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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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Anderson K, Cañadas-Garre M, Chambers R, Maxwell AP, McKnight AJ. The Challenges of Chromosome Y Analysis and the Implications for Chronic Kidney Disease. Front Genet 2019; 10:781. [PMID: 31552093 PMCID: PMC6737325 DOI: 10.3389/fgene.2019.00781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Accepted: 07/24/2019] [Indexed: 12/17/2022] Open
Abstract
The role of chromosome Y in chronic kidney disease (CKD) remains unknown, as chromosome Y is typically excluded from genetic analysis in CKD. The complex, sex-specific presentation of CKD could be influenced by chromosome Y genetic variation, but there is limited published research available to confirm or reject this hypothesis. Although traditionally thought to be associated with male-specific disease, evidence linking chromosome Y genetic variation to common complex disorders highlights a potential gap in CKD research. Chromosome Y variation has been associated with cardiovascular disease, a condition closely linked to CKD and one with a very similar sexual dimorphism. Relatively few sources of genetic variation in chromosome Y have been examined in CKD. The association between chromosome Y aneuploidy and CKD has never been explored comprehensively, while analyses of microdeletions, copy number variation, and single-nucleotide polymorphisms in CKD have been largely limited to the autosomes or chromosome X. In many studies, it is unclear whether the analyses excluded chromosome Y or simply did not report negative results. Lack of imputation, poor cross-study comparability, and requirement for separate or additional analyses in comparison with autosomal chromosomes means that chromosome Y is under-investigated in the context of CKD. Limitations in genotyping arrays could be overcome through use of whole-chromosome sequencing of chromosome Y that may allow analysis of many different types of genetic variation across the chromosome to determine if chromosome Y genetic variation is associated with CKD.
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Affiliation(s)
- Kerry Anderson
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Marisa Cañadas-Garre
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Robyn Chambers
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
| | - Alexander Peter Maxwell
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom.,Regional Nephrology Unit, Belfast City Hospital, Belfast, United Kingdom
| | - Amy Jayne McKnight
- Epidemiology and Public Health Research Group, Centre for Public Health, Queen's University of Belfast, c/o Regional Genetics Centre, Belfast City Hospital, Belfast, United Kingdom
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Khan SI, Andrews KL, Jennings GL, Sampson AK, Chin-Dusting JPF. Y Chromosome, Hypertension and Cardiovascular Disease: Is Inflammation the Answer? Int J Mol Sci 2019; 20:ijms20122892. [PMID: 31200567 PMCID: PMC6627840 DOI: 10.3390/ijms20122892] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 01/17/2023] Open
Abstract
It is now becomingly increasingly evident that the functions of the mammalian Y chromosome are not circumscribed to the induction of male sex. While animal studies have shown variations in the Y are strongly accountable for blood pressure (BP), this is yet to be confirmed in humans. We have recently shown modulation of adaptive immunity to be a significant mechanism underpinning Y-chromosome-dependent differences in BP in consomic strains. This is paralleled by studies in man showing Y chromosome haplogroup is a significant predictor for coronary artery disease through influencing pathways of immunity. Furthermore, recent studies in mice and humans have shown that Y chromosome lineage determines susceptibility to autoimmune disease. Here we review the evidence in animals and humans that Y chromosome lineage influences hypertension and cardiovascular disease risk, with a novel focus on pathways of immunity as a significant pathway involved.
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Affiliation(s)
- Shanzana I Khan
- Department of Pharmacology, Monash University, Clayton, Victoria 3800, Australia.
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia.
| | - Karen L Andrews
- Department of Pharmacology, Monash University, Clayton, Victoria 3800, Australia.
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia.
| | - Garry L Jennings
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia.
| | - Amanda K Sampson
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia.
| | - Jaye P F Chin-Dusting
- Department of Pharmacology, Monash University, Clayton, Victoria 3800, Australia.
- Baker IDI Heart and Diabetes Institute, Melbourne, Victoria 3004, Australia.
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Cunningham CM, Eghbali M. An Introduction to Epigenetics in Cardiovascular Development, Disease, and Sexualization. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1065:31-47. [PMID: 30051375 DOI: 10.1007/978-3-319-77932-4_2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Epigenetic regulation of gene expression is integral to cell differentiation, development, and disease. Modes of epigenetic regulation-including DNA methylation, histone modifications, and ncRNA-based regulation-alter chromatin structure, promotor accessibility, and contribute to posttranscriptional modifications. In the cardiovascular system, epigenetic regulation is necessary for proper cardiovascular development and homeostasis, while epigenetic dysfunction is associated with improper cardiac development and disease.Early sexualization of tissues, including X-inactivation in females and maternal and paternal imprinting, is also orchestrated through epigenetic mechanisms. Furthermore, sex chromosomes encode various sex-specific genes involved in epigenetic regulation, while sex hormones can act as regulatory cofactors that may predispose or protect males and females against developing diseases with a marked sex bias.The following book chapter summarizes the field of epigenetics in the context of cardiovascular development and disease while also highlighting the role of epigenetic regulation as a powerful source of sex differences within the cardiovascular system.
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Affiliation(s)
- Christine M Cunningham
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA
| | - Mansoureh Eghbali
- Department of Anesthesiology and Perioperative Medicine, Division of Molecular Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA, USA.
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Sato Y, Shinka T, Nozawa S, Yoshiike M, Koh E, Kanaya J, Namiki M, Matsumiya K, Tsujimura A, Komatsu K, Itoh N, Eguchi J, Yamauchi A, Iwamoto T, Nakahori Y. Y chromosome haplogroup D2a1 is significantly associated with high levels of luteinizing hormone in Japanese men. Andrology 2015; 3:520-5. [PMID: 25858496 DOI: 10.1111/andr.12026] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 02/04/2015] [Accepted: 02/09/2015] [Indexed: 01/12/2023]
Abstract
The association between the Y chromosome haplogroup D2 and risk of azoospermia and low sperm motility has been previously studied, and it was indicated that haplogroups DE (YAP lineage) are associated with prostate cancer risk in Japanese males. Our assumption had been that Y chromosome haplogroups may be associated with sex hormone levels, because sex hormones have been deemed responsible for spermatogenesis and carcinogenesis. In this study, we assessed the association between Y chromosome haplogroups and sex hormone levels, including those of testosterone, sex hormone-binding globulin (SHBG), follicle-stimulating hormone (FSH), luteinizing hormone (LH), inhibin-B, and calculated free testosterone (cFT), in 901 young men from the general Japanese population (cohort 1) and 786 Japanese men of proven fertility (cohort 2). We found that the haplogroup D2a1 was significantly associated with high LH levels in a combined analysis involving two cohorts (β = 0.068, SE = 0.025, p = 0.0075), following correction for multiple testing. To date, this result is the first evidence that implicates Y chromosome haplogroups in an association with sex hormone levels.
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Affiliation(s)
- Y Sato
- Department of Pharmaceutical Information Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan.,Department of Human Genetics and Public Health, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - T Shinka
- Department of Human Genetics and Public Health, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - S Nozawa
- Department of Urology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - M Yoshiike
- Department of Urology, St. Marianna University School of Medicine, Kawasaki, Japan
| | - E Koh
- Department of Urology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - J Kanaya
- Department of Urology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - M Namiki
- Department of Urology, Kanazawa University Graduate School of Medical Sciences, Kanazawa, Japan
| | - K Matsumiya
- Department of Urology, Osaka Police Hospital, Osaka, Japan
| | - A Tsujimura
- Faculty of Medicine, Department of Urology, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - K Komatsu
- Department of Urology, Harasanshinkai Hospital, Fukuoka, Japan
| | - N Itoh
- Department of Urology, Sapporo Medical University, Sapporo, Japan
| | - J Eguchi
- Department of Urology, Nagasaki University, Nagasaki, Japan
| | - A Yamauchi
- Department of Pharmaceutical Information Science, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
| | - T Iwamoto
- Department of Urology, St. Marianna University School of Medicine, Kawasaki, Japan.,Center for Infertility and IVF, International University of Health and Welfare Hospital, Nasushiobara, Tochigi, Japan
| | - Y Nakahori
- Department of Human Genetics and Public Health, Institute of Health Biosciences, The University of Tokushima Graduate School, Tokushima, Japan
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Case LK, Teuscher C. Y genetic variation and phenotypic diversity in health and disease. Biol Sex Differ 2015; 6:6. [PMID: 25866616 PMCID: PMC4392626 DOI: 10.1186/s13293-015-0024-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/15/2014] [Accepted: 02/22/2015] [Indexed: 11/10/2022] Open
Abstract
Sexually dimorphic traits arise through the combined effects of sex hormones and sex chromosomes on sex-biased gene expression, and experimental mouse models have been instrumental in determining their relative contribution in modulating sex differences. A role for the Y chromosome (ChrY) in mediating sex differences outside of development and reproduction has historically been overlooked due to its unusual genetic composition and the predominant testes-specific expression of ChrY-encoded genes. However, ample evidence now exists supporting ChrY as a mediator of other physiological traits in males, and genetic variation in ChrY has been linked to several diseases, including heart disease, cancer, and autoimmune diseases in experimental animal models, as well as humans. The genetic and molecular mechanisms by which ChrY modulates phenotypic variation in males remain unknown but may be a function of copy number variation between homologous X-Y multicopy genes driving differential gene expression. Here, we review the literature identifying an association between ChrY polymorphism and phenotypic variation and present the current evidence depicting the mammalian ChrY as a member of the regulatory genome in males and as a factor influencing paternal parent-of-origin effects in female offspring.
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Affiliation(s)
- Laure K Case
- Department of Medicine, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA
| | - Cory Teuscher
- Department of Medicine, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA ; Department of Pathology, University of Vermont, 89 Beaumont Ave, Burlington, VT 05405 USA ; University of Vermont, Given Medical Building C317, Burlington, VT 05405 USA
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Suto JI, Satou K. Effect of the Y chromosome on plasma high-density lipoprotein-cholesterol levels in Y-chromosome-consomic mouse strains. BMC Res Notes 2014; 7:393. [PMID: 24962540 PMCID: PMC4080985 DOI: 10.1186/1756-0500-7-393] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2014] [Accepted: 06/20/2014] [Indexed: 01/01/2023] Open
Abstract
Background Plasma high-density lipoprotein (HDL)-cholesterol level is a clinically important quantitative phenotype that widely varies among inbred mouse strains. Several genes or loci associated with plasma HDL-cholesterol levels have been identified on autosomes and the X chromosome. In contrast, genes or loci on the Y chromosome have not attracted significant attention hitherto. Therefore, we investigated the effects of the Y chromosome on plasma HDL-cholesterol levels in Y- chromosome-consomic (Y-consomic) mouse strains. Findings Plasma HDL-cholesterol level data from 16 Y-consomic strains demonstrated that the Y chromosome substitutions significantly altered plasma HDL-cholesterol levels, i.e., variations in the plasma HDL-cholesterol level could be partially explained by Y chromosome genes. We obtained the following results from the genotype data on 30 single nucleotide polymorphisms (SNPs), including nonsynonymous and synonymous SNPs and 9 polymorphisms in Sry: (1) Variation in rs46947134 of Uty was significantly associated with plasma HDL-cholesterol levels. (2) A CAG repeat number polymorphism in Sry was significantly associated with plasma HDL-cholesterol levels. (3) Strains with a certain haplotype of the Mus musculus domesticus-type Y chromosome had significantly lower plasma HDL-cholesterol levels than strains with a certain haplotype of the M. m. musculus-type Y chromosome. Conclusions The effect of the Y chromosome on plasma HDL-cholesterol levels was confirmed in the Y-consomic strains. We identified several variants associated with plasma HDL-cholesterol levels. Because the physiological significance of various Y-linked genes remains unclear, the results of this study will provide further insights into the functions of Y-linked genes in lipid metabolism.
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Affiliation(s)
- Jun-ichi Suto
- Agrogenomics Research Center, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8634, Japan.
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Kostrzewa G, Broda G, Konarzewska M, Krajewki P, Płoski R. Genetic polymorphism of human Y chromosome and risk factors for cardiovascular diseases: a study in WOBASZ cohort. PLoS One 2013; 8:e68155. [PMID: 23935855 PMCID: PMC3723826 DOI: 10.1371/journal.pone.0068155] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2011] [Accepted: 05/30/2013] [Indexed: 11/18/2022] Open
Abstract
Genetic variants of Y chromosome predispose to hypertension in rodents, whereas in humans the evidence is conflicting. Our purpose was to study the distribution of a panel of Y chromosome markers in a cohort from a cross-sectional population-based study on the prevalence of cardiovascular risk factors in Poland (WOBASZ study). The HindIII, YAP Y chromosome variants, previously shown to influence blood pressure, lipid traits or height, as well as SNPs defining main Y chromosome haplogroups, were typed in 3026, 2783 and 2652 samples, respectively. In addition, 4 subgroups (N∼100 each) representing extremes of LDL concentration or blood pressure (BP) were typed for a panel of 17 STRs. The HindIII and YAP polymorphism were not associated with any of the studied traits. Analysis of the haplogroup distribution showed an association between higher HDL level and hg I-M170 (P = 0.02), higher LDL level and hg F*(xI-M170, J2-M172, K-M9) (P = 0.03) and lower BMI and hg N3-Tat (P = 0.04). Analysis of STRs did not show statistically significant differences. Since all these associations lost statistical significance after Bonferroni correction, we conclude that a major role of Y chromosome genetic variation (defined by HindIII, YAP or main Y chromosome haplogroups) in determining cardiovascular risk in Poles is unlikely.
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Affiliation(s)
- Grażyna Kostrzewa
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
| | - Grażyna Broda
- Department of Cardiovascular Epidemiology and Prevention, and Health Promotion, Institute of Cardiology, Warsaw, Poland
| | | | - Paweł Krajewki
- Department of Forensic Medicine, Medical University of Warsaw, Warsaw, Poland
| | - Rafał Płoski
- Department of Medical Genetics, Medical University of Warsaw, Warsaw, Poland
- * E-mail:
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