Stroke Scale), smoking, and diabetes mellitus. In sex-stratified analyses, we found a statistically significant association in women (adjusted OR 1.20, 95% CI 1.08–1.33). In men, the association was in the same direction (adjusted OR 1.04, 95% CI 0.95–1.14), and we observed no significant genotype-sex interaction. Discussion In this exploratory study, we found associations between genetic variants predisposing to mLOY and stroke outcome. The significant association in women suggests underlying mechanisms related to genomic instability that operate in both sexes. These findings need replication and mechanistic exploration.
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Affiliation(s)
- Malin Johansson
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Annie Pedersen
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - John W Cole
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Cecilia Lagging
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Arne Lindgren
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Jane M Maguire
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Natalia S Rost
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Martin Söderholm
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Bradford B Worrall
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Tara M Stanne
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
| | - Christina Jern
- Institute of Biomedicine (M.J., A.P., C.L., T.M.S., C.J.), Sahlgrenska Academy at the University of Gothenburg; Department of Clinical Genetics and Genomics (A.P., C.L., C.J.), Sahlgrenska University Hospital, Gothenburg, Sweden; Department of Neurology (J.W.C.), Baltimore VA Medical Center and University of Maryland School of Medicine, Baltimore, MD; Department of Clinical Sciences Lund (A.L., M.S.), Neurology, Lund University; Department of Neurology (A.L., M.S.), Skåne University Hospital, Lund and Malmö, Sweden; Faculty of Health (J.M.M.), University of Technology Sydney, Australia; Hunter Medical Research Centre (J.M.M.), Newcastle, Australia; J. Philip Kistler Stroke Research Center (N.S.R.), Department of Neurology, Massachusetts General Hospital, Harvard Medical School, Boston; and Departments of Neurology and Health Evaluation Sciences (B.B.W.), University of Virginia, Charlottesville, VA
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35
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Adachi H, Sadato D, Toya T, Hirama C, Haraguchi K, Mukae J, Shingai N, Shimizu H, Najima Y, Kobayashi T, Okuyama Y, Oboki K, Harada H, Sakamaki H, Ohashi K, Harada Y, Doki N. Donor-derived gene mutations in sex chromosome loss after stem cell transplantation. Br J Haematol 2021; 195:e142-e146. [PMID: 34312849 DOI: 10.1111/bjh.17716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 06/30/2021] [Accepted: 07/06/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Hiroto Adachi
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Daichi Sadato
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Takashi Toya
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Chizuko Hirama
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.,Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Kyoko Haraguchi
- Division of Transfusion and Cell Therapy, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Junichi Mukae
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Naoki Shingai
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Hiroaki Shimizu
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Yuho Najima
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Takeshi Kobayashi
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Yoshiki Okuyama
- Division of Transfusion and Cell Therapy, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Keisuke Oboki
- Research Center for Genome & Medical Sciences, Tokyo Metropolitan Institute of Medical Science, Tokyo, Japan
| | - Hironori Harada
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan.,Laboratory of Oncology, School of Life Sciences, Tokyo University of Pharmacy & Life Sciences, Tokyo, Japan
| | - Hisashi Sakamaki
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Kazuteru Ohashi
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Yuka Harada
- Clinical Research Support Center, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
| | - Noriko Doki
- Hematology Division, Tokyo Metropolitan Cancer and Infectious Diseases Center, Komagome Hospital, Tokyo, Japan
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36
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Mattisson J, Danielsson M, Hammond M, Davies H, Gallant CJ, Nordlund J, Raine A, Edén M, Kilander L, Ingelsson M, Dumanski JP, Halvardson J, Forsberg LA. Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99. Sci Rep 2021; 11:15160. [PMID: 34312421 PMCID: PMC8313698 DOI: 10.1038/s41598-021-94588-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
Mosaic loss of chromosome Y (LOY) in immune cells is a male-specific mutation associated with increased risk for morbidity and mortality. The CD99 gene, positioned in the pseudoautosomal regions of chromosomes X and Y, encodes a cell surface protein essential for several key properties of leukocytes and immune system functions. Here we used CITE-seq for simultaneous quantification of CD99 derived mRNA and cell surface CD99 protein abundance in relation to LOY in single cells. The abundance of CD99 molecules was lower on the surfaces of LOY cells compared with cells without this aneuploidy in all six types of leukocytes studied, while the abundance of CD proteins encoded by genes located on autosomal chromosomes were independent from LOY. These results connect LOY in single cells with immune related cellular properties at the protein level, providing mechanistic insight regarding disease vulnerability in men affected with mosaic chromosome Y loss in blood leukocytes.
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Affiliation(s)
- Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Hammond
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Malin Edén
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lena Kilander
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Faculty of Pharmacy, 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
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37
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Lin SH, Brown DW, Rose B, Day F, Lee OW, Khan SM, Hislop J, Chanock SJ, Perry JRB, Machiela MJ. Incident disease associations with mosaic chromosomal alterations on autosomes, X and Y chromosomes: insights from a phenome-wide association study in the UK Biobank. Cell Biosci 2021; 11:143. [PMID: 34301302 PMCID: PMC8299574 DOI: 10.1186/s13578-021-00651-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 07/06/2021] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Mosaic chromosomal alterations (mCAs) are large chromosomal gains, losses and copy-neutral losses of heterozygosity (LOH) in peripheral leukocytes. While many individuals with detectable mCAs have no notable adverse outcomes, mCA-associated gene dosage alterations as well as clonal expansion of mutated leukocyte clones could increase susceptibility to disease. RESULTS We performed a phenome-wide association study (PheWAS) using existing data from 482,396 UK Biobank (UKBB) participants to investigate potential associations between mCAs and incident disease. Of the 1290 ICD codes we examined, our adjusted analysis identified a total of 50 incident disease outcomes associated with mCAs at PheWAS significance levels. We observed striking differences in the diseases associated with each type of alteration, with autosomal mCAs most associated with increased hematologic malignancies, incident infections and possibly cancer therapy-related conditions. Alterations of chromosome X were associated with increased lymphoid leukemia risk and, mCAs of chromosome Y were linked to potential reduced metabolic disease risk. CONCLUSIONS Our findings demonstrate that a wide range of diseases are potential sequelae of mCAs and highlight the critical importance of careful covariate adjustment in mCA disease association studies.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Brandon Rose
- University of Miami Miller School of Medicine, Miami, FL, 33136, USA
| | - Felix Day
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Jada Hislop
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA
| | - John R B Perry
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Drive, Rockville, MD, 20892, USA.
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Kananen L, Marttila S. Ageing-associated changes in DNA methylation in X and Y chromosomes. Epigenetics Chromatin 2021; 14:33. [PMID: 34215292 PMCID: PMC8254238 DOI: 10.1186/s13072-021-00407-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ageing displays clear sexual dimorphism, evident in both morbidity and mortality. Ageing is also associated with changes in DNA methylation, but very little focus has been on the sex chromosomes, potential biological contributors to the observed sexual dimorphism. Here, we sought to identify DNA methylation changes associated with ageing in the Y and X chromosomes, by utilizing datasets available in data repositories, comprising in total of 1240 males and 1191 females, aged 14–92 years. Results In total, we identified 46 age-associated CpG sites in the male Y, 1327 age-associated CpG sites in the male X, and 325 age-associated CpG sites in the female X. The X chromosomal age-associated CpGs showed significant overlap between females and males, with 122 CpGs identified as age-associated in both sexes. Age-associated X chromosomal CpGs in both sexes were enriched in CpG islands and depleted from gene bodies and showed no strong trend towards hypermethylation nor hypomethylation. In contrast, the Y chromosomal age-associated CpGs were enriched in gene bodies, and showed a clear trend towards hypermethylation with age. Conclusions Significant overlap in X chromosomal age-associated CpGs identified in males and females and their shared features suggest that despite the uneven chromosomal dosage, differences in ageing-associated DNA methylation changes in the X chromosome are unlikely to be a major contributor of sex dimorphism in ageing. While age-associated CpGs showed good replication across datasets in the present study, only a limited set of previously reported age-associated CpGs were replicated. One contributor to the limited overlap are differences in the age range of individuals included in each data set. Further study is needed to identify biologically significant age-associated CpGs in the sex chromosomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00407-6.
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Affiliation(s)
- Laura Kananen
- Faculty of Social Sciences (Health Sciences), Tampere University, Tampere, Finland. .,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Saara Marttila
- Gerontology Research Center, Tampere University, Tampere, Finland. .,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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39
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Dai X, Guo X. Decoding and rejuvenating human ageing genomes: Lessons from mosaic chromosomal alterations. Ageing Res Rev 2021; 68:101342. [PMID: 33866012 DOI: 10.1016/j.arr.2021.101342] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/10/2023]
Abstract
One of the most curious findings emerged from genome-wide studies over the last decade was that genetic mosaicism is a dominant feature of human ageing genomes. The clonal dominance of genetic mosaicism occurs preceding the physiological and physical ageing and associates with propensity for diseases including cancer, Alzheimer's disease, cardiovascular disease and diabetes. These findings are revolutionizing the ways biologists thinking about health and disease pathogenesis. Among all mosaic mutations in ageing genomes, mosaic chromosomal alterations (mCAs) have the most significant functional consequences because they can produce intercellular genomic variations simultaneously involving dozens to hundreds or even thousands genes, and therefore have most profound effects in human ageing and disease etiology. Here, we provide a comprehensive picture of the landscapes, causes, consequences and rejuvenation of mCAs at multiple scales, from cell to human population, by reviewing data from cytogenetic, genetic and genomic studies in cells, animal models (fly and mouse) and, more frequently, large-cohort populations. A detailed decoding of ageing genomes with a focus on mCAs may yield important insights into the genomic architecture of human ageing, accelerate the risk stratification of age-related diseases (particularly cancers) and development of novel targets and strategies for delaying or rejuvenating human (genome) ageing.
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Affiliation(s)
- Xueqin Dai
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Xihan Guo
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China; The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, 650500, China; Yunnan Environmental Mutagen Society, Kunming, Yunnan, 650500, China.
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40
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Spasova V, Mladenov B, Rangelov S, Hammoudeh Z, Nesheva D, Serbezov D, Staneva R, Hadjidekova S, Ganev M, Balabanski L, Vazharova R, Slavov C, Toncheva D, Antonova O. Clinical impact of copy number variation changes in bladder cancer samples. Exp Ther Med 2021; 22:901. [PMID: 34257714 PMCID: PMC8243332 DOI: 10.3892/etm.2021.10333] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Accepted: 02/18/2021] [Indexed: 12/19/2022] Open
Abstract
The aim of the present study was to detect copy number variations (CNVs) related to tumour progression and metastasis of urothelial carcinoma through whole-genome scanning. A total of 30 bladder cancer samples staged from pTa to pT4 were included in the study. DNA was extracted from freshly frozen tissue via standard phenol-chloroform extraction and CNV analysis was performed on two alternative platforms (CytoChip Oligo aCGH, 4x44K and Infinium OncoArray-500K BeadChip; Illumina, Inc.). Data were analysed with BlueFuse Multi software and Karyostudio, respectively. The results highlight the role of genomic imbalances in regions containing genes with metastatic and proliferative potential for tumour invasion. A high level of genomic instability in uroepithelial tumours was observed and a total of 524 aberrations, including 175 losses and 349 gains, were identified. The most prevalent genetic imbalances affected the following regions: 1p, 1q, 2q, 4p, 4q, 5p, 5q, 6p, 6q, 7q, 8q, 9p, 9q, 10p, 10q, 11q, 13q and 17q. High-grade tumours more frequently harboured genomic imbalances (n=227) than low-grade tumours (n=103). A total of 36 CNVs in high-grade bladder tumours were detected in chromosomes 1-5, 8-11, 14, 17, 19 and 20. Furthermore, five loss of heterozygosity variants containing 176 genes were observed in high-grade bladder cancer and may be used as potential targets for precision therapy. Revealing specific chromosomal regions related to the metastatic potential of uroepithelial tumours may lay a foundation for implementing molecular CNV profiling of bladder tumours as part of a routine progression risk estimation strategy, thus expanding the personalized therapeutic approach.
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Affiliation(s)
- Victoria Spasova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Boris Mladenov
- Department of Urology, UMBALSM N.I. Pirogov, 1606 Sofia, Bulgaria
| | - Simeon Rangelov
- Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia, Bulgaria
| | - Zora Hammoudeh
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Desislava Nesheva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Dimitar Serbezov
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Rada Staneva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia, Bulgaria
| | - Savina Hadjidekova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, Nadezhda Women's Health Hospital, 1373 Sofia, Bulgaria
| | - Mihail Ganev
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Lubomir Balabanski
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria.,Medical Genetics Laboratory, GARH Malinov, 1680 Sofia, Bulgaria
| | - Radoslava Vazharova
- Medical Genetics Laboratory, GARH Malinov, 1680 Sofia, Bulgaria.,Department of Biology, Medical Genetics and Microbiology, Faculty of Medicine, Sofia University St. Kliment Ohridski, 1407 Sofia, Bulgaria
| | - Chavdar Slavov
- Department of Urology, Tsaritsa Yoanna University Hospital, 1527 Sofia, Bulgaria
| | - Draga Toncheva
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
| | - Olga Antonova
- Department of Medical Genetics, Medical University-Sofia, 1431 Sofia, Bulgaria
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41
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Y disruption, autosomal hypomethylation and poor male lung cancer survival. Sci Rep 2021; 11:12453. [PMID: 34127738 PMCID: PMC8203787 DOI: 10.1038/s41598-021-91907-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/26/2021] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the most frequent cause of cancer death worldwide. It affects more men than women, and men generally have worse survival outcomes. We compared gene co-expression networks in affected and unaffected lung tissue from 126 consecutive patients with Stage IA-IV lung cancer undergoing surgery with curative intent. We observed marked degradation of a sex-associated transcription network in tumour tissue. This disturbance, detected in 27.7% of male tumours in the discovery dataset and 27.3% of male tumours in a further 123-sample replication dataset, was coincident with partial losses of the Y chromosome and extensive autosomal DNA hypomethylation. Central to this network was the epigenetic modifier and regulator of sexually dimorphic gene expression, KDM5D. After accounting for prognostic and epidemiological covariates including stage and histology, male patients with tumour KDM5D deficiency showed a significantly increased risk of death (Hazard Ratio [HR] 3.80, 95% CI 1.40-10.3, P = 0.009). KDM5D deficiency was confirmed as a negative prognostic indicator in a further 1100 male lung tumours (HR 1.67, 95% CI 1.4-2.0, P = 1.2 × 10-10). Our findings identify tumour deficiency of KDM5D as a prognostic marker and credible mechanism underlying sex disparity in lung cancer.
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42
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Hägg S, Jylhävä J. Sex differences in biological aging with a focus on human studies. eLife 2021; 10:e63425. [PMID: 33982659 PMCID: PMC8118651 DOI: 10.7554/elife.63425] [Citation(s) in RCA: 131] [Impact Index Per Article: 43.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 05/04/2021] [Indexed: 02/06/2023] Open
Abstract
Aging is a complex biological process characterized by hallmark features accumulating over the life course, shaping the individual's aging trajectory and subsequent disease risks. There is substantial individual variability in the aging process between men and women. In general, women live longer than men, consistent with lower biological ages as assessed by molecular biomarkers, but there is a paradox. Women are frailer and have worse health at the end of life, while men still perform better in physical function examinations. Moreover, many age-related diseases show sex-specific patterns. In this review, we aim to summarize the current knowledge on sexual dimorphism in human studies, with support from animal research, on biological aging and illnesses. We also attempt to place it in the context of the theories of aging, as well as discuss the explanations for the sex differences, for example, the sex-chromosome linked mechanisms and hormonally driven differences.
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Affiliation(s)
- Sara Hägg
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
| | - Juulia Jylhävä
- Department of Medical Epidemiology and Biostatistics, Karolinska InstitutetStockholmSweden
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43
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Molecular characterization of the Yp11.2 region deletion in the Chinese Han population. Int J Legal Med 2021; 135:1351-1358. [PMID: 33903958 PMCID: PMC8205872 DOI: 10.1007/s00414-021-02596-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 04/03/2021] [Indexed: 12/28/2022]
Abstract
The Y chromosome is male-specific and is important for spermatogenesis and male fertility. However, the Y chromosome is poorly characterized due to massive palindromes and inverted repeats, which increase the likelihood of genomic rearrangements, resulting in short tandem repeats on the Y chromosome or long fragment deletions. The present study reports a large-scale (2.573~2.648 Mb) deletion in the Yp11.2 region in a Chinese population based on the analysis of 34 selected Y-specific sequence-tagged sites and subsequent sequencing of the breakpoint junctions on the Y chromosome from 5,068,482–5,142,391 bp to 7,715,462–7,716,695 bp. The results of sequence analysis indicated that the deleted region included part or all of the following five genes: PCDH11Y, TSPY, AMELY, TBL1Y, and RKY. These genes are associated with spermatogenesis or amelogenesis and various other processes; however, specific physiological functions and molecular mechanisms of these genes remain unclear. Notably, individuals with this deletion pattern did not have an obvious pathological phenotype but manifested some degree of amelogenesis imperfecta.
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44
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Vidaki A, Montiel González D, Planterose Jiménez B, Kayser M. Male-specific age estimation based on Y-chromosomal DNA methylation. Aging (Albany NY) 2021; 13:6442-6458. [PMID: 33744870 PMCID: PMC7993701 DOI: 10.18632/aging.202775] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 02/25/2021] [Indexed: 11/29/2022]
Abstract
Although DNA methylation variation of autosomal CpGs provides robust age predictive biomarkers, no male-specific age predictor exists based on Y-CpGs yet. Since sex chromosomes play an important role in aging, a Y-chromosome-based age predictor would allow studying male-specific aging effects and would also be useful in forensics. Here, we used blood-based DNA methylation microarray data of 1,057 males from six cohorts aged 15-87 and identified 75 Y-CpGs with an interquartile range of ≥0.1. Of these, 22 and six were significantly hyper- and hypomethylated with age (p(cor)<0.05, Bonferroni), respectively. Amongst several machine learning algorithms, a model based on support vector machines with radial kernel performed best in male-specific age prediction. We achieved a mean absolute deviation (MAD) between true and predicted age of 7.54 years (cor=0.81, validation) when using all 75 Y-CpGs, and a MAD of 8.46 years (cor=0.73, validation) based on the most predictive 19 Y-CpGs. The accuracies of both age predictors did not worsen with increased age, in contrast to autosomal CpG-based age predictors that are known to predict age with reduced accuracy in the elderly. Overall, we introduce the first-of-its-kind male-specific epigenetic age predictor for future applications in aging research and forensics.
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Affiliation(s)
- Athina Vidaki
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Diego Montiel González
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Benjamin Planterose Jiménez
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
| | - Manfred Kayser
- Department of Genetic Identification, Erasmus University Medical Center Rotterdam, Rotterdam 3000, CA, The Netherlands
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45
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Evaluation of the usefulness of saliva for mosaic loss of chromosome Y analysis. Sci Rep 2021; 11:3769. [PMID: 33580176 PMCID: PMC7881200 DOI: 10.1038/s41598-021-83308-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
Mosaic loss of chromosome Y (mLOY) in leukocytes has attracted much attention as an emerging biomarker of aging and aging-related diseases. We evaluated the usefulness of saliva for mLOY analysis and showed that saliva-derived mLOY is significantly associated with aging and increased physical activity, but not with smoking. While these data support the robust association between saliva-derived mLOY and aging, caution is required when comparing data from saliva-derived and blood-derived mLOY.
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46
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Ouseph MM, Hasserjian RP, Dal Cin P, Lovitch SB, Steensma DP, Nardi V, Weinberg OK. Genomic alterations in patients with somatic loss of the Y chromosome as the sole cytogenetic finding in bone marrow cells. Haematologica 2021; 106:555-564. [PMID: 32193254 PMCID: PMC7849577 DOI: 10.3324/haematol.2019.240689] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/19/2020] [Indexed: 01/23/2023] Open
Abstract
Loss of the Y chromosome (LOY) is one of the most common somatic genomic alterations in hematopoietic cells in men. However, due to the high prevalence of LOY as the sole cytogenetic finding in the healthy older population, differentiating isolated LOY associated with clonal hematologic processes from aging-associated mosaicism can be difficult in the absence of definitive morphological features of disease. In the past, various investigators have proposed that a high percentage of metaphases with LOY is more likely to represent expansion of a clonal myeloid disease-associated population. It is unknown whether the proportion of metaphases with LOY is associated with the incidence of myeloid neoplasia-associated genomic alterations. To address this question, we identified bone marrow samples with LOY as an isolated cytogenetic finding and used targeted next generation sequencing-based molecular analysis to identify common myeloid neoplasia-associated somatic mutations. Among 73 patients with a median age of 75 years (range, 29-90), the percentage of metaphases with LOY was <25% in 23 patients, 25-49% in 10, 50-74% in 8 and ≥75% in 32. A threshold of ≥75% LOY was significantly associated with a morphological diagnosis of myeloid neoplasm (P=0.004). Furthermore, ≥75% LOY was associated with a higher lifetime incidence of a diagnosis of myelodysplastic syndromes (MDS) (P<0.0001), and in multivariate analysis ≥75% LOY was a statistically significant independent predictor of myeloid neoplasia (odds ratio 6.17; 95% confidence interval: 2.15-17.68; P=0.0007]. Higher LOY percentage (≥75%) was associated with greater likelihood of having somatic mutations (P=0.0009) and a higher number of these mutations (P=0.0002). Our findings indicate that ≥75% LOY in bone marrow cells is associated with an increased likelihood of molecular aberrations in genes commonly seen to be altered in myeloid neoplasia and with morphological features of MDS. These observations suggest that ≥75% LOY in bone marrow should be considered an MDS-associated cytogenetic aberration.
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Affiliation(s)
- Madhu M Ouseph
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | | | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - David P Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children Hospital, Boston, USA
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47
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Baliakas P, Forsberg LA. Chromosome Y loss and drivers of clonal hematopoiesis in myelodysplastic syndrome. Haematologica 2021; 106:329-331. [PMID: 33522783 PMCID: PMC7849334 DOI: 10.3324/haematol.2020.266601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; The Beijer Laboratory, Uppsala University, Uppsala.
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48
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Sherman MA, Rodin RE, Genovese G, Dias C, Barton AR, Mukamel RE, Berger B, Park PJ, Walsh CA, Loh PR. Large mosaic copy number variations confer autism risk. Nat Neurosci 2021; 24:197-203. [PMID: 33432194 PMCID: PMC7854495 DOI: 10.1038/s41593-020-00766-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2020] [Accepted: 11/21/2020] [Indexed: 01/29/2023]
Abstract
Although germline de novo copy number variants (CNVs) are known causes of autism spectrum disorder (ASD), the contribution of mosaic (early-developmental) copy number variants (mCNVs) has not been explored. In this study, we assessed the contribution of mCNVs to ASD by ascertaining mCNVs in genotype array intensity data from 12,077 probands with ASD and 5,500 unaffected siblings. We detected 46 mCNVs in probands and 19 mCNVs in siblings, affecting 2.8-73.8% of cells. Probands carried a significant burden of large (>4-Mb) mCNVs, which were detected in 25 probands but only one sibling (odds ratio = 11.4, 95% confidence interval = 1.5-84.2, P = 7.4 × 10-4). Event size positively correlated with severity of ASD symptoms (P = 0.016). Surprisingly, we did not observe mosaic analogues of the short de novo CNVs recurrently observed in ASD (eg, 16p11.2). We further experimentally validated two mCNVs in postmortem brain tissue from 59 additional probands. These results indicate that mCNVs contribute a previously unexplained component of ASD risk.
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Affiliation(s)
- Maxwell A. Sherman
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA,Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Correspondence should be addressed to M.A.S. (), P.J.P. (), C.A.W. (), or P.-R.L. ()
| | - Rachel E. Rodin
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA
| | - Giulio Genovese
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Caroline Dias
- Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA,Division of Developmental Medicine, Boston Children’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Alison R. Barton
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Ronen E. Mukamel
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Bonnie Berger
- Computer Science and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA,Department of Mathematics, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA
| | - Peter J. Park
- Department of Biomedical Informatics, Harvard Medical School, Boston, Massachusetts, USA,Correspondence should be addressed to M.A.S. (), P.J.P. (), C.A.W. (), or P.-R.L. ()
| | - Christopher A. Walsh
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Division of Genetics and Genomics, Manton Center for Orphan Disease, and Howard Hughes Medical Institute, Boston Children’s Hospital, Boston, Massachusetts, USA,Correspondence should be addressed to M.A.S. (), P.J.P. (), C.A.W. (), or P.-R.L. ()
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, Massachusetts, USA,Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA,Correspondence should be addressed to M.A.S. (), P.J.P. (), C.A.W. (), or P.-R.L. ()
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49
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Reply to Veitia. Eur J Hum Genet 2021; 29:1323-1324. [PMID: 33462398 PMCID: PMC8440652 DOI: 10.1038/s41431-020-00802-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/10/2022] Open
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50
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Kirsch-Volders M, Fenech M. Inflammatory cytokine storms severity may be fueled by interactions of micronuclei and RNA viruses such as COVID-19 virus SARS-CoV-2. A hypothesis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108395. [PMID: 34893160 PMCID: PMC8479308 DOI: 10.1016/j.mrrev.2021.108395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022]
Abstract
In this review we bring together evidence that (i) RNA viruses are a cause of chromosomal instability and micronuclei (MN), (ii) those individuals with high levels of lymphocyte MN have a weakened immune response and are more susceptible to RNA virus infection and (iii) both RNA virus infection and MN formation can induce inflammatory cytokine production. Based on these observations we propose a hypothesis that those who harbor elevated frequencies of MN within their cells are more prone to RNA virus infection and are more likely, through combined effects of leakage of self-DNA from MN and RNA from viruses, to escalate pro-inflammatory cytokine production via the cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING) and the Senescence Associated Secretory Phenotype (SASP) mechanisms to an extent that is unresolvable and therefore confers high risk of causing tissue damage by an excessive and overtly toxic immune response. The corollaries from this hypothesis are (i) those with abnormally high MN frequency are more prone to infection by RNA viruses; (ii) the extent of cytokine production and pro-inflammatory response to infection by RNA viruses is enhanced and possibly exceeds threshold levels that may be unresolvable in those with elevated MN levels in affected organs; (iii) reduction of MN frequency by improving nutrition and life-style factors increases resistance to RNA virus infection and moderates inflammatory cytokine production to a level that is immunologically efficacious and survivable.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA, 5048, Australia; Clinical and Health Sciences, University of South Australia, SA, 5000, Australia; Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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