1
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Fischer J, Shutta KH, Chen C, Fanfani V, Saha E, Mandros P, Ben Guebila M, Xiu J, Nieva J, Liu S, Uprety D, Spetzler D, Lopes-Ramos CM, DeMeo D, Quackenbush J. Selective loss of Y chromosomes in lung adenocarcinoma modulates the tumor immune environment through cancer/testis antigens. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.09.19.613876. [PMID: 39345481 PMCID: PMC11430018 DOI: 10.1101/2024.09.19.613876] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/01/2024]
Abstract
There is increasing recognition that the sex chromosomes, X and Y, play an important role in health and disease that goes beyond the determination of biological sex. Loss of the Y chromosome (LOY) in blood, which occurs naturally in aging men, has been found to be a driver of cardiac fibrosis and heart failure mortality. LOY also occurs in most solid tumors in males and is often associated with worse survival, suggesting that LOY may give tumor cells a growth or survival advantage. We analyzed LOY in lung adenocarcinoma (LUAD) using both bulk and single-cell expression data and found evidence suggesting that LOY affects the tumor immune environment by altering cancer/testis antigen expression and consequently facilitating tumor immune evasion. Analyzing immunotherapy data, we show that LOY and changes in expression of particular cancer/testis antigens are associated with response to pembrolizumab treatment and outcome, providing a new and powerful biomarker for predicting immunotherapy response in LUAD tumors in males.
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Affiliation(s)
- Jonas Fischer
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
- Department for Computer Vision and Machine Learning, Max Planck Institute for Informatics, Stuhlsatzenhausweg E1 4, Saarbrücken, 66123, Germany
| | - Katherine H. Shutta
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, 02115, MA, United States
| | - Chen Chen
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
| | - Viola Fanfani
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
| | - Enakshi Saha
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
| | - Panagiotis Mandros
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
| | - Marouen Ben Guebila
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
| | - Joanne Xiu
- Caris Life Sciences, 4610 South 44th Place, Phoenix, 85040, AZ, United States
| | - Jorge Nieva
- Department of Medicine, Keck School of Medicine of USC, 1975 Zonal Avenue, Los Angeles, 90033, CA, United States
| | - Stephen Liu
- Department of Medicine, Georgetown University School of Medicine, 3900 Reservoir Road NW, Washington, 20007, DC, United States
| | - Dipesh Uprety
- Karmanos Cancer Center, 4100 John R , Detroit, 48201, MI, United States
| | - David Spetzler
- Caris Life Sciences, 4610 South 44th Place, Phoenix, 85040, AZ, United States
| | - Camila M. Lopes-Ramos
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, 02115, MA, United States
- Department of Medicine, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, United States
| | - Dawn DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, 02115, MA, United States
- Department of Medicine, Harvard Medical School, 25 Shattuck St, Boston, 02115, MA, United States
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, 677 Huntington Ave, Boston, 02115, MA, United States
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Avenue, Boston, 02115, MA, United States
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2
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Hozakowska-Roszkowska DM, Mengel-From J, Hristozova TK, Pedersen JK, Jeune B, Andersen-Ranberg K, Hjelmborg JVB, Christensen K, Röttger R, Nygaard M. Mosaic loss of Y chromosome and the association to mortality in Danish men aged 56-100 years. Mech Ageing Dev 2024; 222:111979. [PMID: 39265710 DOI: 10.1016/j.mad.2024.111979] [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: 05/25/2024] [Revised: 08/16/2024] [Accepted: 09/02/2024] [Indexed: 09/14/2024]
Abstract
Mosaic loss of the Y chromosome (mLOY) is a common somatic mutation in the blood of elderly men and several studies have found mLOY in blood cells to be associated with an increased risk of various diseases and mortality. However, most of these studies have focused on middle-aged and older adults, meaning that mLOY in extremely old individuals like centenarians is understudied. To explore mLOY across a wider age range compared to earlier studies and to specifically focus on centenarians, mLOY was estimated in 917 Danish men aged 56-100 years. We found that the percentage of men with LOY increased with age until age 85, after which it plateaued at around 40 %. Consistently, a longitudinal comparison of mLOY revealed that mLOY predominantly increased with age, although inter-individual variation was seen. Using a twin sub-sample, the broad-sense heritability of mLOY was estimated at 72 %, indicating a substantial genetic influence. Supporting previous findings, mLOY was found to associate with increased mortality across all study participants and in men younger than 80 years. In centenarians, however, a higher level of mLOY associated with better survival, most likely due to selection, although confirmation of our findings in larger studies is needed.
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Affiliation(s)
| | - Jonas Mengel-From
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Teodora K Hristozova
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Jacob Krabbe Pedersen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Bernard Jeune
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Karen Andersen-Ranberg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Department of Clinical Research, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Department of Geriatric Medicine, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense C, Denmark.
| | - Jacob V B Hjelmborg
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Kaare Christensen
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark; Department of Clinical Genetics, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense C, Denmark; Department of Clinical Biochemistry, Odense University Hospital, J.B. Winsløws Vej 4, 5000 Odense C, Denmark.
| | - Richard Röttger
- Department of Mathematics and Computer Science, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
| | - Marianne Nygaard
- Epidemiology, Biostatistics and Biodemography, Department of Public Health, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark.
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3
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Shi Y, Ma J, Li S, Liu C, Liu Y, Chen J, Liu N, Liu S, Huang H. Sex difference in human diseases: mechanistic insights and clinical implications. Signal Transduct Target Ther 2024; 9:238. [PMID: 39256355 PMCID: PMC11387494 DOI: 10.1038/s41392-024-01929-7] [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: 12/20/2023] [Revised: 06/26/2024] [Accepted: 07/23/2024] [Indexed: 09/12/2024] Open
Abstract
Sex characteristics exhibit significant disparities in various human diseases, including prevalent cardiovascular diseases, cancers, metabolic disorders, autoimmune diseases, and neurodegenerative diseases. Risk profiles and pathological manifestations of these diseases exhibit notable variations between sexes. The underlying reasons for these sex disparities encompass multifactorial elements, such as physiology, genetics, and environment. Recent studies have shown that human body systems demonstrate sex-specific gene expression during critical developmental stages and gene editing processes. These genes, differentially expressed based on different sex, may be regulated by androgen or estrogen-responsive elements, thereby influencing the incidence and presentation of cardiovascular, oncological, metabolic, immune, and neurological diseases across sexes. However, despite the existence of sex differences in patients with human diseases, treatment guidelines predominantly rely on male data due to the underrepresentation of women in clinical trials. At present, there exists a substantial knowledge gap concerning sex-specific mechanisms and clinical treatments for diverse diseases. Therefore, this review aims to elucidate the advances of sex differences on human diseases by examining epidemiological factors, pathogenesis, and innovative progress of clinical treatments in accordance with the distinctive risk characteristics of each disease and provide a new theoretical and practical basis for further optimizing individualized treatment and improving patient prognosis.
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Affiliation(s)
- Yuncong Shi
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Jianshuai Ma
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Sijin Li
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Chao Liu
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Yuning Liu
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China
| | - Jie Chen
- Department of Radiotherapy, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Ningning Liu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Shiming Liu
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
| | - Hui Huang
- Department of Cardiology, the Eighth Affiliated Hospital, Joint Laboratory of Guangdong-Hong Kong-Macao Universities for Nutritional Metabolism and Precise Prevention and Control of Major Chronic Diseases, Sun Yat-sen University, Shenzhen, China.
- Department of Cardiology, Guangzhou Institute of Cardiovascular Disease, Guangdong Key Laboratory of Vascular Diseases, the Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China.
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4
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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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5
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Otsuka I, Uchiyama S, Shirai T, Liu X, Takahashi M, Kamatani Y, Terao C, Hishimoto A. Increased somatic mosaicism in autosomal and X chromosomes for suicide death. Mol Psychiatry 2024:10.1038/s41380-024-02718-y. [PMID: 39215187 DOI: 10.1038/s41380-024-02718-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/22/2024] [Revised: 08/21/2024] [Accepted: 08/22/2024] [Indexed: 09/04/2024]
Abstract
Mosaic chromosomal alterations (mCAs) are classified as mosaic deletions (loss), copy-neutral loss of heterozygosity (CN-LOH), and duplications (gain), attracting special attention as biological aging-related acquired genetic alterations. While these mCAs have been linked with aging and various diseases, no study has investigated their association with suicide risk which is associated with abnormal biological aging. Here, we examined the association between suicide deaths and mCAs, including mosaic loss of the X (mLOX) and Y chromosomes, by leveraging blood-derived single nucleotide polymorphism-array data. The first (410 suicide decedents and 88,870 controls) and the second (363 suicide decedents and 88,870 controls) cohorts were analyzed and integrated using meta-analyses (773 suicide decedents and 177,740 controls). Total mCAs in autosomal chromosomes were significantly increased in suicide (p = 1.28 × 10-6, odds ratio [OR] = 1.78), mostly driven by loss (p = 4.05 × 10-9, OR = 2.70) and gain (p = 1.08 × 10-3, OR = 2.23). mLOX were significantly increased in female suicide (p = 2.66 × 10-21, OR = 4.00). The directions of effects of all mCAs in autosomal and sex chromosomes on suicide were the same in the first and second sets. Subgroup analyses suggest that our findings were mostly driven by suicide itself, and not confounded by comorbid psychiatric disorders or physical diseases, smoking status, sample location, or postmortem sample status. In conclusion, we provide the first evidence for aberrant mCAs in somatic autosomal and X chromosomes in suicide, which may contribute to an improved understanding of the genomic pathophysiology underlying suicide.
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Affiliation(s)
- Ikuo Otsuka
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Shunsuke Uchiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Department of Allergy and Rheumatology, Nippon Medical School, Tokyo, Japan
| | - Toshiyuki Shirai
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
| | - Motonori Takahashi
- Division of Legal Medicine, Department of Community Medicine and Social Health Science, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Yoichiro Kamatani
- Laboratory of Complex Trait Genomics, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, 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.
| | - Akitoyo Hishimoto
- Department of Psychiatry, Kobe University Graduate School of Medicine, Kobe, Japan.
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6
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Adjeroh DA, Zhou X, Paschoal AR, Dimitrova N, Derevyanchuk EG, Shkurat TP, Loeb JA, Martinez I, Lipovich L. Challenges in LncRNA Biology: Views and Opinions. Noncoding RNA 2024; 10:43. [PMID: 39195572 DOI: 10.3390/ncrna10040043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Revised: 06/26/2024] [Accepted: 07/04/2024] [Indexed: 08/29/2024] Open
Abstract
This is a mini-review capturing the views and opinions of selected participants at the 2021 IEEE BIBM 3rd Annual LncRNA Workshop, held in Dubai, UAE. The views and opinions are expressed on five broad themes related to problems in lncRNA, namely, challenges in the computational analysis of lncRNAs, lncRNAs and cancer, lncRNAs in sports, lncRNAs and COVID-19, and lncRNAs in human brain activity.
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Affiliation(s)
- Donald A Adjeroh
- Lane Department of Computer Science and Electrical Engineering, West Virginia University (WVU), Morgantown, WV 26506, USA
| | - Xiaobo Zhou
- Department of Bioinformatics and Systems Medicine, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Alexandre Rossi Paschoal
- Department of Computer Science, Bioinformatics and Pattern Recognition Group, Federal University of Technology-Paraná-UTFPR, Curitiba 86300-000, Brazil
- Rosalind Franklin Institute, Harwell Science and Innovation Campus, Didcot OX11 0FA, UK
| | - Nadya Dimitrova
- Department of Molecular, Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
| | | | - Tatiana P Shkurat
- Department of Genetics, Southern Federal University, Rostov-on-Don 344090, Russia
| | - Jeffrey A Loeb
- Department of Neurology and Rehabilitation, The Center for Clinical and Translational Science, The University of Illinois NeuroRepository, University of Illinois, Chicago, IL 60607, USA
| | - Ivan Martinez
- Department of Microbiology, Immunology & Cell Biology, WVU Cancer Institute, West Virginia University (WVU) School of Medicine, Morgantown, WV 26505, USA
| | - Leonard Lipovich
- Shenzhen Huayuan Biological Science Research Institute, Shenzhen Huayuan Biotechnology Co., Ltd., Shenzhen 518000, China
- Center for Molecular Medicine and Genetics, School of Medicine, Wayne State University, Detroit, MI 48201, USA
- College of Science, Mathematics and Technology, Wenzhou-Kean University, Wenzhou 325060, China
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7
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Petrone G, Turker I, Natarajan P, Bolton KL. Clinical and Therapeutic Implications of Clonal Hematopoiesis. Annu Rev Genomics Hum Genet 2024; 25:329-351. [PMID: 39190914 DOI: 10.1146/annurev-genom-120722-100409] [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] [Indexed: 08/29/2024]
Abstract
Clonal hematopoiesis (CH) is an age-related process whereby hematopoietic stem and progenitor cells (HSPCs) acquire mutations that lead to a proliferative advantage and clonal expansion. The most commonly mutated genes are epigenetic regulators, DNA damage response genes, and splicing factors, which are essential to maintain functional HSPCs and are frequently involved in the development of hematologic malignancies. Established risk factors for CH, including age, prior cytotoxic therapy, and smoking, increase the risk of acquiring CH and/or may increase CH fitness. CH has emerged as a novel risk factor in many age-related diseases, such as hematologic malignancies, cardiovascular disease, diabetes, and autoimmune disorders, among others. Future characterization of the mechanisms driving CH evolution will be critical to develop preventative and therapeutic approaches.
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Affiliation(s)
- Giulia Petrone
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA;
| | - Isik Turker
- Division of Cardiology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Pradeep Natarajan
- Cardiovascular Research Center and Center for Genomic Medicine, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Cardiovascular Disease Initiative, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
| | - Kelly L Bolton
- Division of Oncology, Department of Medicine, Washington University School of Medicine, St. Louis, Missouri, USA;
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8
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Hislop JM, Went M, Mills C, Sud A, Law PJ, Houlston RS. Using Mendelian Randomisation to search for modifiable risk factors influencing the development of clonal haematopoiesis. Blood Cancer J 2024; 14:114. [PMID: 39013866 PMCID: PMC11252326 DOI: 10.1038/s41408-024-01101-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Revised: 07/05/2024] [Accepted: 07/10/2024] [Indexed: 07/18/2024] Open
Affiliation(s)
- Jessica M Hislop
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK.
| | - Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Charlie Mills
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Amit Sud
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Harvard Medical School, Boston, MA, USA
- Centre for Immuno-Oncology, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
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9
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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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10
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Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat SM, Kentistou KA, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman BR, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman ND, Song L, Gardner EJ, Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ. Genetic drivers and cellular selection of female mosaic X chromosome loss. Nature 2024; 631:134-141. [PMID: 38867047 DOI: 10.1038/s41586-024-07533-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 05/07/2024] [Indexed: 06/14/2024]
Abstract
Mosaic loss of the X chromosome (mLOX) is the most common clonal somatic alteration in leukocytes of female individuals1,2, but little is known about its genetic determinants or phenotypic consequences. Here, to address this, we used data from 883,574 female participants across 8 biobanks; 12% of participants exhibited detectable mLOX in approximately 2% of leukocytes. Female participants with mLOX had an increased risk of myeloid and lymphoid leukaemias. Genetic analyses identified 56 common variants associated with mLOX, implicating genes with roles in chromosomal missegregation, cancer predisposition and autoimmune diseases. Exome-sequence analyses identified rare missense variants in FBXO10 that confer a twofold increased risk of mLOX. Only a small fraction of associations was shared with mosaic Y chromosome loss, suggesting that distinct biological processes drive formation and clonal expansion of sex chromosome missegregation. Allelic shift analyses identified X chromosome alleles that are preferentially retained in mLOX, demonstrating variation at many loci under cellular selection. A polygenic score including 44 allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Our results support a model in which germline variants predispose female individuals to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of clonal expansion.
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Affiliation(s)
- Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA.
- 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.
| | - 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.
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Public Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Seyedeh M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Department of Ophthalmology, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Katherine A Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - 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
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bryan R Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Valdislav Tuzov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
- Institute of Molecular and Cell Biology, University of Tartu, Tartu, Estonia
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal D Freedman
- 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
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- 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
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Anesthesia, Critical Care and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
- 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
| | - Alexander Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 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
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland.
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA.
- 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.
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA.
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11
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Guan X, Meng X, Zhong G, Zhang Z, Wang C, Xiao Y, Fu M, Zhao H, Zhou Y, Hong S, Xu X, Bai Y, Kan H, Chen R, Wu T, Guo H. Particulate matter pollution, polygenic risk score and mosaic loss of chromosome Y in middle-aged and older men from the Dongfeng-Tongji cohort study. JOURNAL OF HAZARDOUS MATERIALS 2024; 471:134315. [PMID: 38678703 DOI: 10.1016/j.jhazmat.2024.134315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 04/04/2024] [Accepted: 04/14/2024] [Indexed: 05/01/2024]
Abstract
Mosaic loss of chromosome Y (mLOY) is the most common somatic alteration as men aging and may reflect genome instability. PM exposure is a major health concern worldwide, but its effects with genetic factors on mLOY has never been investigated. Here we explored the associations of PM2.5 and PM10 exposure with mLOY of 10,158 males measured via signal intensity of 2186 probes in male-specific chromosome-Y region from Illumina array data. The interactive and joint effects of PM2.5 and PM10 with genetic factors and smoking on mLOY were further evaluated. Compared with the lowest tertiles of PM2.5 levels in each exposure window, the highest tertiles in the same day, 7-, 14-, 21-, and 28-day showed a 0.005, 0.006, 0.007, 0.007, and 0.006 decrease in mLRR-Y, respectively (all P < 0.05), with adjustment for age, BMI, smoking pack-years, alcohol drinking status, physical activity, education levels, season of blood draw, and experimental batch. Such adverse effects were also observed in PM10-mLOY associations. Moreover, the unweighted and weighted PRS presented significant negative associations with mLRR-Y (both P < 0.001). Participants with high PRS and high PM2.5 or PM10 exposure in the 28-day separately showed a 0.018 or 0.019 lower mLRR-Y level [β (95 %CI) = -0.018 (-0.023, -0.012) and - 0.019 (-0.025, -0.014), respectively, both P < 0.001], when compared to those with low PRS and low PM2.5 or PM10 exposure. We also observed joint effects of PM with smoking on exacerbated mLOY. This large study is the first to elucidate the impacts of PM2.5 exposure on mLOY, and provides key evidence regarding the interactive and joint effects of PM with genetic factors on mLOY, which may promote understanding of mLOY development, further modifying and increasing healthy aging in males.
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Affiliation(s)
- Xin Guan
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Xia Meng
- Department of Environment Health, School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Guorong Zhong
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Zirui Zhang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Chenming Wang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Yang Xiao
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Ming Fu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Hui Zhao
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Yuhan Zhou
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Shiru Hong
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Xuedan Xu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Yansen Bai
- Institute for Chemical Carcinogenesis, School of Public Health, Guangzhou Medical University, Xinzao, Panyu District, Guangzhou 511436, China
| | - Haidong Kan
- Department of Environment Health, School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Renjie Chen
- Department of Environment Health, School of Public Health, Key Lab of Public Health Safety of the Ministry of Education and National Health Commission Key Lab of Health Technology Assessment, Fudan University, Shanghai, China
| | - Tangchun Wu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Huan Guo
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China.
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12
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Lim J, Hubbard AK, Blechter B, Shi J, Zhou W, Loftfield E, Machiela MJ, Wong JYY. Associations between mosaic loss of sex chromosomes and incident hospitalization for atrial fibrillation in the United Kingdom. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.05.29.24308171. [PMID: 38903105 PMCID: PMC11188119 DOI: 10.1101/2024.05.29.24308171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/22/2024]
Abstract
Background Mosaic loss of chromosome Y (mLOY) in leukocytes of men reflects genomic instability from aging, smoking, and environmental exposures. A similar mosaic loss of chromosome X (mLOX) occurs among women. However, the associations between mLOY, mLOX, and risk of incident heart diseases are unclear. Methods We estimated associations between mLOY, mLOX, and risk of incident heart diseases requiring hospitalization, including atrial fibrillation, myocardial infarction, ischemic heart disease, cardiomyopathy, and heart failure. We analyzed 190,613 men and 224,853 women with genotyping data from the UK Biobank. Among these participants, we analyzed 37,037 men with mLOY and 13,978 women with mLOX detected using Mosaic Chromosomal Alterations caller. Multivariable Cox regression was used to estimate hazard ratios (HRs) and 95% confidence intervals (CIs) of each incident heart disease in relation to mLOY in men and mLOX in women. Additionally, Mendelian randomization (MR) was conducted to estimate causal associations. Results Among men, detectable mLOY was associated with elevated risk of atrial fibrillation (HR=1.06, 95%CI:1.03-1.11). The associations were apparent in both never-smokers (HR=1.07, 95%:1.01-1.14) and ever-smokers (HR=1.05, 95%CI:1.01-1.11) as well as men > and ≤60 years of age. MR analyses supported causal associations between mLOY and atrial fibrillation (HRMR-PRESSO=1.15, 95%CI:1.13-1.18). Among post-menopausal women, we found a suggestive inverse association between detectable mLOX and atrial fibrillation risk (HR=0.90, 95%CI:0.83-0.98). However, associations with mLOY and mLOX were not found for other heart diseases. Conclusions Our findings suggest that mLOY and mLOX reflect sex-specific biological processes or exposure profiles related to incident atrial fibrillation requiring hospitalization.
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Affiliation(s)
- Jungeun Lim
- Epidemiology and Community Health Branch, National Heart Lung and Blood Institute, Bethesda, MD, USA
| | - Aubrey K Hubbard
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Batel Blechter
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jianxin Shi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Leidos Biomedical Research, Inc, Frederick, MD, USA
| | - Erikka Loftfield
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Jason Y Y Wong
- Epidemiology and Community Health Branch, National Heart Lung and Blood Institute, Bethesda, MD, USA
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13
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Wang D, Hadad N, Moss S, Lopez-Jimenez E, Johnson SR, Maher TM, Molyneaux PL, Zhao Y, Perry JRB, Wolters PJ, Kropski JA, Jenkins RG, Banovich NE, Stewart I. Association between mosaic loss of chromosome Y and pulmonary fibrosis susceptibility and severity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.25.595885. [PMID: 38853935 PMCID: PMC11160640 DOI: 10.1101/2024.05.25.595885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
Background Pulmonary fibrosis (PF) is a rare lung disease with diverse pathogenesis and multiple interconnected underlying biological mechanisms. Mosaic loss of chromosome Y (mLOY) is one of the most common forms of acquired chromosome abnormality in men, which has been reported to be associated with increased risk of various chronic progressive diseases including fibrotic diseases. However, the exact role of mLOY in the development of PF remains elusive and to be elucidated. Methods We adopted three complementary approaches to explore the role of mLOY in the pathogenesis of PF. We used copy number on chromosome Y to estimate mLOY comparing patients in PROFILE and gnomAD cohorts and between cases and control patients from the GE100KGP cohort. Correlation of mLOY with demographic and clinical variables was tested using patients from PROFILE cohort. Lung single-cell transcriptomic data were analysed to assess the cell types implicated in mLOY. We performed Mendelian randomisation to examine the causal relationship between mLOY, IPF, and telomere length. Results The genetic analysis suggests that mLOY is found in PF from both case cohorts but when compared with an age matched population the effect is minimal (P = 0.0032). mLOY is related to age (P = 0.00021) and shorter telomere length (P = 0.0081) rather than PF severity or progression. Single-cell analysis indicates that mLOY appears to be found primarily in immune cells and appears to be related to presence and severity of fibrosis. Mendelian randomisation demonstrates that mLOY is not on the causal pathway for IPF, but partial evidence supports that telomere shortening is on the causal pathway for mLOY. Conclusion Our study confirms the existence of mLOY in PF patients and suggests that mLOY is not a major driver of IPF. The combined evidence suggests a triangulation model where telomere shortening leads to both IPF and mLOY.
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14
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Wójcik M, Juhas U, Mohammadi E, Mattisson J, Drężek-Chyła K, Rychlicka-Buniowska E, Bruhn-Olszewska B, Davies H, Chojnowska K, Olszewski P, Bieńkowski M, Jankowski M, Rostkowska O, Hellmann A, Pęksa R, Kowalski J, Zdrenka M, Kobiela J, Zegarski W, Biernat W, Szylberg Ł, Remiszewski P, Mieczkowski J, Filipowicz N, Dumanski JP. Loss of Y in regulatory T lymphocytes in the tumor micro-environment of primary colorectal cancers and liver metastases. Sci Rep 2024; 14:9458. [PMID: 38658633 PMCID: PMC11043399 DOI: 10.1038/s41598-024-60049-y] [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: 08/24/2023] [Accepted: 04/18/2024] [Indexed: 04/26/2024] Open
Abstract
Male sex is a risk factor for colorectal cancer (CRC) with higher illness burden and earlier onset. Thus, we hypothesized that loss of chromosome Y (LOY) in the tumor micro-environment (TME) might be involved in oncogenesis. Previous studies show that LOY in circulating leukocytes of aging men was associated with shorter survival and non-hematological cancer, as well as higher LOY in CD4 + T-lymphocytes in men with prostate cancer vs. controls. However, nothing is known about LOY in leukocytes infiltrating TME and we address this aspect here. We studied frequency and functional effects of LOY in blood, TME and non-tumorous tissue. Regulatory T-lymphocytes (Tregs) in TME had the highest frequency of LOY (22%) in comparison to CD4 + T-lymphocytes and cytotoxic CD8 + T-lymphocytes. LOY score using scRNA-seq was also linked to higher expression of PDCD1, TIGIT and IKZF2 in Tregs. PDCD1 and TIGIT encode immune checkpoint receptors involved in the regulation of Tregs function. Our study sets the direction for further functional research regarding a probable role of LOY in intensifying features related to the suppressive phenotype of Tregs in TME and consequently a possible influence on immunotherapy response in CRC patients.
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Affiliation(s)
- Magdalena Wójcik
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Ulana Juhas
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
- Department of Bioenergetics and Physiology of Exercise, Medical University of Gdańsk, Dębinki 1, 80-211, Gdańsk, Poland
| | - Elyas Mohammadi
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | | | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Katarzyna Chojnowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Paweł Olszewski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Olga Rostkowska
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Andrzej Hellmann
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Jacek Kowalski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jarek Kobiela
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier's Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center - Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Bydgoszcz, Poland
| | - Piotr Remiszewski
- Department of Oncological, Transplant and General Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jakub Mieczkowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland.
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211, Gdańsk, Poland.
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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15
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Jakubek YA, Ma X, Stilp AM, Yu F, Bacon J, Wong JW, Aguet F, Ardlie K, Arnett D, Barnes K, Bis JC, Blackwell T, Becker LC, Boerwinkle E, Bowler RP, Budoff MJ, Carson AP, Chen J, Cho MH, Coresh J, Cox N, de Vries PS, DeMeo DL, Fardo DW, Fornage M, Guo X, Hall ME, Heard-Costa N, Hidalgo B, Irvin MR, Johnson AD, Kenny EE, Levy D, Li Y, Lima JA, Liu Y, Loos RJF, Machiela MJ, Mathias RA, Mitchell BD, Murabito J, Mychaleckyj JC, North K, Orchard P, Parker SC, Pershad Y, Peyser PA, Pratte KA, Psaty BM, Raffield LM, Redline S, Rich SS, Rotter JI, Shah SJ, Smith JA, Smith AP, Smith A, Taub M, Tiwari HK, Tracy R, Tuftin B, Bick AG, Sankaran VG, Reiner AP, Scheet P, Auer PL. Genomic and phenotypic correlates of mosaic loss of chromosome Y in blood. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.04.16.24305851. [PMID: 38699360 PMCID: PMC11065036 DOI: 10.1101/2024.04.16.24305851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2024]
Abstract
Mosaic loss of Y (mLOY) is the most common somatic chromosomal alteration detected in human blood. The presence of mLOY is associated with altered blood cell counts and increased risk of Alzheimer's disease, solid tumors, and other age-related diseases. We sought to gain a better understanding of genetic drivers and associated phenotypes of mLOY through analyses of whole genome sequencing of a large set of genetically diverse males from the Trans-Omics for Precision Medicine (TOPMed) program. This approach enabled us to identify differences in mLOY frequencies across populations defined by genetic similarity, revealing a higher frequency of mLOY in the European American (EA) ancestry group compared to those of Hispanic American (HA), African American (AA), and East Asian (EAS) ancestry. Further, we identified two genes ( CFHR1 and LRP6 ) that harbor multiple rare, putatively deleterious variants associated with mLOY susceptibility, show that subsets of human hematopoietic stem cells are enriched for activity of mLOY susceptibility variants, and that certain alleles on chromosome Y are more likely to be lost than others.
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16
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Gutiérrez-Hurtado IA, Sánchez-Méndez AD, Becerra-Loaiza DS, Rangel-Villalobos H, Torres-Carrillo N, Gallegos-Arreola MP, Aguilar-Velázquez JA. Loss of the Y Chromosome: A Review of Molecular Mechanisms, Age Inference, and Implications for Men's Health. Int J Mol Sci 2024; 25:4230. [PMID: 38673816 PMCID: PMC11050192 DOI: 10.3390/ijms25084230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 03/29/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Until a few years ago, it was believed that the gradual mosaic loss of the Y chromosome (mLOY) was a normal age-related process. However, it is now known that mLOY is associated with a wide variety of pathologies in men, such as cardiovascular diseases, neurodegenerative disorders, and many types of cancer. Nevertheless, the mechanisms that generate mLOY in men have not been studied so far. This task is of great importance because it will allow focusing on possible methods of prophylaxis or therapy for diseases associated with mLOY. On the other hand, it would allow better understanding of mLOY as a possible marker for inferring the age of male samples in cases of human identification. Due to the above, in this work, a comprehensive review of the literature was conducted, presenting the most relevant information on the possible molecular mechanisms by which mLOY is generated, as well as its implications for men's health and its possible use as a marker to infer age.
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Affiliation(s)
- Itzae Adonai Gutiérrez-Hurtado
- Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
| | - Astrid Desireé Sánchez-Méndez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
- Doctorado en Genética Humana, Departamento de Biología Molecular y Genómica, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | | | - Héctor Rangel-Villalobos
- Instituto de Investigación en Genética Molecular, Departamento de Ciencias Médicas y de la Vida, Centro Universitario de la Ciénega, Universidad de Guadalajara, Ocotlán 47820, Jalisco, Mexico
| | - Norma Torres-Carrillo
- Departamento de Microbiología y Patología, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara, Guadalajara 44340, Jalisco, Mexico
| | - Martha Patricia Gallegos-Arreola
- División de Genética, Centro de Investigación Biomédica de Occidente (CIBO), Instituto Mexicano del Seguro Social (IMSS), Guadalajara 44340, Jalisco, Mexico
| | - José Alonso Aguilar-Velázquez
- Laboratorio de Ciencias Morfológico Forenses y Medicina Molecular, Departamento de Morfología, Centro Universitario de Ciencias de la Salud, Guadalajara 44340, Jalisco, Mexico
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17
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Westemeier-Rice ES, Winters MT, Rawson TW, Martinez I. More than the SRY: The Non-Coding Landscape of the Y Chromosome and Its Importance in Human Disease. Noncoding RNA 2024; 10:21. [PMID: 38668379 PMCID: PMC11054740 DOI: 10.3390/ncrna10020021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 03/31/2024] [Accepted: 04/08/2024] [Indexed: 04/29/2024] Open
Abstract
Historically, the Y chromosome has presented challenges to classical methodology and philosophy of understanding the differences between males and females. A genetic unsolved puzzle, the Y chromosome was the last chromosome to be fully sequenced. With the advent of the Human Genome Project came a realization that the human genome is more than just genes encoding proteins, and an entire universe of RNA was discovered. This dark matter of biology and the black box surrounding the Y chromosome have collided over the last few years, as increasing numbers of non-coding RNAs have been identified across the length of the Y chromosome, many of which have played significant roles in disease. In this review, we will uncover what is known about the connections between the Y chromosome and the non-coding RNA universe that originates from it, particularly as it relates to long non-coding RNAs, microRNAs and circular RNAs.
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Affiliation(s)
- Emily S. Westemeier-Rice
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
| | - Michael T. Winters
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| | - Travis W. Rawson
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
| | - Ivan Martinez
- West Virginia University Cancer Institute, West Virginia University School of Medicine, Morgantown, WV 26506, USA;
- Department of Microbiology, Immunology and Cell Biology, West Virginia University School of Medicine, Morgantown, WV 26506, USA; (M.T.W.); (T.W.R.)
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18
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Wang Y, Sano S. Why Y matters? The implication of loss of Y chromosome in blood and cancer. Cancer Sci 2024; 115:706-714. [PMID: 38258457 PMCID: PMC10921008 DOI: 10.1111/cas.16072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Revised: 12/23/2023] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
Hematopoietic mosaic loss of Y chromosome (mLOY) has emerged as a potential male-specific accelerator of biological aging, increasing the risk of various age-related diseases, including cancer. Importantly, mLOY is not confined to hematopoietic cells; its presence has also been observed in nonhematological cancer cells, with the impact of this presence previously unknown. Recent studies have revealed that, whether occurring in leukocytes or cancer cells, mLOY plays a role in promoting the development of an immunosuppressive tumor microenvironment. This occurs through the modulation of tumor-infiltrating immune cells, ultimately enabling cancer cells to evade the vigilant immune system. In this review, we illuminate recent progress concerning the effects of hematopoietic mLOY and cancer mLOY on cancer progression. Examining cancer progression from the perspective of LOY adds a new layer to our understanding of cancer immunity, promising insights that hold the potential to identify innovative and potent immunotherapy targets for cancer.
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Affiliation(s)
- Ying Wang
- Department of CardiologyThe Second Affiliated Hospital of Army Medical UniversityChongqingChina
| | - Soichi Sano
- Laboratory of Cardiovascular MosaicismNational Cerebral and Cardiovascular CenterOsakaJapan
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19
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Stańkowska W, Sarkisyan D, Bruhn-Olszewska B, Duzowska K, Bieńkowski M, Jąkalski M, Wójcik-Zalewska M, Davies H, Drężek-Chyła K, Pęksa R, Harazin-Lechowska A, Ambicka A, Przewoźnik M, Adamczyk A, Sasim K, Makarewicz W, Matuszewski M, Biernat W, Järhult JD, Lipcsey M, Hultström M, Frithiof R, Jaszczyński J, Ryś J, Genovese G, Piotrowski A, Filipowicz N, Dumanski JP. Tumor Predisposing Post-Zygotic Chromosomal Alterations in Bladder Cancer-Insights from Histologically Normal Urothelium. Cancers (Basel) 2024; 16:961. [PMID: 38473323 DOI: 10.3390/cancers16050961] [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: 11/30/2023] [Revised: 01/15/2024] [Accepted: 02/23/2024] [Indexed: 03/14/2024] Open
Abstract
Bladder urothelial carcinoma (BLCA) is the 10th most common cancer with a low survival rate and strong male bias. We studied the field cancerization in BLCA using multi-sample- and multi-tissue-per-patient protocol for sensitive detection of autosomal post-zygotic chromosomal alterations and loss of chromosome Y (LOY). We analysed 277 samples of histologically normal urothelium, 145 tumors and 63 blood samples from 52 males and 15 females, using the in-house adapted Mosaic Chromosomal Alterations (MoChA) pipeline. This approach allows identification of the early aberrations in urothelium from BLCA patients. Overall, 45% of patients exhibited at least one alteration in at least one normal urothelium sample. Recurrence analysis resulted in 16 hotspots composed of either gains and copy number neutral loss of heterozygosity (CN-LOH) or deletions and CN-LOH, encompassing well-known and new BLCA cancer driver genes. Conservative assessment of LOY showed 29%, 27% and 18% of LOY-cells in tumors, blood and normal urothelium, respectively. We provide a proof of principle that our approach can characterize the earliest alterations preconditioning normal urothelium to BLCA development. Frequent LOY in blood and urothelium-derived tissues suggest its involvement in BLCA.
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Affiliation(s)
- Wiktoria Stańkowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Daniil Sarkisyan
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Bożena Bruhn-Olszewska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Katarzyna Duzowska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Marcin Jąkalski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Magdalena Wójcik-Zalewska
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Kinga Drężek-Chyła
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Wojciech Makarewicz
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Piechowskiego 36, 83-400 Kościerzyna, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Wojciech Biernat
- Department of Pathomorphology, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Josef D Järhult
- Zoonosis Science Center, Department of Medical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Miklós Lipcsey
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Hedenstierna Laboratory, Department of Surgical Sciences, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Michael Hultström
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
- Integrative Physiology, Department of Medical Cell Biology, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
| | - Robert Frithiof
- Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Akademiska Sjukhuset, 751 85 Uppsala, Sweden
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Garncarska 11, 31-115 Kraków, Poland
| | - Giulio Genovese
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
| | - Natalia Filipowicz
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
| | - Jan P Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, M. Sklodowskiej-Curie 3A, 80-210 Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, BMC, Husargatan 3, 751 08 Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Hallera 107, 80-416 Gdańsk, Poland
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20
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Bridgers J, Alexander K, Karsan A. Operationalizing Quality Assurance for Clinical Illumina Somatic Next-Generation Sequencing Pipelines. J Mol Diagn 2024; 26:96-105. [PMID: 38086510 DOI: 10.1016/j.jmoldx.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 09/01/2023] [Accepted: 11/07/2023] [Indexed: 01/26/2024] Open
Abstract
Quality assurance (QA) is essential for precision oncology workflows, in particular in the clinical setting. However, because of numerous variations in laboratory and bioinformatics pipelines, QA practices remain non-standardized, are often ad hoc, and are lacking longitudinal tracking. A selected review of existing software was performed for quality control of Illumina next-generation sequencing data, focusing specifically on generalizable tools that can be integrated into any bioinformatics workflow to easily develop a QA workflow with longitudinal tracking. Although all implementations need to be integrated, validated, and iterated upon to suit individual operations, providing a base suite of options will enable better validation and use of QA in clinical somatic mutation testing for workflows using Illumina next-generation sequencing and beyond.
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Affiliation(s)
- Joshua Bridgers
- Genome Sciences Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
| | - Kenyon Alexander
- Genome Sciences Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Aly Karsan
- Genome Sciences Centre, Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada.
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21
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Fedder J, Fagerberg C, Jørgensen MW, Gravholt CH, Berglund A, Knudsen UB, Skakkebæk A. Complete or partial loss of the Y chromosome in an unselected cohort of 865 non-vasectomized, azoospermic men. Basic Clin Androl 2023; 33:37. [PMID: 38093178 PMCID: PMC10720143 DOI: 10.1186/s12610-023-00212-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Accepted: 10/26/2023] [Indexed: 12/17/2023] Open
Abstract
BACKGROUND Structural abnormalities as well as minor variations of the Y chromosome may cause disorders of sex differentiation or, more frequently, azoospermia. This study aimed to determine the prevalence of loss of Y chromosome material within the spectrum ranging from small microdeletions in the azoospermia factor region (AZF) to complete loss of the Y chromosome in azoospermic men. RESULTS Eleven of 865 azoospermic men (1.3%) collected from 1997 to 2022 were found to have a karyotype including a 45,X cell line. Two had a pure 45,X karyotype and nine had a 45,X/46,XY mosaic karyotype. The AZF region, or part of it, was deleted in eight of the nine men with a structural abnormal Y-chromosome. Seven men had a karyotype with a structural abnormal Y chromosome in a non-mosaic form. In addition, Y chromosome microdeletions were found in 34 men with a structural normal Y chromosome. No congenital malformations were detected by echocardiography and ultrasonography of the kidneys of the 11 men with a 45,X mosaic or non-mosaic cell line. CONCLUSIONS In men with azoospermia, Y chromosome loss ranging from small microdeletions to complete loss of the Y chromosome was found in 6.1% (53/865). Partial AZFb microdeletions may give a milder testicular phenotype compared to complete AZFb microdeletions.
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Affiliation(s)
- J Fedder
- Centre of Andrology & Fertility Clinic, Odense University Hospital, Kløvervænget 23, DK-5000, Odense, Denmark.
- Department of Clinical Medicine, University of Southern Denmark, Odense, Denmark.
- Fertility Clinic, Horsens Hospital, Horsens, Denmark.
| | - C Fagerberg
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
| | - M W Jørgensen
- Department of Clinical Genetics, Lillebaelt Hospital, Vejle, Denmark
| | - C H Gravholt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Endocrinology, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - A Berglund
- Department of Clinical Genetics, Odense University Hospital, Odense, Denmark
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - U B Knudsen
- Fertility Clinic, Horsens Hospital, Horsens, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - A Skakkebæk
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
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22
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Chang VC, Zhou W, Berndt SI, Andreotti G, Yeager M, Parks CG, Sandler DP, Rothman N, Beane Freeman LE, Machiela MJ, Hofmann JN. Glyphosate Use and Mosaic Loss of Chromosome Y among Male Farmers in the Agricultural Health Study. ENVIRONMENTAL HEALTH PERSPECTIVES 2023; 131:127006. [PMID: 38055050 PMCID: PMC10699410 DOI: 10.1289/ehp12834] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 11/01/2023] [Accepted: 11/15/2023] [Indexed: 12/07/2023]
Abstract
BACKGROUND Glyphosate is the most commonly used herbicide worldwide and has been implicated in the development of certain hematologic cancers. Although mechanistic studies in human cells and animals support the genotoxic effects of glyphosate, evidence in human populations is scarce. OBJECTIVES We evaluated the association between lifetime occupational glyphosate use and mosaic loss of chromosome Y (mLOY) as a marker of genotoxicity among male farmers. METHODS We analyzed blood-derived DNA from 1,606 farmers ≥ 50 years of age in the Biomarkers of Exposure and Effect in Agriculture study, a subcohort of the Agricultural Health Study. mLOY was detected using genotyping array intensity data in the pseudoautosomal region of the sex chromosomes. Cumulative lifetime glyphosate use was assessed using self-reported pesticide exposure histories. Using multivariable logistic regression, we estimated odds ratios (ORs) and 95% confidence intervals (CIs) for the associations between glyphosate use and any detectable mLOY (overall mLOY) or mLOY affecting ≥ 10 % of cells (expanded mLOY). RESULTS Overall, mLOY was detected in 21.4% of farmers, and 9.8% of all farmers had expanded mLOY. Increasing total lifetime days of glyphosate use was associated with expanded mLOY [highest vs. lowest quartile; OR = 1.75 (95% CI: 1.00, 3.07), p trend = 0.03 ] but not with overall mLOY; the associations with expanded mLOY were most apparent among older (≥ 70 years of age) men [OR = 2.30 (95% CI: 1.13, 4.67), p trend = 0.01 ], never smokers [OR = 2.32 (95% CI: 1.04, 5.21), p trend = 0.04 ], and nonobese men [OR = 2.04 (95% CI: 0.99, 4.19), p trend = 0.03 ]. Similar patterns of associations were observed for intensity-weighted lifetime days of glyphosate use. DISCUSSION High lifetime glyphosate use could be associated with mLOY affecting a larger fraction of cells, suggesting glyphosate could confer genotoxic or selective effects relevant for clonal expansion. As the first study to investigate this association, our findings contribute novel evidence regarding the carcinogenic potential of glyphosate and require replication in future studies. https://doi.org/10.1289/EHP12834.
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Affiliation(s)
- Vicky C. Chang
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Weiyin Zhou
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, USA
| | - Sonja I. Berndt
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Gabriella Andreotti
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Meredith Yeager
- Cancer Genomics Research Laboratory, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, USA
| | - Christine G. Parks
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, North Carolina, USA
| | - Dale P. Sandler
- Epidemiology Branch, National Institute of Environmental Health Sciences, NIH, DHHS, Durham, North Carolina, USA
| | - Nathaniel Rothman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Laura E. Beane Freeman
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
| | - Mitchell J. Machiela
- Integrative Tumor Epidemiology Branch, Division of Cancer Epidemiology and Genetics, NCI, NIH, DHHS, Bethesda, Maryland, USA
| | - Jonathan N. Hofmann
- Occupational and Environmental Epidemiology Branch, Division of Cancer Epidemiology and Genetics, National Cancer Institute (NCI), National Institutes of Health (NIH), Department of Health and Human Services (DHHS), Bethesda, Maryland, USA
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23
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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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24
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Dyrskjøt L, Hansel DE, Efstathiou JA, Knowles MA, Galsky MD, Teoh J, Theodorescu D. Bladder cancer. Nat Rev Dis Primers 2023; 9:58. [PMID: 37884563 PMCID: PMC11218610 DOI: 10.1038/s41572-023-00468-9] [Citation(s) in RCA: 61] [Impact Index Per Article: 61.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 09/20/2023] [Indexed: 10/28/2023]
Abstract
Bladder cancer is a global health issue with sex differences in incidence and prognosis. Bladder cancer has distinct molecular subtypes with multiple pathogenic pathways depending on whether the disease is non-muscle invasive or muscle invasive. The mutational burden is higher in muscle-invasive than in non-muscle-invasive disease. Commonly mutated genes include TERT, FGFR3, TP53, PIK3CA, STAG2 and genes involved in chromatin modification. Subtyping of both forms of bladder cancer is likely to change considerably with the advent of single-cell analysis methods. Early detection signifies a better disease prognosis; thus, minimally invasive diagnostic options are needed to improve patient outcomes. Urine-based tests are available for disease diagnosis and surveillance, and analysis of blood-based cell-free DNA is a promising tool for the detection of minimal residual disease and metastatic relapse. Transurethral resection is the cornerstone treatment for non-muscle-invasive bladder cancer and intravesical therapy can further improve oncological outcomes. For muscle-invasive bladder cancer, radical cystectomy with neoadjuvant chemotherapy is the standard of care with evidence supporting trimodality therapy. Immune-checkpoint inhibitors have demonstrated benefit in non-muscle-invasive, muscle-invasive and metastatic bladder cancer. Effective management requires a multidisciplinary approach that considers patient characteristics and molecular disease characteristics.
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Affiliation(s)
- Lars Dyrskjøt
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark
| | - Donna E Hansel
- Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jason A Efstathiou
- Department of Radiation Oncology, Massachusetts General Hospital, Harvard Medical School, Boston, MA, USA
| | - Margaret A Knowles
- Division of Molecular Medicine, Leeds Institute of Medical Research at St James's, St James's University Hospital, Leeds, UK
| | - Matthew D Galsky
- Division of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Jeremy Teoh
- S.H. Ho Urology Centre, Department of Surgery, The Chinese University of Hong Kong, Hong Kong, China
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
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25
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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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Kuznetsova IL, Uralsky LI, Tyazhelova TV, Andreeva TV, Rogaev EI. Mosaic loss of the Y chromosome in human neurodegenerative and oncological diseases. Vavilovskii Zhurnal Genet Selektsii 2023; 27:502-511. [PMID: 37808213 PMCID: PMC10551935 DOI: 10.18699/vjgb-23-61] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 10/10/2023] Open
Abstract
The development of new biomarkers for prediction and early detection of human diseases, as well as for monitoring the response to therapy is one of the most relevant areas of modern human genetics and genomics. Until recently, it was believed that the function of human Y chromosome genes was limited to determining sex and controlling spermatogenesis. Thanks to occurance of large databases of the genome-wide association study (GWAS), there has been a transition to the use of large samples for analyzing genetic changes in both normal and pathological conditions. This has made it possible to assess the association of mosaic aneuploidy of the Y chromosome in somatic cells with a shorter lifespan in men compared to women. Based on data from the UK Biobank, an association was found between mosaic loss of the Y chromosome (mLOY) in peripheral blood leukocytes and the age of men over 70, as well as a number of oncological, cardiac, metabolic, neurodegenerative, and psychiatric diseases. As a result, mLOY in peripheral blood cells has been considered a potential marker of biological age in men and as a marker of certain age-related diseases. Currently, numerous associations have been identified between mLOY and genes based on GWAS and transcriptomes in affected tissues. However, the exact cause of mLOY and the impact and consequences of this phenomenon at the whole organism level have not been established. In particular, it is unclear whether aneuploidy of the Y chromosome in blood cells may affect the development of pathologies that manifest in other organs, such as the brain in Alzheimer's disease, or whether it is a neutral biomarker of general genomic instability. This review examines the main pathologies and genetic factors associated with mLOY, as well as the hypotheses regarding their interplay. Special attention is given to recent studies on mLOY in brain cells in Alzheimer's disease.
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Affiliation(s)
- I L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - L I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - T V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia
| | - T V Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
| | - E I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
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27
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Kuroki Y, Fukami M. Y Chromosome Genomic Variations and Biological Significance in Human Diseases and Health. Cytogenet Genome Res 2023; 163:5-13. [PMID: 37562362 DOI: 10.1159/000531933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 07/10/2023] [Indexed: 08/12/2023] Open
Abstract
The Y chromosome is a haploid genome unique to males with no genes essential for life. It is easily transmitted to the next generation without being repaired by recombination, even if a major genomic structural alteration occurs. On the other hand, the Y chromosome genome is basically a region transmitted only from father to son, reflecting a male-specific inheritance between generations. The Y chromosome exhibits genomic structural differences among different ethnic groups and individuals. The Y chromosome was previously thought to affect only male-specific phenotypes, but recent studies have revealed associations between the Y chromosomes and phenotypes common to both males and females, such as certain types of cancer and neuropsychiatric disorders. This evidence was discovered with the finding of the mosaic loss of the Y chromosome in somatic cells. This phenomenon is also affected by environmental factors, such as smoking and aging. In the past, functional analysis of the Y chromosome has been elucidated by assessing the function of Y chromosome-specific genes and the association between Y chromosome haplogroups and human phenotypes. These studies are currently being conducted intensively. Additionally, the recent advance of large-scale genome cohort studies has increased the amount of Y chromosome genomic information available for analysis, making it possible to conduct more precise studies of the relationship between genome structures and phenotypes. In this review, we will introduce recent analyses using large-scale genome cohort data and previously reported association studies between Y chromosome haplogroups and human phenotypes, such as male infertility, cancer, cardiovascular system traits, and neuropsychiatric disorders. The function and biological role of the Y chromosome in human phenotypes will also be discussed.
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Affiliation(s)
- Yoko Kuroki
- Department of Genome Medicine, National Center for Child Health and Development, Tokyo, Japan
- Division of Collaborative Research, National Center for Child Health and Development, Tokyo, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Maki Fukami
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Molecular Endocrinology, National Center for Child Health and Development, Tokyo, Japan
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28
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Demanelis K, Delgado DA, Tong L, Jasmine F, Ahmed A, Islam T, Parvez F, Kibriya MG, Graziano JH, Ahsan H, Pierce BL. Somatic loss of the Y chromosome is associated with arsenic exposure among Bangladeshi men. Int J Epidemiol 2023; 52:1035-1046. [PMID: 36130227 PMCID: PMC10695470 DOI: 10.1093/ije/dyac176] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Accepted: 09/01/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Arsenic exposure increases the risk of several cancers in humans and contributes to genomic instability. Somatic loss of the Y chromosome (LoY) is a potential biomarker of genomic instability and cancer risk. Smoking is associated with LoY, but few other carcinogens have been investigated. We tested the cross-sectional association between arsenic exposure and LoY in leukocytes among genotyped Bangladeshi men (age 20-70 years) from the Health Effects of Arsenic Longitudinal Study. METHODS We extracted the median of logR-ratios from probes on the Y chromosome (mLRR-chrY) from genotyping arrays (n = 1364) and estimated the percentage of cells with LoY (% LoY) from mLRR-chrY. We evaluated the association between arsenic exposure (measured in drinking water and urine) and LoY using multivariable linear and logistic regression models. The association between LoY and incident arsenic-induced skin lesions was also examined. RESULTS Ten percent of genotyped men had LoY in at least 5% of cells and % LoY increased with age. Among men randomly selected for genotyping (n = 778), higher arsenic in drinking water, arsenic consumed and urinary arsenic were associated with increased % LoY (P = 0.006, P = 0.06 and P = 0.13, respectively). LoY was associated with increased risk of incident skin lesions (P = 0.008). CONCLUSION Arsenic exposure was associated with increased LoY, providing additional evidence that arsenic contributes to genomic instability. LoY was associated with developing skin lesions, a risk factor for cancer, suggesting that LoY may be a biomarker of susceptibility in arsenic-exposed populations. The effect of arsenic on somatic events should be further explored in cancer-prone tissue types.
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Affiliation(s)
- Kathryn Demanelis
- Division of Hematology/Oncology, Department of Medicine, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Dayana A Delgado
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Lin Tong
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Farzana Jasmine
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | | | | | - Faruque Parvez
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Muhammad G Kibriya
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
| | - Joseph H Graziano
- Department of Environmental Health Sciences, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Habibul Ahsan
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
- Departments of Medicine and Human Genetics, The University of Chicago, Chicago, IL, USA
| | - Brandon L Pierce
- Department of Public Health Sciences, The University of Chicago, Chicago, IL, USA
- Department of Human Genetics, The University of Chicago, Chicago, IL, USA
- Comprehensive Cancer Center, The University of Chicago, Chicago, IL, USA
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29
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Cheng C, Hong W, Li Y, Xiao X, McKay J, Han Y, Byun J, Peng B, Albanes D, Lam S, Tardon A, Chen C, Bojesen SE, Landi MT, Johansson M, Risch A, Bickeböller H, Wichmann HE, Christiani DC, Rennert G, Arnold S, Goodman G, Field JK, Davies MPA, Shete SS, Le Marchand L, Liu G, Hung RJ, Andrew AS, Kiemeney LA, Zhu M, Shen H, Zienolddiny S, Grankvist K, Johansson M, Cox A, Hong YC, Yuan JM, Lazarus P, Schabath MB, Aldrich MC, Brennan P, Li Y, Gorlova O, Gorlov I, Amos CI. Mosaic Chromosomal Alterations Are Associated With Increased Lung Cancer Risk: Insight From the INTEGRAL-ILCCO Cohort Analysis. J Thorac Oncol 2023; 18:1003-1016. [PMID: 37150255 PMCID: PMC10435278 DOI: 10.1016/j.jtho.2023.05.001] [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: 03/14/2023] [Revised: 04/21/2023] [Accepted: 05/01/2023] [Indexed: 05/09/2023]
Abstract
INTRODUCTION Mosaic chromosomal alterations (mCAs) detected in white blood cells represent a type of clonal hematopoiesis (CH) that is understudied compared with CH-related somatic mutations. A few recent studies indicated their potential link with nonhematological cancers, especially lung cancer. METHODS In this study, we investigated the association between mCAs and lung cancer using the high-density genotyping data from the OncoArray study of INTEGRAL-ILCCO, the largest single genetic study of lung cancer with 18,221 lung cancer cases and 14,825 cancer-free controls. RESULTS We identified a comprehensive list of autosomal mCAs, ChrX mCAs, and mosaic ChrY (mChrY) losses from these samples. Autosomal mCAs were detected in 4.3% of subjects, in addition to ChrX mCAs in 3.6% of females and mChrY losses in 9.6% of males. Multivariable logistic regression analysis indicated that the presence of autosomal mCAs in white blood cells was associated with an increased lung cancer risk after adjusting for key confounding factors, including age, sex, smoking status, and race. This association was mainly driven by a specific type of mCAs: copy-neutral loss of heterozygosity on autosomal chromosomes. The association between autosome copy-neutral loss of heterozygosity and increased risk of lung cancer was further confirmed in two major histologic subtypes, lung adenocarcinoma and squamous cell carcinoma. In addition, we observed a significant increase of ChrX mCAs and mChrY losses in smokers compared with nonsmokers and racial differences in certain types of mCA events. CONCLUSIONS Our study established a link between mCAs in white blood cells and increased risk of lung cancer.
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Affiliation(s)
- Chao Cheng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Wei Hong
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - Yafang Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Xiangjun Xiao
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas
| | - James McKay
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Younghun Han
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Jinyoung Byun
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Bo Peng
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas
| | - Demetrios Albanes
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Stephen Lam
- Department of Integrative Oncology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Adonina Tardon
- Public Health Department, University of Oviedo, ISPA and CIBERESP, Asturias, Spain
| | - Chu Chen
- Program in Epidemiology, Public Health Sciences Division, Fred Hutchinson Cancer Center, Seattle, Washington
| | - Stig E Bojesen
- Department of Clinical Biochemistry, Copenhagen University Hospital, Copenhagen, Denmark; Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Maria T Landi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland
| | - Mattias Johansson
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Angela Risch
- Thoraxklinik at University Hospital Heidelberg, Heidelberg, Germany; Translational Lung Research Center Heidelberg (TLRC-H), Heidelberg, Germany; University of Salzburg and Cancer Cluster Salzburg, Salzburg, Austria
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center, Georg-August-University Göttingen, Göttingen, Germany
| | - H-Erich Wichmann
- Institute of Medical Statistics and Epidemiology, Technical University Munich, Munich, Germany
| | - David C Christiani
- Department of Environmental Health, Harvard T.H. Chan School of Public Health, Boston, Massachusetts; Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Gad Rennert
- Clalit National Cancer Control Center at Carmel Medical Center and Technion Faculty of Medicine, Haifa, Israel
| | - Susanne Arnold
- University of Kentucky, Markey Cancer Center, Lexington, Kentucky
| | | | - John K Field
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Michael P A Davies
- Department of Molecular and Clinical Cancer Medicine, University of Liverpool, Liverpool, United Kingdom
| | - Sanjay S Shete
- Department of Biostatistics, The University of Texas M. D. Anderson Cancer Center, Houston, Texas; Department of Epidemiology, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, Hawaii
| | - Geoffrey Liu
- University Health Network- The Princess Margaret Cancer Centre, Toronto, California
| | - Rayjean J Hung
- Luenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Canada; Division of Epidemiology, Dalla Lana School of Public Health, University of Toronto, Toronto, Canada
| | - Angeline S Andrew
- Department of Epidemiology, Dartmouth College, Hanover, New Hampshire; Department of Community and Family Medicine, Dartmouth College, Hanover, New Hampshire
| | | | - Meng Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | | | - Kjell Grankvist
- Department of Medical Biosciences, Umeå University, Umeå, Sweden
| | | | - Angela Cox
- Academic Unit of Clinical Oncology University of Sheffield, Weston Park Hospital, Whitham Road, Sheffield, United Kingdom
| | - Yun-Chul Hong
- Department of Preventive Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Jian-Min Yuan
- University of Pittsburgh Medical Center (UPMC) Hillman Cancer Center, Pittsburgh, Pennsylvania
| | - Philip Lazarus
- Department of Pharmaceutical Sciences, College of Pharmacy and Pharmaceutical Sciences, Washington State University, Spokane, Washington
| | - Matthew B Schabath
- Department of Cancer Epidemiology, H. Lee Moffitt Cancer Center and Research Institute, Tampa, Florida
| | - Melinda C Aldrich
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Paul Brennan
- Section of Genetics, International Agency for Research on Cancer, WHO, Lyon, France
| | - Yong Li
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Olga Gorlova
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Ivan Gorlov
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Christopher I Amos
- Institute for Clinical and Translational Research, Baylor College of Medicine, Houston, Texas; Section of Epidemiology and Population Sciences, Department of Medicine, Baylor College of Medicine, Houston, Texas; Dan L Duncan Comprehensive Cancer Center, Baylor College of Medicine, Houston, Texas.
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30
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Abdel-Hafiz HA, Schafer JM, Chen X, Xiao T, Gauntner TD, Li Z, Theodorescu D. Y chromosome loss in cancer drives growth by evasion of adaptive immunity. Nature 2023; 619:624-631. [PMID: 37344596 PMCID: PMC10975863 DOI: 10.1038/s41586-023-06234-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 51.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Accepted: 05/18/2023] [Indexed: 06/23/2023]
Abstract
Loss of the Y chromosome (LOY) is observed in multiple cancer types, including 10-40% of bladder cancers1-6, but its clinical and biological significance is unknown. Here, using genomic and transcriptomic studies, we report that LOY correlates with poor prognoses in patients with bladder cancer. We performed in-depth studies of naturally occurring LOY mutant bladder cancer cells as well as those with targeted deletion of Y chromosome by CRISPR-Cas9. Y-positive (Y+) and Y-negative (Y-) tumours grew similarly in vitro, whereas Y- tumours were more aggressive than Y+ tumours in immune-competent hosts in a T cell-dependent manner. High-dimensional flow cytometric analyses demonstrated that Y- tumours promote striking dysfunction or exhaustion of CD8+ T cells in the tumour microenvironment. These findings were validated using single-nuclei RNA sequencing and spatial proteomic evaluation of human bladder cancers. Of note, compared with Y+ tumours, Y- tumours exhibited an increased response to anti-PD-1 immune checkpoint blockade therapy in both mice and patients with cancer. Together, these results demonstrate that cancer cells with LOY mutations alter T cell function, promoting T cell exhaustion and sensitizing them to PD-1-targeted immunotherapy. This work provides insights into the basic biology of LOY mutation and potential biomarkers for improving cancer immunotherapy.
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Affiliation(s)
- Hany A Abdel-Hafiz
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Johanna M Schafer
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
- Roche Diagnostics Solutions, Oro Valley, AZ, USA
| | - Xingyu Chen
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Timothy D Gauntner
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Dan Theodorescu
- Department of Urology, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA.
- Cedars-Sinai Cancer Center, Los Angeles, CA, USA.
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31
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Sano S, Thel MC, Walsh K. Mosaic Loss of Y Chromosome in White Blood Cells: Its Impact on Men's Health. Physiology (Bethesda) 2023; 38:0. [PMID: 36976266 PMCID: PMC10281780 DOI: 10.1152/physiol.00008.2023] [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: 02/27/2023] [Revised: 03/27/2023] [Accepted: 03/27/2023] [Indexed: 03/29/2023] Open
Abstract
We present a brief introduction of loss of Y chromosome (LOY) in blood and describe the known risk factors for this condition. We then overview the associations between LOY and age-related disease traits. Finally, we discuss murine models and the potential mechanisms by which LOY contributes to disease.
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Affiliation(s)
- Soichi Sano
- Department of Cardiovascular Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka, Japan
- Laboratory of Cardiovascular Mosaicism, National Cerebral and Cardiovascular Center, Osaka, Japan
| | - Mark C Thel
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, United States
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, United States
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32
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Jiang L, Song M, Song F, Zhou Y, Yao H, Li G, Luo H. Characterization of loss of chromosome Y in peripheral blood cells in male Han Chinese patients with schizophrenia. BMC Psychiatry 2023; 23:469. [PMID: 37370034 DOI: 10.1186/s12888-023-04929-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/06/2023] [Indexed: 06/29/2023] Open
Abstract
BACKGROUND Schizophrenia (SCZ) has a global prevalence of 1% and increases the risk of mortality, reducing life expectancy. There is growing evidence that the risk of this disorder is higher in males than in females and it tends to develop in early adulthood. The Y chromosome is thought to be involved in biological processes other than sex determination and spermatogenesis. Studies have shown that loss of chromosome Y (LOY) in peripheral blood cells is associated with a variety of diseases (including cancer) and increased all-cause mortality. An analysis of the relationship between LOY and schizophrenia is warranted. METHODS A total of 442 Chinese males (271 patients with schizophrenia vs. 171 controls) were included in this study. The copy numbers of the Y and X chromosomes were detected by positive droplets targeting the amelogenin gene (AMEL) on the Y chromosome and X chromosome (AMELY and AMELX, respectively), using droplet digital PCR (ddPCR). The LOY percentage was defined as the difference between the concentration of AMELX and the concentration of AMELY divided by the concentration of AMELX, denoted as (X - Y)/X. RESULTS In the Han Chinese population, the LOY percentage was higher in the schizophrenia group than in the control group (p < 0.05), although there was no significant difference in the presence of LOY between the two groups. A strong correlation was found between the average of the disease duration and the average of the LOY percentage (R2 = 0.506, p = 0.032). The logistic regression analysis implied that the risk of LOY increases by 0.058 and 0.057 per year according to age at onset and duration of disease, respectively (ponset = 0.013, pduration = 0.017). CONCLUSIONS In the Han Chinese population, the LOY percentage of the disease group was significantly different from that of the control group. The age of onset and duration of schizophrenia might be risk factors for LOY in peripheral blood cells. A larger sample size and expanded clinical information are needed for more in-depth and specific analyses.
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Affiliation(s)
- Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, Sichuan, China
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Yuxiang Zhou
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Hewen Yao
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China
| | - Gangqin Li
- Department of Forensic Psychiatry, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China.
| | - Haibo Luo
- Department of Forensic Genetics, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan Province, China.
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Abstract
Although sex differences have been noted in cellular function and behavior, therapy efficacy, and disease incidence and outcomes, the adoption of sex as a biological variable in tissue engineering and regenerative medicine remains limited. Furthering the development of personalized, precision medicine requires considering biological sex at the bench and in the clinic. This review provides the basis for considering biological sex when designing tissue-engineered constructs and regenerative therapies by contextualizing sex as a biological variable within the tissue engineering triad of cells, matrices, and signals. To achieve equity in biological sex within medicine requires a cultural shift in science and engineering research, with active engagement by researchers, clinicians, companies, policymakers, and funding agencies.
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Affiliation(s)
- Josephine B Allen
- Department of Materials Science and Engineering, University of Florida, Gainesville, Florida, USA;
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA;
| | - Christopher Ludtka
- J. Crayton Pruitt Family Department of Biomedical Engineering, University of Florida, Gainesville, Florida, USA;
| | - Bryan D James
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA;
- Department of Biology, Woods Hole Oceanographic Institution, Woods Hole, Massachusetts, USA
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Song M, Jiang L, Wang X, Zhou W, Wang N, Hou Y, Song F. Loss of Y chromosome in leukocytes can be regarded as a male-specific age predictor for age group estimation in forensic genetics. Mol Genet Genomics 2023:10.1007/s00438-023-02039-9. [PMID: 37285076 DOI: 10.1007/s00438-023-02039-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/18/2023] [Indexed: 06/08/2023]
Abstract
Age prediction is an important field in forensic and aging research. Traditional methods used DNA methylation, telomere shortening, and mitochondrial DNA mutations to conduct age prediction models. Sex chromosomes, like the Y chromosome, have a significant role in aging as previously reported in hematopoietic disease and many non-reproductive cancers. Until now, there is no age predictor based on the percentage of loss of Y chromosome (LOY). LOY has been previously revealed to be correlated with Alzheimer's disease, short survival, and higher risk of cancer. The possible correlation of LOY between normal aging was not fully explored. In this study, we conducted age prediction by measuring LOY percentage by droplet digital PCR (ddPCR), based on 232 healthy male samples, including 171 blood samples, 49 saliva samples, 12 semen samples. The age group of samples ranges from 0 to 99 years, with two individuals in almost every single age. Pearson correlation method was performed to calculate the correlation index. The result indicated a correlation index of 0.21 (p = 0.0059) between age and LOY percentage in blood samples, with the regression formula being y = - 0.016823 + 0.001098x. The correlation between LOY percentage and age is obvious only when the individuals were divided into different age groups (R = 0.73, p = 0.016). In the studied saliva and semen samples, p-values of the correlation are 0.11 and 0.20, respectively, showing no significant association between age and LOY percentage in these two biological materials. For the first time, we investigated male-specific age predictor based on LOY. The study showed that LOY in leukocytes can be regarded as a male-specific age predictor for age group estimation in forensic genetics. This study might be indicative for forensic applications and aging research.
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Affiliation(s)
- Mengyuan Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Lanrui Jiang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Xindi Wang
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Wenjing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Nian Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, People's Republic of China
| | - Yiping Hou
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China.
| | - Feng Song
- Department of Forensic Genetics, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, People's Republic of China.
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35
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Kobayashi T, Hachiya T, Ikehata Y, Horie S. Genetic association of mosaic loss of chromosome Y with prostate cancer in men of European and East Asian ancestries: a Mendelian randomization study. FRONTIERS IN AGING 2023; 4:1176451. [PMID: 37323536 PMCID: PMC10264619 DOI: 10.3389/fragi.2023.1176451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023]
Abstract
Background: Genomic instability is a significant hallmark of aging and has a major impact on aging biology. Mosaic loss of chromosome Y (mLOY) in blood cells is a common chromosomal abnormality in aging men and is considered an indicator of genomic instability. Previous studies have indicated a connection between mLOY and prostate cancer risk, but the causal relationship has not been fully established. Methods: To determine the causal effect of mLOY on prostate cancer, we conducted a Mendelian Randomization (MR) study in two ancestral groups. We utilized 125 and 42 mLOY-associated variants as instrumental variables (IVs) in European and East Asian GWAS of prostate cancer, respectively. Summary-level data on prostate cancer was obtained from the PRACTICAL consortium (79,148 cases and 61,106 controls of European ancestry) and the Biobank Japan consortium (5,408 cases and 103,939 controls of East Asian ancestry). A single population was used to assess the causal relationship in East Asian ancestry. Our main method for obtaining MR results was inverse-variance weighted (IVW), and we conducted sensitivity analyses to confirm the robustness of our results. Finally, we combined the estimates from both sources using a fixed-effects meta-analysis. Results: Our MR analysis using the IVW method showed that a one-unit increase in genetically predicted mLOY was associated with an increased risk of prostate cancer in the PRACTICAL consortium (OR = 1.09%, 95% CI: 1.05-1.13, p = 1.2 × 10-5), but not in the Biobank Japan consortium (OR = 1.13%, 95% CI: 0.88-1.45, p = 0.34). Sensitivity analyses robustly indicated increased odds ratios for prostate cancer with every one-unit increase in genetically predicted mLOY for the PRACTICAL consortium. Furthermore, mLOY was found to be associated with prostate cancer risk in a meta-analysis of both sources (OR = 1.09%, 95% CI: 1.05-1.13, p = 8.0 × 10-6). Conclusion: Our MR study provides strong evidence that higher mLOY increases the risk of prostate cancer. Preventing mLOY may be a means of reducing the risk of developing prostate cancer.
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Affiliation(s)
- Takuro Kobayashi
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Tsuyoshi Hachiya
- Department of Advanced Informatics for Genetic Diseases, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Yoshihiro Ikehata
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
| | - Shigeo Horie
- Department of Urology, Graduate School of Medicine, Juntendo University, Tokyo, Japan
- Department of Advanced Informatics for Genetic Diseases, Graduate School of Medicine, Juntendo University, Tokyo, Japan
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36
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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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37
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Sano S, Thel MC, Walsh K. Clonal hematopoiesis: the nonhereditary genetics of age-associated cardiovascular disease. Curr Opin Cardiol 2023; 38:201-206. [PMID: 36811645 PMCID: PMC10079606 DOI: 10.1097/hco.0000000000001032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
Abstract
PURPOSE OF REVIEW Somatic mutations, described as noninherited changes in DNA that arise and are passed on to descendant cells, are well known to cause cancers; however, it is increasingly appreciated that the propagation of somatic mutations within a tissue may have a role in causing nonneoplastic disorders and abnormalities in elderly individuals. The nonmalignant clonal expansion of somatic mutations in the hematopoietic system is termed clonal hematopoiesis. This review will briefly discuss how this condition has been linked to various age-related diseases outside the hematopoietic system. RECENT FINDINGS Clonal hematopoiesis, resulting from leukemic driver gene mutations or mosaic loss of the Y chromosome in leukocytes, is associated with the development of various forms of cardiovascular disease, including atherosclerosis and heart failure, in a mutation-dependent manner. SUMMARY Accumulating evidence shows that clonal hematopoiesis represents a new mechanism for cardiovascular disease and a new risk factor that is as prevalent and consequential as the traditional risk factors that have been studied for decades.
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Affiliation(s)
- Soichi Sano
- National Cerebral and Cardiovascular Center, Osaka 564-8565, Japan
| | - Mark C. Thel
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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38
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Dawoud AA, Tapper WJ, Cross NC. Age-related loss of chromosome Y is associated with levels of sex hormone binding globulin and clonal hematopoiesis defined by TET2, TP53, and CBL mutations. SCIENCE ADVANCES 2023; 9:eade9746. [PMID: 37083525 PMCID: PMC10121166 DOI: 10.1126/sciadv.ade9746] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Figures] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Mosaic loss of the Y-chromosome (LOY) in peripheral blood leukocytes is the most common somatic alteration in men and linked to wide range of malignant and nonmalignant conditions. LOY is associated with age, smoking, and constitutional genetics. Here, we aimed to assess the relationships between LOY, serum biomarkers, and clonal hematopoiesis (CH). LOY in U.K. Biobank was strongly associated with levels of sex hormone binding globulin (SHBG), a key regulator of testosterone bioavailability. Mendelian randomization suggested a causal effect of SHBG on LOY but there was no evidence for an effect of LOY on SHBG. In contrast, age-related CH defined by somatic driver mutations was not associated with SHBG but was associated with LOY at clonal fractions above 30%. TET2, TP53, and CBL mutations were enriched in LOY cases, but JAK2 V617F was depleted. Our findings thus identify independent relationships between LOY, sex hormone levels, and CH.
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Affiliation(s)
- Ahmed A. Z. Dawoud
- School of Medicine, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire SP2 8BJ, UK
| | - William J. Tapper
- School of Medicine, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
| | - Nicholas C. P. Cross
- School of Medicine, University of Southampton, Southampton, Hampshire SO17 1BJ, UK
- Wessex Regional Genetics Laboratory, Salisbury NHS Foundation Trust, Salisbury, Wiltshire SP2 8BJ, UK
- Corresponding author.
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39
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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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40
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Liu A, Genovese G, Zhao Y, Pirinen M, Zekavat MM, Kentistou K, Yang Z, Yu K, Vlasschaert C, Liu X, Brown DW, Hudjashov G, Gorman B, Dennis J, Zhou W, Momozawa Y, Pyarajan S, Tuzov V, Pajuste FD, Aavikko M, Sipilä TP, Ghazal A, Huang WY, Freedman N, Song L, Gardner EJ, Sankaran VG, Palotie A, Ollila HM, Tukiainen T, Chanock SJ, Mägi R, Natarajan P, Daly MJ, Bick A, McCarroll SA, Terao C, Loh PR, Ganna A, Perry JRB, Machiela MJ. Population analyses of mosaic X chromosome loss identify genetic drivers and widespread signatures of cellular selection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.01.28.23285140. [PMID: 36778285 PMCID: PMC9915812 DOI: 10.1101/2023.01.28.23285140] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Mosaic loss of the X chromosome (mLOX) is the most commonly occurring clonal somatic alteration detected in the leukocytes of women, yet little is known about its genetic determinants or phenotypic consequences. To address this, we estimated mLOX in >900,000 women across eight biobanks, identifying 10% of women with detectable X loss in approximately 2% of their leukocytes. Out of 1,253 diseases examined, women with mLOX had an elevated risk of myeloid and lymphoid leukemias and pneumonia. Genetic analyses identified 49 common variants influencing mLOX, implicating genes with established roles in chromosomal missegregation, cancer predisposition, and autoimmune diseases. Complementary exome-sequence analyses identified rare missense variants in FBXO10 which confer a two-fold increased risk of mLOX. A small fraction of these associations were shared with mosaic Y chromosome loss in men, suggesting different biological processes drive the formation and clonal expansion of sex chromosome missegregation events. Allelic shift analyses identified alleles on the X chromosome which are preferentially retained, demonstrating that variation at many loci across the X chromosome is under cellular selection. A novel polygenic score including 44 independent X chromosome allelic shift loci correctly inferred the retained X chromosomes in 80.7% of mLOX cases in the top decile. Collectively our results support a model where germline variants predispose women to acquiring mLOX, with the allelic content of the X chromosome possibly shaping the magnitude of subsequent clonal expansion.
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Affiliation(s)
- Aoxing Liu
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally: Aoxing Liu, Giulio Genovese, Yajie Zhao
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- These authors contributed equally: Aoxing Liu, Giulio Genovese, Yajie Zhao
| | - Yajie Zhao
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- These authors contributed equally: Aoxing Liu, Giulio Genovese, Yajie Zhao
| | - Matti Pirinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Department of Publich Health, University of Helsinki, Helsinki, Finland
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland
| | - Maryam M Zekavat
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
| | - Katherine Kentistou
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Zhiyu Yang
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kai Yu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Xiaoxi Liu
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - 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
| | - Georgi Hudjashov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Bryan Gorman
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Booz Allen Hamilton, McLean, VA, USA
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saiju Pyarajan
- Center for Data and Computational Sciences (C-DACS), VA Cooperative Studies Program, VA Boston Healthcare System, Boston, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Vlad Tuzov
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Fanny-Dhelia Pajuste
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Mervi Aavikko
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Timo P Sipilä
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Awaisa Ghazal
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Wen-Yi Huang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Neal Freedman
- 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
| | - Eugene J Gardner
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Vijay G Sankaran
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Hanna M Ollila
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Anesthesia, Critical Care, and Pain Medicine, Massachusetts General Hospital, Boston, MA, USA
- Center of Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Taru Tukiainen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Reedik Mägi
- Estonian Genome Centre, Institute of Genomics, University of Tartu, Tartu, Estonia
| | - Pradeep Natarajan
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA, USA
- Center of Genomic Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Mark J Daly
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
| | - Alexander Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Steven A McCarroll
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
| | - Andrea Ganna
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Stanley Center, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA, USA
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
| | - John R B Perry
- MRC Epidemiology Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
- These authors jointly supervised this work: Po-Ru Loh, Andrea Ganna, John R.B. Perry, Mitchell J. Machiela
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41
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Evans MA, Walsh K. Clonal hematopoiesis, somatic mosaicism, and age-associated disease. Physiol Rev 2023; 103:649-716. [PMID: 36049115 PMCID: PMC9639777 DOI: 10.1152/physrev.00004.2022] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Revised: 07/19/2022] [Accepted: 08/02/2022] [Indexed: 12/15/2022] Open
Abstract
Somatic mosaicism, the occurrence of multiple genetically distinct cell clones within the same tissue, is an evitable consequence of human aging. The hematopoietic system is no exception to this, where studies have revealed the presence of expanded blood cell clones carrying mutations in preleukemic driver genes and/or genetic alterations in chromosomes. This phenomenon is referred to as clonal hematopoiesis and is remarkably prevalent in elderly individuals. While clonal hematopoiesis represents an early step toward a hematological malignancy, most individuals will never develop blood cancer. Somewhat unexpectedly, epidemiological studies have found that clonal hematopoiesis is associated with an increase in the risk of all-cause mortality and age-related disease, particularly in the cardiovascular system. Studies using murine models of clonal hematopoiesis have begun to shed light on this relationship, suggesting that driver mutations in mature blood cells can causally contribute to aging and disease by augmenting inflammatory processes. Here we provide an up-to-date review of clonal hematopoiesis within the context of somatic mosaicism and aging and describe recent epidemiological studies that have reported associations with age-related disease. We will also discuss the experimental studies that have provided important mechanistic insight into how driver mutations promote age-related disease and how this knowledge could be leveraged to treat individuals with clonal hematopoiesis.
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Affiliation(s)
- Megan A Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia
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Bruhn-Olszewska B, Davies H, Sarkisyan D, Juhas U, Rychlicka-Buniowska E, Wójcik M, Horbacz M, Jąkalski M, Olszewski P, Westholm JO, Smialowska A, Wierzba K, Torinsson Naluai Å, Jern N, Andersson LM, Järhult JD, Filipowicz N, Tiensuu Janson E, Rubertsson S, Lipcsey M, Gisslén M, Hultström M, Frithiof R, Dumanski JP. Loss of Y in leukocytes as a risk factor for critical COVID-19 in men. Genome Med 2022; 14:139. [PMID: 36514076 PMCID: PMC9747543 DOI: 10.1186/s13073-022-01144-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 11/23/2022] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The COVID-19 pandemic, which has a prominent social and economic impact worldwide, shows a largely unexplained male bias for the severity and mortality of the disease. Loss of chromosome Y (LOY) is a risk factor candidate in COVID-19 due to its prior association with many chronic age-related diseases, and its impact on immune gene transcription. METHODS Publicly available scRNA-seq data of PBMC samples derived from male patients critically ill with COVID-19 were reanalyzed, and LOY status was added to the annotated cells. We further studied LOY in whole blood for 211 COVID-19 patients treated at intensive care units (ICU) from the first and second waves of the pandemic. Of these, 139 patients were subject to cell sorting for LOY analysis in granulocytes, low-density neutrophils (LDNs), monocytes, and PBMCs. RESULTS Reanalysis of available scRNA-seq data revealed LDNs and monocytes as the cell types most affected by LOY. Subsequently, DNA analysis indicated that 46%, 32%, and 29% of critically ill patients showed LOY above 5% cut-off in LDNs, granulocytes, and monocytes, respectively. Hence, the myeloid lineage that is crucial for the development of severe COVID-19 phenotype is affected by LOY. Moreover, LOY correlated with increasing WHO score (median difference 1.59%, 95% HDI 0.46% to 2.71%, p=0.025), death during ICU treatment (median difference 1.46%, 95% HDI 0.47% to 2.43%, p=0.0036), and history of vessel disease (median difference 2.16%, 95% HDI 0.74% to 3.7%, p=0.004), among other variables. In 16 recovered patients, sampled during ICU stay and 93-143 days later, LOY decreased significantly in whole blood and PBMCs. Furthermore, the number of LDNs at the recovery stage decreased dramatically (median difference 76.4 per 10,000 cell sorting events, 95% HDI 55.5 to 104, p=6e-11). CONCLUSIONS We present a link between LOY and an acute, life-threatening infectious disease. Furthermore, this study highlights LOY as the most prominent clonal mutation affecting the myeloid cell lineage during emergency myelopoiesis. The correlation between LOY level and COVID-19 severity might suggest that this mutation affects the functions of monocytes and neutrophils, which could have consequences for male innate immunity.
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Affiliation(s)
- Bożena Bruhn-Olszewska
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Daniil Sarkisyan
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulana Juhas
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Edyta Rychlicka-Buniowska
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Magdalena Wójcik
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Monika Horbacz
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Marcin Jąkalski
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Paweł Olszewski
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Jakub O. Westholm
- grid.10548.380000 0004 1936 9377National Bioinformatics Infrastructure Sweden, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden
| | - Agata Smialowska
- grid.10548.380000 0004 1936 9377National Bioinformatics Infrastructure Sweden, Department of Biochemistry and Biophysics, Stockholm University, Science for Life Laboratory, Stockholm, Sweden
| | - Karol Wierzba
- grid.11451.300000 0001 0531 3426Department and Clinic of Rheumatology, Clinical Immunology, Geriatrics and Internal Medicine, Medical University of Gdańsk, Gdańsk, Poland
| | - Åsa Torinsson Naluai
- grid.8761.80000 0000 9919 9582Department of Laboratory Medicine, Institute of Biomedicine and Biobank Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Niklas Jern
- grid.8761.80000 0000 9919 9582Department of Laboratory Medicine, Institute of Biomedicine and Biobank Core Facility, Sahlgrenska Academy at the University of Gothenburg, Gothenburg, Sweden
| | - Lars-Magnus Andersson
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Josef D. Järhult
- grid.8993.b0000 0004 1936 9457Zoonosis Science Center, Department of Medical Sciences, Uppsala, Sweden, Uppsala University, Uppsala, Sweden
| | - Natalia Filipowicz
- grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
| | - Eva Tiensuu Janson
- grid.8993.b0000 0004 1936 9457Department of Medical Sciences, Endocrine Oncology Unit, Uppsala University, Uppsala, Sweden
| | - Sten Rubertsson
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Uppsala, Sweden
| | - Miklós Lipcsey
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Hedenstierna laboratory, Department of Surgical Sciences, Uppsala University, Uppsala, Sweden
| | - Magnus Gisslén
- grid.8761.80000 0000 9919 9582Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden ,grid.1649.a000000009445082XDepartment of Infectious Diseases, Region Västra Götaland, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Michael Hultström
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Uppsala, Sweden ,grid.8993.b0000 0004 1936 9457Integrative Physiology, Department of Medical Cell Biology, Uppsala University, Uppsala, Sweden
| | - Robert Frithiof
- grid.8993.b0000 0004 1936 9457Department of Surgical Sciences, Anesthesiology and Intensive Care, Uppsala University, Uppsala, Sweden
| | - Jan P. Dumanski
- grid.8993.b0000 0004 1936 9457Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden ,grid.11451.300000 0001 0531 34263P-Medicine Laboratory, Medical University of Gdańsk, Dębinki 7, 80-211 Gdańsk, Poland
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Kirtane K, St. John M, Fuentes-Bayne H, Patel SP, Mardiros A, Xu H, Ng EW, Go WY, Wong DJ, Sunwoo JB, Welch JS. Genomic Immune Evasion: Diagnostic and Therapeutic Opportunities in Head and Neck Squamous Cell Carcinomas. J Clin Med 2022; 11:jcm11247259. [PMID: 36555876 PMCID: PMC9781632 DOI: 10.3390/jcm11247259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Revised: 11/29/2022] [Accepted: 12/04/2022] [Indexed: 12/13/2022] Open
Abstract
Head and neck squamous cell cancers (HNSCCs) represent a diverse group of tumors emerging within different mucosal surfaces of the oral cavity, nasopharynx, oropharynx, larynx, and hypopharynx. HNSCCs share common clinical risk factors and genomic features, including smoking, alcohol, age, male sex, aneuploidy, and TP53 mutations. Viral initiating and contributing events are increasingly recognized in HNSCCs. While both Epstein-Barr Virus (EBV) and human papilloma virus (HPV) are observed, EBV is more frequently associated with nasopharyngeal cancers whereas HPV is associated with oropharyngeal cancers. HNSCCs are associated with high tumor mutational burden and loss of tumor suppressor gene function, especially in TP53 and X-linked genes. Multiple lines of evidence suggest that HNSCCs are subject to immunologic surveillance and immune-induced evolutionary pressure that correlate with negative clinical outcomes. This review will discuss genomic mechanisms related to immune-mediated pressures and propose prognostic and therapeutic implications of detectable immune escape mechanisms that drive tumorigenesis and disease progression.
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Affiliation(s)
| | - Maie St. John
- Otolaryngology, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | | | - Sandip P. Patel
- Moores Cancer Center, UCSD School of Medicine, San Diego, CA 92093, USA
| | | | - Han Xu
- A2 Biotherapeutics, Agoura Hills, CA 91301, USA
| | - Eric W. Ng
- A2 Biotherapeutics, Agoura Hills, CA 91301, USA
| | | | - Deborah J. Wong
- Otolaryngology, UCLA School of Medicine, Los Angeles, CA 90095, USA
| | - John B. Sunwoo
- Otolaryngology, Stanford University, Palo Alto, CA 94305, USA
| | - John S. Welch
- A2 Biotherapeutics, Agoura Hills, CA 91301, USA
- Correspondence:
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44
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Lam CM, Li Z, Theodorescu D, Li X. Mechanism of Sex Differences in Bladder Cancer: Evident and Elusive Sex-biasing Factors. Bladder Cancer 2022; 8:241-254. [PMID: 36277328 PMCID: PMC9536425 DOI: 10.3233/blc-211658] [Citation(s) in RCA: 6] [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: 12/27/2021] [Accepted: 06/14/2022] [Indexed: 11/26/2022]
Abstract
Bladder cancer incidence is drastically higher in males than females across geographical, racial, and socioeconomic strata. Despite potential differences in tumor biology, however, male and female bladder cancer patients are still clinically managed in highly similar ways. While sex hormones and sex chromosomes have been shown to promote observed sex differences, a more complex story lies beneath these evident sex-biasing factors than previously appreciated. Advances in genomic technology have spurred numerous preclinical studies characterizing elusive sex-biasing factors such as epigenetics, X chromosome inactivation escape genes, single nucleotide polymorphism, transcription regulation, metabolism, immunity, and many more. Sex-biasing effects, if properly understood, can be leveraged by future efforts in precision medicine based on a patient's biological sex. In this review, we will highlight key findings from the last half century that demystify the intricate ways in which sex-specific biology contribute to differences in pathogenesis as well as discuss future research directions.
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Affiliation(s)
- Christa M. Lam
- Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center – The James, Columbus, OH, USA
| | - Dan Theodorescu
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Department of Surgery, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Xue Li
- Department of Medicine and Department of Biomedical Sciences, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
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45
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Sano S, Horitani K, Ogawa H, Halvardson J, Chavkin NW, Wang Y, Sano M, Mattisson J, Hata A, Danielsson M, Miura-Yura E, Zaghlool A, Evans MA, Fall T, De Hoyos HN, Sundström J, Yura Y, Kour A, Arai Y, Thel MC, Arai Y, Mychaleckyj JC, Hirschi KK, Forsberg LA, Walsh K. Hematopoietic loss of Y chromosome leads to cardiac fibrosis and heart failure mortality. Science 2022; 377:292-297. [PMID: 35857592 PMCID: PMC9437978 DOI: 10.1126/science.abn3100] [Citation(s) in RCA: 88] [Impact Index Per Article: 44.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Hematopoietic mosaic loss of Y chromosome (mLOY) is associated with increased risk of mortality and age-related diseases in men, but the causal and mechanistic relationships have yet to be established. Here, we show that male mice reconstituted with bone marrow cells lacking the Y chromosome display increased mortality and age-related profibrotic pathologies including reduced cardiac function. Cardiac macrophages lacking the Y chromosome exhibited polarization toward a more fibrotic phenotype, and treatment with a transforming growth factor β1-neutralizing antibody ameliorated cardiac dysfunction in mLOY mice. A prospective study revealed that mLOY in blood is associated with an increased risk for cardiovascular disease and heart failure-associated mortality. Together, these results indicate that hematopoietic mLOY causally contributes to fibrosis, cardiac dysfunction, and mortality in men.
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Affiliation(s)
- Soichi Sano
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Cardiovascular Medicine, Osaka Metropolitan University Graduate School of Medicine, Osaka 545-8585, Japan
| | - Keita Horitani
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Hayato Ogawa
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75108 Uppsala, Sweden
| | - Nicholas W Chavkin
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA.,Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ying Wang
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Miho Sano
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75108 Uppsala, Sweden
| | - Atsushi Hata
- Chiba University Graduate School of Medicine, Department of General Thoracic Surgery, Chiba 260-8670, Japan
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75108 Uppsala, Sweden
| | - Emiri Miura-Yura
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Ammar Zaghlool
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75108 Uppsala, Sweden
| | - Megan A Evans
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Tove Fall
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Henry N De Hoyos
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Johan Sundström
- Department of Medical Sciences, Uppsala University, Sweden, and Uppsala Clinical Research Center, 78185 Uppsala, Sweden
| | - Yoshimitsu Yura
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Anupreet Kour
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yohei Arai
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Mark C Thel
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Yuka Arai
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Josyf C Mychaleckyj
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Karen K Hirschi
- Department of Cell Biology, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75108 Uppsala, Sweden.,The Beijer Laboratory, Uppsala University, 75185 Uppsala, Sweden
| | - Kenneth Walsh
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, VA 22908, USA
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46
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Cīrulis A, Hansson B, Abbott JK. Sex-limited chromosomes and non-reproductive traits. BMC Biol 2022; 20:156. [PMID: 35794589 PMCID: PMC9261002 DOI: 10.1186/s12915-022-01357-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 06/22/2022] [Indexed: 12/03/2022] Open
Abstract
Sex chromosomes are typically viewed as having originated from a pair of autosomes, and differentiated as the sex-limited chromosome (e.g. Y) has degenerated by losing most genes through cessation of recombination. While often thought that degenerated sex-limited chromosomes primarily affect traits involved in sex determination and sex cell production, accumulating evidence suggests they also influence traits not sex-limited or directly involved in reproduction. Here, we provide an overview of the effects of sex-limited chromosomes on non-reproductive traits in XY, ZW or UV sex determination systems, and discuss evolutionary processes maintaining variation at sex-limited chromosomes and molecular mechanisms affecting non-reproductive traits.
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Affiliation(s)
- Aivars Cīrulis
- Department of Biology, Lund University, 223 62, Lund, Sweden.
| | - Bengt Hansson
- Department of Biology, Lund University, 223 62, Lund, Sweden
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Levin MG, Nakao T, Zekavat SM, Koyama S, Bick AG, Niroula A, Ebert B, Damrauer SM, Natarajan P. Genetics of smoking and risk of clonal hematopoiesis. Sci Rep 2022; 12:7248. [PMID: 35508625 PMCID: PMC9068754 DOI: 10.1038/s41598-022-09604-z] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Accepted: 03/25/2022] [Indexed: 11/12/2022] Open
Abstract
Clonal hematopoiesis of indeterminate potential (CHIP) and mosaic chromosomal alterations (mCAs) represent two forms of clonal hematopoiesis where clones bearing expanded somatic mutations have been linked to both oncologic and non-oncologic clinical outcomes including atherosclerosis and all-cause mortality. Epidemiologic studies have highlighted smoking as an important driver of somatic mutations across multiple tissues. However, establishing the causal role of smoking in clonal hematopoiesis has been limited by observational study designs, which may suffer from confounding and reverse-causality. We performed two complementary analyses to investigate the role of smoking in mCAs and CHIP. First, using an observational study design among UK Biobank participants, we confirmed strong associations between smoking and mCAs. Second, using two-sample Mendelian randomization, smoking was strongly associated with mCA but not with CHIP. Overall, these results support a causal association between smoking and mCAs and suggest smoking may variably shape the fitness of clones bearing somatic mutations.
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Affiliation(s)
- Michael G Levin
- Division of Cardiovascular Medicine, Department of Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
| | - Tetsushi Nakao
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, CPZN 3.184, Boston, MA, 02114, USA
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Division of Cardiovascular Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Seyedeh M Zekavat
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Satoshi Koyama
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Alexander G Bick
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Abhishek Niroula
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Cancer Program, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Laboratory Medicine, Lund University, Lund, Sweden
| | - Benjamin Ebert
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, MA, USA
- Howard Hughes Medical Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Scott M Damrauer
- Corporal Michael J. Crescenz VA Medical Center, Philadelphia, PA, USA
- Department of Surgery, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Pradeep Natarajan
- Program in Medical and Population Genetics and Cardiovascular Disease Initiative, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Cardiovascular Research Center, Massachusetts General Hospital, 185 Cambridge Street, CPZN 3.184, Boston, MA, 02114, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
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48
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Filipowicz N, Drężek K, Horbacz M, Wojdak A, Szymanowski J, Rychlicka-Buniowska E, Juhas U, Duzowska K, Nowikiewicz T, Stańkowska W, Chojnowska K, Andreou M, Ławrynowicz U, Wójcik M, Davies H, Śrutek E, Bieńkowski M, Milian-Ciesielska K, Zdrenka M, Ambicka A, Przewoźnik M, Harazin-Lechowska A, Adamczyk A, Kowalski J, Bała D, Wiśniewski D, Tkaczyński K, Kamecki K, Drzewiecka M, Wroński P, Siekiera J, Ratnicka I, Jankau J, Wierzba K, Skokowski J, Połom K, Przydacz M, Bełch Ł, Chłosta P, Matuszewski M, Okoń K, Rostkowska O, Hellmann A, Sasim K, Remiszewski P, Sierżęga M, Hać S, Kobiela J, Kaska Ł, Jankowski M, Hodorowicz-Zaniewska D, Jaszczyński J, Zegarski W, Makarewicz W, Pęksa R, Szpor J, Ryś J, Szylberg Ł, Piotrowski A, Dumanski JP. Comprehensive cancer-oriented biobanking resource of human samples for studies of post-zygotic genetic variation involved in cancer predisposition. PLoS One 2022; 17:e0266111. [PMID: 35390022 PMCID: PMC8989288 DOI: 10.1371/journal.pone.0266111] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2021] [Accepted: 03/14/2022] [Indexed: 11/17/2022] Open
Abstract
The progress in translational cancer research relies on access to well-characterized samples from a representative number of patients and controls. The rationale behind our biobanking are explorations of post-zygotic pathogenic gene variants, especially in non-tumoral tissue, which might predispose to cancers. The targeted diagnoses are carcinomas of the breast (via mastectomy or breast conserving surgery), colon and rectum, prostate, and urinary bladder (via cystectomy or transurethral resection), exocrine pancreatic carcinoma as well as metastases of colorectal cancer to the liver. The choice was based on the high incidence of these cancers and/or frequent fatal outcome. We also collect age-matched normal controls. Our still ongoing collection originates from five clinical centers and after nearly 2-year cooperation reached 1711 patients and controls, yielding a total of 23226 independent samples, with an average of 74 donors and 1010 samples collected per month. The predominant diagnosis is breast carcinoma, with 933 donors, followed by colorectal carcinoma (383 donors), prostate carcinoma (221 donors), bladder carcinoma (81 donors), exocrine pancreatic carcinoma (15 donors) and metachronous colorectal cancer metastases to liver (14 donors). Forty percent of the total sample count originates from macroscopically healthy cancer-neighboring tissue, while contribution from tumors is 12%, which adds to the uniqueness of our collection for cancer predisposition studies. Moreover, we developed two program packages, enabling registration of patients, clinical data and samples at the participating hospitals as well as the central system of sample/data management at coordinating center. The approach used by us may serve as a model for dispersed biobanking from multiple satellite hospitals. Our biobanking resource ought to stimulate research into genetic mechanisms underlying the development of common cancers. It will allow all available "-omics" approaches on DNA-, RNA-, protein- and tissue levels to be applied. The collected samples can be made available to other research groups.
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Affiliation(s)
| | - Kinga Drężek
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Monika Horbacz
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Agata Wojdak
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Jakub Szymanowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Bioenit Jakub Szymanowski, Gdańsk, Poland
| | | | - Ulana Juhas
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Tomasz Nowikiewicz
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | | | | | - Maria Andreou
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Magdalena Wójcik
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ewa Śrutek
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Michał Bieńkowski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | | | - Marek Zdrenka
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Aleksandra Ambicka
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Agnieszka Adamczyk
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Jacek Kowalski
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Dariusz Bała
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Dorian Wiśniewski
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Karol Tkaczyński
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Krzysztof Kamecki
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Marta Drzewiecka
- Department of Breast Cancer and Reconstructive Surgery, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Paweł Wroński
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Jerzy Siekiera
- Department of Urology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Izabela Ratnicka
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jerzy Jankau
- Department of Plastic Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Wierzba
- Department of Internal Medicine, Connective Tissue Diseases and Geriatrics, Medical University of Gdańsk, Gdańsk, Poland
| | - Jarosław Skokowski
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
- Department of Medical Laboratory Diagnostics-Biobank, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Połom
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
| | - Mikołaj Przydacz
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Łukasz Bełch
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Piotr Chłosta
- Department of Urology, Jagiellonian University Medical College, Kraków, Poland
| | - Marcin Matuszewski
- Department and Clinic of Urology, Medical University of Gdańsk, Gdańsk, Poland
| | - Krzysztof Okoń
- Department of Pathomorphology, Jagiellonian University Medical College, Kraków, Poland
| | - Olga Rostkowska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Andrzej Hellmann
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Karol Sasim
- Clinic of Urology and Oncological Urology, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Piotr Remiszewski
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Marek Sierżęga
- Department of General, Oncological, and Gastrointestinal Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Stanisław Hać
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Jarosław Kobiela
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Łukasz Kaska
- Department of General, Endocrine and Transplant Surgery, Medical University of Gdańsk, Gdańsk, Poland
| | - Michał Jankowski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Diana Hodorowicz-Zaniewska
- Department of General, Oncological, and Gastrointestinal Surgery, Jagiellonian University Medical College, Kraków, Poland
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Wojciech Zegarski
- Surgical Oncology, Ludwik Rydygier’s Collegium Medicum, Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
- Department of Surgical Oncology, Oncology Center—Prof. Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
| | - Wojciech Makarewicz
- Department of Surgical Oncology, Medical University of Gdańsk, Gdańsk, Poland
- Clinic of General and Oncological Surgery, Specialist Hospital of Kościerzyna, Kościerzyna, Poland
| | - Rafał Pęksa
- Department of Pathomorphology, Medical University of Gdańsk, Gdańsk, Poland
| | - Joanna Szpor
- Department of Pathomorphology, Jagiellonian University Medical College, Kraków, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, Maria Skłodowska-Curie National Research Institute of Oncology, Kraków, Poland
| | - Łukasz Szylberg
- Department of Tumor Pathology and Pathomorphology, Oncology Center—Prof Franciszek Łukaszczyk Memorial Hospital, Bydgoszcz, Poland
- Department of Clinical Pathomorphology, Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University, Toruń, Poland
| | - Arkadiusz Piotrowski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
| | - Jan P. Dumanski
- 3P-Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Department of Biology and Pharmaceutical Botany, Medical University of Gdańsk, Gdańsk, Poland
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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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Abstract
Contrary to earlier beliefs, every cell in the individual is genetically different due to somatic mutations. Consequently, tissues become a mixture of cells with distinct genomes, a phenomenon termed somatic mosaicism. Recent advances in genome sequencing technology have unveiled possible causes of mutations and how they shape the unique mutational landscape of the tissues. Moreover, the analysis of sequencing data in combination with clinical information has revealed the impacts of somatic mosaicism on disease processes. In this review, we discuss somatic mosaicism in various tissues and its clinical implications for human disease.
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Affiliation(s)
- Hayato Ogawa
- Department of Cardiology, Meijo Hospital, Nagoya, Japan
- Department of Cardiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keita Horitani
- Hematovascular Biology Center, Robert M. Berne Cardiovascular Research Center, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Medicine II, Kansai Medical University, Hirakata, Japan
| | - Yasuhiro Izumiya
- Department of Cardiovascular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan;
| | - Soichi Sano
- Department of Cardiovascular Medicine, Osaka City University Graduate School of Medicine, Osaka, Japan;
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