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Dai Z, Chen H, Feng K, Li T, Liu W, Zhou Y, Yang D, Xue B, Zhu J. Promoter hypermethylation of Y-chromosome gene PRKY as a potential biomarker for the early diagnosis of prostate cancer. Epigenomics 2024:1-16. [PMID: 38979582 DOI: 10.1080/17501911.2024.2365625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/04/2024] [Indexed: 07/10/2024] Open
Abstract
Aim: To develop a methylation marker of Y-chromosome gene in the early diagnosis of prostate cancer (PCa). Materials & methods: We utilized bioinformatics analysis to identify the expression and promoter methylation of Y-chromosome gene PRKY in PCa and other common malignancies. Single-center experiments were conducted to validate the diagnostic value of PRKY promoter methylation in PCa. Results: PRKY expression was significantly down-regulated in PCa and its mechanism may be related to promoter methylation. PRKY promoter methylation is highly specific for the diagnosis of early PCa, which may be superior to prostate-specific antigen, mpMRI and other excellent molecular biomarkers. Conclusion: PRKY promoter methylation may be a potential marker for the early and accurate diagnosis of PCa.
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Affiliation(s)
- Zheng Dai
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
- Department of Urology, The Third Affiliated Hospital of Anhui Medical University, Hefei, 230061, China
| | - Hongbing Chen
- Department of Urology, The Third Affiliated Hospital of Anhui Medical University, Hefei, 230061, China
| | - Kaiwen Feng
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Tuoxin Li
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Weifeng Liu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Yibin Zhou
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Dongrong Yang
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Boxin Xue
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
| | - Jin Zhu
- Department of Urology, The Second Affiliated Hospital of Soochow University, Suzhou, 215004, China
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Morgan R, Loh E, Singh D, Mendizabal I, Yi SV. DNA methylation differences between the female and male X chromosomes in human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589778. [PMID: 38659923 PMCID: PMC11042362 DOI: 10.1101/2024.04.16.589778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The mechanisms of X chromosome inactivation suggest fundamental epigenetic differences between the female and male X chromosomes. However, DNA methylation studies often exclude the X chromosomes. In addition, many previous studies relied on techniques that examine non-randomly selected subsets of positions such as array-based methods, rather than assessing the whole X chromosome. Consequently, our understanding of X chromosome DNA methylation lags behind that of autosomes. Here we addressed this gap of knowledge by studying X chromosome DNA methylation using 89 whole genome bisulfite sequencing (WGBS) maps from neurons and oligodendrocytes. Using this unbiased and comprehensive data, we show that DNA methylation of the female X chromosomes is globally reduced (hypomethylated) across the entire chromosome compared to the male X chromosomes and autosomes. On the other hand, the majority of X-linked promoters were more highly methylated (hypermethylated) in females compared to males, consistent with the role of DNA methylation in X chromosome inactivation and dosage compensation. Remarkably, hypermethylation of female X promoters was limited to a group of previously lowly methylated promoters. The other group of highly methylated promoters were both hyper- and hypo-methylated in females with no obvious association with gene expression. Therefore, X chromosome inactivation by DNA methylation was exclusive to a subset of promoters with distinctive epigenetic feature. Apart from this group of promoters, differentially methylated regions in the female and male X chromosomes were dominated by female hypomethylation. Our study furthers the understanding of X-chromosome dosage regulation by DNA methylation on the chromosomal level as well as on individual gene level.
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Affiliation(s)
- Robert Morgan
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140
| | - Eddie Loh
- Department of Ecology and Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara
| | - Devika Singh
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Current address: Foundation Medicine, Inc., Boston, MA, 02210
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Translational prostate cancer Research lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
| | - Soojin V Yi
- Department of Ecology and Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara
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Christians JK, Reue K. The role of gonadal hormones and sex chromosomes in sex-dependent effects of early nutrition on metabolic health. Front Endocrinol (Lausanne) 2023; 14:1304050. [PMID: 38189044 PMCID: PMC10770830 DOI: 10.3389/fendo.2023.1304050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Accepted: 12/11/2023] [Indexed: 01/09/2024] Open
Abstract
Early-life conditions such as prenatal nutrition can have long-term effects on metabolic health, and these effects may differ between males and females. Understanding the biological mechanisms underlying sex differences in the response to early-life environment will improve interventions, but few such mechanisms have been identified, and there is no overall framework for understanding sex differences. Biological sex differences may be due to chromosomal sex, gonadal sex, or interactions between the two. This review describes approaches to distinguish between the roles of chromosomal and gonadal sex, and summarizes findings regarding sex differences in metabolism. The Four Core Genotypes (FCG) mouse model allows dissociation of the sex chromosome genotype from gonadal type, whereas the XY* mouse model can be used to distinguish effects of X chromosome dosage vs the presence of the Y chromosome. Gonadectomy can be used to distinguish between organizational (permanent) and activational (reversible) effects of sex hormones. Baseline sex differences in a variety of metabolic traits are influenced by both activational and organizational effects of gonadal hormones, as well as sex chromosome complement. Thus far, these approaches have not been widely applied to examine sex-dependent effects of prenatal conditions, although a number of studies have found activational effects of estradiol to be protective against the development of hypertension following early-life adversity. Genes that escape X chromosome inactivation (XCI), such as Kdm5c, contribute to baseline sex-differences in metabolism, while Ogt, another XCI escapee, leads to sex-dependent responses to prenatal maternal stress. Genome-wide approaches to the study of sex differences include mapping genetic loci influencing metabolic traits in a sex-dependent manner. Seeking enrichment for binding sites of hormone receptors among genes showing sexually-dimorphic expression can elucidate the relative roles of hormones. Using the approaches described herein to identify mechanisms underlying sex-dependent effects of early nutrition on metabolic health may enable the identification of fundamental mechanisms and potential interventions.
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Affiliation(s)
- Julian K. Christians
- Department of Biological Sciences, Simon Fraser University, Burnaby, BC, Canada
- Centre for Cell Biology, Development and Disease, Simon Fraser University, Burnaby, BC, Canada
- British Columbia Children’s Hospital Research Institute, Vancouver, BC, Canada
- Women’s Health Research Institute, BC Women’s Hospital and Health Centre, Vancouver, BC, Canada
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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Saha E, Ghosal R. Gender difference in the effects of chronic diseases on daily physical activity patterns in older adults: analysis of objectively measured physical activity in NHATS 2021. Ann Epidemiol 2023; 86:110-118.e4. [PMID: 37625499 DOI: 10.1016/j.annepidem.2023.08.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2023] [Revised: 08/14/2023] [Accepted: 08/16/2023] [Indexed: 08/27/2023]
Abstract
PURPOSE Many chronic diseases have detrimental impact on the physical activity (PA) patterns of older adults. Often such diseases have different degrees of severity in males and females. Quantifying this gender difference would not only enhance our understanding of diseases but would also help design individual-specific PA interventions, thereby improving health outcomes for both genders. METHODS PA data for 747 participants from round 11 (2021) of the National Health and Aging Trends Study were analyzed. Multilevel functional regression models were used to study gender difference in the effects of chronic diseases on daily PA patterns while adjusting for confounders. RESULTS Females with dementia (or Alzheimer's disease), hypertension, heart and lung disease had lower PA at different times of day compared to females without these diseases, whereas males with and without these diseases had comparable daily PA. Males with diabetes had higher midnight PA and lower noon PA compared to males without diabetes, while females' PA with and without diabetes were similar. CONCLUSIONS Our analysis demonstrates that although for most diseases, the daily PA patterns of individuals with the disease are negatively altered compared to healthy individuals, the extent of decline varies by gender and time of day. Designing personalized physical activity interventions considering gender and diurnal PA pattern can potentially improve quality of life across both genders.
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Affiliation(s)
- Enakshi Saha
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA.
| | - Rahul Ghosal
- Department of Epidemiology and Biostatistics, University of South Carolina, Columbia
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Pinto BJ, O’Connor B, Schatz MC, Zarate S, Wilson MA. Concerning the eXclusion in human genomics: the choice of sex chromosome representation in the human genome drastically affects the number of identified variants. G3 (BETHESDA, MD.) 2023; 13:jkad169. [PMID: 37497639 PMCID: PMC10542555 DOI: 10.1093/g3journal/jkad169] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 06/28/2023] [Accepted: 07/05/2023] [Indexed: 07/28/2023]
Abstract
Over the past 30 years, a community of scientists has pieced together every base pair of the human reference genome from telomere to telomere. Interestingly, most human genomics studies omit more than 5% of the genome from their analyses. Under "normal" circumstances, omitting any chromosome(s) from an analysis of the human genome would be a cause for concern, with the exception being sex chromosomes. Sex chromosomes in eutherians share an evolutionary origin as an ancestral pair of autosomes. In humans, they share 3 regions of high-sequence identity (∼98-100%), which, along with the unique transmission patterns of the sex chromosomes, introduce technical artifacts in genomic analyses. However, the human X chromosome bears numerous important genes, including more "immune response" genes than any other chromosome, which makes its exclusion irresponsible when sex differences across human diseases are widespread. To better characterize the possible effect of the inclusion/exclusion of the X chromosome on variants called, we conducted a pilot study on the Terra cloud platform to replicate a subset of standard genomic practices using both the CHM13 reference genome and the sex chromosome complement-aware reference genome. We compared the quality of variant calling, expression quantification, and allele-specific expression using these 2 reference genome versions across 50 human samples from the Genotype-Tissue Expression consortium annotated as females. We found that after correction, the whole X chromosome (100%) can generate reliable variant calls, allowing for the inclusion of the whole genome in human genomics analyses as a departure from the status quo of omitting the sex chromosomes from empirical and clinical genomics studies.
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Affiliation(s)
- Brendan J Pinto
- School of Life Sciences, Arizona State University, Tempe, AZ 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85282, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218, USA
| | - Melissa A Wilson
- School of Life Sciences, Arizona State University, Tempe, AZ 85282, USA
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85282, USA
- The Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85282, USA
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Pinto BJ, O’Connor B, Schatz MC, Zarate S, Wilson MA. Concerning the eXclusion in human genomics: The choice of sex chromosome representation in the human genome drastically affects number of identified variants. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.22.529542. [PMID: 36865318 PMCID: PMC9980147 DOI: 10.1101/2023.02.22.529542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
Over the past 30 years, a community of scientists have pieced together every base pair of the human reference genome from telomere-to-telomere. Interestingly, most human genomics studies omit more than 5% of the genome from their analyses. Under 'normal' circumstances, omitting any chromosome(s) from analysis of the human genome would be reason for concern-the exception being the sex chromosomes. Sex chromosomes in eutherians share an evolutionary origin as an ancestral pair of autosomes. In humans, they share three regions of high sequence identity (~98-100%), which-along with the unique transmission patterns of the sex chromosomes-introduce technical artifacts into genomic analyses. However, the human X chromosome bears numerous important genes-including more "immune response" genes than any other chromosome-which makes its exclusion irresponsible when sex differences across human diseases are widespread. To better characterize the effect that including/excluding the X chromosome may have on variants called, we conducted a pilot study on the Terra cloud platform to replicate a subset of standard genomic practices using both the CHM13 reference genome and sex chromosome complement-aware (SCC-aware) reference genome. We compared quality of variant calling, expression quantification, and allele-specific expression using these two reference genome versions across 50 human samples from the Genotype-Tissue-Expression consortium annotated as females. We found that after correction, the whole X chromosome (100%) can generate reliable variant calls-allowing for the inclusion of the whole genome in human genomics analyses as a departure from the status quo of omitting the sex chromosomes from empirical and clinical genomics studies.
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Affiliation(s)
- Brendan J. Pinto
- School of Life Sciences, Arizona State University, Tempe AZ 85282 USA
- Center for Evolution and Medicine, Arizona State University, Tempe AZ 85282 USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233 USA
| | | | - Michael C. Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Samantha Zarate
- Department of Computer Science, Johns Hopkins University, Baltimore, MD 21218 USA
| | - Melissa A. Wilson
- School of Life Sciences, Arizona State University, Tempe AZ 85282 USA
- Center for Evolution and Medicine, Arizona State University, Tempe AZ 85282 USA
- The Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe AZ 85282 USA
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Fernández-Carrión R, Sorlí JV, Asensio EM, Pascual EC, Portolés O, Alvarez-Sala A, Francès F, Ramírez-Sabio JB, Pérez-Fidalgo A, Villamil LV, Tinahones FJ, Estruch R, Ordovas JM, Coltell O, Corella D. DNA-Methylation Signatures of Tobacco Smoking in a High Cardiovascular Risk Population: Modulation by the Mediterranean Diet. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2023; 20:3635. [PMID: 36834337 PMCID: PMC9964856 DOI: 10.3390/ijerph20043635] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 02/15/2023] [Accepted: 02/16/2023] [Indexed: 06/18/2023]
Abstract
Biomarkers based on DNA methylation are relevant in the field of environmental health for precision health. Although tobacco smoking is one of the factors with a strong and consistent impact on DNA methylation, there are very few studies analyzing its methylation signature in southern European populations and none examining its modulation by the Mediterranean diet at the epigenome-wide level. We examined blood methylation smoking signatures on the EPIC 850 K array in this population (n = 414 high cardiovascular risk subjects). Epigenome-wide methylation studies (EWASs) were performed analyzing differential methylation CpG sites by smoking status (never, former, and current smokers) and the modulation by adherence to a Mediterranean diet score was explored. Gene-set enrichment analysis was performed for biological and functional interpretation. The predictive value of the top differentially methylated CpGs was analyzed using receiver operative curves. We characterized the DNA methylation signature of smoking in this Mediterranean population by identifying 46 differentially methylated CpGs at the EWAS level in the whole population. The strongest association was observed at the cg21566642 (p = 2.2 × 10-32) in the 2q37.1 region. We also detected other CpGs that have been consistently reported in prior research and discovered some novel differentially methylated CpG sites in subgroup analyses. In addition, we found distinct methylation profiles based on the adherence to the Mediterranean diet. Particularly, we obtained a significant interaction between smoking and diet modulating the cg5575921 methylation in the AHRR gene. In conclusion, we have characterized biomarkers of the methylation signature of tobacco smoking in this population, and suggest that the Mediterranean diet can increase methylation of certain hypomethylated sites.
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Affiliation(s)
- Rebeca Fernández-Carrión
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - José V. Sorlí
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva M. Asensio
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Eva C. Pascual
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Olga Portolés
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | - Andrea Alvarez-Sala
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
| | - Francesc Francès
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
| | | | - Alejandro Pérez-Fidalgo
- Department of Medical Oncology, University Clinic Hospital of Valencia, 46010 Valencia, Spain
- Biomedical Research Networking Centre on Cancer (CIBERONC), Health Institute Carlos III, 28029 Madrid, Spain
- INCLIVA Biomedical Research Institute, 46010 Valencia, Spain
| | - Laura V. Villamil
- Department of Physiology, School of Medicine, University Antonio Nariño, Bogotá 111511, Colombia
| | - Francisco J. Tinahones
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Endocrinology and Nutrition, Virgen de la Victoria University Hospital, Instituto de Investigación Biomédica de Málaga (IBIMA), University of Málaga, 29590 Málaga, Spain
| | - Ramon Estruch
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Internal Medicine, Institut d’Investigacions Biomèdiques August Pi Sunyer (IDIBAPS), Hospital Clinic, University of Barcelona, 08036 Barcelona, Spain
| | - Jose M. Ordovas
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Nutrition and Genomics Laboratory, JM-USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA 02111, USA
- Nutritional Control of the Epigenome Group, Precision Nutrition and Obesity Program, IMDEA Food, UAM + CSIC, 28049 Madrid, Spain
| | - Oscar Coltell
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
- Department of Computer Languages and Systems, Universitat Jaume I, 12071 Castellón, Spain
| | - Dolores Corella
- Department of Preventive Medicine and Public Health, School of Medicine, University of Valencia, 46010 Valencia, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición, Instituto de Salud Carlos III, 28029 Madrid, Spain
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