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Hirata W, Tomoda T, Yuri S, Isotani A. Generation of the Y-chromosome linked red fluorescent protein transgenic mouse model and sexing at the preimplantation stage. Exp Anim 2022; 71:82-89. [PMID: 34544911 PMCID: PMC8828399 DOI: 10.1538/expanim.21-0119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 08/30/2021] [Indexed: 12/04/2022] Open
Abstract
In mammals, sexual fate is determined by the chromosomes of the male and female gametes during fertilization. Males (XY) or females (XX) are produced when a sperm containing a Y or X-chromosome respectively fertilizes an X-chromosome-containing unfertilized egg. However, sexing of preimplantation stage embryos cannot be conducted visually. To address this, transgenic male mouse models with the ubiquitously expressed green fluorescent protein (GFP) transgene on X- (X-GFP) or Y-chromosomes (Y-GFP) have been established. However, when crossed with wild-type females, sexing of the preimplantation stage embryos by observing the GFP signal is problematic in some cases due to X-inactivation, loss of Y-chromosome (LOY), or loss of transgene fluorescence. In this study, a mouse model with the ubiquitously expressed red fluorescent protein (RFP) transgene on the Y-chromosome was generated since RFP is easily distinguishable from GFP signals. Unfortunately, the ubiquitously expressed tdTomato RFP transgene on the Y-chromosome (Y-RFP) mouse showed the lethal phenotype after birth. No lethal phenotypes were observed when the mitochondrial locating signal N-terminal of tdTomato (mtRFP) was included in the transgene construct. Almost half of the collected fertilized eggs from Y-mtRFP male mice crossed with wild-type females had an RFP signal at the preimplantation stage (E1.5). Therefore, XY eggs were recognized as RFP-positive embryos at the preimplantation stage. Furthermore, 100% sexing was observed at the preimplantation stage using the X-linked GFP/Y-linked RFP male mouse. The established Y-mtRFP mouse models may be used to study sex chromosome related research.
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Affiliation(s)
- Wataru Hirata
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Taiki Tomoda
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Shunsuke Yuri
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
| | - Ayako Isotani
- Division of Biological Science, Graduate School of Science and Technology, Nara Institute of Science and Technology, 8916-5 Takayama-cho, Ikoma, Nara 630-0192, Japan
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52
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Zhang Q, Zhao L, Yang Y, Li S, Liu Y, Chen C. Mosaic loss of chromosome Y promotes leukemogenesis and clonal hematopoiesis. JCI Insight 2022; 7:153768. [PMID: 35132955 PMCID: PMC8855789 DOI: 10.1172/jci.insight.153768] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 12/23/2021] [Indexed: 12/21/2022] Open
Abstract
Mosaic loss of chromosome Y (mLOY) in blood cells is one of the most frequent chromosome alterations in adult males. It is strongly associated with clonal hematopoiesis, hematopoietic malignancies, and other hematopoietic and nonhematopoietic diseases. However, whether there is a causal relationship between mLOY and human diseases is unknown. Here, we generated mLOY in murine hematopoietic stem and progenitor cells (HSPCs) with CRISPR/Cas9 genome editing. We found that mLOY led to dramatically increased DNA damage in HSPCs. Interestingly, HSPCs with mLOY displayed significantly enhanced reconstitution capacity and gave rise to clonal hematopoiesis in vivo. mLOY, which is associated with AML1-ETO translocation and p53 defects in patients with acute myeloid leukemia (AML), promoted AML in mice. Mechanistically, loss of KDM5D, a chromosome Y-specific histone 3 lysine 4 demethylase in both humans and mice, partially recapitulated mLOY in DNA damage and leukemogenesis. Thus, our study validates mLOY as a functional driver for clonal hematopoiesis and leukemogenesis.
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MESH Headings
- Animals
- Carcinogenesis/genetics
- Chromosomes, Human, Y/genetics
- Clonal Hematopoiesis/genetics
- Core Binding Factor Alpha 2 Subunit/genetics
- Core Binding Factor Alpha 2 Subunit/metabolism
- Gene Editing
- Hematopoietic Stem Cells/metabolism
- Hematopoietic Stem Cells/pathology
- Humans
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/pathology
- Male
- Mice
- Mice, Transgenic
- Models, Animal
- Mutation
- Neoplasms, Experimental
- Translocation, Genetic
- Tumor Cells, Cultured
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53
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Fukami M, Miyado M. Mosaic loss of the Y chromosome and men's health. Reprod Med Biol 2022; 21:e12445. [PMID: 35386373 PMCID: PMC8967293 DOI: 10.1002/rmb2.12445] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 01/21/2022] [Accepted: 01/24/2022] [Indexed: 11/08/2022] Open
Abstract
Background Although Y chromosomal genes are involved in male sex development, spermatogenesis, and height growth, these genes play no role in the survival or mitosis of somatic cells. Therefore, somatic cells lacking the Y chromosome can stay and proliferate in the body. Methods Several molecular technologies, including next-generation sequencing and multiplex PCR-based assays, are used to detect mosaic loss of the Y chromosome (mLOY) in the blood of men. Main findings Accumulating evidence suggests that mLOY represents the most common acquired chromosomal alteration in humans, affecting >40% of men over 70 years of age. Advanced age, tobacco smoking, and some SNPs in cell cycle genes are known to increase the frequency of mLOY. The developmental process of mLOY in elderly men remains to be clarified, but it possibly reflects recurrent mitotic elimination of Y chromosomes or clonal expansion of 45,X cell lineages. In rare cases, mLOY also occurs in young men and fetuses. MLOY has been associated with early death, cancers, and other disorders in elderly men, infertility in reproductive-aged men, and developmental defects in children. Conclusion Y chromosomes in men can be lost at every life stage and Y chromosomal loss is associated with various health problems.
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Affiliation(s)
- Maki Fukami
- Department of Molecular EndocrinologyNational Research Institute for Child Health and DevelopmentTokyoJapan
| | - Mami Miyado
- Department of Molecular EndocrinologyNational Research Institute for Child Health and DevelopmentTokyoJapan
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54
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Abstract
Mosaic loss of the Y chromosome (LOY) is the most frequent chromosomal aberration in aging men and is strongly correlated with mortality and disease. To date, studies of LOY have only been performed in humans, and so it is unclear whether LOY is a natural consequence of our relatively long lifespan or due to exposure to human-specific external stressors. Here, we explored whether LOY could be detected in rats. We applied a locus-specific PCR and target sequencing approach that we used as a proxy to estimate LOY in 339 samples covering eleven tissues from young and old individuals. We detected LOY in four tissues of older rats. To confirm the results from the PCR screening, we re-sequenced 60 full genomes from old rats, which revealed that the Y chromosome is the sole chromosome with low copy numbers. Finally, our results suggest that LOY is associated with other structural aberrations on the Y chromosome and possibly linked to the mosaic loss of the X chromosome. This is the first report, to our knowledge, demonstrating that the patterns of LOY observed in aging men are also present in a rodent, and conclude that LOY may be a natural process in placental mammals.
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55
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Matsunaga M, Ohtsubo Y, Masuda T, Noguchi Y, Yamasue H, Ishii K. A Genetic Variation in the Y Chromosome Among Modern Japanese Males Related to Several Physiological and Psychological Characteristics. Front Behav Neurosci 2021; 15:774879. [PMID: 34924970 PMCID: PMC8675941 DOI: 10.3389/fnbeh.2021.774879] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2021] [Accepted: 11/12/2021] [Indexed: 01/04/2023] Open
Abstract
Previous studies in population genetics have proposed that the Y-chromosomal (Y-DNA) haplogroup D ancestor likely originated from Africa. The haplogroup D branch next started Out-of-Africa migration, rapidly expanded across Eurasia, and later diversified in East Asia. Y-DNA haplogroup D-M55, one of the branches of haplogroup D, is only found in modern Japanese males, suggesting that individuals with Y-DNA haplogroup D migrated from the Eurasian continent. Based on previous observations, Y-DNA haplogroup D is expected to be associated with some male characteristics including personality. Therefore, this study investigated whether the Y-DNA haplogroup D-M55 is associated with several physiological and psychological characteristics, including exploratory motivation and human relationship-related perception. We recruited Japanese young adult males and females and investigated the association between Y-DNA haplogroup D-M55, physiological [body mass index (BMI)], and several psychological parameters [perceived number of close friends, behavioral inhibition system/behavioral activation system (BIS/BAS), perceived happiness, and perceived loneliness]. The results indicated that males with haplogroup D-M55 had a higher BMI and more close friends, compared with non-carrier males. Additional multiple regression analyses, which tested the hypothesis that haplogroup D-M55 predicts BMI and perceived number of close friends, confirmed our hypothesis, even after controlling for the potentially confounding variables of age and sex. We also analyzed the gene-gene interaction between haplogroup D-M55 and an autosomal gene polymorphism associated with BMI and human relationships, such as the dopamine D2 receptor gene (DRD2: rs1800497). Results showed gene-gene interactions between haplogroups D-M55 and DRD2 in BMI. Based on these findings, it is demonstrated that Y-DNA haplogroup D is associated with human personality.
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Affiliation(s)
- Masahiro Matsunaga
- Department of Health and Psychosocial Medicine, Aichi Medical University School of Medicine, Nagakute, Japan
| | - Yohsuke Ohtsubo
- Department of Social Psychology, Graduate School of Humanities and Sociology, The University of Tokyo, Bunkyō, Japan
| | - Takahiko Masuda
- Department of Psychology, University of Alberta, Edmonton, AB, Canada
| | - Yasuki Noguchi
- Department of Psychology, Graduate School of Humanities, Kobe University, Kobe, Japan
| | - Hidenori Yamasue
- Department of Psychiatry, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Keiko Ishii
- Department of Cognitive and Psychological Sciences, Graduate School of Informatics, Nagoya University, Nagoya, Japan
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56
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Riaz M, Mattisson J, Polekhina G, Bakshi A, Halvardson J, Danielsson M, Ameur A, McNeil J, Forsberg LA, Lacaze P. A polygenic risk score predicts mosaic loss of chromosome Y in circulating blood cells. Cell Biosci 2021; 11:205. [PMID: 34895331 PMCID: PMC8667399 DOI: 10.1186/s13578-021-00716-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Accepted: 11/19/2021] [Indexed: 11/23/2022] Open
Abstract
Background Mosaic loss of Y chromosome (LOY) is the most common somatic change that occurs in circulating white blood cells of older men. LOY in leukocytes is associated with increased risk for all-cause mortality and a range of common disease such as hematological and non-hematological cancer, Alzheimer’s disease, and cardiovascular events. Recent genome-wide association studies identified up to 156 germline variants associated with risk of LOY. The objective of this study was to use these variants to calculate a novel polygenic risk score (PRS) for LOY, and to assess the predictive performance of this score in a large independent population of older men. Results We calculated a PRS for LOY in 5131 men aged 70 years and older. Levels of LOY were estimated using microarrays and validated by whole genome sequencing. After adjusting for covariates, the PRS was a significant predictor of LOY (odds ratio [OR] = 1.74 per standard deviation of the PRS, 95% confidence intervals [CI] 1.62–1.86, p < 0.001). Men in the highest quintile of the PRS distribution had > fivefold higher risk of LOY than the lowest (OR = 5.05, 95% CI 4.05–6.32, p < 0.001). Adding the PRS to a LOY prediction model comprised of age, smoking and alcohol consumption significantly improved prediction (AUC = 0.628 [CI 0.61–0.64] to 0.695 [CI 0.67–0.71], p < 0.001). Conclusions Our results suggest that a PRS for LOY could become a useful tool for risk prediction and targeted intervention for common disease in men. Supplementary Information The online version contains supplementary material available at 10.1186/s13578-021-00716-z.
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Affiliation(s)
- Moeen Riaz
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Galina Polekhina
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Andrew Bakshi
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - John McNeil
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
| | - Paul Lacaze
- Department of Epidemiology and Preventive Medicine, School of Public Health and Preventive Medicine, Monash University, Melbourne, Australia.
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57
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Guo X, Li J, Xue J, Fenech M, Wang X. Loss of Y chromosome: An emerging next-generation biomarker for disease prediction and early detection? MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108389. [PMID: 34893154 DOI: 10.1016/j.mrrev.2021.108389] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Revised: 07/01/2021] [Accepted: 07/01/2021] [Indexed: 12/25/2022]
Abstract
As human life expectancy increases substantially and aging is the primary risk factor for most chronic diseases, there is an urgent need for advancing the development of post-genomic era biomarkers that can be used for disease prediction and early detection (DPED). Mosaic loss of Y chromosome (LOY) is the state of nullisomy Y in sub-groups of somatic cells acquired from different post-zygotic development stages and onwards throughout the lifespan. Multiple large-cohort based epidemiology studies have found that LOY in blood cells is a significant risk factor for future mortality and various diseases in males. Many features intrinsic to LOY analysis may be leveraged to enhance its use as a non-invasive, sensitive, reliable, high throughput-biomarker for DPED. Here, we review the emerging literatures in LOY studies and highlight ten strengths for using LOY as a novel biomarker for genomics-driven DPED diagnostics. Meanwhile, the current limitations in this area are also discussed. We conclude by identifying some important knowledge gaps regarding the consequences of malsegregation of the Y chromosome and propose further steps that are required before clinical implementation of LOY. Taken together, we think that LOY has substantial potential as a biomarker for DPED, despite some hurdles that still need to be addressed before its integration into healthcare becomes acceptable.
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Affiliation(s)
- Xihan Guo
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China; Yunnan Environmental Mutagen Society, Kunming, Yunnan, 650500, China.
| | - Jianfei Li
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Jinglun Xue
- State Key Laboratory of Genetic Engineering, Institute of Genetics, School of Life Sciences, Fudan University, Shanghai, 200433, China
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA, 5048, Australia; University of South Australia, School of Pharmacy and Medical Sciences, Adelaide, SA, 5000, Australia; Centre of Healthy Ageing and Wellness, Faculty of Health Sciences, Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
| | - Xu Wang
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China; Yunnan Environmental Mutagen Society, Kunming, Yunnan, 650500, China.
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58
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Loss of Y and clonal hematopoiesis in blood-two sides of the same coin? Leukemia 2021; 36:889-891. [PMID: 34725452 PMCID: PMC8885420 DOI: 10.1038/s41375-021-01456-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/14/2021] [Accepted: 10/15/2021] [Indexed: 11/23/2022]
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59
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Abstract
Clonal haematopoiesis (CH) is a common, age-related expansion of blood cells with somatic mutations that is associated with an increased risk of haematological malignancies, cardiovascular disease and all-cause mortality. CH may be caused by point mutations in genes associated with myeloid neoplasms, chromosomal copy number changes and loss of heterozygosity events. How inherited and environmental factors shape the incidence of CH is incompletely understood. Even though the several varieties of CH may have distinct phenotypic consequences, recent research points to an underlying genetic architecture that is highly overlapping. Moreover, there are numerous commonalities between the inherited variation associated with CH and that which has been linked to age-associated biomarkers and diseases. In this Review, we synthesize what is currently known about how inherited variation shapes the risk of CH and how this genetic architecture intersects with the biology of diseases that occur with ageing.
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Affiliation(s)
- Alexander J Silver
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Alexander G Bick
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Michael R Savona
- Program in Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Vanderbilt-Ingram Cancer Center, Vanderbilt University School of Medicine, Nashville, TN, USA.
- Center for Immunobiology, Vanderbilt University School of Medicine, Nashville, TN, USA.
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60
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Sultan I, Amarin JZ, Mansour R, Sultan H, Al-Hussaini M. Sex Differences in Cancer-Specific Survival Are Pronounced during Adolescence and Young Adulthood: A SEER Population-Based Study. EPIDEMIOLGIA (BASEL, SWITZERLAND) 2021; 2:391-401. [PMID: 36417233 PMCID: PMC9620934 DOI: 10.3390/epidemiologia2030029] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Revised: 08/28/2021] [Accepted: 08/30/2021] [Indexed: 12/14/2022]
Abstract
Sex differences in cancer survival may be related to hormonal changes during puberty and menopause; therefore, we investigated sex differences in the cancer-specific survival rates of children, adolescents and young adults (AYAs), and older adults with sex-nonspecific cancers. We interrogated the November 2019 submission of the SEER 18 database and included microscopically confirmed cases of first primary malignant tumors. We stratified the dataset into children (<15 years), AYAs (modified; 15-49 years), and older adults (≥50 years). For each age group, we used the Kaplan-Meier method to estimate the sex-stratified 5-year all-site cancer-specific survival probabilities. Of 3,386,276 eligible patients, 45,124 (1.3%) were children, 548,158 (16.2%) were AYAs, and 2,792,994 (82.5%) were older adults. The 5-year all-site cancer-specific survival probabilities were 84.0% (95% CI, 83.5%-84.5%) for boys, 84.8% (95% CI, 84.3%-85.3%) for girls, 70.4% (95% CI, 70.2%-70.6%) for male AYAs, 80.8% (95% CI, 80.6%-81.0%) for female AYAs, 52.0% (95% CI, 51.9%-52.1%) for older adult men, and 52.2% (95% CI, 52.1%-52.3%) for older adult women. The all-site survival rate for female patients with cancer is markedly higher than for male patients with cancer during adolescence and young adulthood, although this difference diminishes in older adulthood.
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Affiliation(s)
- Iyad Sultan
- Department of Pediatrics, King Hussein Cancer Center, Amman 11941, Jordan;
| | - Justin Z. Amarin
- Office of Scientific Affairs and Research, King Hussein Cancer Center, Amman 11941, Jordan; (J.Z.A.); (R.M.)
| | - Razan Mansour
- Office of Scientific Affairs and Research, King Hussein Cancer Center, Amman 11941, Jordan; (J.Z.A.); (R.M.)
| | - Hala Sultan
- School of Medicine, The University of Jordan, Amman 11942, Jordan;
| | - Maysa Al-Hussaini
- Department of Pathology and Laboratory Medicine, King Hussein Cancer Center, Amman 11941, Jordan
- Correspondence:
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Lin SH, Wang Y, Hartley SW, Karyadi DM, Lee OW, Zhu B, Zhou W, Brown DW, Beilstein-Wedel E, Hazra R, Kacanek D, Chadwick EG, Marsit CJ, Poirier MC, Brummel SS, Chanock SJ, Engels EA, Machiela MJ. In-utero exposure to zidovudine-containing antiretroviral therapy and clonal hematopoiesis in HIV-exposed uninfected newborns. AIDS 2021; 35:1525-1535. [PMID: 33756513 PMCID: PMC8286286 DOI: 10.1097/qad.0000000000002894] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
OBJECTIVE Zidovudine (ZDV) has been extensively used in pregnant women to prevent vertical transmission of HIV but few studies have evaluated potential mutagenic effects of ZDV during fetal development. DESIGN Our study investigated clonal hematopoiesis in HIV-exposed uninfected (HEU) newborns, 94 of whom were ZDV-exposed and 91 antiretroviral therapy (ART)-unexposed and matched for potential confounding factors. METHODS Utilizing high depth sequencing and genotyping arrays, we comprehensively examined blood samples collected during the first week after birth for potential clonal hematopoiesis associated with fetal ZDV exposure, including clonal single nucleotide variants (SNVs), small insertions and deletions (indels), and large structural copy number or copy neutral alterations. RESULTS We observed no statistically significant difference in the number of SNVs and indels per person in ZDV-exposed children (adjusted ratio [95% confidence interval, CI] for expected number of mutations = 0.79 [0.50--1.22], P = 0.3), and no difference in the number of large structural alterations. Mutations in common clonal hematopoiesis driver genes were not found in the study population. Mutational signature analyses on SNVs detected no novel signatures unique to the ZDV-exposed children and the mutational profiles were similar between the two groups. CONCLUSION Our results suggest that clonal hematopoiesis at levels detectable in our study is not strongly influenced by in-utero ZDV exposure; however, additional follow-up studies are needed to further evaluate the safety and potential long-term impacts of in-utero ZDV exposure in HEU children as well as better investigate genomic aberrations occurring late in pregnancy.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Youjin Wang
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Stephen W Hartley
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Danielle M Karyadi
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Olivia W Lee
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Bin Zhu
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
- Cancer Genomics Research Laboratory, Leidos Biomedical Research, Inc., Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Derek W Brown
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Erin Beilstein-Wedel
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Rohan Hazra
- Maternal and Pediatric Infectious Disease Branch, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, Maryland
| | - Deborah Kacanek
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Ellen G Chadwick
- Department of Pediatrics, Feinberg School of Medicine, Northwestern University, Chicago, Illinois
| | - Carmen J Marsit
- Departments of Environmental Health and Epidemiology, Rollins School of Public Health, Emory University, Atlanta, Georgia
| | - Miriam C Poirier
- Carcinogen-DNA Interactions Section, Laboratory of Cancer Biology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Sean S Brummel
- Center for Biostatistics in AIDS Research, Harvard T.H. Chan School of Public Health, Boston, Massachusetts
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Eric A Engels
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville
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62
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Mattisson J, Danielsson M, Hammond M, Davies H, Gallant CJ, Nordlund J, Raine A, Edén M, Kilander L, Ingelsson M, Dumanski JP, Halvardson J, Forsberg LA. Leukocytes with chromosome Y loss have reduced abundance of the cell surface immunoprotein CD99. Sci Rep 2021; 11:15160. [PMID: 34312421 PMCID: PMC8313698 DOI: 10.1038/s41598-021-94588-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2021] [Accepted: 07/12/2021] [Indexed: 01/02/2023] Open
Abstract
Mosaic loss of chromosome Y (LOY) in immune cells is a male-specific mutation associated with increased risk for morbidity and mortality. The CD99 gene, positioned in the pseudoautosomal regions of chromosomes X and Y, encodes a cell surface protein essential for several key properties of leukocytes and immune system functions. Here we used CITE-seq for simultaneous quantification of CD99 derived mRNA and cell surface CD99 protein abundance in relation to LOY in single cells. The abundance of CD99 molecules was lower on the surfaces of LOY cells compared with cells without this aneuploidy in all six types of leukocytes studied, while the abundance of CD proteins encoded by genes located on autosomal chromosomes were independent from LOY. These results connect LOY in single cells with immune related cellular properties at the protein level, providing mechanistic insight regarding disease vulnerability in men affected with mosaic chromosome Y loss in blood leukocytes.
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Affiliation(s)
- Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Maria Hammond
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Caroline J Gallant
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Amanda Raine
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Malin Edén
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lena Kilander
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences / Geriatrics, Uppsala University, Uppsala, Sweden
| | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden.,Faculty of Pharmacy, 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
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63
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Bai Y, Guan X, Wei W, Feng Y, Meng H, Li G, Li H, Li M, Wang C, Fu M, Jie J, Zhang X, He M, Guo H. Effects of polycyclic aromatic hydrocarbons and multiple metals co-exposure on the mosaic loss of chromosome Y in peripheral blood. JOURNAL OF HAZARDOUS MATERIALS 2021; 414:125519. [PMID: 33676251 DOI: 10.1016/j.jhazmat.2021.125519] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Revised: 02/21/2021] [Accepted: 02/22/2021] [Indexed: 06/12/2023]
Abstract
Mosaic loss of chromosome Y (mLOY) is an indicator of genome instability, but the environmental stressors of mLOY remained largely unknown. In this study, we detected the internal exposure levels of 11 polycyclic aromatic hydrocarbon (PAH) metabolites and 22 metals among 888 coke-oven workers, and calculated their blood mLOY based on genome-wide SNP genotyping data and presented as median log R ratio (mLRR-Y). The generalized linear model (GLM), LASSO, and Bayesian kernel machine regression (BKMR), were used to select mLOY-relevant chemicals. The results of these models consistently suggested the negative dose-response relationships of urinary 1-hydroxynaphthalene (1-OHNa), antimony (Sb), and molybdenum (Mo) with mLRR-Y. There were no pairwise interactions between these three chemicals (Pinteraction > 0.05), but subjects with high exposure to ≥ 2 kinds of these chemicals showed reducing mLRR-Y [β(95%CI) = - 0.015(- 0.023, - 0.008)], increasing oxidative DNA damage (marked by 8-hydroxydeoxyguanosine) [β(95%CI) = 0.625(0.454, 0.796)] and chromosome damage (marked by micronucleus frequency in lymphocytes) [frequency ratio (FR) and 95%CI = 1.146(1.047, 1.225)] than those with low exposure to all these chemicals. The combined effects of 1-OHNa, Sb, and Mo on elevating DNA damage may partly explain their joint effects on increased blood mLOY. These results provided a new insight into environmental hazards co-exposure on chromosome-Y deletions.
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Affiliation(s)
- Yansen Bai
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xin Guan
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Wei Wei
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Yue Feng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hua Meng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Guyanan Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Hang Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Mengying Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Chenming Wang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Ming Fu
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Jiali Jie
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Meian He
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China
| | - Huan Guo
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, Wuhan 430030, China.
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64
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GIGYF1 loss of function is associated with clonal mosaicism and adverse metabolic health. Nat Commun 2021; 12:4178. [PMID: 34234147 PMCID: PMC8263756 DOI: 10.1038/s41467-021-24504-y] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Accepted: 06/21/2021] [Indexed: 12/01/2022] Open
Abstract
Mosaic loss of chromosome Y (LOY) in leukocytes is the most common form of clonal mosaicism, caused by dysregulation in cell-cycle and DNA damage response pathways. Previous genetic studies have focussed on identifying common variants associated with LOY, which we now extend to rarer, protein-coding variation using exome sequences from 82,277 male UK Biobank participants. We find that loss of function of two genes—CHEK2 and GIGYF1—reach exome-wide significance. Rare alleles in GIGYF1 have not previously been implicated in any complex trait, but here loss-of-function carriers exhibit six-fold higher susceptibility to LOY (OR = 5.99 [3.04–11.81], p = 1.3 × 10−10). These same alleles are also associated with adverse metabolic health, including higher susceptibility to Type 2 Diabetes (OR = 6.10 [3.51–10.61], p = 1.8 × 10−12), 4 kg higher fat mass (p = 1.3 × 10−4), 2.32 nmol/L lower serum IGF1 levels (p = 1.5 × 10−4) and 4.5 kg lower handgrip strength (p = 4.7 × 10−7) consistent with proposed GIGYF1 enhancement of insulin and IGF-1 receptor signalling. These associations are mirrored by a common variant nearby associated with the expression of GIGYF1. Our observations highlight a potential direct connection between clonal mosaicism and metabolic health. Mosaic loss of chromosome Y (LOY) is a common form of clonal mosaicism in leukocytes. Here, the authors extend genetic association analyses to rare variation using exome-sequence data from 82,277 males, finding that loss-of-function alleles in GIGYF1 are associated with six-fold higher susceptibility to both LOY and Type 2 Diabetes.
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65
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Kirsch-Volders M, Fenech M. Inflammatory cytokine storms severity may be fueled by interactions of micronuclei and RNA viruses such as COVID-19 virus SARS-CoV-2. A hypothesis. MUTATION RESEARCH. REVIEWS IN MUTATION RESEARCH 2021; 788:108395. [PMID: 34893160 PMCID: PMC8479308 DOI: 10.1016/j.mrrev.2021.108395] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Revised: 09/23/2021] [Accepted: 09/23/2021] [Indexed: 12/25/2022]
Abstract
In this review we bring together evidence that (i) RNA viruses are a cause of chromosomal instability and micronuclei (MN), (ii) those individuals with high levels of lymphocyte MN have a weakened immune response and are more susceptible to RNA virus infection and (iii) both RNA virus infection and MN formation can induce inflammatory cytokine production. Based on these observations we propose a hypothesis that those who harbor elevated frequencies of MN within their cells are more prone to RNA virus infection and are more likely, through combined effects of leakage of self-DNA from MN and RNA from viruses, to escalate pro-inflammatory cytokine production via the cyclic GMP-AMP synthase (cGAS), stimulator of interferon genes (STING) and the Senescence Associated Secretory Phenotype (SASP) mechanisms to an extent that is unresolvable and therefore confers high risk of causing tissue damage by an excessive and overtly toxic immune response. The corollaries from this hypothesis are (i) those with abnormally high MN frequency are more prone to infection by RNA viruses; (ii) the extent of cytokine production and pro-inflammatory response to infection by RNA viruses is enhanced and possibly exceeds threshold levels that may be unresolvable in those with elevated MN levels in affected organs; (iii) reduction of MN frequency by improving nutrition and life-style factors increases resistance to RNA virus infection and moderates inflammatory cytokine production to a level that is immunologically efficacious and survivable.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050, Brussels, Belgium.
| | - Michael Fenech
- Genome Health Foundation, North Brighton, SA, 5048, Australia; Clinical and Health Sciences, University of South Australia, SA, 5000, Australia; Universiti Kebangsaan Malaysia, Kuala Lumpur, Malaysia.
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66
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Dai X, Guo X. Decoding and rejuvenating human ageing genomes: Lessons from mosaic chromosomal alterations. Ageing Res Rev 2021; 68:101342. [PMID: 33866012 DOI: 10.1016/j.arr.2021.101342] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 04/05/2021] [Accepted: 04/07/2021] [Indexed: 01/10/2023]
Abstract
One of the most curious findings emerged from genome-wide studies over the last decade was that genetic mosaicism is a dominant feature of human ageing genomes. The clonal dominance of genetic mosaicism occurs preceding the physiological and physical ageing and associates with propensity for diseases including cancer, Alzheimer's disease, cardiovascular disease and diabetes. These findings are revolutionizing the ways biologists thinking about health and disease pathogenesis. Among all mosaic mutations in ageing genomes, mosaic chromosomal alterations (mCAs) have the most significant functional consequences because they can produce intercellular genomic variations simultaneously involving dozens to hundreds or even thousands genes, and therefore have most profound effects in human ageing and disease etiology. Here, we provide a comprehensive picture of the landscapes, causes, consequences and rejuvenation of mCAs at multiple scales, from cell to human population, by reviewing data from cytogenetic, genetic and genomic studies in cells, animal models (fly and mouse) and, more frequently, large-cohort populations. A detailed decoding of ageing genomes with a focus on mCAs may yield important insights into the genomic architecture of human ageing, accelerate the risk stratification of age-related diseases (particularly cancers) and development of novel targets and strategies for delaying or rejuvenating human (genome) ageing.
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Affiliation(s)
- Xueqin Dai
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China
| | - Xihan Guo
- School of Life Sciences, Yunnan Normal University, Kunming, Yunnan, 650500, China; The Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, Yunnan, 650500, China; Yunnan Environmental Mutagen Society, Kunming, Yunnan, 650500, China.
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67
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Fazel A, Quabius ES, Fabian A, Gonzales Donate M, Schleicher T, Kress K, Laudien M, Huber K, Hoffmann M. [The impact of smoking habit alteration on prognosis of head and neck cancer patients]. Laryngorhinootologie 2021; 100:634-643. [PMID: 34139775 DOI: 10.1055/a-1509-8851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
INTRODUCTION The influence of smoking on survival in patients with HNSCC is well documented in the literature. There is little data on changes in smoking habits after diagnosis. Here, the effect on survival of the reduction of smoking compared to full smoking cessation is investigated. PATIENTS AND METHODS Patient records and tumor documentation of 643 consecutive HNSCC cases of the Head and Neck Tumor Center of the University Hospital Kiel are evaluated retrospectively: smoking habits before and after treatment and survival are evaluated. RESULTS Change in smoking behavior at the initial diagnosis of HNSCC leads to a significant positive effect on the prognosis compared to continued smoking. There is no difference between smoke reduction and weaning. This effect is based solely on those patients who are treated exclusively by surgery. Lifelong non-smokers have a significant survival advantage over active and ex-smokers, with no difference between the latter two groups. CONCLUSIONS The positive influence of changed smoking habits on the prognosis runs parallel to the negative direct effect of active smoking on therapy, which is attributed to peritumoral hypoxia with a negative effect on the effectiveness of R(C)T. The positive effect of the change in smoking behaviour during surgery alone is most likely due to reduced peri-operative complications. Patients should be encouraged to at least minimize smoking with the cancer diagnosis. In addition, former smokers should be considered active smokers for survival estimates and therapy planning.
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Affiliation(s)
- Asita Fazel
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | | | - Alexander Fabian
- Klinik für Strahlentherapie, Christian-Albrechts-Universität zu Kiel, Germany
| | - Mireia Gonzales Donate
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Thilo Schleicher
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Konstantin Kress
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Martin Laudien
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Karen Huber
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
| | - Markus Hoffmann
- Klinik für Hals-Nasen-Ohrenheilkunde, Kopf- und Halschirurgie, Universitätsklinikum Schleswig-Holstein, Kiel, Germany
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68
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Y disruption, autosomal hypomethylation and poor male lung cancer survival. Sci Rep 2021; 11:12453. [PMID: 34127738 PMCID: PMC8203787 DOI: 10.1038/s41598-021-91907-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 05/26/2021] [Indexed: 01/27/2023] Open
Abstract
Lung cancer is the most frequent cause of cancer death worldwide. It affects more men than women, and men generally have worse survival outcomes. We compared gene co-expression networks in affected and unaffected lung tissue from 126 consecutive patients with Stage IA-IV lung cancer undergoing surgery with curative intent. We observed marked degradation of a sex-associated transcription network in tumour tissue. This disturbance, detected in 27.7% of male tumours in the discovery dataset and 27.3% of male tumours in a further 123-sample replication dataset, was coincident with partial losses of the Y chromosome and extensive autosomal DNA hypomethylation. Central to this network was the epigenetic modifier and regulator of sexually dimorphic gene expression, KDM5D. After accounting for prognostic and epidemiological covariates including stage and histology, male patients with tumour KDM5D deficiency showed a significantly increased risk of death (Hazard Ratio [HR] 3.80, 95% CI 1.40-10.3, P = 0.009). KDM5D deficiency was confirmed as a negative prognostic indicator in a further 1100 male lung tumours (HR 1.67, 95% CI 1.4-2.0, P = 1.2 × 10-10). Our findings identify tumour deficiency of KDM5D as a prognostic marker and credible mechanism underlying sex disparity in lung cancer.
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69
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Structural and numerical Y chromosomal variations in elderly men identified through multiplex ligation-dependent probe amplification. J Hum Genet 2021; 66:1181-1184. [PMID: 34108640 DOI: 10.1038/s10038-021-00943-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Revised: 05/09/2021] [Accepted: 05/27/2021] [Indexed: 11/08/2022]
Abstract
Human Y chromosomes frequently acquire structural and numerical alterations. Known alterations include germline copy-number variations (CNVs) in the azoospermia factor (AZF) region and somatic mosaic loss of the Y chromosome (mLOY). Here, we explored Y chromosomal variations in 160 Japanese men aged 75-90 years. Multiplex ligation-dependent probe amplification (MLPA) identified ten types of AZF-linked CNVs in 77 men and mLOY of various degrees in 37. Seventeen men carried both a CNV and mLOY. MLOY levels estimated by MLPA were closely correlated with those determined by droplet digital PCR. No association was found between AZF-linked CNVs and the frequency or levels of mLOY. These results emphasize the high frequency and large inter-individual variability of AZF-linked CNVs and mLOY, and demonstrate the usefulness of MLPA in the detection of these variations. More importantly, this study provides the first evidence that AZF-linked CNVs do not increase the risk of aging-related mLOY.
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70
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Cáceres A, Jene A, Esko T, Pérez-Jurado LA, González JR. Extreme Downregulation of Chromosome Y and Cancer Risk in Men. J Natl Cancer Inst 2021; 112:913-920. [PMID: 31945786 DOI: 10.1093/jnci/djz232] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/31/2019] [Accepted: 12/11/2019] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Understanding the biological differences between sexes in cancer is essential for personalized treatment and prevention. We hypothesized that the extreme downregulation of chromosome Y gene expression (EDY) is a signature of cancer risk in men and the functional mediator of the reported association between the mosaic loss of chromosome Y (LOY) and cancer. METHODS We advanced a method to measure EDY from transcriptomic data. We studied EDY across 47 nondiseased tissues from the Genotype Tissue-Expression Project (n = 371) and its association with cancer status across 12 cancer studies from The Cancer Genome Atlas (n = 1774) and seven other studies (n = 7562). Associations of EDY with cancer status and presence of loss-off function mutations in chromosome X were tested with logistic regression models, and a Fisher's test was used to assess genome-wide association of EDY with the proportion of copy number gains. All statistical tests were two-sided. RESULTS EDY was likely to occur in multiple nondiseased tissues (P < .001) and was statistically significantly associated with the EGFR tyrosine kinase inhibitor resistance pathway (false discovery rate = 0.028). EDY strongly associated with cancer risk in men (odds ratio [OR] = 3.66, 95% confidence interval [CI] = 1.58 to 8.46, P = .002), adjusted by LOY and age, and its variability was largely explained by several genes of the nonrecombinant region whose chromosome X homologs showed loss-of-function mutations that co-occurred with EDY during cancer (OR = 2.82, 95% CI = 1.32 to 6.01, P = .007). EDY associated with a high proportion of EGFR amplifications (OR = 5.64, 95% CI = 3.70 to 8.59, false discovery rate < 0.001) and EGFR overexpression along with SRY hypomethylation and nonrecombinant region hypermethylation, indicating alternative causes of EDY in cancer other than LOY. EDY associations were independently validated for different cancers and exposure to smoking, and its status was accurately predicted from individual methylation patterns. CONCLUSIONS EDY is a male-specific signature of cancer susceptibility that supports the escape from X-inactivation tumor suppressor hypothesis for genes that protect women compared with men from cancer risk.
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Affiliation(s)
- Alejandro Cáceres
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain
| | - Aina Jene
- Center for Genomics Regulation, Barcelona, Spain
| | - Tonu Esko
- Estonian Genome Centre Science Centre, University of Tartu, Tartu, Estonia
| | - Luis A Pérez-Jurado
- Genetics Unit, Universitat Pompeu Fabra, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain.,Women's and Children's Hospital, South Australian Health and Medical Research Institute & University of Adelaide, Adelaide, Australia
| | - Juan R González
- Barcelona Institute for Global Health (ISGlobal), Barcelona, Spain.,Centro de Investigación Biomédica en Red en Epidemiología y Salud Pública (CIBERESP), Barcelona, Spain.,Department of Mathematics, Universitat Autònoma de Barcelona, Bellaterra, Spain
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71
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Dumanski JP, Halvardson J, Davies H, Rychlicka-Buniowska E, Mattisson J, Moghadam BT, Nagy N, Węglarczyk K, Bukowska-Strakova K, Danielsson M, Olszewski P, Piotrowski A, Oerton E, Ambicka A, Przewoźnik M, Bełch Ł, Grodzicki T, Chłosta PL, Imreh S, Giedraitis V, Kilander L, Nordlund J, Ameur A, Gyllensten U, Johansson Å, Józkowicz A, Siedlar M, Klich-Rączka A, Jaszczyński J, Enroth S, Baran J, Ingelsson M, Perry JRB, Ryś J, Forsberg LA. Immune cells lacking Y chromosome show dysregulation of autosomal gene expression. Cell Mol Life Sci 2021; 78:4019-4033. [PMID: 33837451 PMCID: PMC8106578 DOI: 10.1007/s00018-021-03822-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Revised: 03/01/2021] [Accepted: 03/25/2021] [Indexed: 01/09/2023]
Abstract
Epidemiological investigations show that mosaic loss of chromosome Y (LOY) in leukocytes is associated with earlier mortality and morbidity from many diseases in men. LOY is the most common acquired mutation and is associated with aberrant clonal expansion of cells, yet it remains unclear whether this mosaicism exerts a direct physiological effect. We studied DNA and RNA from leukocytes in sorted- and single-cells in vivo and in vitro. DNA analyses of sorted cells showed that men diagnosed with Alzheimer's disease was primarily affected with LOY in NK cells whereas prostate cancer patients more frequently displayed LOY in CD4 + T cells and granulocytes. Moreover, bulk and single-cell RNA sequencing in leukocytes allowed scoring of LOY from mRNA data and confirmed considerable variation in the rate of LOY across individuals and cell types. LOY-associated transcriptional effect (LATE) was observed in ~ 500 autosomal genes showing dysregulation in leukocytes with LOY. The fraction of LATE genes within specific cell types was substantially larger than the fraction of LATE genes shared between different subsets of leukocytes, suggesting that LOY might have pleiotropic effects. LATE genes are involved in immune functions but also encode proteins with roles in other diverse biological processes. Our findings highlight a surprisingly broad role for chromosome Y, challenging the view of it as a "genetic wasteland", and support the hypothesis that altered immune function in leukocytes could be a mechanism linking LOY to increased risk for disease.
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Affiliation(s)
- Jan P Dumanski
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland.
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Hanna Davies
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Edyta Rychlicka-Buniowska
- International Research Agendas Programme, 3P Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Behrooz Torabi Moghadam
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Noemi Nagy
- Department of Cell and Molecular Biology, Karolinska Institutet, Stockholm, Sweden
| | - Kazimierz Węglarczyk
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Karolina Bukowska-Strakova
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Marcus Danielsson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Paweł Olszewski
- International Research Agendas Programme, 3P Medicine Laboratory, Medical University of Gdańsk, Gdańsk, Poland
| | - Arkadiusz Piotrowski
- Faculty of Pharmacy and 3P Medicine Laboratory, International Research Agendas Programme, Medical University of Gdańsk, Gdańsk, Poland
| | - Erin Oerton
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Aleksandra Ambicka
- Department of Tumour Pathology, Kraków Branch, Maria Skłodowska-Curie Memorial Cancer Centre and Institute of Oncology, Kraków, Poland
| | - Marcin Przewoźnik
- Department of Tumour Pathology, Kraków Branch, Maria Skłodowska-Curie Memorial Cancer Centre and Institute of Oncology, Kraków, Poland
| | - Łukasz Bełch
- Department and Clinic of Urology, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Tomasz Grodzicki
- Department and Clinic of Internal Medicine and Gerontology, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Piotr L Chłosta
- Department and Clinic of Urology, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Stefan Imreh
- Department Oncology-Pathology, Karolinska Institutet, Stockholm, Sweden
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Lena Kilander
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Jessica Nordlund
- Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Adam Ameur
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Ulf Gyllensten
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Åsa Johansson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Alicja Józkowicz
- Department of Medical Biotechnology, Faculty of Biochemistry, Biophysics and Biotechnology, Jagiellonian University, Kraków, Poland
| | - Maciej Siedlar
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Alicja Klich-Rączka
- Department and Clinic of Internal Medicine and Gerontology, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Janusz Jaszczyński
- Department of Urology, Maria Skłodowska-Curie Memorial Cancer Centre, Institute of Oncology, Kraków Branch, Kraków, Poland
| | - Stefan Enroth
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jarosław Baran
- Department of Clinical Immunology, Institute of Paediatrics, Jagiellonian University, Collegium Medicum, Kraków, Poland
| | - Martin Ingelsson
- Department of Public Health and Caring Sciences/Geriatrics, Uppsala University, Uppsala, Sweden
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Janusz Ryś
- Department of Tumour Pathology, Kraków Branch, Maria Skłodowska-Curie Memorial Cancer Centre and Institute of Oncology, Kraków, Poland
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden. .,The Beijer Laboratory, Uppsala University, Uppsala, Sweden.
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72
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Evaluation of the usefulness of saliva for mosaic loss of chromosome Y analysis. Sci Rep 2021; 11:3769. [PMID: 33580176 PMCID: PMC7881200 DOI: 10.1038/s41598-021-83308-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Accepted: 01/27/2021] [Indexed: 11/30/2022] Open
Abstract
Mosaic loss of chromosome Y (mLOY) in leukocytes has attracted much attention as an emerging biomarker of aging and aging-related diseases. We evaluated the usefulness of saliva for mLOY analysis and showed that saliva-derived mLOY is significantly associated with aging and increased physical activity, but not with smoking. While these data support the robust association between saliva-derived mLOY and aging, caution is required when comparing data from saliva-derived and blood-derived mLOY.
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73
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Ouseph MM, Hasserjian RP, Dal Cin P, Lovitch SB, Steensma DP, Nardi V, Weinberg OK. Genomic alterations in patients with somatic loss of the Y chromosome as the sole cytogenetic finding in bone marrow cells. Haematologica 2021; 106:555-564. [PMID: 32193254 PMCID: PMC7849577 DOI: 10.3324/haematol.2019.240689] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 03/19/2020] [Indexed: 01/23/2023] Open
Abstract
Loss of the Y chromosome (LOY) is one of the most common somatic genomic alterations in hematopoietic cells in men. However, due to the high prevalence of LOY as the sole cytogenetic finding in the healthy older population, differentiating isolated LOY associated with clonal hematologic processes from aging-associated mosaicism can be difficult in the absence of definitive morphological features of disease. In the past, various investigators have proposed that a high percentage of metaphases with LOY is more likely to represent expansion of a clonal myeloid disease-associated population. It is unknown whether the proportion of metaphases with LOY is associated with the incidence of myeloid neoplasia-associated genomic alterations. To address this question, we identified bone marrow samples with LOY as an isolated cytogenetic finding and used targeted next generation sequencing-based molecular analysis to identify common myeloid neoplasia-associated somatic mutations. Among 73 patients with a median age of 75 years (range, 29-90), the percentage of metaphases with LOY was <25% in 23 patients, 25-49% in 10, 50-74% in 8 and ≥75% in 32. A threshold of ≥75% LOY was significantly associated with a morphological diagnosis of myeloid neoplasm (P=0.004). Furthermore, ≥75% LOY was associated with a higher lifetime incidence of a diagnosis of myelodysplastic syndromes (MDS) (P<0.0001), and in multivariate analysis ≥75% LOY was a statistically significant independent predictor of myeloid neoplasia (odds ratio 6.17; 95% confidence interval: 2.15-17.68; P=0.0007]. Higher LOY percentage (≥75%) was associated with greater likelihood of having somatic mutations (P=0.0009) and a higher number of these mutations (P=0.0002). Our findings indicate that ≥75% LOY in bone marrow cells is associated with an increased likelihood of molecular aberrations in genes commonly seen to be altered in myeloid neoplasia and with morphological features of MDS. These observations suggest that ≥75% LOY in bone marrow should be considered an MDS-associated cytogenetic aberration.
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Affiliation(s)
- Madhu M Ouseph
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | | | - Paola Dal Cin
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - Scott B Lovitch
- Department of Pathology, Brigham and Women's Hospital, Boston, USA
| | - David P Steensma
- Department of Medical Oncology, Dana-Farber Cancer Institute, Boston, USA
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Boston, USA
| | - Olga K Weinberg
- Department of Pathology, Boston Children Hospital, Boston, USA
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74
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Baliakas P, Forsberg LA. Chromosome Y loss and drivers of clonal hematopoiesis in myelodysplastic syndrome. Haematologica 2021; 106:329-331. [PMID: 33522783 PMCID: PMC7849334 DOI: 10.3324/haematol.2020.266601] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Indexed: 11/25/2022] Open
Affiliation(s)
- Panagiotis Baliakas
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University; The Beijer Laboratory, Uppsala University, Uppsala.
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75
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Reply to Veitia. Eur J Hum Genet 2021; 29:1323-1324. [PMID: 33462398 PMCID: PMC8440652 DOI: 10.1038/s41431-020-00802-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 12/11/2020] [Indexed: 11/10/2022] Open
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76
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James BD, Guerin P, Allen JB. Let's Talk About Sex-Biological Sex Is Underreported in Biomaterial Studies. Adv Healthc Mater 2021; 10:e2001034. [PMID: 33043626 PMCID: PMC7791002 DOI: 10.1002/adhm.202001034] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Revised: 08/26/2020] [Indexed: 12/13/2022]
Abstract
Precision medicine aims to better individualize healthcare. It requires that biomaterials be designed for the physiological characteristics of a specific patient. To make this a reality, biomaterials research and development must address differences of biological sex. More specifically, biomaterials should be designed with properties optimized and appropriate for male and female patients. In analyzing research articles from seven prominent biomaterials journals, sex as a biological variable is missing from an overwhelming majority of in vitro biomaterial studies. From the survey, the reporting of the sex of primary cell cultures happened only 10.3% of the time. Contributing to this trend is that commercial vendors bias cell lines toward one sex or another by not disclosing information of cell line sex at the time of purchase; researchers do not communicate this pertinent information in published studies; and many journal policies have little to no requirements for reporting cell line characteristics. Omitting this valuable information leads to a gap in the understanding of sex-specific cell-biomaterial interactions and it creates a bias in research findings towards one sex or another. To curb this concerning trend and make precision biomaterials a reality will require the biomaterials field to "talk about sex" by reporting cell sex more broadly.
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Affiliation(s)
- Bryan D James
- Department of Materials Science and Engineering, University of Florida, 206 Rhines Hall, PO Box 116400, Gainesville, FL, 32611-6400, USA
| | - Paxton Guerin
- Department of Materials Science and Engineering, University of Florida, 206 Rhines Hall, PO Box 116400, Gainesville, FL, 32611-6400, USA
| | - Josephine B Allen
- Department of Materials Science and Engineering, University of Florida, 206 Rhines Hall, PO Box 116400, Gainesville, FL, 32611-6400, USA
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77
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Klutstein M. Cause and effect in epigenetics - where lies the truth, and how can experiments reveal it?: Epigenetic self-reinforcing loops obscure causation in cancer and aging. Bioessays 2020; 43:e2000262. [PMID: 33236359 DOI: 10.1002/bies.202000262] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 10/14/2020] [Accepted: 10/15/2020] [Indexed: 12/19/2022]
Abstract
Epigenetic changes are implicated in aging and cancer. Sometimes, it is clear whether the causing agent of the condition is a genetic factor or epigenetic. In other cases, the causative factor is unclear, and could be either genetic or epigenetic. Is there a general role for epigenetic changes in cancer and aging? Here, I present the paradigm of causative roles executed by epigenetic changes. I discuss cases with clear roles of the epigenome in cancer and aging, and other cases showing involvement of other factors. I also present the possibility that sometimes causality is difficult to assign because of the presence of self-reinforcing loops in epigenetic regulation. Such loops hinder the identification of the causative factor. I provide an experimental framework by which the role of the epigenome can be examined in a better setting and where the presence of such loops could be investigated in more detail.
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Affiliation(s)
- Michael Klutstein
- Institute of Dental Sciences, Faculty of Dental Medicine, The Hebrew University of Jerusalem, Ein Kerem, Jerusalem, Israel
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78
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Jaiswal S. Clonal hematopoiesis and nonhematologic disorders. Blood 2020; 136:1606-1614. [PMID: 32736379 PMCID: PMC8209629 DOI: 10.1182/blood.2019000989] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/01/2020] [Indexed: 12/18/2022] Open
Abstract
Clonal expansions of mutated hematopoietic cells, termed clonal hematopoiesis, are common in aging humans. One expected consequence of mutation-associated clonal hematopoiesis is an increased risk of hematologic cancers, which has now been shown in several studies. However, the hematopoietic stem cells that acquire these somatic mutations also give rise to mutated immune effector cells, such as monocytes, granulocytes, and lymphocytes. These effector cells can potentially influence many disease states, especially those with a chronic inflammatory component. Indeed, several studies have now shown that clonal hematopoiesis associates with increased risk of atherosclerotic cardiovascular disease. Emerging data also associate clonal hematopoiesis with other nonhematologic diseases. Here, we will review recent studies linking clonal hematopoiesis to altered immune function, inflammation, and nonmalignant diseases of aging.
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Affiliation(s)
- Siddhartha Jaiswal
- Department of Pathology, Institute for Stem Cell Biology and Regenerative Medicine, and Program in Immunology, School of Medicine, Stanford University, Stanford, CA
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79
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Kirsch-Volders M, Bolognesi C, Ceppi M, Bruzzone M, Fenech M. Micronuclei, inflammation and auto-immune disease. MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH 2020; 786:108335. [PMID: 33339583 DOI: 10.1016/j.mrrev.2020.108335] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/11/2020] [Revised: 08/28/2020] [Accepted: 09/03/2020] [Indexed: 12/16/2022]
Abstract
Auto-immune diseases (AUD) are characterized by an immune response to antigenic components of the host itself. The etiology of AUD is not well understood. The available evidence points to an interaction between genetic, epigenetic, environmental, infectious and life-style factors. AUD are more prevalent in women than in men; sex hormones play a crucial role in this sex bias. Micronuclei (MN) emerged as a new player in the induction of AUD, based on the capacity of DNA-sensors to detect self-DNA that leaks into the cytoplasm from disrupted MN and induce the cGAS-STING pathway triggering an innate auto-immune response and chronic inflammation. It was found that inflammation can induce MN and MN can induce inflammation, leading to a vicious inflammation-oxidative-DNA damage-MN-formation-chromothripsis cycle. MN originating from sex chromosome-loss may induce inflammation and AUD. We performed a systematic review of studies reporting MN in patients with systemic or organ-specific AUD. A meta-analysis was performed on lymphocyte MN in diabetes mellitus (10 studies, 457 patients/290 controls) and Behcet's disease (3 studies, 100 patients/70 controls) and for buccal MN in diabetes mellitus (11 studies, 507 patients/427 controls). A statistically significant increase in patients compared to controls was found in the meta-analyses providing an indication of an association between MN and AUD. A 36%-higher mean-MRi in buccal cells (3.8+/-0.7) was found compared to lymphocytes (2.8+/-0.7)(P = 0.01). The meta-MRi in lymphocytes and buccal cells (1.7 and 3.0 respectively) suggest that buccal cells may be more sensitive. To assess their relative sensitivity, studies with measurements from the same subjects would be desirable. It is important that future studies (i) investigate, in well-designed powered studies, the prospective association of MN-formation with AUD and (ii) explore the molecular mechanisms by which chromosome shattering in MN and the release of chromatin fragments from MN lead to the formation of auto-antibodies.
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Affiliation(s)
- Micheline Kirsch-Volders
- Laboratory for Cell Genetics, Department Biology, Faculty of Sciences and Bio-engineering Sciences, Vrije Universiteit Brussel, Pleinlaan 2, 1050 Brussels, Belgium
| | - Claudia Bolognesi
- Environmental Carcinogenesis Unit, Ospedale Policlinico San Martino, 16132 Genoa, Italy.
| | - Marcello Ceppi
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Marco Bruzzone
- Unit of Clinical Epidemiology, IRCCS Ospedale Policlinico San Martino, 16132 Genoa, Italy
| | - Michael Fenech
- Genome Health Foundation, North Brighton, 5048, Australia; Clinical and Health Sciences, University of South Australia, SA 5000, Australia
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80
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Fazel A, Quabius ES, Gonzales-Donate M, Laudien M, Herzog A, Kress K, Schleicher T, Fabian A, Huber K, Hoffmann M. Alteration of smoking habit at time of first diagnosis influences survival of patients with HNSCC. Mol Clin Oncol 2020; 13:50. [PMID: 32874580 PMCID: PMC7453390 DOI: 10.3892/mco.2020.2120] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 06/02/2020] [Indexed: 11/23/2022] Open
Abstract
The impact of smoking on survival in patients with squamous cell carcinoma of the head and neck is well established, despite some conflicting data in the literature. However, data on alterations of smoking habit following cancer diagnosis is sparse. In the present study, the effect of reduction of smoking compared with cessation on the course of disease was studied. Data from 643 patients with HNSCC from the tumor documentation registry of the Department of Otorhinolaryngology, Head and Neck Surgery of the Christian-Albrechts-University Kiel were collected and statistically analyzed, looking at pre- and post-treatment smoking habit and survival. Alteration of smoking at the first diagnosis of HNSCC led to a significantly beneficial effect on survival outcomes compared with continued smoking, without significant differences between reduction and cessation of smoking. Detailed analysis revealed that this effect was solely dependent on patients treated by surgery only. Lifelong non-smokers exhibited a significant survival advantage compared with active and former smokers, with no difference in survival between these last two groups. The positive influence of altered smoking habit following first time diagnosis on disease-specific survival paralleled the negative direct effect of active smoking on therapy, which is predominantly attributed to peritumoral tissue hypoxia leading to impaired efficacy of radiochemotherapy (RCT). In the present study cohort, the positive effect of smoking habit alterations were primarily observed in patients treated by surgery only instead of RCT, possibly due to fewer perioperative complications. These findings indicated that patients should be encouraged to at least minimize smoking following cancer diagnosis. Furthermore, for survival estimates and therapy planning, former smokers should be considered as active smokers.
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Affiliation(s)
- Asita Fazel
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Elgar Susanne Quabius
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany.,Institute of Immunology, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Mireia Gonzales-Donate
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Martin Laudien
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Arved Herzog
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Konstantin Kress
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Thilo Schleicher
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Alexander Fabian
- Department of Radiooncology, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Karen Huber
- Department of Radiooncology, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
| | - Markus Hoffmann
- Department of Otorhinolaryngology, Head and Neck Surgery, Christian-Albrechts-University, University Hospital Schleswig-Holstein, D-24105 Kiel, Germany
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81
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Muscogiuri G, Altieri B, Albertelli M, Dotto A, Modica R, Barrea L, Fanciulli G, Feola T, Baldelli R, Ruggeri RM, Gallo M, Guarnotta V, Malandrino P, Messina E, Venneri MA, Giannetta E, Ferone D, Colao A, Faggiano A. Epidemiology of pancreatic neuroendocrine neoplasms: a gender perspective. Endocrine 2020; 69:441-450. [PMID: 32468269 DOI: 10.1007/s12020-020-02331-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 04/25/2020] [Indexed: 01/10/2023]
Abstract
PURPOSE Pancreatic neuroendocrine neoplasms (PNENs) are a group of clinically rare and heterogeneous tumors of the pancreas. Currently there are no studies investigating the gender difference in PNEN susceptibility. Thus, the purpose of this study was aimed at examining how gender shapes risk factors, clinicopathological features, and comorbidities in PNENs. METHODS The study design consisted of an Italian multicenter, retrospective study. The study included all consecutive patients with PNENs followed at the participating centers. Two hundred and twenty-nine patients (105 males,124 females, age 54 ± 0.98 years) with PNENs were enrolled at the participating centers. The clinicopathological features (age, gender, BMI, histology, tumor size, tumor grade, distant metastasis, hormonal function, and diagnostic circumstances), comorbidities (cardiovascular diseases (CVD), pancreatitis, type 2 diabetes (T2DM), and potential risk factors (smoking and drinking) were included in the analysis. RESULTS Females were slightly prevalent (54.15%). PNENs were diagnosed at younger age in females compared to males (p = 0.04). The prevalence of CVD was significantly higher in males than in females (p = 0.006). In the female group, the presence of T2DM was significantly associated with higher tumor grade (p = 0.04) and metastatic disease (p = 0.02). The proportion of smokers and alcohol drinkers was significantly higher in the male group (p < 0.001). No significant gender differences were detected regarding the other parameters included in the analysis. CONCLUSIONS This study has identified gender differences of PNENs in terms of age at diagnosis, associated comorbidities, and potential risk factors. A gender-tailored approach could become a potential strategy to better understand the natural history of PNENs and improve the effectiveness of PNENs clinical management.
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Affiliation(s)
- Giovanna Muscogiuri
- Department of Clinical Medicine and Surgery, University "Federico II", Naples, Italy.
| | - Barbara Altieri
- Department of Clinical Medicine and Surgery, University "Federico II", Naples, Italy
- Division of Endocrinology and Diabetes, Department of Internal Medicine I, University Hospital, University of Würzburg, Würzburg, Germany
| | - Manuela Albertelli
- Endocrinology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Endocrinology Unit, Department of Internal Medicine and Medical Specialities (DIMI) and Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Andrea Dotto
- Endocrinology Unit, Department of Internal Medicine and Medical Specialities (DIMI), University of Genoa, Genoa, Italy
| | - Roberta Modica
- Department of Clinical Medicine and Surgery, University "Federico II", Naples, Italy
| | - Luigi Barrea
- Department of Clinical Medicine and Surgery, University "Federico II", Naples, Italy
| | - Giuseppe Fanciulli
- Department of Surgical, Medical and Experimental Sciences, University of Sassari-Endocrine Unit, AOU Sassari, Sassari, Italy
| | - Tiziana Feola
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Roberto Baldelli
- Endocrinological Oncology, Service of Endocrinology, A.O. San Camillo-Forlanini, Rome, Italy
| | | | - Marco Gallo
- Department of Medical Sciences, Oncological Endocrinology Unit, University of Turin, Turin, Italy
| | - Valentina Guarnotta
- Section of Endocrine-Metabolic Diseases, Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties (ProMISE), University of Palermo, Palermo, Italy
| | - Pasqualino Malandrino
- Endocrinology, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - Erika Messina
- Department of Clinical and Experimental Medicine, University of Messina, Messina, Italy
| | - Mary Anna Venneri
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Elisa Giannetta
- Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Diego Ferone
- Endocrinology Unit, IRCCS Ospedale Policlinico San Martino, Genoa, Italy
- Endocrinology Unit, Department of Internal Medicine and Medical Specialities (DIMI) and Centre of Excellence for Biomedical Research (CEBR), University of Genoa, Genoa, Italy
| | - Annamaria Colao
- Department of Clinical Medicine and Surgery, University "Federico II", Naples, Italy
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82
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Y Chromosome Loss is a Frequent Event in Barrett's Adenocarcinoma and Associated with Poor Outcome. Cancers (Basel) 2020; 12:cancers12071743. [PMID: 32629877 PMCID: PMC7408596 DOI: 10.3390/cancers12071743] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2020] [Revised: 06/23/2020] [Accepted: 06/26/2020] [Indexed: 01/06/2023] Open
Abstract
Background: The loss of the Y chromosome in various malignant diseases has been described previously. There are no reliable information on the actual frequency, significance and homogeneity of Y chromosome loss (LoY) in esophageal adenocarcinoma (EAC). Methods: 400 male EAC including lymph-node metastases were analyzed with commercially available Y chromosome specific fluorescence in-situ probes. The results were correlated with molecular and immunohistochemical markers and clinicopathological aspects. Results: The entire cohort (n = 400) showed a singular LoY of one chromosome arm in 1.0% (q-arm) and 2.8% (p-arm), complete LoY in 52.5%. LoY was strongly associated with shortened overall-survival (OS). Patients with preserved Y chromosome had a median OS of 58.8 months, patients with LoY an OS of 19.4 months (p < 0.001). Multivariate analysis showed LoY as an independent prognostic marker with a hazard ratio of 1.835 (95% CI 1.233–2.725). LoY correlated with TP53 mutations (p = 0.003), KRAS amplification (p = 0.004), loss of ARID1a (p = 0.045) and presence of LAG3 (p = 0.018). Conclusions: Loss of the Y chromosome is a very common phenomenon in EAC. The LoY is heterogeneously distributed within the tumor, but corresponding lymph node metastases frequently show homogeneous LoY, indicating a selection and metastasizing advantage with poor prognosis. To date, the male predominance of EAC (7–9:1) is unclear, so genetic explanatory models are favored. The LoY in EAC may be biologically and functionally relevant and additional genomic or functional analyses are needed.
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83
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Caceres A, Jene A, Esko T, Perez-Jurado LA, Gonzalez JR. Extreme downregulation of chromosome Y and Alzheimer's disease in men. Neurobiol Aging 2020; 90:150.e1-150.e4. [DOI: 10.1016/j.neurobiolaging.2020.02.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 09/16/2019] [Accepted: 02/04/2020] [Indexed: 12/31/2022]
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84
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Association Between Psychoactive Substance Abuse and Health Disorders in Colombian Problem Drug Users: Second Study. Int J Ment Health Addict 2020. [DOI: 10.1007/s11469-018-9881-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
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85
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Chen Y, Xu Y, Cao X, Zheng C, Lin L, Zhu Z, Hu J. Three patients with 46,X,inv(Y)(p11.2q11.2)pat/45,X and their pedigree analysis. Ann Hum Genet 2020; 84:331-338. [PMID: 32162681 PMCID: PMC7318165 DOI: 10.1111/ahg.12381] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 01/09/2020] [Accepted: 01/10/2020] [Indexed: 11/29/2022]
Abstract
The present study aimed to perform chromosome examination and pedigree analysis on three patients with semen abnormality who had undergone in vitro fertilization–embryo transfer (IVF‐ET). Peripheral blood cell culture and chromosome karyotyping were performed on 4,200 individuals who had undergone chromosome examination. Among them, 155 pregnant women who had successfully conceived were subjected to amniotic cell culture and chromosome karyotyping and those with abnormal chromosome karyotype were further subjected to C‐banding and whole‐genome sequencing. Mosaicism for a 46,X,inv(Y)(p11.2q11.2)pat/45,X karyotype was identified in the probands and immediate adult male relatives. The incidence of this mosaicism in the study population was only 0.07% (3/4,200), which is reported for the first time. For the proband of pedigree A, the results of whole‐genome sequencing and other tests were normal, and the chromosome karyotype of IVF fetuses was 46,X,inv(Y)(p11.2q11.2)pat. All the male members of three pedigrees have normal phenotypes, with no features of Turner's syndrome (45,X) or hermaphroditism (45,X/46,XY), suggesting that the inverted Y chromosome is extremely unstable and particularly susceptible to loss in somatic cells. So we speculate this karyotype may be a unique type of inverted Y chromosome in somatic cells.
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Affiliation(s)
- Yunchun Chen
- Department of Laboratory Medicine, Haikou Branch of Yue Yang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine (Haikou Hospital of Traditional Chinese Medicine), Hainan, Haikou, China
| | - Yuni Xu
- Department of Laboratory Medicine, Second Affiliated Hospital of Hainan Medical University, Hainan, Haikou, China
| | - Xiaoqiang Cao
- Department of Laboratory Medicine, Second Affiliated Hospital of Hainan Medical University, Hainan, Haikou, China
| | - Chunqiao Zheng
- Department of Laboratory Medicine, Second Affiliated Hospital of Hainan Medical University, Hainan, Haikou, China
| | - Liying Lin
- Department of Laboratory Medicine, Second Affiliated Hospital of Hainan Medical University, Hainan, Haikou, China
| | - Zhongyuan Zhu
- Department of Laboratory Medicine, Second Affiliated Hospital of Hainan Medical University, Hainan, Haikou, China
| | - Jiandong Hu
- Internal Medicine, Haikou Branch of Yue Yang Hospital of Integrated Traditional Chinese and Western Medicine, Shanghai University of Traditional Chinese Medicine (Haikou Hospital of Traditional Chinese Medicine), Hainan, Haikou, China
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86
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Liu Y, Bai Y, Wu X, Li G, Wei W, Fu W, Wang G, Feng Y, Meng H, Li H, Li M, Guan X, Zhang X, He M, Wu T, Guo H. Polycyclic aromatic hydrocarbons exposure and their joint effects with age, smoking, and TCL1A variants on mosaic loss of chromosome Y among coke-oven workers. ENVIRONMENTAL POLLUTION (BARKING, ESSEX : 1987) 2020; 258:113655. [PMID: 31818624 DOI: 10.1016/j.envpol.2019.113655] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/10/2019] [Accepted: 11/19/2019] [Indexed: 06/10/2023]
Abstract
Mosaic loss of chromosome Y (mLOY) is the most common structure somatic event that related to increased risks of various diseases and mortality. Environmental pollution and genetic susceptibility were important contributors to mLOY. We aimed to explore the associations of polycyclic aromatic hydrocarbons (PAHs) exposure, as well as their joint effects with age, smoking, and genetic variants on peripheral blood mLOY. A total of 1005 male coke-oven workers were included in this study and their internal PAHs exposure levels of 10 urinary PAH metabolites and plasma benzo[a]pyrene-r-7,t-8,t-9,c-10-tetrahydotetrol-albumin (BPDE-Alb) adducts were measured. mLOY was defined by the median log R ratio(mLRR) of 1480 probes in male-specific region of chromosome-Y from genotyping array. We found that the PAHs exposure levels were linearly associated with mLOY. A 10-fold increase in urinary 1-hydroxynaphthalene (1-OHNa), 1-hydroxyphenanthrene (1-OHPh), 2-OHPh, 1-hydroxypyrene (1-OHP), ΣOH-PAHs, and plasma BPDE-Alb adducts could generate 0.0111, 0.0085, 0.0069, 0.0103, 0.0134, and 0.0152 decrease in mLRR-Y, respectively. Additionally, mLOY accelerated with age, smoking pack-years, and TCL1A rs1122138-C allele, and we observed the most severe mLOY among subjects carrying more than 3 of the above risk factors. Our results revealed the linear dose-effect associations between PAHs exposure and mLOY. Elder male smokers carrying rs1122138CC genotype were the most susceptible subpopulations to mLOY, who should be given protections for PAHs exposure induced chromosome-Y aberration.
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Affiliation(s)
- Yuhang Liu
- 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
- 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
| | - Xiulong 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
| | - Guyanan Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Wei Wei
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Wenshan 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
| | - Gege 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
| | - Yue Feng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Hua Meng
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Hang Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Mengying Li
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Xin Guan
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Xiaomin Zhang
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, China
| | - Meian He
- Department of Occupational and Environmental Health, State Key Laboratory of Environmental Health (Incubating), School of Public Health, Tongji Medical College, Huazhong University of Science and Technology, 13 Hangkong Rd, Wuhan, 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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87
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Xirocostas ZA, Everingham SE, Moles AT. The sex with the reduced sex chromosome dies earlier: a comparison across the tree of life. Biol Lett 2020; 16:20190867. [PMID: 32126186 PMCID: PMC7115182 DOI: 10.1098/rsbl.2019.0867] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2019] [Accepted: 02/10/2020] [Indexed: 01/02/2023] Open
Abstract
Many taxa show substantial differences in lifespan between the sexes. However, these differences are not always in the same direction. In mammals, females tend to live longer than males, while in birds, males tend to live longer than females. One possible explanation for these differences in lifespan is the unguarded X hypothesis, which suggests that the reduced or absent chromosome in the heterogametic sex (e.g. the Y chromosome in mammals and the W chromosome in birds) exposes recessive deleterious mutations on the other sex chromosome. While the unguarded X hypothesis is intuitively appealing, it had never been subject to a broad test. We compiled male and female longevity data for 229 species spanning 99 families, 38 orders and eight classes across the tree of life. Consistent with the unguarded X hypothesis, a meta-analysis showed that the homogametic sex, on average, lives 17.6% longer than the heterogametic sex. Surprisingly, we found substantial differences in lifespan dimorphism between female heterogametic species (in which the homogametic sex lives 7.1% longer) and male heterogametic species (in which the homogametic sex lives 20.9% longer). Our findings demonstrate the importance of considering chromosome morphology in addition to sexual selection and environment as potential drivers of sexual dimorphism, and advance our fundamental understanding of the mechanisms that shape an organism's lifespan.
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Affiliation(s)
- Zoe A. Xirocostas
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
| | - Susan E. Everingham
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
- The Australian PlantBank, Royal Botanic Gardens and Domain Trust, Australian Botanic Garden, Mount Annan, New South Wales 2567, Australia
| | - Angela T. Moles
- Evolution & Ecology Research Centre, School of Biological, Earth and Environmental Sciences, UNSW Sydney, Sydney, New South Wales 2052, Australia
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88
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Lin SH, Loftfield E, Sampson JN, Zhou W, Yeager M, Freedman ND, Chanock SJ, Machiela MJ. Mosaic chromosome Y loss is associated with alterations in blood cell counts in UK Biobank men. Sci Rep 2020; 10:3655. [PMID: 32108144 PMCID: PMC7046668 DOI: 10.1038/s41598-020-59963-8] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Accepted: 02/04/2020] [Indexed: 12/31/2022] Open
Abstract
Mosaic loss of Y chromosome (mLOY) is the most frequently detected somatic copy number alteration in leukocytes of men. In this study, we investigate blood cell counts as a potential mechanism linking mLOY to disease risk in 206,353 UK males. Associations between mLOY, detected by genotyping arrays, and blood cell counts were assessed by multivariable linear models adjusted for relevant risk factors. Among the participants, mLOY was detected in 39,809 men. We observed associations between mLOY and reduced erythrocyte count (−0.009 [−0.014, −0.005] × 1012 cells/L, p = 2.75 × 10−5) and elevated thrombocyte count (5.523 [4.862, 6.183] × 109 cells/L, p = 2.32 × 10−60) and leukocyte count (0.218 [0.198, 0.239] × 109 cells/L, p = 9.22 × 10−95), particularly for neutrophil count (0.174 × [0.158, 0.190]109 cells/L, p = 1.24 × 10−99) and monocyte count (0.021 [0.018 to 0.024] × 109 cells/L, p = 6.93 × 10−57), but lymphocyte count was less consistent (0.016 [0.007, 0.025] × 109 cells/L, p = 8.52 × 10−4). Stratified analyses indicate these associations are independent of the effects of aging and smoking. Our findings provide population-based evidence for associations between mLOY and blood cell counts that should stimulate investigation of the underlying biological mechanisms linking mLOY to cancer and chronic disease risk.
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Affiliation(s)
- Shu-Hong Lin
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Erikka Loftfield
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Josh N Sampson
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Weiyin Zhou
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Meredith Yeager
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.,Cancer Genomics Research Laboratory, Frederick National Laboratory for Cancer Research, Frederick, Maryland, 8717 Grovemont Circle, Gaithersburg, MD, 20877, USA
| | - Neal D Freedman
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, 9609 Medical Center Drive MSC 9776, Bethesda, Maryland, 20892, USA.
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Abstract
PURPOSE OF REVIEW Genetic mosaicism is the presence of a somatic mutation in a subset of cells that differs from the inherited germline genome. Detectable genetic mosaicism is attractive as a potential early biomarker for cancer risk because of its established relationship with aging, introduction of potentially deleterious mutations, and clonal selection and expansion of mutated cells. The aim of this review is to survey shared risk factors associated with genetic mosaicism, aging and cancer risk. RECENT FINDINGS Studies have associated aging, cigarette smoking and several genetic susceptibility loci with increased risk of acquiring genetic mosaicism. Genetic mosaicism has also been associated with numerous outcomes including cancer risk and cancer mortality; however, the level of evidence supporting these associations varies considerably. SUMMARY Ample evidence exists for shared risk factors for genetic mosaicism and cancer risk as well as abundant support linking genetic mosaicism in leukocytes to hematologic malignancies. The relationship between genetic mosaicism in circulating leukocytes and solid malignancies remains an active area of research.
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90
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Guo X, Dai X, Zhou T, Wang H, Ni J, Xue J, Wang X. Mosaic loss of human Y chromosome: what, how and why. Hum Genet 2020; 139:421-446. [DOI: 10.1007/s00439-020-02114-w] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Accepted: 01/06/2020] [Indexed: 02/07/2023]
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91
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Dumont M, Gamba R, Gestraud P, Klaasen S, Worrall JT, De Vries SG, Boudreau V, Salinas‐Luypaert C, Maddox PS, Lens SMA, Kops GJPL, McClelland SE, Miga KH, Fachinetti D. Human chromosome-specific aneuploidy is influenced by DNA-dependent centromeric features. EMBO J 2020; 39:e102924. [PMID: 31750958 PMCID: PMC6960447 DOI: 10.15252/embj.2019102924] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/21/2019] [Accepted: 10/29/2019] [Indexed: 12/11/2022] Open
Abstract
Intrinsic genomic features of individual chromosomes can contribute to chromosome-specific aneuploidy. Centromeres are key elements for the maintenance of chromosome segregation fidelity via a specialized chromatin marked by CENP-A wrapped by repetitive DNA. These long stretches of repetitive DNA vary in length among human chromosomes. Using CENP-A genetic inactivation in human cells, we directly interrogate if differences in the centromere length reflect the heterogeneity of centromeric DNA-dependent features and whether this, in turn, affects the genesis of chromosome-specific aneuploidy. Using three distinct approaches, we show that mis-segregation rates vary among different chromosomes under conditions that compromise centromere function. Whole-genome sequencing and centromere mapping combined with cytogenetic analysis, small molecule inhibitors, and genetic manipulation revealed that inter-chromosomal heterogeneity of centromeric features, but not centromere length, influences chromosome segregation fidelity. We conclude that faithful chromosome segregation for most of human chromosomes is biased in favor of centromeres with high abundance of DNA-dependent centromeric components. These inter-chromosomal differences in centromere features can translate into non-random aneuploidy, a hallmark of cancer and genetic diseases.
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Affiliation(s)
- Marie Dumont
- Institut CuriePSL Research UniversityCNRSUMR144ParisFrance
| | - Riccardo Gamba
- Institut CuriePSL Research UniversityCNRSUMR144ParisFrance
| | - Pierre Gestraud
- Institut CuriePSL Research UniversityCNRSUMR144ParisFrance
- PSL Research UniversityInstitut Curie Research CenterINSERM U900ParisFrance
- MINES ParisTechPSL Research UniversityCBIO‐Centre for Computational BiologyParisFrance
| | - Sjoerd Klaasen
- Oncode InstituteHubrecht Institute—KNAW (Royal Netherlands Academy of Arts and Sciences)UtrechtThe Netherlands
| | | | - Sippe G De Vries
- Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Vincent Boudreau
- Department of BiologyUniversity of North CarolinaChapel HillNCUSA
| | | | - Paul S Maddox
- Department of BiologyUniversity of North CarolinaChapel HillNCUSA
| | - Susanne MA Lens
- Oncode InstituteCenter for Molecular MedicineUniversity Medical Center UtrechtUtrecht UniversityUtrechtThe Netherlands
| | - Geert JPL Kops
- Oncode InstituteHubrecht Institute—KNAW (Royal Netherlands Academy of Arts and Sciences)UtrechtThe Netherlands
| | | | - Karen H Miga
- Center for Biomolecular Science & EngineeringUniversity of California Santa CruzSanta CruzCAUSA
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92
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Micronuclei and disease - Report of HUMN project workshop at Rennes 2019 EEMGS conference. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2020; 850-851:503133. [PMID: 32247551 DOI: 10.1016/j.mrgentox.2020.503133] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Revised: 12/05/2019] [Accepted: 01/07/2020] [Indexed: 02/07/2023]
Abstract
The "Micronuclei and Disease" workshop was organized by the HUMN Project consortium and hosted by the European Environmental Mutagen and Genomics Society at their annual meeting in Rennes, France, on 23 May 2019. The program of the workshop focused on addressing the emerging evidence linking micronucleus (MN) frequency to human disease. The first objective was to review what has been published and evaluate the level and quality of evidence for the connection between MN frequency and various diseases through all life stages. The second objective was to identify the knowledge gaps and what else needs to be done to determine the clinical utility of MN assays as predictors of disease risk and of prognosis when disease is active. Speakers at the workshop discussed the association of MN frequency with inflammation, infertility, pregnancy complications, obesity, diabetes, cardiovascular disease, kidney disease, cervical and bladder cancer, oral head and neck cancer, lung cancer, accelerated ageing syndromes, neurodegenerative diseases, and a road-map on how to utilise this knowledge was proposed. The outcomes of the workshop indicated that there are significant opportunities for translating the application of MN assays into clinical practice to improve disease prevention and risk management and to inform public health policy.
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93
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Thompson DJ, Genovese G, Halvardson J, Ulirsch JC, Wright DJ, Terao C, Davidsson OB, Day FR, Sulem P, Jiang Y, Danielsson M, Davies H, Dennis J, Dunlop MG, Easton DF, Fisher VA, Zink F, Houlston RS, Ingelsson M, Kar S, Kerrison ND, Kinnersley B, Kristjansson RP, Law PJ, Li R, Loveday C, Mattisson J, McCarroll SA, Murakami Y, Murray A, Olszewski P, Rychlicka-Buniowska E, Scott RA, Thorsteinsdottir U, Tomlinson I, Moghadam BT, Turnbull C, Wareham NJ, Gudbjartsson DF, Kamatani Y, Hoffmann ER, Jackson SP, Stefansson K, Auton A, Ong KK, Machiela MJ, Loh PR, Dumanski JP, Chanock SJ, Forsberg LA, Perry JRB. Genetic predisposition to mosaic Y chromosome loss in blood. Nature 2019; 575:652-657. [PMID: 31748747 PMCID: PMC6887549 DOI: 10.1038/s41586-019-1765-3] [Citation(s) in RCA: 187] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 10/04/2019] [Indexed: 12/13/2022]
Abstract
Mosaic loss of chromosome Y (LOY) in circulating white blood cells is the most common form of clonal mosaicism1-5, yet our knowledge of the causes and consequences of this is limited. Here, using a computational approach, we estimate that 20% of the male population represented in the UK Biobank study (n = 205,011) has detectable LOY. We identify 156 autosomal genetic determinants of LOY, which we replicate in 757,114 men of European and Japanese ancestry. These loci highlight genes that are involved in cell-cycle regulation and cancer susceptibility, as well as somatic drivers of tumour growth and targets of cancer therapy. We demonstrate that genetic susceptibility to LOY is associated with non-haematological effects on health in both men and women, which supports the hypothesis that clonal haematopoiesis is a biomarker of genomic instability in other tissues. Single-cell RNA sequencing identifies dysregulated expression of autosomal genes in leukocytes with LOY and provides insights into why clonal expansion of these cells may occur. Collectively, these data highlight the value of studying clonal mosaicism to uncover fundamental mechanisms that underlie cancer and other ageing-related diseases.
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Affiliation(s)
- Deborah J Thompson
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Giulio Genovese
- Department of Genetics, Harvard Medical School, 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
| | - Jonatan Halvardson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jacob C Ulirsch
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Program in Biological and Biomedical Sciences, Harvard Medical School, Boston, MA, USA
| | - Daniel J Wright
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Open Targets Core Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Chikashi Terao
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- Department of Applied Genetics, School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
| | | | - Felix R Day
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | | | - Marcus Danielsson
- 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
| | - Joe Dennis
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Malcolm G Dunlop
- Colon Cancer Genetics Group, Medical Research Council Human Genetics Unit and CRUK Cancer Research Centre, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh, UK
| | - Douglas F Easton
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK
| | - Victoria A Fisher
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | | | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Martin Ingelsson
- Geriatrics Research Group, Department of Public Health and Caring Sciences, Uppsala University, Uppsala, Sweden
| | - Siddhartha Kar
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, UK
| | - Nicola D Kerrison
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | | | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Rong Li
- Department of Cell Biology, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Chey Loveday
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Jonas Mattisson
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Steven A McCarroll
- Department of Genetics, Harvard Medical School, 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
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Anna Murray
- Genetics of Complex Traits, University of Exeter Medical School, University of Exeter, Exeter, UK
| | - Pawel Olszewski
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Edyta Rychlicka-Buniowska
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Robert A Scott
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Amgen, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | - Ian Tomlinson
- Cancer Genetics and Evolution Laboratory, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Behrooz Torabi Moghadam
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Clare Turnbull
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
- William Harvey Research Institute, Queen Mary University, London, UK
| | - Nicholas J Wareham
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics, Amgen, Reykjavík, Iceland
- School of Engineering and Natural Sciences, University of Iceland, Reykjavík, Iceland
| | - Yoichiro Kamatani
- Laboratory for Statistical Analysis, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, Japan
- Kyoto-McGill International Collaborative School in Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Eva R Hoffmann
- DNRF Center for Chromosome Stability, Department of Cellular and Molecular Medicine, Faculty of Health Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Steve P Jackson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
- Wellcome Trust and Cancer Research UK Gurdon Institute, University of Cambridge, Cambridge, UK
| | - Kari Stefansson
- deCODE Genetics, Amgen, Reykjavík, Iceland
- Faculty of Medicine, University of Iceland, Reykjavík, Iceland
| | | | - Ken K Ong
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK
| | - Mitchell J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Po-Ru Loh
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Jan P Dumanski
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Faculty of Pharmacy, Medical University of Gdansk, Gdansk, Poland
| | - Stephen J Chanock
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, USA
| | - Lars A Forsberg
- Department of Immunology, Genetics and Pathology and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
- Beijer Laboratory of Genome Research, Uppsala University, Uppsala, Sweden
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, UK.
- Department of Internal Medicine, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
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94
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Longitudinal changes in the frequency of mosaic chromosome Y loss in peripheral blood cells of aging men varies profoundly between individuals. Eur J Hum Genet 2019; 28:349-357. [PMID: 31654039 PMCID: PMC7028735 DOI: 10.1038/s41431-019-0533-z] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/10/2019] [Accepted: 10/13/2019] [Indexed: 11/18/2022] Open
Abstract
Mosaic loss of chromosome Y (LOY) is the most common somatic genetic aberration and is associated with increased risk for all-cause mortality, various forms of cancer and Alzheimer’s disease, as well as other common human diseases. By tracking LOY frequencies in subjects from which blood samples have been serially collected up to five times during up to 22 years, we observed a pronounced intra-individual variation of changes in the frequency of LOY within individual men over time. We observed that in some individuals the frequency of LOY in blood clearly progressed over time and that in other men, the frequency was constant or showed other types of longitudinal development. The predominant method used for estimating LOY is calculation of the median Log R Ratio of probes located in the male specific part of chromosome Y (mLRRY) from intensity data generated by SNP-arrays, which is difficult to interpret due to its logarithmic and inversed scale. We present here a formula to transform mLRRY-values to percentage of LOY that is a more comprehensible unit. The formula was derived using measurements of LOY from matched samples analysed using SNP-array, whole genome sequencing and a new AMELX/AMELY-based assay for droplet digital PCR. The methods described could be applied for analyses of the vast amount of SNP-array data already generated in the scientific community, allowing further discoveries of LOY associated diseases and outcomes.
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95
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Terao C, Momozawa Y, Ishigaki K, Kawakami E, Akiyama M, Loh PR, Genovese G, Sugishita H, Ohta T, Hirata M, Perry JRB, Matsuda K, Murakami Y, Kubo M, Kamatani Y. GWAS of mosaic loss of chromosome Y highlights genetic effects on blood cell differentiation. Nat Commun 2019; 10:4719. [PMID: 31624269 PMCID: PMC6797717 DOI: 10.1038/s41467-019-12705-5] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2019] [Accepted: 09/18/2019] [Indexed: 12/28/2022] Open
Abstract
Mosaic loss of chromosome Y (mLOY) is frequently observed in the leukocytes of ageing men. However, the genetic architecture and biological mechanisms underlying mLOY are not fully understood. In a cohort of 95,380 Japanese men, we identify 50 independent genetic markers in 46 loci associated with mLOY at a genome-wide significant level, 35 of which are unreported. Lead markers overlap enhancer marks in hematopoietic stem cells (HSCs, P ≤ 1.0 × 10−6). mLOY genome-wide association study signals exhibit polygenic architecture and demonstrate strong heritability enrichment in regions surrounding genes specifically expressed in multipotent progenitor (MPP) cells and HSCs (P ≤ 3.5 × 10−6). ChIP-seq data demonstrate that binding sites of FLI1, a fate-determining factor promoting HSC differentiation into platelets rather than red blood cells (RBCs), show a strong heritability enrichment (P = 1.5 × 10−6). Consistent with these findings, platelet and RBC counts are positively and negatively associated with mLOY, respectively. Collectively, our observations improve our understanding of the mechanisms underlying mLOY. Mosaic loss of chromosome Y (mLOY) is associated with age and smoking but also genetic factors play a role. Here, Terao et al. perform GWAS for mLOY in 95,380 Japanese men and identify 46 loci that overlap with hematopoietic stem cell enhancers and transcription factor binding sites critical for hematopoiesis.
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Affiliation(s)
- Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan. .,Clinical Research Center, Shizuoka General Hospital, Shizuoka, 420-8527, Japan. .,The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, 422-8526, Japan.
| | - Yukihide Momozawa
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Kazuyoshi Ishigaki
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan
| | - Eiryo Kawakami
- Healthcare and Medical Data Driven AI based Predictive Reasoning Development Unit, Medical Sciences Innovation Hub Program (MIH), RIKEN, Kanagawa, 230-0045, Japan.,Laboratory for Developmental Genetics, Center for Integrative Medical Sciences (IMS), RIKEN, Yokohama, Kanagawa, 230-0045, Japan.,Artificial Intelligence Medicine, Graduate School of Medicine, Chiba University, Chiba, 260-8670, Japan
| | - Masato Akiyama
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan.,Department of Ophthalmology, Graduate School of Medical Sciences, Kyushu University, Fukuoka, 812-8582, Japan
| | - Po-Ru Loh
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, 02115, USA.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Giulio Genovese
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA.,Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA
| | - Hiroki Sugishita
- Laboratory for Developmental Genetics, RIKEN Center for Integrative Medical Science (IMS), Yokohama, Kanagawa, 230-0045, Japan
| | - Tazro Ohta
- Database Center for Life Science, Joint Support-Center for Data Science Research, Research Organization of Information and Systems, Mishima, Shizuoka, 411-8540, Japan
| | - Makoto Hirata
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - John R B Perry
- MRC Epidemiology Unit, School of Clinical Medicine, University of Cambridge, Cambridge, CB2 0SP, UK
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.,Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yoshinori Murakami
- Division of Molecular Pathology, Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Michiaki Kubo
- Laboratory for Genotyping Development, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, 230-0045, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Kanagawa, 230-0045, Japan. .,Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan.
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96
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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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97
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Network analysis of canine brain morphometry links tumour risk to oestrogen deficiency and accelerated brain ageing. Sci Rep 2019; 9:12506. [PMID: 31467332 PMCID: PMC6715702 DOI: 10.1038/s41598-019-48446-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 08/02/2019] [Indexed: 12/24/2022] Open
Abstract
Structural ‘brain age’ is a valuable but complex biomarker for several brain disorders. The dog is an unrivalled comparator for neurological disease modeling, however canine brain morphometric diversity creates computational and statistical challenges. Using a data-driven approach, we explored complex interactions between patient metadata, brain morphometry, and neurological disease. Twenty-four morphometric parameters measured from 286 canine brain magnetic resonance imaging scans were combined with clinical parameters to generate 9,438 data points. Network analysis was used to cluster patients according to their brain morphometry profiles. An ‘aged-brain’ profile, defined by a small brain width and volume combined with ventriculomegaly, was revealed in the Boxer breed. Key features of this profile were paralleled in neutered female dogs which, relative to un-neutered females, had an 11-fold greater risk of developing brain tumours. Boxer dog and geriatric dog groups were both enriched for brain tumour diagnoses, despite a lack of geriatric Boxers within the cohort. Our findings suggest that advanced brain ageing enhances brain tumour risk in dogs and may be influenced by oestrogen deficiency—a risk factor for dementia and brain tumours in humans. Morphometric features of brain ageing in dogs, like humans, might better predict neurological disease risk than patient chronological age.
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98
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Tang D, Han Y, Lun Y, Jiang H, Xin S, Duan Z, Zhang J. Y chromosome loss is associated with age-related male patients with abdominal aortic aneurysms. Clin Interv Aging 2019; 14:1227-1241. [PMID: 31413553 PMCID: PMC6662525 DOI: 10.2147/cia.s202188] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2019] [Accepted: 04/15/2019] [Indexed: 11/23/2022] Open
Abstract
Purpose Abdominal aortic aneurysm (AAA) demonstrates many features of autoimmune diseases. Y chromosome, sex-determining region of the Y chromosome (SRY) gene, androgen receptor (AR) gene, and androgen appear as potential candidates for influence of the male immune function. This study investigated Y chromosome numbers, SRY gene, AR gene, and androgen levels in male AAAs. We also investigated the correlation between Y chromosome loss (LOY) ratio, SRY expression, androgen levels, and age. Patients and methods We investigated LOY by fluorescence in situ hybridization (FISH) in 37 AAAs and compared with 12 patients with abdominal aortic atherosclerotic occlusive disease (AOD) and 91 healthy controls (HC). We investigated SRY and AR expression at mRNA level by real-time PCR in peripheral T lymphocytes in AAA compared with AOD and HC, and AR protein levels by immunohistochemistry (IHC) in AAA. LOY, SRY expression, androgen levels, and age were examined for correlations using the Spearman’s rank correlation coefficient. Results LOY ratio in peripheral T lymphocytes was significantly higher in the AAA group compared with the HC (9.11% vs 5.56%, P<0.001) and AOD groups (9.11% vs 6.42%, P=0.029). The SRY mRNA expression in peripheral T lymphocytes was 4.7-fold lower expressed in the AAA group than in the HC group (P<0.001). Free plasma testosterone levels were lower in the AAA group compared with the HC group (P=0.036), whereas sex hormone-binding globulin levels were higher (P=0.020). LOY ratio and expression of SRY mRNA level increased with age in the AAA group (R=0.402 and, R=0.366, respectively). A significant correlation between AR mRNA level (R=0.692) and aortic diameter was detected. Simultaneously, in AAA tissue, the rate of LOY increased with age (R=0.547) and also positively associated with LOY in peripheral blood T lymphocytes (R=0.661). Conclusion This study identified a prominent Y chromosome loss in male AAAs, which is correlated to age, lower level of SRY expression and free testosterone, providing a new clue for the mechanisms of AAA.
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Affiliation(s)
- Dianjun Tang
- Department of Vascular Surgery, The First Hospital of China Medical University, Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm Liaoning Province, Shenyang, People's Republic of China.,Department of Vascular Surgery, The Second Hospital of Shandong University, Jinan, People's Republic of China
| | - Yanshuo Han
- Department of General Surgery, Shengjing Hospital of China Medical University, Shenyang, People's Republic of China
| | - Yu Lun
- Department of Vascular Surgery, The First Hospital of China Medical University, Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm Liaoning Province, Shenyang, People's Republic of China
| | - Han Jiang
- Department of Vascular Surgery, The First Hospital of China Medical University, Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm Liaoning Province, Shenyang, People's Republic of China
| | - Shijie Xin
- Department of Vascular Surgery, The First Hospital of China Medical University, Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm Liaoning Province, Shenyang, People's Republic of China
| | - Zhiquan Duan
- Department of Vascular Surgery, The First Hospital of China Medical University, Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm Liaoning Province, Shenyang, People's Republic of China
| | - Jian Zhang
- Department of Vascular Surgery, The First Hospital of China Medical University, Key Laboratory of Pathogenesis, Prevention and Therapeutics of Aortic Aneurysm Liaoning Province, Shenyang, People's Republic of China
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99
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Dumanski JP, Sundström J, Forsberg LA. Loss of Chromosome Y in Leukocytes and Major Cardiovascular Events. ACTA ACUST UNITED AC 2019; 10:e001820. [PMID: 28768755 DOI: 10.1161/circgenetics.117.001820] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jan P Dumanski
- From the Department of Immunology, Genetics, and Pathology (J.P.D., L.A.F.), Science for Life Laboratory (J.P.D., L.A.F.), Department of Medical Sciences (J.S.), and Beijer Laboratory of Genome Research (L.A.F.), Uppsala University, Sweden; and Faculty of Pharmacy, Medical University of Gdansk, Poland (J.P.D.)
| | - Johan Sundström
- From the Department of Immunology, Genetics, and Pathology (J.P.D., L.A.F.), Science for Life Laboratory (J.P.D., L.A.F.), Department of Medical Sciences (J.S.), and Beijer Laboratory of Genome Research (L.A.F.), Uppsala University, Sweden; and Faculty of Pharmacy, Medical University of Gdansk, Poland (J.P.D.)
| | - Lars A Forsberg
- From the Department of Immunology, Genetics, and Pathology (J.P.D., L.A.F.), Science for Life Laboratory (J.P.D., L.A.F.), Department of Medical Sciences (J.S.), and Beijer Laboratory of Genome Research (L.A.F.), Uppsala University, Sweden; and Faculty of Pharmacy, Medical University of Gdansk, Poland (J.P.D.).
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100
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Hollows R, Wei W, Cazier J, Mehanna H, Parry G, Halford G, Murray P. Association between loss of Y chromosome and poor prognosis in male head and neck squamous cell carcinoma. Head Neck 2019; 41:993-1006. [PMID: 30582241 PMCID: PMC6492017 DOI: 10.1002/hed.25537] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2018] [Accepted: 10/01/2018] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Head and neck squamous cell carcinoma (HNSCC) is more prevalent in men than women and this disparity cannot be fully explained by known risk factors. Recent studies have shown that loss of Y chromosome (LoY) confers an increased risk of solid cancer and reduces life expectancy in men. METHODS Using publicly available data from The Cancer Genome Atlas, we investigated the prevalence of LoY and its association with clinicopathological features in male HNSCC. RESULTS LoY was detectable in around 25% of male HNSCC. Men with human papillomavirus-negative tumors exhibiting LoY experienced significantly worse overall survival than those with no LoY. Moreover, LoY tumors exhibited overexpression of genes involved in redox processes, including genes previously implicated in resistance to both radiotherapy and cisplatin-based chemotherapeutics. CONCLUSION LoY may be an indicator of poor prognosis in male HNSCC that is linked to the overexpression of genes associated with resistance to standard care therapies.
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Affiliation(s)
- Robert Hollows
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
- Centre for Computational BiologyUniversity of BirminghamBirminghamUnited Kingdom
| | - Wenbin Wei
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
- Sheffield Institute of Translational NeuroscienceUniversity of SheffieldSheffieldUnited Kingdom
| | - Jean‐Baptiste Cazier
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
- Centre for Computational BiologyUniversity of BirminghamBirminghamUnited Kingdom
| | - Hisham Mehanna
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
- Institute of Head and Neck Studies and Education (InHANSE)University of BirminghamBirminghamUnited Kingdom
| | - Gabriella Parry
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
| | - Graham Halford
- Regional Genetics LaboratoryBirmingham Women's HospitalBirminghamUnited Kingdom
| | - Paul Murray
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUnited Kingdom
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