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Abou Abdallah F, Abdel Massih C, Attieh C, Chebly A. The impact of mosaic loss of the Y chromosome (mLOY) in men of advanced age. Biogerontology 2024:10.1007/s10522-024-10133-7. [PMID: 39223433 DOI: 10.1007/s10522-024-10133-7] [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: 05/30/2024] [Accepted: 08/23/2024] [Indexed: 09/04/2024]
Abstract
The Y chromosome has long been considered to be a "genetic wasteland" harboring only few genes essentially involved in male sex development and spermatogenesis. However, the discovery of mosaic loss of the Y chromosome (mLOY) in older men has led to revisiting of the potential impact of the Y chromosome on health and the pathophysiological processes of multiple diseases such as cancer, Alzheimer's disease and cardiovascular disease. Hence, developing more sensitive techniques for the detection of mLOY has become an emergent concern. In this article, we present a comprehensive review of the literature regarding mLOY. Additionally, we discuss the emerging discoveries concerning mLOY as well as the underlying mechanisms promoting disease in men of advanced age.
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Affiliation(s)
| | | | - Charbel Attieh
- Center Jacques Loiselet for Medical Genetics and Genomics (CGGM), Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon
| | - Alain Chebly
- Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon.
- Center Jacques Loiselet for Medical Genetics and Genomics (CGGM), Faculty of Medicine, Saint Joseph University of Beirut, Beirut, Lebanon.
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2
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Dauber EM, Haas OA, Nebral K, Gassner C, Haslinger S, Geyeregger R, Hustinx H, Lejon Crottet S, Scharberg EA, Müller-Steinhardt M, Schönbacher M, Mayr WR, Körmöczi GF. Body-wide chimerism and mosaicism are predominant causes of naturally occurring ABO discrepancies. Br J Haematol 2024. [PMID: 38973155 DOI: 10.1111/bjh.19618] [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: 04/24/2024] [Accepted: 06/18/2024] [Indexed: 07/09/2024]
Abstract
Routine ABO blood group typing of apparently healthy individuals sporadically uncovers unexplained mixed-field reactions. Such blood group discrepancies can either result from a haematopoiesis-confined or body-wide dispersed chimerism or mosaicism. Taking the distinct clinical consequences of these four different possibilities into account, we explored the responsible cause in nine affected individuals. Genotype analyses revealed that more than three-quarters were chimaeras (two same-sex females, four same-sex males, one sex-mismatched male), while two were mosaics. Short tandem repeat analyses of buccal swab, hair root and nail DNA suggested a body-wide involvement in all instances. Moreover, genome-wide array analyses unveiled that in both mosaic cases the causative genetic defect was a unique copy-neutral loss of heterozygosity encompassing the entire long arm of chromosome 9. The practical transfusion- or transplantation-associated consequences of such incidental discoveries are well known and therefore easily manageable. Far less appreciated is the fact that such findings also call attention to potential problems that directly ensue from their specific genetic make-up. In case of chimerism, these are the appearance of seemingly implausible family relationships and pitfalls in forensic testing. In case of mosaicism, they concern with the necessity to delineate innocuous pre-existent or age-related from disease-predisposing and disease-indicating cell clones.
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Affiliation(s)
- Eva-Maria Dauber
- Department of Transfusion Medicine and Cell Therapy, Medical University of Vienna, Vienna, Austria
| | - Oskar A Haas
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
- Department of Pediatrics, St. Anna Children's Hospital, Medical University of Vienna, Vienna, Austria
| | - Karin Nebral
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - Christoph Gassner
- Institute of Translational Medicine, Private University in the Principality of Liechtenstein, Triesen, Liechtenstein
| | - Sabrina Haslinger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
- Labdia Labordiagnostik, Vienna, Austria
| | - René Geyeregger
- St. Anna Children's Cancer Research Institute (CCRI), Vienna, Austria
| | - Hein Hustinx
- Interregional Blood Transfusion SRC Ltd., Berne, Switzerland
| | | | - Erwin A Scharberg
- Institute for Transfusion Medicine and Immunohematology, German Red Cross Blood Service Baden-Württemberg-Hessen, Baden-Baden, Germany
| | - Michael Müller-Steinhardt
- Institute for Transfusion Medicine and Immunohematology, German Red Cross Blood Service Baden-Württemberg-Hessen, Baden-Baden, Germany
| | - Marlies Schönbacher
- Department of Transfusion Medicine and Cell Therapy, Medical University of Vienna, Vienna, Austria
| | - Wolfgang R Mayr
- Department of Transfusion Medicine and Cell Therapy, Medical University of Vienna, Vienna, Austria
| | - Günther F Körmöczi
- Department of Transfusion Medicine and Cell Therapy, Medical University of Vienna, Vienna, Austria
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3
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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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4
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJF, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun JH, DeMeo D, Levy D, Johnson AD, Mathias RA, Taub MA, Arnett D, North KE, Raffield LM, Carson AP, Doyle MF, Rich SS, Rotter JI, Guo X, Cox NJ, Roden DM, Franceschini N, Desai P, Reiner AP, Auer PL, Scheet PA, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. Nat Commun 2024; 15:3800. [PMID: 38714703 PMCID: PMC11076528 DOI: 10.1038/s41467-024-48190-8] [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: 11/08/2023] [Accepted: 04/23/2024] [Indexed: 05/10/2024] Open
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate as PACER scores for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our mCA fitness estimates, derived by aggregating per-individual PACER scores, were correlated (R2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using population-level distributions of clonal fraction. Among individuals with JAK2 V617F clonal hematopoiesis of indeterminate potential or mCAs affecting the JAK2 gene on chromosome 9, PACER score was strongly correlated with erythrocyte count. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified a TCL1A locus variant associated with mCA clonal expansion rate, with suggestive variants in NRIP1 and TERT.
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Affiliation(s)
- Yash Pershad
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Taralynn Mack
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Hannah Poisner
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, USA
| | - Yasminka A Jakubek
- Internal Medicine, Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Adrienne M Stilp
- Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Braxton D Mitchell
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Joshua P Lewis
- Dept of Medicine, Endocrinology, Diabetes, and Nutrition, University of Maryland, Baltimore, Baltimore, MD, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Nathalie Chami
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Zhe Wang
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Kathleen Barnes
- Division of Biomedical Informatics & Personalized Medicine, University of Colorado Anschutz, Aurora, CO, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Myriam Fornage
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
- Brown Foundation Institute of Molecular Medicine, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology, and Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Ali Shojaie
- Biostatistics, University of Washington, Seattle, WA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jeong H Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Daniel Levy
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute, Population Sciences Branch, Framingham, MA, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Donna Arnett
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Kari E North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Margaret F Doyle
- Department of Pathology & Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Xiuqing Guo
- Pediatrics, Genomic Outcomes, The Institute for Translational Genomics and Population Sciences, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Nancy J Cox
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA
| | - Dan M Roden
- Departments of Medicine, Pharmacology, and Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Weill Cornell Medical College, New York, NY, USA
| | - Alex P Reiner
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Paul L Auer
- Division of Biostatistics, Insitute for Health & Equity and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Paul A Scheet
- Dept of Epidemiology, University of Texas M. D. Anderson Cancer Center, Houston, TX, USA
| | | | - Joshua S Weinstock
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University and Vanderbilt University Medical Center, Nashville, TN, USA.
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Borsi E, Vigliotta I, Poletti A, Mazzocchetti G, Solli V, Zazzeroni L, Martello M, Armuzzi S, Taurisano B, Kanapari A, Pistis I, Zamagni E, Pantani L, Rocchi S, Mancuso K, Tacchetti P, Rizzello I, Rizzi S, Dan E, Sinigaglia B, Cavo M, Terragna C. Single-Cell DNA Sequencing Reveals an Evolutionary Pattern of CHIP in Transplant Eligible Multiple Myeloma Patients. Cells 2024; 13:657. [PMID: 38667272 PMCID: PMC11049155 DOI: 10.3390/cells13080657] [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: 02/21/2024] [Revised: 03/26/2024] [Accepted: 04/06/2024] [Indexed: 04/28/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) refers to the phenomenon where a hematopoietic stem cell acquires fitness-increasing mutation(s), resulting in its clonal expansion. CHIP is frequently observed in multiple myeloma (MM) patients, and it is associated with a worse outcome. High-throughput amplicon-based single-cell DNA sequencing was performed on circulating CD34+ cells collected from twelve MM patients before autologous stem cell transplantation (ASCT). Moreover, in four MM patients, longitudinal samples either before or post-ASCT were collected. Single-cell sequencing and data analysis were assessed using the MissionBio Tapestri® platform, with a targeted panel of 20 leukemia-associated genes. We detected CHIP pathogenic mutations in 6/12 patients (50%) at the time of transplant. The most frequently mutated genes were TET2, EZH2, KIT, DNMT3A, and ASXL1. In two patients, we observed co-occurring mutations involving an epigenetic modifier (i.e., DNMT3A) and/or a gene involved in splicing machinery (i.e., SF3B1) and/or a tyrosine kinase receptor (i.e., KIT) in the same clone. Longitudinal analysis of paired samples revealed a positive selection of mutant high-fitness clones over time, regardless of their affinity with a major or minor sub-clone. Copy number analysis of the panel of all genes did not show any numerical alterations present in stem cell compartment. Moreover, we observed a tendency of CHIP-positive patients to achieve a suboptimal response to therapy compared to those without. A sub-clone dynamic of high-fitness mutations over time was confirmed.
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Affiliation(s)
- Enrica Borsi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Ilaria Vigliotta
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Andrea Poletti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Gaia Mazzocchetti
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Vincenza Solli
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Luca Zazzeroni
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Marina Martello
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Silvia Armuzzi
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Barbara Taurisano
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ajsi Kanapari
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ignazia Pistis
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Elena Zamagni
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Lucia Pantani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Serena Rocchi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Katia Mancuso
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Paola Tacchetti
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Ilaria Rizzello
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Simonetta Rizzi
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Elisa Dan
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Barbara Sinigaglia
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
| | - Michele Cavo
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
- Department of Medical and Surgical Sciences (DIMEC), University of Bologna, 40126 Bologna, Italy
| | - Carolina Terragna
- IRCCS Azienda Ospedaliero-Universitaria di Bologna, Istituto di Ematologia “Seràgnoli”, 40138 Bologna, Italy
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Pérez-Jurado LA, Cáceres A, Balagué-Dobón L, Esko T, López de Heredia M, Quintela I, Cruz R, Lapunzina P, Carracedo Á, González JR. Clonal chromosomal mosaicism and loss of chromosome Y in elderly men increase vulnerability for SARS-CoV-2. Commun Biol 2024; 7:202. [PMID: 38374351 PMCID: PMC10876565 DOI: 10.1038/s42003-024-05805-6] [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: 02/18/2022] [Accepted: 01/11/2024] [Indexed: 02/21/2024] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2, COVID-19) had an estimated overall case fatality ratio of 1.38% (pre-vaccination), being 53% higher in males and increasing exponentially with age. Among 9578 individuals diagnosed with COVID-19 in the SCOURGE study, we found 133 cases (1.42%) with detectable clonal mosaicism for chromosome alterations (mCA) and 226 males (5.08%) with acquired loss of chromosome Y (LOY). Individuals with clonal mosaic events (mCA and/or LOY) showed a 54% increase in the risk of COVID-19 lethality. LOY is associated with transcriptomic biomarkers of immune dysfunction, pro-coagulation activity and cardiovascular risk. Interferon-induced genes involved in the initial immune response to SARS-CoV-2 are also down-regulated in LOY. Thus, mCA and LOY underlie at least part of the sex-biased severity and mortality of COVID-19 in aging patients. Given its potential therapeutic and prognostic relevance, evaluation of clonal mosaicism should be implemented as biomarker of COVID-19 severity in elderly people.
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Affiliation(s)
- Luis A Pérez-Jurado
- Genetics Unit, Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain.
- Genetics Service, Hospital del Mar & Hospital del Mar Research Institute (IMIM), Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain.
| | - Alejandro Cáceres
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Laura Balagué-Dobón
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Tonu Esko
- Estonian Genome Science Centre, University of Tartu, Tartu, Estonia
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Miguel López de Heredia
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
| | - Inés Quintela
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Raquel Cruz
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Pablo Lapunzina
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
- Instituto de Genética Médica y Molecular (INGEMM), Hospital Universitario La Paz-IDIPAZ, Madrid, Spain
- ERN-ITHACA-European Reference Network, Paris, France
| | - Ángel Carracedo
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), ISCIII, Barcelona, Spain
- Centro Nacional de Genotipado (CEGEN), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain
- Centro Singular de Investigación en Medicina Molecular y Enfermedades Crónicas (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain
- Fundación Pública Galega de Medicina Xenómica, Sistema Galego de Saúde (SERGAS), Santiago de Compostela, Spain
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.
- Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.
- Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra, Spain.
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7
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Kanagal-Shamanna R, Beck DB, Calvo KR. Clonal Hematopoiesis, Inflammation, and Hematologic Malignancy. ANNUAL REVIEW OF PATHOLOGY 2024; 19:479-506. [PMID: 37832948 DOI: 10.1146/annurev-pathmechdis-051222-122724] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/15/2023]
Abstract
Somatic or acquired mutations are postzygotic genetic variations that can occur within any tissue. These mutations accumulate during aging and have classically been linked to malignant processes. Tremendous advancements over the past years have led to a deeper understanding of the role of somatic mutations in benign and malignant age-related diseases. Here, we review the somatic mutations that accumulate in the blood and their connection to disease states, with a particular focus on inflammatory diseases and myelodysplastic syndrome. We include a definition of clonal hematopoiesis (CH) and an overview of the origins and implications of these mutations. In addition, we emphasize somatic disorders with overlapping inflammation and hematologic disease beyond CH, including paroxysmal nocturnal hemoglobinuria and aplastic anemia, focusing on VEXAS (vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic) syndrome. Finally, we provide a practical view of the implications of somatic mutations in clinical hematology, pathology, and beyond.
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology and Molecular Diagnostics, Division of Pathology and Laboratory Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - David B Beck
- Center for Human Genetics and Genomics, New York University Grossman School of Medicine, New York, New York, USA
- Department of Medicine, New York University Grossman School of Medicine, New York, New York, USA
| | - Katherine R Calvo
- Hematology Section, Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA;
- Myeloid Malignancies Program, National Institutes of Health, Bethesda, Maryland, USA
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8
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Kishtagari A, Khan MAW, Li Y, Vlasschaert C, Marneni N, Silver AJ, von Beck K, Spaulding T, Stockton S, Snider C, Sochacki A, Dorand D, Mack TM, Ferrell PB, Xu Y, Bejan CA, Savona MR, Bick AG. Driver mutation zygosity is a critical factor in predicting clonal hematopoiesis transformation risk. Blood Cancer J 2024; 14:6. [PMID: 38225345 PMCID: PMC10789770 DOI: 10.1038/s41408-023-00974-9] [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: 09/05/2023] [Revised: 12/15/2023] [Accepted: 12/21/2023] [Indexed: 01/17/2024] Open
Abstract
Clonal hematopoiesis (CH) can be caused by either single gene mutations (eg point mutations in JAK2 causing CHIP) or mosaic chromosomal alterations (e.g., loss of heterozygosity at chromosome 9p). CH is associated with a significantly increased risk of hematologic malignancies. However, the absolute rate of transformation on an annualized basis is low. Improved prognostication of transformation risk is urgently needed for routine clinical practice. We hypothesized that the co-occurrence of CHIP and mCAs at the same locus (e.g., transforming a heterozygous JAK2 CHIP mutation into a homozygous mutation through concomitant loss of heterozygosity at chromosome 9) might have important prognostic implications for malignancy transformation risk. We tested this hypothesis using our discovery cohort, the UK Biobank (n = 451,180), and subsequently validated it in the BioVU cohort (n = 91,335). We find that individuals with a concurrent somatic mutation and mCA were at significantly increased risk of hematologic malignancy (for example, In BioVU cohort incidence of hematologic malignancies is higher in individuals with co-occurring JAK2 V617F and 9p CN-LOH; HR = 54.76, 95% CI = 33.92-88.41, P < 0.001 vs. JAK2 V617F alone; HR = 44.05, 95% CI = 35.06-55.35, P < 0.001). Currently, the 'zygosity' of the CHIP mutation is not routinely reported in clinical assays or considered in prognosticating CHIP transformation risk. Based on these observations, we propose that clinical reports should include 'zygosity' status of CHIP mutations and that future prognostication systems should take mutation 'zygosity' into account.
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Affiliation(s)
- Ashwin Kishtagari
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - M A Wasay Khan
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yajing Li
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | | | - Naimisha Marneni
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Kelly von Beck
- Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Travis Spaulding
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Shannon Stockton
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christina Snider
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Andrew Sochacki
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Dixon Dorand
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Taralynn M Mack
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - P Brent Ferrell
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Yaomin Xu
- Department of Biostatistics, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Quantitative Sciences, Vanderbilt University School of Medicine, Nashville, TN, USA
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Cosmin A Bejan
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Division of Hematology/Oncology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA.
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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9
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Cacic AM, Schulz FI, Germing U, Dietrich S, Gattermann N. Molecular and clinical aspects relevant for counseling individuals with clonal hematopoiesis of indeterminate potential. Front Oncol 2023; 13:1303785. [PMID: 38162500 PMCID: PMC10754976 DOI: 10.3389/fonc.2023.1303785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 11/28/2023] [Indexed: 01/03/2024] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) has fascinated the medical community for some time. Discovered about a decade ago, this phenomenon links age-related alterations in hematopoiesis not only to the later development of hematological malignancies but also to an increased risk of early-onset cardiovascular disease and some other disorders. CHIP is detected in the blood and is characterized by clonally expanded somatic mutations in cancer-associated genes, predisposing to the development of hematologic neoplasms such as MDS and AML. CHIP-associated mutations often involve DNA damage repair genes and are frequently observed following prior cytotoxic cancer therapy. Genetic predisposition seems to be a contributing factor. It came as a surprise that CHIP significantly elevates the risk of myocardial infarction and stroke, and also contributes to heart failure and pulmonary hypertension. Meanwhile, evidence of mutant clonal macrophages in vessel walls and organ parenchyma helps to explain the pathophysiology. Besides aging, there are some risk factors promoting the appearance of CHIP, such as smoking, chronic inflammation, chronic sleep deprivation, and high birth weight. This article describes fundamental aspects of CHIP and explains its association with hematologic malignancies, cardiovascular disorders, and other medical conditions, while also exploring potential progress in the clinical management of affected individuals. While it is important to diagnose conditions that can lead to adverse, but potentially preventable, effects, it is equally important not to stress patients by confronting them with disconcerting findings that cannot be remedied. Individuals with diagnosed or suspected CHIP should receive counseling in a specialized outpatient clinic, where professionals from relevant medical specialties may help them to avoid the development of CHIP-related health problems. Unfortunately, useful treatments and clinical guidelines for managing CHIP are still largely lacking. However, there are some promising approaches regarding the management of cardiovascular disease risk. In the future, strategies aimed at restoration of gene function or inhibition of inflammatory mediators may become an option.
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Affiliation(s)
- Anna Maria Cacic
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Felicitas Isabel Schulz
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Ulrich Germing
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Sascha Dietrich
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
| | - Norbert Gattermann
- Department of Hematology, Oncology and Clinical Immunology, Medical Faculty and University Hospital Düsseldorf, Heinrich Heine Universität Düsseldorf, Düsseldorf, Germany
- Center for Integrated Oncology Aachen Bonn Cologne Düsseldorf (CIO ABCD), Düsseldorf, Germany
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10
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Zhou W, Fischer A, Ogwang MD, Luo W, Kerchan P, Reynolds SJ, Tenge CN, Were PA, Kuremu RT, Wekesa WN, Masalu N, Kawira E, Kinyera T, Otim I, Legason ID, Nabalende H, Ayers LW, Bhatia K, Goedert JJ, Gouveia MH, Cole N, Hicks B, Jones K, Hummel M, Schlesner M, Chagaluka G, Mutalima N, Borgstein E, Liomba GN, Kamiza S, Mkandawire N, Mitambo C, Molyneux EM, Newton R, Glaser S, Kretzmer H, Manning M, Hutchinson A, Hsing AW, Tettey Y, Adjei AA, Chanock SJ, Siebert R, Yeager M, Prokunina-Olsson L, Machiela MJ, Mbulaiteye SM. Mosaic chromosomal alterations in peripheral blood leukocytes of children in sub-Saharan Africa. Nat Commun 2023; 14:8081. [PMID: 38057307 PMCID: PMC10700489 DOI: 10.1038/s41467-023-43881-0] [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: 02/09/2023] [Accepted: 11/22/2023] [Indexed: 12/08/2023] Open
Abstract
In high-income countries, mosaic chromosomal alterations in peripheral blood leukocytes are associated with an elevated risk of adverse health outcomes, including hematologic malignancies. We investigate mosaic chromosomal alterations in sub-Saharan Africa among 931 children with Burkitt lymphoma, an aggressive lymphoma commonly characterized by immunoglobulin-MYC chromosomal rearrangements, 3822 Burkitt lymphoma-free children, and 674 cancer-free men from Ghana. We find autosomal and X chromosome mosaic chromosomal alterations in 3.4% and 1.7% of Burkitt lymphoma-free children, and 8.4% and 3.7% of children with Burkitt lymphoma (P-values = 5.7×10-11 and 3.74×10-2, respectively). Autosomal mosaic chromosomal alterations are detected in 14.0% of Ghanaian men and increase with age. Mosaic chromosomal alterations in Burkitt lymphoma cases include gains on chromosomes 1q and 8, the latter spanning MYC, while mosaic chromosomal alterations in Burkitt lymphoma-free children include copy-neutral loss of heterozygosity on chromosomes 10, 14, and 16. Our results highlight mosaic chromosomal alterations in sub-Saharan African populations as a promising area of research.
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Affiliation(s)
- Weiyin Zhou
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Anja Fischer
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | | | - Wen Luo
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | | | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Constance N Tenge
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Pamela A Were
- EMBLEM Study, Academic Model Providing Access To Healthcare (AMPATH), Eldoret, Kenya
| | - Robert T Kuremu
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | - Walter N Wekesa
- EMBLEM Study, Moi University College of Health Sciences, Eldoret, Kenya
| | | | - Esther Kawira
- EMBLEM Study, Shirati Health, Education, and Development Foundation, Shirati, Tanzania
| | - Tobias Kinyera
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Isaac Otim
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Ismail D Legason
- EMBLEM Study, Kuluva Hospital, Arua, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Hadijah Nabalende
- EMBLEM Study, St. Mary's Hospital, Lacor, Gulu, Uganda
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH, USA
| | - Kishor Bhatia
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - James J Goedert
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mateus H Gouveia
- Center for Research on Genomics & Global Health, NHGRI, National Institutes of Health, Bethesda, MD, USA
| | - Nathan Cole
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Belynda Hicks
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Kristine Jones
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Michael Hummel
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Berlin, Germany
- Humboldt-Universität zu Berlin, and Berlin Institute of Health, Institute of Pathology, D-10117, Berlin, Germany
| | - Mathias Schlesner
- Biomedical Informatics, Data Mining and Data Analytics, University of Augsburg, Augsburg, Germany
| | - George Chagaluka
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nora Mutalima
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
- Cancer Epidemiology Unit, University of Oxford, Oxford, UK
| | - Eric Borgstein
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - George N Liomba
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Steve Kamiza
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Nyengo Mkandawire
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Collins Mitambo
- Research Department, Ministry of Health, P.O. Box 30377, Lilongwe 3, Malawi
| | - Elizabeth M Molyneux
- Departments of Pediatrics and Surgery, College of Medicine, University of Malawi, Blantyre, Malawi
| | - Robert Newton
- Epidemiology and Cancer Statistics Group, Department of Health Sciences, University of York, York, UK
| | - Selina Glaser
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Helene Kretzmer
- Department of Genome Regulation, Max Planck Institute for Molecular Genetics, Berlin, Germany
| | - Michelle Manning
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Amy Hutchinson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ann W Hsing
- Stanford Cancer Institute, Stanford University, Stanford, Palo Alto, CA, USA
| | - Yao Tettey
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, P.O. Box KB 52, Korle-Bu, Accra, Ghana
| | - Andrew A Adjei
- Department of Pathology, University of Ghana Medical School, College of Health Sciences, P.O. Box KB 52, Korle-Bu, Accra, Ghana
| | - Stephen J Chanock
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Reiner Siebert
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Meredith Yeager
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Ludmila Prokunina-Olsson
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA
| | - Sam M Mbulaiteye
- Division of Cancer Epidemiology & Genetics, National Cancer Institute, National Institutes of Health, US Department of Health and Human Services, Bethesda, MD, USA.
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11
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Klausner M, Phan B, Morsberger L, Parish R, Shane A, Park R, Gocke CD, Xian RR, Jones RJ, Bolaños-Meade J, Gondek LP, Phan M, Zou YS. Donor cell-derived genetic abnormalities after sex mismatched allogeneic cell transplantation: a unique challenge of donor cell leukemia. Blood Cancer J 2023; 13:163. [PMID: 37926709 PMCID: PMC10625970 DOI: 10.1038/s41408-023-00938-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2023] [Revised: 10/16/2023] [Accepted: 10/25/2023] [Indexed: 11/07/2023] Open
Affiliation(s)
- Melanie Klausner
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Brian Phan
- The College of William and Mary, Williamsburg, VA, USA
| | - Laura Morsberger
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Parish
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Alison Shane
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rebecca Park
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Christopher D Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rena R Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Rick John Jones
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Javier Bolaños-Meade
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Lukasz P Gondek
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Michael Phan
- The Johns Hopkins University, Baltimore, MD, USA
| | - Ying S Zou
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD, USA.
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12
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Hubbard AK, Brown DW, Zhou W, Lin SH, Genovese G, Chanock SJ, Machiela MJ. Serum biomarkers are altered in UK Biobank participants with mosaic chromosomal alterations. Hum Mol Genet 2023; 32:3146-3152. [PMID: 37565819 PMCID: PMC10630237 DOI: 10.1093/hmg/ddad133] [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: 02/22/2023] [Revised: 06/09/2023] [Accepted: 08/03/2023] [Indexed: 08/12/2023] Open
Abstract
Age-related clonal expansion of cells harbouring mosaic chromosomal alterations (mCAs) is one manifestation of clonal haematopoiesis. Identifying factors that influence the generation and promotion of clonal expansion of mCAs are key to investigate the role of mCAs in health and disease. Herein, we report on widely measured serum biomarkers and their possible association with mCAs, which could provide new insights into molecular alterations that promote acquisition and clonal expansion. We performed a cross-sectional investigation of the association of 32 widely measured serum biomarkers with autosomal mCAs, mosaic loss of the Y chromosome, and mosaic loss of the X chromosome in 436 784 cancer-free participants from the UK Biobank. mCAs were associated with a range of commonly measured serum biomarkers such as lipid levels, circulating sex hormones, blood sugar homeostasis, inflammation and immune function, vitamins and minerals, kidney function, and liver function. Biomarker levels in participants with mCAs were estimated to differ by up to 5% relative to mCA-free participants, and individuals with higher cell fraction mCAs had greater deviation in mean biomarker values. Polygenic scores associated with sex hormone binding globulin, vitamin D, and total cholesterol were also associated with mCAs. Overall, we observed commonly used clinical serum biomarkers related to disease risk are associated with mCAs, suggesting mechanisms involved in these diseases could be related to mCA proliferation and clonal expansion.
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Affiliation(s)
- Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD 20850, United States
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA 02142, United States
- Department of Genetics, Harvard Medical School, Boston, MA 02115, United States
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD 20850, United States
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13
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Jakubek YA, Zhou Y, Stilp A, Bacon J, Wong JW, Ozcan Z, Arnett D, Barnes K, Bis JC, Boerwinkle E, Brody JA, Carson AP, Chasman DI, Chen J, Cho M, Conomos MP, Cox N, Doyle MF, Fornage M, Guo X, Kardia SLR, Lewis JP, Loos RJF, Ma X, Machiela MJ, Mack TM, Mathias RA, Mitchell BD, Mychaleckyj JC, North K, Pankratz N, Peyser PA, Preuss MH, Psaty B, Raffield LM, Vasan RS, Redline S, Rich SS, Rotter JI, Silverman EK, Smith JA, Smith AP, Taub M, Taylor KD, Yun J, Li Y, Desai P, Bick AG, Reiner AP, Scheet P, Auer PL. Mosaic chromosomal alterations in blood across ancestries using whole-genome sequencing. Nat Genet 2023; 55:1912-1919. [PMID: 37904051 PMCID: PMC10632132 DOI: 10.1038/s41588-023-01553-1] [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: 11/04/2022] [Accepted: 09/27/2023] [Indexed: 11/01/2023]
Abstract
Megabase-scale mosaic chromosomal alterations (mCAs) in blood are prognostic markers for a host of human diseases. Here, to gain a better understanding of mCA rates in genetically diverse populations, we analyzed whole-genome sequencing data from 67,390 individuals from the National Heart, Lung, and Blood Institute Trans-Omics for Precision Medicine program. We observed higher sensitivity with whole-genome sequencing data, compared with array-based data, in uncovering mCAs at low mutant cell fractions and found that individuals of European ancestry have the highest rates of autosomal mCAs and the lowest rates of chromosome X mCAs, compared with individuals of African or Hispanic ancestry. Although further studies in diverse populations will be needed to replicate our findings, we report three loci associated with loss of chromosome X, associations between autosomal mCAs and rare variants in DCPS, ADM17, PPP1R16B and TET2 and ancestry-specific variants in ATM and MPL with mCAs in cis.
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Affiliation(s)
- Yasminka A Jakubek
- Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Ying Zhou
- Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, WA, USA
| | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Jason Bacon
- Department of Computer Science, Department of Biological Sciences, University of Wisconsin-Milwaukee, Milwaukee, WI, USA
| | - Justin W Wong
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | - Zuhal Ozcan
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA
| | | | - Kathleen Barnes
- Division of Biomedical Informatics and Personalized Medicine, School of Medicine University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Eric Boerwinkle
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, The University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington Seattle, Seattle, WA, USA
| | - April P Carson
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Jiawen Chen
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Michael Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew P Conomos
- Department of Biostatistics, University of Washington, Seattle, WA, USA
| | - Nancy Cox
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Margaret F Doyle
- Department of Pathology and Laboratory Medicine, The University of Vermont Larner College of Medicine, Colchester, VT, USA
| | - Myriam Fornage
- University of Texas Health Science Center at Houston, Houston, TX, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Sharon L R Kardia
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Joshua P Lewis
- Department of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Xiaolong Ma
- Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | | | - Taralynn M Mack
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Rasika A Mathias
- Division of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MA, USA
| | - Braxton D Mitchell
- Department of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Kari North
- Department of Epidemiology, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Patricia A Peyser
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Michael H Preuss
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Bruce Psaty
- Cardiovascular Health Research Unit, Department of Medicine, Department of Epidemiology, Department of Health Systems and Population Health, University of Washington, Seattle, WA, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | | | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA, USA
| | - Stephen S Rich
- Center for Public Health Genomics, Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, VA, USA
| | - Jerome I Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Edwin K Silverman
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Jennifer A Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI, USA
- Institute for Social Research, Survey Research Center, University of Michigan, Ann Arbor, MI, USA
| | - Aaron P Smith
- Institute for Biomedical Informatics, University of Kentucky, Lexington, KY, USA
| | - Margaret Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MA, USA
| | - Kent D Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jeong Yun
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Yun Li
- Department of Biostatistics, Department of Genetics, Department of Computer Science, University of North Carolina Chapel-Hill, Chapel Hill, NC, USA
| | - Pinkal Desai
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Paul Scheet
- Department of Epidemiology, University of Texas M.D. Anderson Cancer Center, Houston, TX, USA.
| | - Paul L Auer
- Division of Biostatistics, Institute for Health and Equity, and Cancer Center, Medical College of Wisconsin, Milwaukee, WI, USA.
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Pershad Y, Mack T, Poisner H, Jakubek YA, Stilp AM, Mitchell BD, Lewis JP, Boerwinkle E, Loos RJ, Chami N, Wang Z, Barnes K, Pankratz N, Fornage M, Redline S, Psaty BM, Bis JC, Shojaie A, Silverman EK, Cho MH, Yun J, DeMeo D, Levy D, Johnson A, Mathias R, Taub M, Arnett D, North K, Raffield LM, Carson A, Doyle MF, Rich SS, Rotter JI, Guo X, Cox N, Roden DM, Franceschini N, Desai P, Reiner A, Auer PL, Scheet P, Jaiswal S, Weinstock JS, Bick AG. Determinants of mosaic chromosomal alteration fitness. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.10.20.23297280. [PMID: 37905118 PMCID: PMC10615010 DOI: 10.1101/2023.10.20.23297280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/02/2023]
Abstract
Clonal hematopoiesis (CH) is characterized by the acquisition of a somatic mutation in a hematopoietic stem cell that results in a clonal expansion. These driver mutations can be single nucleotide variants in cancer driver genes or larger structural rearrangements called mosaic chromosomal alterations (mCAs). The factors that influence the variations in mCA fitness and ultimately result in different clonal expansion rates are not well-understood. We used the Passenger-Approximated Clonal Expansion Rate (PACER) method to estimate clonal expansion rate for 6,381 individuals in the NHLBI TOPMed cohort with gain, loss, and copy-neutral loss of heterozygosity mCAs. Our estimates of mCA fitness were correlated (R 2 = 0.49) with an alternative approach that estimated fitness of mCAs in the UK Biobank using a theoretical probability distribution. Individuals with lymphoid-associated mCAs had a significantly higher white blood cell count and faster clonal expansion rate. In a cross-sectional analysis, genome-wide association study of estimates of mCA expansion rate identified TCL1A , NRIP1 , and TERT locus variants as modulators of mCA clonal expansion rate.
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15
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Brown DW, Cato LD, Zhao Y, Nandakumar SK, Bao EL, Gardner EJ, Hubbard AK, DePaulis A, Rehling T, Song L, Yu K, Chanock SJ, Perry JRB, Sankaran VG, Machiela MJ. Shared and distinct genetic etiologies for different types of clonal hematopoiesis. Nat Commun 2023; 14:5536. [PMID: 37684235 PMCID: PMC10491829 DOI: 10.1038/s41467-023-41315-5] [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: 01/10/2023] [Accepted: 08/29/2023] [Indexed: 09/10/2023] Open
Abstract
Clonal hematopoiesis (CH)-age-related expansion of mutated hematopoietic clones-can differ in frequency and cellular fitness by CH type (e.g., mutations in driver genes (CHIP), gains/losses and copy-neutral loss of chromosomal segments (mCAs), and loss of sex chromosomes). Co-occurring CH raises questions as to their origin, selection, and impact. We integrate sequence and genotype array data in up to 482,378 UK Biobank participants to demonstrate shared genetic architecture across CH types. Our analysis suggests a cellular evolutionary trade-off between different types of CH, with LOY occurring at lower rates in individuals carrying mutations in established CHIP genes. We observed co-occurrence of CHIP and mCAs with overlap at TET2, DNMT3A, and JAK2, in which CHIP precedes mCA acquisition. Furthermore, individuals carrying overlapping CH had high risk of future lymphoid and myeloid malignancies. Finally, we leverage shared genetic architecture of CH traits to identify 15 novel loci associated with leukemia risk.
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Affiliation(s)
- Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Liam D Cato
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Yajie Zhao
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Satish K Nandakumar
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
- Department of Cell Biology, Albert Einstein College of Medicine, Albert Einstein Cancer Center, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Bronx, NY, 10461, USA
| | - Erik L Bao
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Eugene J Gardner
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK
| | - Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alexander DePaulis
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Thomas Rehling
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lei Song
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - John R B Perry
- MRC Epidemiology Unit, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.
- Metabolic Research Laboratory, Wellcome-MRC Institute of Metabolic Science, University of Cambridge School of Clinical Medicine, Cambridge, CB2 0QQ, UK.
| | - Vijay G Sankaran
- Division of Hematology/Oncology, Boston Children's Hospital and Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, 02115, USA.
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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16
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Lin SH, Khan SM, Zhou W, Brown DW, Vergara C, Wolinsky SM, Martínez-Maza O, Margolick JB, Martinson JJ, Hussain SK, Engels EA, Machiela MJ. Mosaic chromosomal alterations detected in men living with HIV and the relationship to non-Hodgkin lymphoma. AIDS 2023; 37:1307-1313. [PMID: 36927626 PMCID: PMC10500031 DOI: 10.1097/qad.0000000000003545] [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: 03/18/2023]
Abstract
OBJECTIVES People with HIV (PWH) have an elevated risk of non-Hodgkin lymphoma (NHL) and other diseases. Studying clonal hematopoiesis (CH), the clonal expansion of mutated hematopoietic stem cells, could provide insights regarding elevated NHL risk. DESIGN Cohort analysis of participants in the Multicenter AIDS Cohort Study ( N = 5979). METHODS Mosaic chromosomal alterations (mCAs), a type of CH, were detected from genotyping array data using MoChA. We compared CH prevalence in men with HIV (MWH) to HIV-uninfected men using logistic regression, and among MWH, assessed the associations of CH with NHL incidence and overall mortality using Poisson regression. RESULTS Comparing MWH to HIV-uninfected men, we observed no difference in the frequency of autosomal mCAs (3.9% vs. 3.6%, P -value = 0.09) or mosaic loss of the Y chromosome (mLOY) (1.4% vs. 2.9%, P -value = 0.13). Autosomal mCAs involving copy-neutral loss of heterozygosity (CN-LOH) of chromosome 14q were more common in MWH. Among MWH, mCAs were not associated with subsequent NHL incidence (autosomal mCA P -value = 0.65, mLOY P -value = 0.48). However, two MWH with diffuse large B-cell lymphoma had overlapping CN-LOH mCAs on chromosome 19 spanning U2AF2 (involved in RNA splicing), and one MWH with Burkitt lymphoma had high-frequency mCAs involving chromosome 1 gain and chromosome 17 CN-LOH (cell fractions 22.1% and 25.0%, respectively). mCAs were not associated with mortality among MWH (autosomal mCA P -value = 0.52, mLOY P -value = 0.93). CONCLUSIONS We found limited evidence for a relationship between HIV infection and mCAs. Although mCAs were not significantly associated with NHL, mCAs detected in several NHL cases indicate a need for further investigation.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Sairah M Khan
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Candelaria Vergara
- Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD
| | | | - Otoniel Martínez-Maza
- UCLA AIDS Institute and Jonsson Comprehensive Cancer Center at UCLA, Los Angeles, CA
| | - Joseph B Margolick
- Bloomberg School of Public Health, The Johns Hopkins University, Baltimore, MD
| | | | - Shehnaz K Hussain
- University of California Davis Comprehensive Cancer Center, Sacramento, CA, USA
| | - Eric A Engels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
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17
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Zhou X, Cao J, Zhu L, Farrell K, Wang M, Guo L, Yang J, McKenzie A, Crary JF, Cai D, Tu Z, Zhang B. Molecular differences in brain regional vulnerability to aging between males and females. Front Aging Neurosci 2023; 15:1153251. [PMID: 37284017 PMCID: PMC10239962 DOI: 10.3389/fnagi.2023.1153251] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2023] [Accepted: 05/02/2023] [Indexed: 06/08/2023] Open
Abstract
Background Aging-related cognitive decline is associated with brain structural changes and synaptic loss. However, the molecular mechanisms of cognitive decline during normal aging remain elusive. Results Using the GTEx transcriptomic data from 13 brain regions, we identified aging-associated molecular alterations and cell-type compositions in males and females. We further constructed gene co-expression networks and identified aging-associated modules and key regulators shared by both sexes or specific to males or females. A few brain regions such as the hippocampus and the hypothalamus show specific vulnerability in males, while the cerebellar hemisphere and the anterior cingulate cortex regions manifest greater vulnerability in females than in males. Immune response genes are positively correlated with age, whereas those involved in neurogenesis are negatively correlated with age. Aging-associated genes identified in the hippocampus and the frontal cortex are significantly enriched for gene signatures implicated in Alzheimer's disease (AD) pathogenesis. In the hippocampus, a male-specific co-expression module is driven by key synaptic signaling regulators including VSNL1, INA, CHN1 and KCNH1; while in the cortex, a female-specific module is associated with neuron projection morphogenesis, which is driven by key regulators including SRPK2, REPS2 and FXYD1. In the cerebellar hemisphere, a myelination-associated module shared by males and females is driven by key regulators such as MOG, ENPP2, MYRF, ANLN, MAG and PLP1, which have been implicated in the development of AD and other neurodegenerative diseases. Conclusions This integrative network biology study systematically identifies molecular signatures and networks underlying brain regional vulnerability to aging in males and females. The findings pave the way for understanding the molecular mechanisms of gender differences in developing neurodegenerative diseases such as AD.
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Affiliation(s)
- Xianxiao Zhou
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jiqing Cao
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Research & Development, James J. Peters VA Medical Center, Bronx, NY, United States
| | - Li Zhu
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Research & Development, James J. Peters VA Medical Center, Bronx, NY, United States
| | - Kurt Farrell
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Minghui Wang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Lei Guo
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Jialiang Yang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Andrew McKenzie
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - John F. Crary
- Neuropathology Brain Bank & Research CoRE, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Dongming Cai
- Department of Neurology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Research & Development, James J. Peters VA Medical Center, Bronx, NY, United States
- Alzheimer’s Disease Research Center, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Ronald M. Loeb Center for Alzheimer’s Disease, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Zhidong Tu
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Bin Zhang
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Mount Sinai Center for Transformative Disease Modeling, Icahn School of Medicine at Mount Sinai, New York, NY, United States
- Icahn Institute for Data Science and Genomic Technology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
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18
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Jakubek YA, Reiner AP, Honigberg MC. Risk factors for clonal hematopoiesis of indeterminate potential and mosaic chromosomal alterations. Transl Res 2023; 255:171-180. [PMID: 36414227 PMCID: PMC10135440 DOI: 10.1016/j.trsl.2022.11.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/12/2022] [Revised: 11/11/2022] [Accepted: 11/15/2022] [Indexed: 11/21/2022]
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) of the autosomes, X, and Y chromosomes are aging-related somatic mutations detectable in peripheral blood. The presence of these acquired mutations predisposes otherwise healthy adults to increased risk of several chronic aging-related conditions including hematologic cancers, atherosclerotic cardiovascular diseases, other inflammatory conditions, and mortality. While the public health impact and disease associations of these blood-derived somatic mutations continue to expand, the inherited, behavioral/lifestyle, environmental risk factors and comorbid conditions that influence their occurrence and progression have been less well characterized. Age is the strongest risk factor for all types of CHIP and mCAs. CHIP and mCAs are generally more common in individuals of European than non-European ancestry. Evidence for a genetic predisposition has been strongest for mosaic loss of Y chromosome in men. Genome-wide association studies have recently begun to identify common and rare germline genetic variants associated with CHIP and mCAs. These loci include genes involving cell cycle regulation, cell proliferation/survival, hematopoietic progenitor cell regulation, DNA damage repair, and telomere maintenance. Some loci, such as TERT, ATM, TP53, CHEK2, and TCL1A, have overlapping associations with different types of CHIP, mCAs, and cancer predisposition. Various environmental or co-morbid contexts associated with presence or expansion of specific CHIP or mCA mutations are beginning to be elucidated, such as cigarette smoking, diet, cancer chemotherapy, particulate matter, and premature menopause. Further characterization of the germline genetic and environmental correlates of CHIP/mCAs may inform our ability to modify their progression and ultimately reduce the risk and burden of chronic diseases associated with these clonal somatic phenomena.
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Affiliation(s)
- Yasminka A Jakubek
- Department of Internal Medicine, College of Medicine, University of Kentucky, Lexington, Kentucky
| | - Alexander P Reiner
- Division of Public Health Sciences, Fred Hutchinson Center Research Center, Seattle, Washington; Department of Epidemiology, University of Washington, Seattle, Washington.
| | - Michael C Honigberg
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Boston, Massachusetts; Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, Massachusetts
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19
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Mendez LM, Patnaik MM. Clonal Hematopoiesis: Origins and determinants of evolution. Leuk Res 2023; 129:107076. [PMID: 37075557 DOI: 10.1016/j.leukres.2023.107076] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2023] [Revised: 03/22/2023] [Accepted: 04/10/2023] [Indexed: 04/21/2023]
Abstract
The accrual of somatic mutations is a byproduct of aging. When a clone bearing a somatic genetic alteration, conferring comparative competitive advantage, displays sufficient outgrowth to become detectable amongst an otherwise polyclonal background in the hematopoietic system, this is called clonal hematopoiesis (CH). Somatic genetic alterations observed in CH include point mutations in cancer related genes, mosaic chromosomal alterations or a combination of these. Interestingly, clonal hematopoiesis (CH) can also occur with somatic variants in genes without a known role in cancer and in the absence of a somatic genetic alteration through a process that has been described as 'genetic drift'. Clonal hematopoiesis of indeterminate significance (CHIP), is age-related and defined by the presence of somatic point mutations in cancer related genes, in the absence of cytopenias or a diagnosis of hematologic neoplasm, with a variant allele fraction ≥ 2 %. Remarkably, the increased mortality associated with CHIP is largely due to cardiovascular disease. Subsequently, CHIP has been associated with a myriad of age-related conditions such as Alzheimer's Disease, osteoporosis, CVA and COPD. CHIP is associated with an increased risk of hematologic malignancies, particularly myeloid neoplasms, with the risk rising with increasing clone size and clonal complexity. Mechanisms regulating clonal evolution and progression to hematologic malignancies remain to be defined. However, observations on context specific CH arising in the setting of bone marrow failure states, or on exposure to chemotherapy and radiation therapy, suggest that CH reflects context specific selection pressures and constraint-escape mechanisms.
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Affiliation(s)
- Lourdes M Mendez
- Section of Hematology, Department of Internal Medicine, Yale Cancer Center and Smilow Cancer Hospital, Yale University School of Medicine, CT, USA
| | - Mrinal M Patnaik
- Division of Hematology, Department of Medicine, Mayo Clinic, MN, USA.
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20
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Hubbard AK, Brown DW, Machiela MJ. Clonal hematopoiesis due to mosaic chromosomal alterations: Impact on disease risk and mortality. Leuk Res 2023; 126:107022. [PMID: 36706615 PMCID: PMC9974917 DOI: 10.1016/j.leukres.2023.107022] [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: 11/21/2022] [Revised: 12/28/2022] [Accepted: 01/22/2023] [Indexed: 01/25/2023]
Abstract
Mosaic chromosomal alterations (mCAs) are the clonal expansion of large somatically acquired structural chromosomal changes present on the autosomes and sex chromosomes. Most studies of mCAs use existing genotype array intensity data from large populations to investigate potential risk factors and disease outcomes associated with mCAs. In this review, we perform a comprehensive examination of existing evidence for mCA disease and mortality associations and provide a framework for interpreting these associations in the context of important biases specific to mCA studies. Our goal is to motivate well-designed mCA studies to assist in unlocking the potential of mCAs to improve understanding of the effects of ageing and accelerate translational applications for improving public health.
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Affiliation(s)
- Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA; Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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21
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Machiela MJ, Huang WY, Wong W, Berndt SI, Sampson J, De Almeida J, Abubakar M, Hislop J, Chen KL, Dagnall C, Diaz-Mayoral N, Ferrell M, Furr M, Gonzalez A, Hicks B, Hubbard AK, Hutchinson A, Jiang K, Jones K, Liu J, Loftfield E, Loukissas J, Mabie J, Merkle S, Miller E, Minasian LM, Nordgren E, Park B, Pinsky P, Riley T, Sandoval L, Saxena N, Vogt A, Wang J, Williams C, Wright P, Yeager M, Zhu B, Zhu C, Chanock SJ, Garcia-Closas M, Freedman ND. GWAS Explorer: an open-source tool to explore, visualize, and access GWAS summary statistics in the PLCO Atlas. Sci Data 2023; 10:25. [PMID: 36635305 PMCID: PMC9837135 DOI: 10.1038/s41597-022-01921-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2022] [Accepted: 12/21/2022] [Indexed: 01/13/2023] Open
Abstract
The Prostate, Lung, Colorectal and Ovarian (PLCO) Cancer Screening Trial is a prospective cohort study of nearly 155,000 U.S. volunteers aged 55-74 at enrollment in 1993-2001. We developed the PLCO Atlas Project, a large resource for multi-trait genome-wide association studies (GWAS), by genotyping participants with available DNA and genomic consent. Genotyping on high-density arrays and imputation was performed, and GWAS were conducted using a custom semi-automated pipeline. Association summary statistics were generated from a total of 110,562 participants of European, African and Asian ancestry. Application programming interfaces (APIs) and open-source software development kits (SKDs) enable exploring, visualizing and open data access through the PLCO Atlas GWAS Explorer website, promoting Findable, Accessible, Interoperable, and Re-usable (FAIR) principles. Currently the GWAS Explorer hosts association data for 90 traits and >78,000,000 genomic markers, focusing on cancer and cancer-related phenotypes. New traits will be posted as association data becomes available. The PLCO Atlas is a FAIR resource of high-quality genetic and phenotypic data with many potential reuse opportunities for cancer research and genetic epidemiology.
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Affiliation(s)
- Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA.
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Wendy Wong
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Sonja I Berndt
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Joshua Sampson
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Jonas De Almeida
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Mustapha Abubakar
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Jada Hislop
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Kai-Ling Chen
- Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA
| | - Casey Dagnall
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Norma Diaz-Mayoral
- BioProcessing and Trial Logistics Laboratory, FNLCR, Leidos Biomedical Research, Inc. Division of Cancer Prevention, NCI, NIH, Rockville, USA
| | - Mary Ferrell
- NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA
| | - Michael Furr
- Information Management Services, Inc., Danbury, USA
| | - Alex Gonzalez
- NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA
| | - Belynda Hicks
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Amy Hutchinson
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Kevin Jiang
- Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA
| | - Kristine Jones
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Jia Liu
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Erikka Loftfield
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Jennifer Loukissas
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Jerome Mabie
- Information Management Services, Inc., Danbury, USA
| | | | - Eric Miller
- Division of Cancer Prevention, NCI, NIH, Rockville, USA
| | | | - Ellen Nordgren
- NCI at Frederick Central Repository, American Type Culture Collection, Rockville, USA
| | - Brian Park
- Essential Software Inc., Center for Biomedical Informatics and Information Technology, NCI, Rockville, USA
| | - Paul Pinsky
- Division of Cancer Prevention, NCI, NIH, Rockville, USA
| | - Thomas Riley
- Information Management Services, Inc., Danbury, USA
| | - Lorena Sandoval
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Neeraj Saxena
- Division of Cancer Prevention, NCI, NIH, Rockville, USA
| | - Aurelie Vogt
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Jiahui Wang
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | | | | | - Meredith Yeager
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Bin Zhu
- Cancer Genomics Research Laboratory, DCEG, NCI, Frederick National Laboratory for Cancer Research (FNLCR), Leidos Biomedical Research, Inc., Rockville, USA
| | - Claire Zhu
- Division of Cancer Prevention, NCI, NIH, Rockville, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Montserrat Garcia-Closas
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics (DCEG), National Cancer Institute (NCI), National Institutes of Health (NIH), Rockville, USA
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22
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Germline-somatic JAK2 interactions are associated with clonal expansion in myelofibrosis. Nat Commun 2022; 13:5284. [PMID: 36075929 PMCID: PMC9458655 DOI: 10.1038/s41467-022-32986-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Accepted: 08/25/2022] [Indexed: 12/13/2022] Open
Abstract
Myelofibrosis is a rare myeloproliferative neoplasm (MPN) with high risk for progression to acute myeloid leukemia. Our integrated genomic analysis of up to 933 myelofibrosis cases identifies 6 germline susceptibility loci, 4 of which overlap with previously identified MPN loci. Virtual karyotyping identifies high frequencies of mosaic chromosomal alterations (mCAs), with enrichment at myelofibrosis GWAS susceptibility loci and recurrently somatically mutated MPN genes (e.g., JAK2). We replicate prior MPN associations showing germline variation at the 9p24.1 risk haplotype confers elevated risk of acquiring JAK2V617F mutations, demonstrating with long-read sequencing that this relationship occurs in cis. We also describe recurrent 9p24.1 large mCAs that selectively retained JAK2V617F mutations. Germline variation associated with longer telomeres is associated with increased myelofibrosis risk. Myelofibrosis cases with high-frequency JAK2 mCAs have marked reductions in measured telomere length – suggesting a relationship between telomere biology and myelofibrosis clonal expansion. Our results advance understanding of the germline-somatic interaction at JAK2 and implicate mCAs involving JAK2 as strong promoters of clonal expansion of those mutated clones. Myelofibrosis is a risk factor for the development of Acute Myeloid Leukaemia. Here, the authors carry out an integrated genomic investigation of 933 myelofibrosis patients, and identified interactions between germline and somatic variation in patients who required haematopoietic cell transplantation.
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23
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Tong S, Devine WP, Shieh JT. Tumor and Constitutional Sequencing for Neurofibromatosis Type 1. JCO Precis Oncol 2022; 6:e2100540. [PMID: 35584348 PMCID: PMC9200388 DOI: 10.1200/po.21.00540] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
NF1 variants in tumors are important to recognize, as multiple mechanisms may give rise to biallelic variants. Both deletions and copy-neutral loss of heterozygosity (LOH) are potential mechanisms of NF1 loss, distinct from point mutations, and additional genes altered may drive different tumor types. This study investigates whether tumors from individuals with neurofibromatosis type 1 (NF1) demonstrate additional gene variants and detects NF1 second hits using paired germline and somatic sequencing. In addition, rare tumor types in NF1 may also be characterized by tumor sequencing. NF1 second hits are primarily copy-neutral LOH and offer opportunity for variant interpretation
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Affiliation(s)
- Schuyler Tong
- Division of Hematology/Oncology, Pediatrics, Benioff Children's Hospital Oakland, University of California San Francisco, San Francisco, CA
| | - W Patrick Devine
- Department of Pathology, University of California San Francisco, San Francisco, CA.,Institute for Human Genetics, University of California San Francisco, San Francisco, CA
| | - Joseph T Shieh
- Institute for Human Genetics, University of California San Francisco, San Francisco, CA.,Division of Medical Genetics, Pediatrics, Benioff Children's Hospital, University of California San Francisco, San Francisco, CA
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24
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Alagpulinsa DA, Toribio MP, Alhallak I, Shmookler Reis RJ. Advances in understanding the molecular basis of clonal hematopoiesis. Trends Mol Med 2022; 28:360-377. [PMID: 35341686 DOI: 10.1016/j.molmed.2022.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 03/02/2022] [Accepted: 03/04/2022] [Indexed: 12/28/2022]
Abstract
Hematopoietic stem cells (HSCs) are polyfunctional, regenerating all blood cells via hematopoiesis throughout life. Clonal hematopoiesis (CH) is said to occur when a substantial proportion of mature blood cells is derived from a single dominant HSC lineage, usually because these HSCs have somatic mutations that confer a fitness and expansion advantage. CH strongly associates with aging and enrichment in some diseases irrespective of age, emerging as an independent causal risk factor for hematologic malignancies, cardiovascular disease, adverse disease outcomes, and all-cause mortality. Defining the molecular mechanisms underlying CH will thus provide a framework to develop interventions for healthy aging and disease treatment. Here, we review the most recent advances in understanding the molecular basis of CH in health and disease.
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Affiliation(s)
- David A Alagpulinsa
- Vaccine & Immunotherapy Center, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02129, USA.
| | - Mabel P Toribio
- Metabolism Unit, Division of Endocrinology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Iad Alhallak
- Metabolism Unit, Division of Endocrinology, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, 02114, USA
| | - Robert J Shmookler Reis
- Central Arkansas Veterans Healthcare System and Department of Geriatrics, University of Arkansas for Medical Sciences, Little Rock, AR 72205, USA
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25
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Abstract
PURPOSE OF REVIEW Loss of chromosome 7 has long been associated with adverse-risk myeloid malignancy. In the last decade, CUX1 has been identified as a critical tumor suppressor gene (TSG) located within a commonly deleted segment of chromosome arm 7q. Additional genes encoded on 7q have also been identified as bona fide myeloid tumor suppressors, further implicating chromosome 7 deletions in disease pathogenesis. This review will discuss the clinical implications of del(7q) and CUX1 mutations, both in disease and clonal hematopoiesis, and synthesize recent literature on CUX1 and other chromosome 7 TSGs. RECENT FINDINGS Two major studies, including a new mouse model, have been published that support a role for CUX1 inactivation in the development of myeloid neoplasms. Additional recent studies describe the cellular and hematopoietic effects from loss of the 7q genes LUC7L2 and KMT2C/MLL3, and the implications of chromosome 7 deletions in clonal hematopoiesis. SUMMARY Mounting evidence supports CUX1 as being a key chromosome 7 TSG. As 7q encodes additional myeloid regulators and tumor suppressors, improved models of chromosome loss are needed to interrogate combinatorial loss of these critical 7q genes.
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Affiliation(s)
| | - Megan E McNerney
- Department of Pathology
- Department of Pediatrics, Section of Hematology/Oncology
- The University of Chicago Medicine Comprehensive Cancer Center, The University of Chicago, Chicago, Illinois, USA
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26
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The spectrum of sex differences in cancer. Trends Cancer 2022; 8:303-315. [PMID: 35190302 PMCID: PMC8930612 DOI: 10.1016/j.trecan.2022.01.013] [Citation(s) in RCA: 46] [Impact Index Per Article: 23.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Revised: 01/08/2022] [Accepted: 01/20/2022] [Indexed: 02/07/2023]
Abstract
Sex differences in cellular and systems biology have been evolutionarily selected to optimize reproductive success in all species with little (sperm) and big (ova) gamete producers. They are evident from the time of fertilization and accrue throughout development through genetic, epigenetic, and circulating sex hormone-dependent mechanisms. Among other effects, they significantly impact on chromatin organization, metabolism, cell cycle regulation, immunity, longevity, and cancer risk and survival. Sex differences in cancer should be expected and accounted for in basic, translational, and clinical oncology research.
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27
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Katsuda T, Sato N, Mogushi K, Hase T, Muramatsu M. Sub-GOFA: A tool for Sub-Gene Ontology function analysis in clonal mosaicism using semantic (logical) similarity. Bioinformation 2022; 18:53-60. [PMID: 35815201 PMCID: PMC9200605 DOI: 10.6026/97320630018053] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/10/2021] [Accepted: 12/16/2021] [Indexed: 11/23/2022] Open
Abstract
Clonal mosaicism (a detectable post-zygotic mutational event in cellular subpopulations) is common in cancer patients. Detected segments of clonal mosaicism are usually bundled into large-locus regions for statistical analysis. However, low-frequency genes are overlooked and are not sufficient to elucidate qualitative differences between cancer patients and non-patients. Therefore, it is of interest to develop and describe a tool named Sub-GOFA for Sub-Gene Ontology function analysis in clonal mosaicism using semantic similarity. Sub-GOFA measures the semantic (logical) similarity among patients using the sub-GO network structures of various sizes segmented from the gene ontology (GO) for clustering analysis. The sub-GO's root-terms with significant differences are extracted as disease-associated genetic functions. Sub-GOFA selected a high ratio of cancer-associated genes under validation with acceptable threshold.
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Affiliation(s)
- Tadaaki Katsuda
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 24F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Noriko Sato
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 24F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
| | - Kaoru Mogushi
- Institute of Education, Tokyo Medical and Dental University, 20F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
| | - Takeshi Hase
- Institute of Education, Tokyo Medical and Dental University, 20F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
- Faculty of Pharmacy, Keio University, 1-5-30 Shibakoen, Minato-ku, Tokyo, 105-8512, Japan
- The Systems Biology Institute, SaiseiIkedayama Bldg. 5-10-25 Higashi Gotanda Shinagawa, Tokyo, 141-0022, Japan
- SBX BioSciences, Inc, 1600 - 925 West Georgia Street, Vancouver, BC V6C 3L2, Canada
| | - Masaaki Muramatsu
- Department of Molecular Epidemiology, Medical Research Institute, Tokyo Medical and Dental University, 24F, M&D Tower, 1-5-45 Yushima, Bunkyo-ku, Tokyo, 113-8510, Japan
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28
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Hong W, Li A, Liu Y, Xiao X, Christiani DC, Hung RJ, McKay J, Field J, Amos CI, Cheng C. Clonal Hematopoiesis Mutations in Patients with Lung Cancer Are Associated with Lung Cancer Risk Factors. Cancer Res 2022; 82:199-209. [PMID: 34815255 PMCID: PMC8815061 DOI: 10.1158/0008-5472.can-21-1903] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/23/2021] [Accepted: 11/15/2021] [Indexed: 01/12/2023]
Abstract
Clonal hematopoiesis (CH) is a phenomenon caused by expansion of white blood cells descended from a single hematopoietic stem cell. While CH can be associated with leukemia and some solid tumors, the relationship between CH and lung cancer remains largely unknown. To help clarify this relationship, we analyzed whole-exome sequencing (WES) data from 1,958 lung cancer cases and controls. Potential CH mutations were identified by a set of hierarchical filtering criteria in different exonic regions, and the associations between the number of CH mutations and clinical traits were investigated. Family history of lung cancer (FHLC) may exert diverse influences on the accumulation of CH mutations in different age groups. In younger subjects, FHLC was the strongest risk factor for CH mutations. Association analysis of genome-wide genetic variants identified dozens of genetic loci associated with CH mutations, including a candidate SNP rs2298110, which may promote CH by increasing expression of a potential leukemia promoter gene OTUD3. Hundreds of potentially novel CH mutations were identified, and smoking was found to potentially shape the CH mutational signature. Genetic variants and lung cancer risk factors, especially FHLC, correlated with CH. These analyses improve our understanding of the relationship between lung cancer and CH, and future experimental studies will be necessary to corroborate the uncovered correlations. SIGNIFICANCE: Analysis of whole-exome sequencing data uncovers correlations between clonal hematopoiesis and lung cancer risk factors, identifies genetic variants correlated with clonal hematopoiesis, and highlights hundreds of potential novel clonal hematopoiesis mutations.
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Affiliation(s)
- Wei Hong
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Ang Li
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Yanhong Liu
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Department of Medicine, Baylor College of Medicine, Houston, Texas
| | | | - Rayjean J Hung
- Mount Sinai Hospital Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - James McKay
- World Health Organization International Agency for Research on Cancer, Lyon CEDEX, France
| | - John Field
- Institute of Systems, Molecular and Integrative Biology, University of Liverpool, Liverpool, United Kingdom
| | | | - Chao Cheng
- Department of Medicine, Baylor College of Medicine, Houston, Texas.
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29
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Liu L, Chen H, Sun C, Zhang J, Wang J, Du M, Li J, Di L, Shen J, Geng S, Pang Y, Luo Y, Wu C, Fu Y, Zheng Z, Wang J, Huang Y. Low-frequency somatic copy number alterations in normal human lymphocytes revealed by large-scale single-cell whole-genome profiling. Genome Res 2021; 32:44-54. [PMID: 34963662 PMCID: PMC8744674 DOI: 10.1101/gr.275453.121] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 11/15/2021] [Indexed: 11/29/2022]
Abstract
Genomic-scale somatic copy number alterations in healthy humans are difficult to investigate because of low occurrence rates and the structural variations’ stochastic natures. Using a Tn5-transposase-assisted single-cell whole-genome sequencing method, we sequenced over 20,000 single lymphocytes from 16 individuals. Then, with the scale increased to a few thousand single cells per individual, we found that about 7.5% of the cells had large-size copy number alterations. Trisomy 21 was the most prevalent aneuploid event among all autosomal copy number alterations, whereas monosomy X occurred most frequently in over-30-yr-old females. In the monosomy X single cells from individuals with phased genomes and identified X-inactivation ratios in bulk, the inactive X Chromosomes were lost more often than the active ones.
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30
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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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31
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Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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32
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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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33
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Wang Y, Zhou W, McReynolds LJ, Katki HA, Griffiths EA, Thota S, Machiela MJ, Yeager M, McCarthy P, Pasquini M, Wang J, Karaesmen E, Rizvi A, Preus L, Tang H, Wang Y, Pooler L, Sheng X, Haiman CA, Van Den Berg D, Spellman SR, Wang T, Kuxhausen M, Chanock SJ, Lee SJ, Hahn TE, Sucheston-Campbell LE, Gadalla SM. Prognostic impact of pre-transplant chromosomal aberrations in peripheral blood of patients undergoing unrelated donor hematopoietic cell transplant for acute myeloid leukemia. Sci Rep 2021; 11:15004. [PMID: 34294836 PMCID: PMC8298542 DOI: 10.1038/s41598-021-94539-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 06/30/2021] [Indexed: 11/24/2022] Open
Abstract
To improve risk stratification and treatment decisions for patients with acute myeloid leukemia (AML) undergoing hematopoietic cell transplantation (HCT). We used SNP-array data from the DISCOVeRY-BMT study to detect chromosomal aberrations in pre-HCT peripheral blood (collected 2–4 weeks before the administration of conditioning regimen) from 1974 AML patients who received HCT between 2000 and 2011. All aberrations detected in ≥ 10 patients were tested for their association with overall survival (OS), separately by remission status, using the Kaplan–Meier estimator. Cox regression models were used for multivariable analyses. Follow-up was through January 2019. We identified 701 unique chromosomal aberrations in 285 patients (7% of 1438 in complete remission (CR) and 36% of 536 not in CR). Copy-neutral loss-of-heterozygosity (CNLOH) in chr17p in CR patients (3-year OS = 20% vs. 50%, with and without chr17p CNLOH, p = 0.0002), and chr13q in patients not in CR (3-year OS = 4% vs. 26%, with and without chr13q CNLOH, p < 0.0001) are risk factors for poor survival. Models adjusted for clinical factors showed approximately three-fold excess risk of post-HCT mortality with chr17p CNLOH in CR patients (hazard ratio, HR = 3.39, 95% confidence interval CI 1.74–6.60, p = 0.0003), or chr13q CNLOH in patients not in CR (HR = 2.68, 95% CI 1.75–4.09, p < 0.0001). The observed mortality was mostly driven by post-HCT relapse (HR = 2.47, 95% CI 1.01–6.02, p = 0.047 for chr17p CNLOH in CR patients, and HR = 2.58, 95% CI 1.63–4.08, p < 0.0001 for chr13q CNLOH in patients not in CR. Pre-transplant CNLOH in chr13q or chr17p predicts risk of poor outcomes after unrelated donor HCT in AML patients. A large prospective study is warranted to validate the results and evaluate novel strategies to improve survival in those patients.
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Affiliation(s)
- Youjin Wang
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Weiyin Zhou
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Lisa J McReynolds
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Hormuzd A Katki
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | | | - Swapna Thota
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Mitchell J Machiela
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Meredith Yeager
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Philip McCarthy
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | - Marcelo Pasquini
- Department of Medicine, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Junke Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Ezgi Karaesmen
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Abbas Rizvi
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Leah Preus
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Hancong Tang
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Yiwen Wang
- College of Pharmacy, The Ohio State University, Columbus, OH, USA
| | - Loreall Pooler
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Xin Sheng
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Christopher A Haiman
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - David Van Den Berg
- Department of Preventive Medicine, University of Southern California, Los Angeles, CA, USA
| | - Stephen R Spellman
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Tao Wang
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, USA.,Division of Biostatistics, Medical College of Wisconsin, Milwaukee, WI, USA
| | - Michelle Kuxhausen
- Center for International Blood and Marrow Transplant Research, Minneapolis, MN, USA
| | - Stephen J Chanock
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA
| | - Stephanie J Lee
- Center for International Blood and Marrow Transplant Research, Medical College of Wisconsin, Milwaukee, WI, USA.,Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Theresa E Hahn
- Department of Medicine, Roswell Park Comprehensive Cancer Center, Buffalo, NY, USA
| | | | - Shahinaz M Gadalla
- Clinical Genetics Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, 9609 Medical Center Dr., Rockville, MD, 20850, USA.
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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: 21] [Impact Index Per Article: 7.0] [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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35
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Zekavat SM, Lin SH, Bick AG, Liu A, Paruchuri K, Wang C, Uddin MM, Ye Y, Yu Z, Liu X, Kamatani Y, Bhattacharya R, Pirruccello JP, Pampana A, Loh PR, Kohli P, McCarroll SA, Kiryluk K, Neale B, Ionita-Laza I, Engels EA, Brown DW, Smoller JW, Green R, Karlson EW, Lebo M, Ellinor PT, Weiss ST, Daly MJ, Terao C, Zhao H, Ebert BL, Reilly MP, Ganna A, Machiela MJ, Genovese G, Natarajan P. Hematopoietic mosaic chromosomal alterations increase the risk for diverse types of infection. Nat Med 2021; 27:1012-1024. [PMID: 34099924 PMCID: PMC8245201 DOI: 10.1038/s41591-021-01371-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 04/23/2021] [Indexed: 12/13/2022]
Abstract
Age is the dominant risk factor for infectious diseases, but the mechanisms linking age to infectious disease risk are incompletely understood. Age-related mosaic chromosomal alterations (mCAs) detected from genotyping of blood-derived DNA, are structural somatic variants indicative of clonal hematopoiesis, and are associated with aberrant leukocyte cell counts, hematological malignancy, and mortality. Here, we show that mCAs predispose to diverse types of infections. We analyzed mCAs from 768,762 individuals without hematological cancer at the time of DNA acquisition across five biobanks. Expanded autosomal mCAs were associated with diverse incident infections (hazard ratio (HR) 1.25; 95% confidence interval (CI) = 1.15-1.36; P = 1.8 × 10-7), including sepsis (HR 2.68; 95% CI = 2.25-3.19; P = 3.1 × 10-28), pneumonia (HR 1.76; 95% CI = 1.53-2.03; P = 2.3 × 10-15), digestive system infections (HR 1.51; 95% CI = 1.32-1.73; P = 2.2 × 10-9) and genitourinary infections (HR 1.25; 95% CI = 1.11-1.41; P = 3.7 × 10-4). A genome-wide association study of expanded mCAs identified 63 loci, which were enriched at transcriptional regulatory sites for immune cells. These results suggest that mCAs are a marker of impaired immunity and confer increased predisposition to infections.
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Affiliation(s)
- Seyedeh M Zekavat
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Shu-Hong Lin
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Alexander G Bick
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Aoxing Liu
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Kaavya Paruchuri
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Chen Wang
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York City, NY, USA
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Md Mesbah Uddin
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Yixuan Ye
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Zhaolong Yu
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Romit Bhattacharya
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - James P Pirruccello
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Akhil Pampana
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Po-Ru Loh
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Puja Kohli
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Vertex Pharmaceuticals, Boston, MA, USA
| | - Steven A McCarroll
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Krzysztof Kiryluk
- Division of Nephrology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
- Irving Institute for Clinical and Translational Research, Columbia University, New York City, NY, USA
| | - Benjamin Neale
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Iuliana Ionita-Laza
- Department of Biostatistics, Mailman School of Public Health, Columbia University, New York City, NY, USA
| | - Eric A Engels
- Infections and Immunoepidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Derek W Brown
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jordan W Smoller
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Department of Psychiatry, Harvard Medical School, Boston, MA, USA
| | - Robert Green
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Elizabeth W Karlson
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women's Hospital, Boston, MA, USA
| | - Matthew Lebo
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Laboratory for Molecular Medicine, Partners Healthcare, Cambridge, MA, USA
| | - Patrick T Ellinor
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hongyu Zhao
- Computational Biology and Bioinformatics Program, Yale University, New Haven, CT, USA
- Department of Biostatistics, Yale School of Public Health, New Haven, CT, USA
| | - Benjamin L Ebert
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | - Muredach P Reilly
- Irving Institute for Clinical and Translational Research, Columbia University, New York City, NY, USA
- Division of Cardiology, Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York City, NY, USA
| | - Andrea Ganna
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Mitchell J Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Giulio Genovese
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Pradeep Natarajan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
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36
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Pre-HCT mosaicism increases relapse risk and lowers survival in acute lymphoblastic leukemia patients post-unrelated HCT. Blood Adv 2021; 5:66-70. [PMID: 33570634 DOI: 10.1182/bloodadvances.2020003366] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 11/13/2020] [Indexed: 12/11/2022] Open
Abstract
Key Points
Pre-HCT mosaicism is related to increased relapse risk and lower survival after unrelated HCT, independent of cytogenetics at diagnosis. Pre-HCT mosaicism could be a useful clinical tool to guide risk stratification in acute lymphoblastic leukemia patients.
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37
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Glessner JT, Chang X, Liu Y, Li J, Khan M, Wei Z, Sleiman PMA, Hakonarson H. MONTAGE: a new tool for high-throughput detection of mosaic copy number variation. BMC Genomics 2021; 22:133. [PMID: 33627065 PMCID: PMC7905641 DOI: 10.1186/s12864-021-07395-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 01/19/2021] [Indexed: 01/21/2023] Open
Abstract
Background Not all cells in a given individual are identical in their genomic makeup. Mosaicism describes such a phenomenon where a mixture of genotypic states in certain genomic segments exists within the same individual. Mosaicism is a prevalent and impactful class of non-integer state copy number variation (CNV). Mosaicism implies that certain cell types or subset of cells contain a CNV in a segment of the genome while other cells in the same individual do not. Several studies have investigated the impact of mosaicism in single patients or small cohorts but no comprehensive scan of mosaic CNVs has been undertaken to accurately detect such variants and interpret their impact on human health and disease. Results We developed a tool called Montage to improve the accuracy of detection of mosaic copy number variants in a high throughput fashion. Montage directly interfaces with ParseCNV2 algorithm to establish disease phenotype genome-wide association and determine which genomic ranges had more or less than expected frequency of mosaic events. We screened for mosaic events in over 350,000 samples using 1% allele frequency as the detection limit. Additionally, we uncovered disease associations of multiple phenotypes with mosaic CNVs at several genomic loci. We additionally investigated the allele imbalance observations genome-wide to define non-diploid and non-integer copy number states. Conclusions Our novel algorithm presents an efficient tool with fast computational runtime and high levels of accuracy of mosaic CNV detection. A curated mosaic CNV callset of 3716 events in 2269 samples is presented with comparability to previous reports and disease phenotype associations. The new algorithm can be freely accessed via: https://github.com/CAG-CNV/MONTAGE. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-07395-7.
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Affiliation(s)
- Joseph T Glessner
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA.
| | - Xiao Chang
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Yichuan Liu
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Jin Li
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Munir Khan
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Zhi Wei
- New Jersey Institute of Technology, Newark, NJ, 07102, USA
| | - Patrick M A Sleiman
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Department of Pediatrics, Children's Hospital of Philadelphia, 3401 Civic Center Blvd, Philadelphia, PA, 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, 3400 Civic Center Blvd, Philadelphia, PA, 19104, USA
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38
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Amico S, Smith P, Tobi S, Perry M, Wallace A, Evans DG. Neurofibromatosis type 2 discordance in monozygous twins. Fam Cancer 2021; 19:37-40. [PMID: 31965447 DOI: 10.1007/s10689-019-00148-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Neurofibromatosis type 2 (NF2) is an autosomal dominant condition caused by pathogenic variants in the NF2 gene. The pathogenic variant is either inherited or obtained by de novo mutation, characterised by the presence of schwannomas, meningiomas and ependymomas. Here we report the presence of NF2 in one twin, with bilateral vestibular schwannomas and a pathogenic variant of the NF2 gene identified in both tumour and lymphocytes, while his monozygous brother remains asymptomatic. Imaging of the unaffected twin showed no tumour load and genetic testing via Sanger sequencing and Amplification Refractory Mutation System assay demonstrated low levels of expression of the NF2 variant in lymphocytes. Further testing on non-haemopoietic tissue showed little expression or absence of the pathogenic variant. Given there is no family history and the low level of the variant, we assume the pathogenic variant is a de novo mutation during embryogenesis. De novo mutations have been described as occurring at three possible time points in the creation of monozygous twins with different genetic make-up; prior to the twinning event, as a cause of the event, or after the twinning event. Of these options, we hypothesise that the discordance in the expression of the NF2 variant between these twins is likely due to a mutational event that occurred as a result of either of the latter two possibilities, between which we cannot determine. The pathogenic variant in lymphocytes was likely transferred between the twins through a shared blood supply in utero, and the non-haemopoietic samples that showed low levels of expression, were likely due to the presence of lymphocytic cells. Therefore, we have a discordance between monozygous twins at the NF2 gene.
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Affiliation(s)
- S Amico
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK.
| | - P Smith
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - S Tobi
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - M Perry
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - A Wallace
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
| | - D G Evans
- Division of Evolution and Genomic Science, Department of Genomic Medicine, St Mary's Hospital, Manchester Academic Health Sciences Centre (MAHSC), University of Manchester, Manchester University Hospital Foundation Trust, Manchester, UK
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39
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Detectable chromosome X mosaicism in males is rarely tolerated in peripheral leukocytes. Sci Rep 2021; 11:1193. [PMID: 33441948 PMCID: PMC7806852 DOI: 10.1038/s41598-020-80948-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Accepted: 12/30/2020] [Indexed: 12/23/2022] Open
Abstract
Age-related male Y and female X chromosome mosaicism is commonly observed in large population-based studies. To investigate the frequency of male X chromosome mosaicism, we scanned for deviations in chromosome X genotyping array intensity data in a population-based survey of 196,219 UK Biobank men. We detected 12 (0.006%) men with mosaic chromosome X gains ≥ 2 Mb and found no evidence for mosaic chromosome X loss, a level of detection substantially lower than for autosomes or other sex chromosomes. The rarity of chromosome X mosaicism in males relative to females reflects the importance of chromosome X gene dosage for leukocyte function.
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40
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Gao T, Ptashkin R, Bolton KL, Sirenko M, Fong C, Spitzer B, Menghrajani K, Ossa JEA, Zhou Y, Bernard E, Levine M, Martinez JSM, Zhang Y, Franch-Expósito S, Patel M, Braunstein LZ, Kelly D, Yabe M, Benayed R, Caltabellotta NM, Philip J, Paraiso E, Mantha S, Solit DB, Diaz LA, Berger MF, Klimek V, Levine RL, Zehir A, Devlin SM, Papaemmanuil E. Interplay between chromosomal alterations and gene mutations shapes the evolutionary trajectory of clonal hematopoiesis. Nat Commun 2021; 12:338. [PMID: 33436578 PMCID: PMC7804935 DOI: 10.1038/s41467-020-20565-7] [Citation(s) in RCA: 60] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 12/01/2020] [Indexed: 01/03/2023] Open
Abstract
Stably acquired mutations in hematopoietic cells represent substrates of selection that may lead to clonal hematopoiesis (CH), a common state in cancer patients that is associated with a heightened risk of leukemia development. Owing to technical and sample size limitations, most CH studies have characterized gene mutations or mosaic chromosomal alterations (mCAs) individually. Here we leverage peripheral blood sequencing data from 32,442 cancer patients to jointly characterize gene mutations (n = 14,789) and mCAs (n = 383) in CH. Recurrent composite genotypes resembling known genetic interactions in leukemia genomes underlie 23% of all detected autosomal alterations, indicating that these selection mechanisms are operative early in clonal evolution. CH with composite genotypes defines a patient group at high risk of leukemia progression (3-year cumulative incidence 14.6%, CI: 7-22%). Multivariable analysis identifies mCA as an independent risk factor for leukemia development (HR = 14, 95% CI: 6-33, P < 0.001). Our results suggest that mCA should be considered in conjunction with gene mutations in the surveillance of patients at risk of hematologic neoplasms.
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Affiliation(s)
- Teng Gao
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ryan Ptashkin
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Kelly L Bolton
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Maria Sirenko
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Christopher Fong
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Barbara Spitzer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Kamal Menghrajani
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Juan E Arango Ossa
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Yangyu Zhou
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Elsa Bernard
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Max Levine
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Juan S Medina Martinez
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Yanming Zhang
- Department of Pathology, Cytogenetics Laboratory, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Sebastià Franch-Expósito
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Minal Patel
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Lior Z Braunstein
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Daniel Kelly
- Department of Information Systems, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Mariko Yabe
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ryma Benayed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Nicole M Caltabellotta
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - John Philip
- Department of Health Informatics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ederlinda Paraiso
- Center for Strategy & Innovation, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Simon Mantha
- Department of Medicine, Hematology Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - David B Solit
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Medicine, Solid Tumor Division, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Luis A Diaz
- Department of Medicine, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Program in Precision Interception and Prevention, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Michael F Berger
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Virginia Klimek
- Department of Medicine, Hematology Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Weill Cornell Medical College, 407 E 61st St, New York, NY, 10065, USA
| | - Ross L Levine
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Department of Medicine, Leukemia Service, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
- Program in Precision Interception and Prevention, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Ahmet Zehir
- Department of Pathology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Sean M Devlin
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA
| | - Elli Papaemmanuil
- Computational Oncology Service, Department of Epidemiology & Biostatistics, Center for Computational Oncology, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
- Center for Hematologic Malignancies, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
- Department of Epidemiology & Biostatistics, Memorial Sloan Kettering Cancer Center, 1275 York Ave, New York, NY, 10065, USA.
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41
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Bazyka D, Hatch M, Gudzenko N, Cahoon EK, Drozdovitch V, Little MP, Chumak V, Bakhanova E, Belyi D, Kryuchkov V, Golovanov I, Mabuchi K, Illienko I, Belayev Y, Bodelon C, Machiela MJ, Hutchinson A, Yeager M, Berrington de González A, Chanock SJ. Field Study of the Possible Effect of Parental Irradiation on the Germline of Children Born to Cleanup Workers and Evacuees of the Chornobyl Nuclear Accident. Am J Epidemiol 2020; 189:1451-1460. [PMID: 32613232 DOI: 10.1093/aje/kwaa095] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Revised: 05/26/2020] [Accepted: 05/27/2020] [Indexed: 01/01/2023] Open
Abstract
Although transgenerational effects of exposure to ionizing radiation have long been a concern, human research to date has been confined to studies of disease phenotypes in groups exposed to high doses and high dose rates, such as the Japanese atomic bomb survivors. Transgenerational effects of parental irradiation can be addressed using powerful new genomic technologies. In collaboration with the Ukrainian National Research Center for Radiation Medicine, the US National Cancer Institute, in 2014-2018, initiated a genomic alterations study among children born in selected regions of Ukraine to cleanup workers and/or evacuees exposed to low-dose-rate radiation after the 1986 Chornobyl (Chernobyl) nuclear accident. To investigate whether parental radiation exposure is associated with germline mutations and genomic alterations in the offspring, we are collecting biospecimens from father-mother-offspring constellations to study de novo mutations, minisatellite mutations, copy-number changes, structural variants, genomic insertions and deletions, methylation profiles, and telomere length. Genomic alterations are being examined in relation to parental gonadal dose, reconstructed using questionnaire and measurement data. Subjects are being recruited in exposure categories that will allow examination of parental origin, duration, and timing of exposure in relation to conception. Here we describe the study methodology and recruitment results and provide descriptive information on the first 150 families (mother-father-child(ren)) enrolled.
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42
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Zekavat SM, Lin SH, Bick AG, Liu A, Paruchuri K, Uddin MM, Ye Y, Yu Z, Liu X, Kamatani Y, Pirruccello JP, Pampana A, Loh PR, Kohli P, McCarroll SA, Neale B, Engels EA, Brown DW, Smoller JW, Green R, Karlson EW, Lebo M, Ellinor PT, Weiss ST, Daly MJ, Terao C, Zhao H, Ebert BL, Ganna A, Machiela MJ, Genovese G, Natarajan P. Hematopoietic mosaic chromosomal alterations and risk for infection among 767,891 individuals without blood cancer. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.11.12.20230821. [PMID: 33236019 PMCID: PMC7685330 DOI: 10.1101/2020.11.12.20230821] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Age is the dominant risk factor for infectious diseases, but the mechanisms linking the two are incompletely understood1,2. Age-related mosaic chromosomal alterations (mCAs) detected from blood-derived DNA genotyping, are structural somatic variants associated with aberrant leukocyte cell counts, hematological malignancy, and mortality3-11. Whether mCAs represent independent risk factors for infection is unknown. Here we use genome-wide genotyping of blood DNA to show that mCAs predispose to diverse infectious diseases. We analyzed mCAs from 767,891 individuals without hematological cancer at DNA acquisition across four countries. Expanded mCA (cell fraction >10%) prevalence approached 4% by 60 years of age and was associated with diverse incident infections, including sepsis, pneumonia, and coronavirus disease 2019 (COVID-19) hospitalization. A genome-wide association study of expanded mCAs identified 63 significant loci. Germline genetic alleles associated with expanded mCAs were enriched at transcriptional regulatory sites for immune cells. Our results link mCAs with impaired immunity and predisposition to infections. Furthermore, these findings may also have important implications for the ongoing COVID-19 pandemic, particularly in prioritizing individual preventive strategies and evaluating immunization responses.
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Affiliation(s)
- Seyedeh M. Zekavat
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Alexander G. Bick
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center
| | - Aoxing Liu
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Kaavya Paruchuri
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Md Mesbah Uddin
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Yixuan Ye
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT
| | - Zhaolong Yu
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
| | - James P. Pirruccello
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Akhil Pampana
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
| | - Po-Ru Loh
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Puja Kohli
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital, Boston, MA
- Vertex Pharmaceuticals, Boston, MA
| | - Steven A. McCarroll
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Genetics, Harvard Medical School, Boston, MA
| | - Benjamin Neale
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Eric A. Engels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Derek W. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Jordan W. Smoller
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA
- Department of Psychiatry, Harvard Medical School, Boston, MA
| | - Robert Green
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Department of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
| | - Elizabeth W. Karlson
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Division of Rheumatology, Inflammation and Immunity, Brigham and Women’s Hospital, Boston, MA
| | - Matthew Lebo
- Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Laboratory for Molecular Medicine, Partners Healthcare, Cambridge, MA
| | - Patrick T. Ellinor
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
| | - Scott T. Weiss
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
- Channing Division of Network Medicine, Brigham and Women’s Hospital, Boston, MA
| | - Mark J. Daly
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | | | | | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, RIKEN, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Hongyu Zhao
- Computational Biology & Bioinformatics Program, Yale University, New Haven, CT
- Department of Biostatistics, Yale School of Public Health, New Haven, CT
| | - Benjamin L. Ebert
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
| | | | - Andrea Ganna
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Institute for Molecular Medicine Finland, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD
| | - Giulio Genovese
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Department of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA
| | - Pradeep Natarajan
- Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA
- Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, MA
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43
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Natarajan P, Zekavat S, Lin SH, Bick A, Liu A, Paruchuri K, Uddin MM, Ye Y, Yu Z, Liu X, Kamatani Y, Pirruccello J, Pampana A, Loh PR, Kohli P, McCarroll S, Neale B, Engels E, Brown D, Smoller J, Green R, Karlson E, Lebo M, Ellinor P, Weiss S, Daly M, Terao C, Zhao H, Ebert B, Machiela M, Genovese G. Hematopoietic mosaic chromosomal alterations and risk for infection among 767,891 individuals without blood cancer. RESEARCH SQUARE 2020. [PMID: 33236004 PMCID: PMC7685327 DOI: 10.21203/rs.3.rs-100817/v1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Age is the dominant risk factor for infectious diseases, but the mechanisms linking the two are incompletely understood1,2. Age-related mosaic chromosomal alterations (mCAs) detected from blood-derived DNA genotyping, are structural somatic variants associated with aberrant leukocyte cell counts, hematological malignancy, and mortality3-11. Whether mCAs represent independent risk factors for infection is unknown. Here we use genome-wide genotyping of blood DNA to show that mCAs predispose to diverse infectious diseases. We analyzed mCAs from 767,891 individuals without hematological cancer at DNA acquisition across four countries. Expanded mCA (cell fraction >10%) prevalence approached 4% by 60 years of age and was associated with diverse incident infections, including sepsis, pneumonia, and coronavirus disease 2019 (COVID-19) hospitalization. A genome-wide association study of expanded mCAs identified 63 significant loci. Germline genetic alleles associated with expanded mCAs were enriched at transcriptional regulatory sites for immune cells. Our results link mCAs with impaired immunity and predisposition to infections. Furthermore, these findings may also have important implications for the ongoing COVID-19 pandemic, particularly in prioritizing individual preventive strategies and evaluating immunization responses.
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44
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Brown DW, Lin SH, Loh PR, Chanock SJ, Savage SA, Machiela MJ. Genetically predicted telomere length is associated with clonal somatic copy number alterations in peripheral leukocytes. PLoS Genet 2020; 16:e1009078. [PMID: 33090998 PMCID: PMC7608979 DOI: 10.1371/journal.pgen.1009078] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Revised: 11/03/2020] [Accepted: 08/24/2020] [Indexed: 12/15/2022] Open
Abstract
Telomeres are DNA-protein structures at the ends of chromosomes essential in maintaining chromosomal stability. Observational studies have identified associations between telomeres and elevated cancer risk, including hematologic malignancies; but biologic mechanisms relating telomere length to cancer etiology remain unclear. Our study sought to better understand the relationship between telomere length and cancer risk by evaluating genetically-predicted telomere length (gTL) in relation to the presence of clonal somatic copy number alterations (SCNAs) in peripheral blood leukocytes. Genotyping array data were acquired from 431,507 participants in the UK Biobank and used to detect SCNAs from intensity information and infer telomere length using a polygenic risk score (PRS) of variants previously associated with leukocyte telomere length. In total, 15,236 (3.5%) of individuals had a detectable clonal SCNA on an autosomal chromosome. Overall, higher gTL value was positively associated with the presence of an autosomal SCNA (OR = 1.07, 95% CI = 1.05–1.09, P = 1.61×10−15). There was high consistency in effect estimates across strata of chromosomal event location (e.g., telomeric ends, interstitial or whole chromosome event; Phet = 0.37) and strata of copy number state (e.g., gain, loss, or neutral events; Phet = 0.05). Higher gTL value was associated with a greater cellular fraction of clones carrying autosomal SCNAs (β = 0.004, 95% CI = 0.002–0.007, P = 6.61×10−4). Our population-based examination of gTL and SCNAs suggests inherited components of telomere length do not preferentially impact autosomal SCNA event location or copy number status, but rather likely influence cellular replicative potential. Telomeres lie at the ends of chromosomes and protect from damage and chromosomal fusions. Recent studies have identified relationships between telomere length and cancer risk; however, exactly how telomere length impacts cancer risk is unknown. We investigated potential associations between telomere length and somatic copy number alterations (SCNAs), as SCNAs are associated with cancer risk and may be responsible for some of the observed association between telomere length and cancer. We analyzed blood-derived DNA from over 430,000 participants in a large UK based study and identified an association between elevated telomere length (as inferred from genetic variants) and increased frequency of SCNAs. We did not find any difference in the relationship between telomere length and SCNAs based on specific regions of chromosomes impacted or whether chromosomes were lost or gained. However, we did note that longer predicted telomere length is associated with higher proportions of cells containing a SCNA. Although further studies are needed, our results provide new evidence indicating SCNAs may be a potential mechanism by which telomere length could impact cancer risk.
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Affiliation(s)
- Derek W. Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
- Cancer Prevention Fellowship Program, Division of Cancer Prevention, National Cancer Institute, Rockville, MD, United States of America
- * E-mail:
| | - Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, United States of America
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, United States of America
| | - Stephen J. Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
| | - Sharon A. Savage
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
| | - Mitchell J. Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, United States of America
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45
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Jaiswal S. Clonal hematopoiesis and nonhematologic disorders. Blood 2020; 136:1606-1614. [PMID: 32736379 PMCID: PMC8209629 DOI: 10.1182/blood.2019000989] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/01/2020] [Indexed: 12/18/2022] Open
Abstract
Clonal expansions of mutated hematopoietic cells, termed clonal hematopoiesis, are common in aging humans. One expected consequence of mutation-associated clonal hematopoiesis is an increased risk of hematologic cancers, which has now been shown in several studies. However, the hematopoietic stem cells that acquire these somatic mutations also give rise to mutated immune effector cells, such as monocytes, granulocytes, and lymphocytes. These effector cells can potentially influence many disease states, especially those with a chronic inflammatory component. Indeed, several studies have now shown that clonal hematopoiesis associates with increased risk of atherosclerotic cardiovascular disease. Emerging data also associate clonal hematopoiesis with other nonhematologic diseases. Here, we will review recent studies linking clonal hematopoiesis to altered immune function, inflammation, and nonmalignant diseases of aging.
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Affiliation(s)
- Siddhartha Jaiswal
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, and Program in Immunology, School of Medicine, Stanford University, Stanford, CA
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46
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Abstract
Mosaicism refers to the occurrence of two or more genomes in an individual derived from a single zygote. Germline mosaicism is a mutation that is limited to the gonads and can be transmitted to offspring. Somatic mosaicism is a postzygotic mutation that occurs in the soma, and it may occur at any developmental stage or in adult tissues. Mosaic variation may be classified in six ways: (a) germline or somatic origin, (b) class of DNA mutation (ranging in scale from single base pairs to multiple chromosomes), (c) developmental context, (d) body location(s), (e) functional consequence (including deleterious, neutral, or advantageous), and (f) additional sources of mosaicism, including mitochondrial heteroplasmy, exogenous DNA sources such as vectors, and epigenetic changes such as imprinting and X-chromosome inactivation. Technological advances, including single-cell and other next-generation sequencing, have facilitated improved sensitivity and specificity to detect mosaicism in a variety of biological contexts.
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Affiliation(s)
- Jeremy Thorpe
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA;
| | - Ikeoluwa A Osei-Owusu
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA;
| | | | - Rossella Tupler
- Department of Molecular, Cell and Cancer Biology, University of Massachusetts Medical School, Worcester, Massachusetts 01605, USA.,Department of Biomedical, Metabolic, and Neural Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy;
| | - Jonathan Pevsner
- Department of Neurology, Kennedy Krieger Institute, Baltimore, Maryland 21205, USA; , .,Program in Biochemistry, Cellular, and Molecular Biology, Johns Hopkins School of Medicine, Baltimore, Maryland 21287, USA; .,Program in Human Genetics, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA; .,Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, Maryland 21205, USA
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47
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Tuke M, Tyrrell J, Ruth KS, Beaumont RN, Wood AR, Murray A, Frayling TM, Weedon MN, Wright CF. Large Copy-Number Variants in UK Biobank Caused by Clonal Hematopoiesis May Confound Penetrance Estimates. Am J Hum Genet 2020; 107:325-329. [PMID: 32574563 DOI: 10.1016/j.ajhg.2020.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Accepted: 06/02/2020] [Indexed: 12/20/2022] Open
Abstract
Large copy-number variants (CNVs) are strongly associated with both developmental delay and cancer, but the type of disease depends strongly on when and where the mutation occurred, i.e., germline versus somatic. We used microarray data from UK Biobank to investigate the prevalence and penetrance of large autosomal CNVs and chromosomal aneuploidies using a standard CNV detection algorithm not designed for detecting mosaic variants. We found 160 individuals that carry >10 Mb copy number changes, including 56 with whole chromosome aneuploidies. Nineteen (12%) individuals had a diagnosis of Down syndrome or other developmental disorder, while 84 (52.5%) individuals had a diagnosis of hematological malignancies or chronic myeloproliferative disorders. Notably, there was no evidence of mosaicism in the blood for many of these large CNVs, so they could easily be mistaken for germline alleles even when caused by somatic mutations. We therefore suggest that somatic mutations associated with blood cancers may result in false estimates of rare variant penetrance from population biobanks.
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Affiliation(s)
- Marcus Tuke
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Jessica Tyrrell
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Katherine S Ruth
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Robin N Beaumont
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Andrew R Wood
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Anna Murray
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Timothy M Frayling
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Michael N Weedon
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK
| | - Caroline F Wright
- Institute of Biomedical and Clinical Science, University of Exeter Medical School, RILD Building, Royal Devon & Exeter Hospital, Barrack Road, Exeter EX2 5DW, UK.
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48
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Loh PR, Genovese G, McCarroll SA. Monogenic and polygenic inheritance become instruments for clonal selection. Nature 2020; 584:136-141. [PMID: 32581363 PMCID: PMC7415571 DOI: 10.1038/s41586-020-2430-6] [Citation(s) in RCA: 99] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/23/2020] [Indexed: 12/30/2022]
Abstract
Clonally expanded blood cells that contain somatic mutations (clonal haematopoiesis) are commonly acquired with age and increase the risk of blood cancer1-9. The blood clones identified so far contain diverse large-scale mosaic chromosomal alterations (deletions, duplications and copy-neutral loss of heterozygosity (CN-LOH)) on all chromosomes1,2,5,6,9, but the sources of selective advantage that drive the expansion of most clones remain unknown. Here, to identify genes, mutations and biological processes that give selective advantage to mutant clones, we analysed genotyping data from the blood-derived DNA of 482,789 participants from the UK Biobank10. We identified 19,632 autosomal mosaic chromosomal alterations and analysed these for relationships to inherited genetic variation. We found 52 inherited, rare, large-effect coding or splice variants in 7 genes that were associated with greatly increased vulnerability to clonal haematopoiesis with specific acquired CN-LOH mutations. Acquired mutations systematically replaced the inherited risk alleles (at MPL) or duplicated them to the homologous chromosome (at FH, NBN, MRE11, ATM, SH2B3 and TM2D3). Three of the genes (MRE11, NBN and ATM) encode components of the MRN-ATM pathway, which limits cell division after DNA damage and telomere attrition11-13; another two (MPL and SH2B3) encode proteins that regulate the self-renewal of stem cells14-16. In addition, we found that CN-LOH mutations across the genome tended to cause chromosomal segments with alleles that promote the expansion of haematopoietic cells to replace their homologous (allelic) counterparts, increasing polygenic drive for blood-cell proliferation traits. Readily acquired mutations that replace chromosomal segments with their homologous counterparts seem to interact with pervasive inherited variation to create a challenge for lifelong cytopoiesis.
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Affiliation(s)
- Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Genetics, Harvard Medical School, Boston, MA, USA.
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49
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Martínez-Glez V, Tenorio J, Nevado J, Gordo G, Rodríguez-Laguna L, Feito M, de Lucas R, Pérez-Jurado LA, Ruiz Pérez VL, Torrelo A, Spinner NB, Happle R, Biesecker LG, Lapunzina P. A six-attribute classification of genetic mosaicism. Genet Med 2020; 22:1743-1757. [PMID: 32661356 PMCID: PMC8581815 DOI: 10.1038/s41436-020-0877-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Revised: 06/12/2020] [Accepted: 06/12/2020] [Indexed: 01/23/2023] Open
Abstract
Mosaicism denotes an individual who has at least two populations of cells with distinct genotypes that are derived from a single fertilized egg. Genetic variation among the cell lines can involve whole chromosomes, structural or copy number variants, small or single nucleotide variants, or epigenetic variants. The mutational events that underlie mosaic variants occur during mitotic cell divisions after fertilization and zygote formation. The initiating mutational event can occur in any types of cell at any time in development, leading to enormous variation in the distribution and phenotypic effect of mosaicism. A number of classification proposals have been put forward to classify genetic mosaicism into categories based on the location, pattern, and mechanisms of the disease. We here propose a new classification of genetic mosaicism that considers the affected tissue, the pattern and distribution of the mosaicism, the pathogenicity of the variant, the direction of the change (benign to pathogenic vs. pathogenic to benign), and the postzygotic mutational mechanism. The accurate and comprehensive categorization and subtyping of mosaicisms is important and has potential clinical utility to define the natural history of these disorders, tailor follow-up frequency and interventions, estimate recurrence risks, and guide therapeutic decisions.
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Affiliation(s)
- Víctor Martínez-Glez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
| | - Jair Tenorio
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Julián Nevado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium
| | - Gema Gordo
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Lara Rodríguez-Laguna
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Marta Feito
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Raúl de Lucas
- Department of Pediatric Dermatology, Hospital Universitario La Paz-UAM, Madrid, Spain
| | - Luis A Pérez-Jurado
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,Genetics Unit, Universitat Pompeu Fabra and Hospital del Mar Research Institute (IMIM), Barcelona, Spain.,Women's and Children's Hospital, South Australia Medical and Health Research Institute (SAHMRI) and University of Adelaide, Adelaide, SA, Australia
| | - Víctor L Ruiz Pérez
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain.,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.,Instituto de Investigaciones Biomédicas de Madrid (CSIC-UAM), Madrid, Spain
| | - Antonio Torrelo
- Department of Pediatrics, Hospital Universitario Niño Jesús, Madrid, Spain
| | - Nancy B Spinner
- Division of Genomic Diagnostics, Department of Pathology and Laboratory Medicines at The Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Rudolf Happle
- Department of Dermatology, Medical Center-University of Freiburg, Freiburg, Germany
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health, Bethesda, MD, USA
| | - Pablo Lapunzina
- CIBERER, Centro de Investigación Biomédica en Red de Enfermedades Raras, ISCIII, Madrid, Spain. .,Institute of Medical and Molecular Genetics (INGEMM)-IdiPAZ, Hospital Universitario La Paz-UAM, Madrid, Spain. .,ITHACA, European Reference Network on Rare Congenital Malformations and Rare Intellectual Disability, Brussels, Belgium.
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Chromosomal alterations among age-related haematopoietic clones in Japan. Nature 2020; 584:130-135. [PMID: 32581364 DOI: 10.1038/s41586-020-2426-2] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2019] [Accepted: 04/02/2020] [Indexed: 12/26/2022]
Abstract
The extent to which the biology of oncogenesis and ageing are shaped by factors that distinguish human populations is unknown. Haematopoietic clones with acquired mutations become common with advancing age and can lead to blood cancers1-10. Here we describe shared and population-specific patterns of genomic mutations and clonal selection in haematopoietic cells on the basis of 33,250 autosomal mosaic chromosomal alterations that we detected in 179,417 Japanese participants in the BioBank Japan cohort and compared with analogous data from the UK Biobank. In this long-lived Japanese population, mosaic chromosomal alterations were detected in more than 35.0% (s.e.m., 1.4%) of individuals older than 90 years, which suggests that such clones trend towards inevitability with advancing age. Japanese and European individuals exhibited key differences in the genomic locations of mutations in their respective haematopoietic clones; these differences predicted the relative rates of chronic lymphocytic leukaemia (which is more common among European individuals) and T cell leukaemia (which is more common among Japanese individuals) in these populations. Three different mutational precursors of chronic lymphocytic leukaemia (including trisomy 12, loss of chromosomes 13q and 13q, and copy-neutral loss of heterozygosity) were between two and six times less common among Japanese individuals, which suggests that the Japanese and European populations differ in selective pressures on clones long before the development of clinically apparent chronic lymphocytic leukaemia. Japanese and British populations also exhibited very different rates of clones that arose from B and T cell lineages, which predicted the relative rates of B and T cell cancers in these populations. We identified six previously undescribed loci at which inherited variants predispose to mosaic chromosomal alterations that duplicate or remove the inherited risk alleles, including large-effect rare variants at NBN, MRE11 and CTU2 (odds ratio, 28-91). We suggest that selective pressures on clones are modulated by factors that are specific to human populations. Further genomic characterization of clonal selection and cancer in populations from around the world is therefore warranted.
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