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Ji Z, Xing Y, Li J, Feng X, Yang F, Zhu B, Yan J. Male-specific age prediction based on Y-chromosome DNA methylation with blood using pyrosequencing. Forensic Sci Int Genet 2024; 71:103050. [PMID: 38703560 DOI: 10.1016/j.fsigen.2024.103050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 04/14/2024] [Accepted: 04/19/2024] [Indexed: 05/06/2024]
Abstract
Age prediction is an important aspect of forensic science that offers valuable insight into identification. In recent years, extensive studies have been conducted on age prediction based on DNA methylation, and numerous studies have demonstrated that DNA methylation is a reliable biomarker for age prediction. However, almost all studies on age prediction based on DNA methylation have focused on age-related CpG sites in autosomes, which are concentrated on single-source DNA samples. Mixed samples, especially male-female mixed samples, are common in forensic casework. The application of Y-STRs and Y-SNPs can provide clues for the genetic typing of male individuals in male-female mixtures, but they cannot provide the age information of male individuals. Studies on Y-chromosome DNA methylation can address this issue. In this study, we identified five age-related CpG sites on the Y chromosome (Y-CpGs) and developed a male-specific age prediction model using pyrosequencing combined with a support vector machine algorithm. The mean absolute deviation of the model was 5.50 years in the training set and 6.74 years in the testing set. When we used a male blood sample to predict age, the deviation between the predicted and chronological age was 1.18 years. Then, we mixed the genomic DNA of the male and a female at ratios of 1:1, 1:5, 1:10, and 1:50, the range of deviation between the predicted and chronological age of the male in the mixture was 1.16-1.74 years. In addition, there was no significant difference between the methylation values of bloodstains and blood in the same sample, which indicates that our model is also suitable for bloodstain samples. Overall, our results show that age prediction using DNA methylation of the Y chromosome has potential applications in forensic science and can be of great help in predicting the age of males in male-female mixtures. Furthermore, this work lays the foundation for future research on age-related applications of Y-CpGs.
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Affiliation(s)
- Zhimin Ji
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Yangfeng Xing
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Junli Li
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Xiaoxiao Feng
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China
| | - Fenglong Yang
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China.
| | - Bofeng Zhu
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China; Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, Guangdong 510515, PR China.
| | - Jiangwei Yan
- School of Forensic Medicine, Shanxi Medical University, Taiyuan, Shanxi 030009, PR China.
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2
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Rubin JB, Abou-Antoun T, Ippolito JE, Llaci L, Marquez CT, Wong JP, Yang L. Epigenetic developmental mechanisms underlying sex differences in cancer. J Clin Invest 2024; 134:e180071. [PMID: 38949020 PMCID: PMC11213507 DOI: 10.1172/jci180071] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/02/2024] Open
Abstract
Cancer risk is modulated by hereditary and somatic mutations, exposures, age, sex, and gender. The mechanisms by which sex and gender work alone and in combination with other cancer risk factors remain underexplored. In general, cancers that occur in both the male and female sexes occur more commonly in XY compared with XX individuals, regardless of genetic ancestry, geographic location, and age. Moreover, XY individuals are less frequently cured of their cancers, highlighting the need for a greater understanding of sex and gender effects in oncology. This will be necessary for optimal laboratory and clinical cancer investigations. To that end, we review the epigenetics of sexual differentiation and its effect on cancer hallmark pathways throughout life. Specifically, we will touch on how sex differences in metabolism, immunity, pluripotency, and tumor suppressor functions are patterned through the epigenetic effects of imprinting, sex chromosome complement, X inactivation, genes escaping X inactivation, sex hormones, and life history.
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Affiliation(s)
| | | | - Joseph E. Ippolito
- Department of Radiology
- Department of Biochemistry and Molecular Biophysics
| | - Lorida Llaci
- Deartment of Genetics Washington University School of Medicine, St. Louis, Missouri, USA
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3
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Xiao T, Lee J, Gauntner TD, Velegraki M, Lathia JD, Li Z. Hallmarks of sex bias in immuno-oncology: mechanisms and therapeutic implications. Nat Rev Cancer 2024; 24:338-355. [PMID: 38589557 DOI: 10.1038/s41568-024-00680-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 02/26/2024] [Indexed: 04/10/2024]
Abstract
Sex differences are present across multiple non-reproductive organ cancers, with male individuals generally experiencing higher incidence of cancer with poorer outcomes. Although some mechanisms underlying these differences are emerging, the immunological basis is not well understood. Observations from clinical trials also suggest a sex bias in conventional immunotherapies with male individuals experiencing a more favourable response and female individuals experiencing more severe adverse events to immune checkpoint blockade. In this Perspective article, we summarize the major biological hallmarks underlying sex bias in immuno-oncology. We focus on signalling from sex hormones and chromosome-encoded gene products, along with sex hormone-independent and chromosome-independent epigenetic mechanisms in tumour and immune cells such as myeloid cells and T cells. Finally, we highlight opportunities for future studies on sex differences that integrate sex hormones and chromosomes and other emerging cancer hallmarks such as ageing and the microbiome to provide a more comprehensive view of how sex differences underlie the response in cancer that can be leveraged for more effective immuno-oncology approaches.
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Affiliation(s)
- Tong Xiao
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Juyeun Lee
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Timothy D Gauntner
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Maria Velegraki
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA
| | - Justin D Lathia
- Department of Cardiovascular and Metabolic Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA.
- Case Comprehensive Cancer Center, Cleveland, OH, USA.
- Rose Ella Burkhardt Brain Tumour Center, Cleveland Clinic, Cleveland, OH, USA.
| | - Zihai Li
- Pelotonia Institute for Immuno-Oncology, The Ohio State University Comprehensive Cancer Center-The James, Columbus, OH, USA.
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4
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Castagnola MJ, Medina-Paz F, Zapico SC. Uncovering Forensic Evidence: A Path to Age Estimation through DNA Methylation. Int J Mol Sci 2024; 25:4917. [PMID: 38732129 PMCID: PMC11084977 DOI: 10.3390/ijms25094917] [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: 03/25/2024] [Revised: 04/27/2024] [Accepted: 04/28/2024] [Indexed: 05/13/2024] Open
Abstract
Age estimation is a critical aspect of reconstructing a biological profile in forensic sciences. Diverse biochemical processes have been studied in their correlation with age, and the results have driven DNA methylation to the forefront as a promising biomarker. DNA methylation, an epigenetic modification, has been extensively studied in recent years for developing age estimation models in criminalistics and forensic anthropology. Epigenetic clocks, which analyze DNA sites undergoing hypermethylation or hypomethylation as individuals age, have paved the way for improved prediction models. A wide range of biomarkers and methods for DNA methylation analysis have been proposed, achieving different accuracies across samples and cell types. This review extensively explores literature from the past 5 years, showing scientific efforts toward the ultimate goal: applying age prediction models to assist in human identification.
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Affiliation(s)
- María Josefina Castagnola
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Francisco Medina-Paz
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
| | - Sara C. Zapico
- Department of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Tiernan Hall 365, Newark, NJ 07102, USA; (M.J.C.); (F.M.-P.)
- Department of Anthropology and Laboratories of Analytical Biology, National Museum of Natural History, MRC 112, Smithsonian Institution, Washington, DC 20560, USA
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5
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Gálvez-Silva M, Arros P, Berríos-Pastén C, Villamil A, Rodas PI, Araya I, Iglesias R, Araya P, Hormazábal JC, Bohle C, Chen Y, Gan YH, Chávez FP, Lagos R, Marcoleta AE. Carbapenem-resistant hypervirulent ST23 Klebsiella pneumoniae with a highly transmissible dual-carbapenemase plasmid in Chile. Biol Res 2024; 57:7. [PMID: 38475927 DOI: 10.1186/s40659-024-00485-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 02/19/2024] [Indexed: 03/14/2024] Open
Abstract
BACKGROUND The convergence of hypervirulence and carbapenem resistance in the bacterial pathogen Klebsiella pneumoniae represents a critical global health concern. Hypervirulent K. pneumoniae (hvKp) strains, frequently from sequence type 23 (ST23) and having a K1 capsule, have been associated with severe community-acquired invasive infections. Although hvKp were initially restricted to Southeast Asia and primarily antibiotic-sensitive, carbapenem-resistant hvKp infections are reported worldwide. Here, within the carbapenemase production Enterobacterales surveillance system headed by the Chilean Public Health Institute, we describe the isolation in Chile of a high-risk ST23 dual-carbapenemase-producing hvKp strain, which carbapenemase genes are encoded in a single conjugative plasmid. RESULTS Phenotypic and molecular tests of this strain revealed an extensive resistance to at least 15 antibiotic classes and the production of KPC-2 and VIM-1 carbapenemases. Unexpectedly, this isolate lacked hypermucoviscosity, challenging this commonly used hvKp identification criteria. Complete genome sequencing and analysis confirmed the K1 capsular type, the KpVP-1 virulence plasmid, and the GIE492 and ICEKp10 genomic islands carrying virulence factors strongly associated with hvKp. Although this isolate belonged to the globally disseminated hvKp clonal group CG23-I, it is unique, as it formed a clade apart from a previously reported Chilean ST23 hvKp isolate and acquired an IncN KPC-2 plasmid highly disseminated in South America (absent in other hvKp genomes), but now including a class-I integron carrying blaVIM-1 and other resistance genes. Notably, this isolate was able to conjugate the double carbapenemase plasmid to an E. coli recipient, conferring resistance to 1st -5th generation cephalosporins (including combinations with beta-lactamase inhibitors), penicillins, monobactams, and carbapenems. CONCLUSIONS We reported the isolation in Chile of high-risk carbapenem-resistant hvKp carrying a highly transmissible conjugative plasmid encoding KPC-2 and VIM-1 carbapenemases, conferring resistance to most beta-lactams. Furthermore, the lack of hypermucoviscosity argues against this trait as a reliable hvKp marker. These findings highlight the rapid evolution towards multi-drug resistance of hvKp in Chile and globally, as well as the importance of conjugative plasmids and other mobile genetic elements in this convergence. In this regard, genomic approaches provide valuable support to monitor and obtain essential information on these priority pathogens and mobile elements.
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Affiliation(s)
- Matías Gálvez-Silva
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Patricio Arros
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Camilo Berríos-Pastén
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Aura Villamil
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Paula I Rodas
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Ingrid Araya
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Rodrigo Iglesias
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | - Pamela Araya
- Instituto de Salud Pública Marathon, Ñuñoa, Santiago, 1000, Chile
| | | | | | - Yahua Chen
- Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore, Singapore
| | - Yunn-Hwen Gan
- Yong Loo Lin School of Medicine, National University of Singapore, MD7, 8 Medical Drive, Singapore, Singapore
| | - Francisco P Chávez
- Laboratorio de Microbiología de Sistemas, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Rosalba Lagos
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile
| | - Andrés E Marcoleta
- Grupo de Microbiología Integrativa, Laboratorio de Biología Estructural y Molecular BEM, Departamento de Biología, Facultad de Ciencias, Universidad de Chile Las Palmeras, Ñuñoa, Santiago, 3425, Chile.
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6
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Boahen CK, Abee H, Ponce IR, Joosten LAB, Netea MG, Kumar V. Sex-biased genetic regulation of inflammatory proteins in the Dutch population. BMC Genomics 2024; 25:154. [PMID: 38326779 PMCID: PMC10851559 DOI: 10.1186/s12864-024-10065-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 01/30/2024] [Indexed: 02/09/2024] Open
Abstract
BACKGROUND Significant differences in immune responses, prevalence or susceptibility of diseases and treatment responses have been described between males and females. Despite this, sex-differentiation analysis of the genetic architecture of inflammatory proteins is largely unexplored. We performed sex-stratified meta-analysis after protein quantitative trait loci (pQTL) mapping using inflammatory biomarkers profiled using targeted proteomics (Olink inflammatory panel) of two population-based cohorts of Europeans. RESULTS Even though, around 67% of the pQTLs demonstrated shared effect between sexes, colocalization analysis identified two loci in the males (LINC01135 and ITGAV) and three loci (CNOT10, SRD5A2, and LILRB5) in the females with evidence of sex-dependent modulation by pQTL variants. Furthermore, we identified pathways with relevant functions in the sex-biased pQTL variants. We also showed through cross-validation that the sex-specific pQTLs are linked with sex-specific phenotypic traits. CONCLUSION Our study demonstrates the relevance of genetic sex-stratified analysis in the context of genetic dissection of protein abundances among individuals and reveals that, sex-specific pQTLs might mediate sex-linked phenotypes. Identification of sex-specific pQTLs associated with sex-biased diseases can help realize the promise of individualized treatment.
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Affiliation(s)
- Collins K Boahen
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Hannah Abee
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Isis Ricaño Ponce
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
| | - Leo A B Joosten
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Medical Genetics, Iuliu Hatieganu University of Medicine and Pharmacia, Cluj-Napoca-Napoca, Romania
| | - Mihai G Netea
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands
- Department for Immunology and Metabolism, Life and Medical Sciences Institute (LIMES), University of Bonn, Bonn, Germany
| | - Vinod Kumar
- Department of Internal Medicine and Radboud Institute of Molecular Life Sciences (RIMLS), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
- Department of Internal Medicine and Radboud Center for Infectious Diseases (RCI), Radboud University Medical Center, Nijmegen, 6525 HP, the Netherlands.
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen, 9700 RB, the Netherlands.
- Nitte (Deemed to Be University), Medical Sciences Complex, Nitte University Centre for Science Education and Research (NUCSER), Deralakatte, Mangalore, 575018, India.
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7
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Ying K, Liu H, Tarkhov AE, Sadler MC, Lu AT, Moqri M, Horvath S, Kutalik Z, Shen X, Gladyshev VN. Causality-enriched epigenetic age uncouples damage and adaptation. NATURE AGING 2024; 4:231-246. [PMID: 38243142 PMCID: PMC11070280 DOI: 10.1038/s43587-023-00557-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Accepted: 12/12/2023] [Indexed: 01/21/2024]
Abstract
Machine learning models based on DNA methylation data can predict biological age but often lack causal insights. By harnessing large-scale genetic data through epigenome-wide Mendelian randomization, we identified CpG sites potentially causal for aging-related traits. Neither the existing epigenetic clocks nor age-related differential DNA methylation are enriched in these sites. These CpGs include sites that contribute to aging and protect against it, yet their combined contribution negatively affects age-related traits. We established a new framework to introduce causal information into epigenetic clocks, resulting in DamAge and AdaptAge-clocks that track detrimental and adaptive methylation changes, respectively. DamAge correlates with adverse outcomes, including mortality, while AdaptAge is associated with beneficial adaptations. These causality-enriched clocks exhibit sensitivity to short-term interventions. Our findings provide a detailed landscape of CpG sites with putative causal links to lifespan and healthspan, facilitating the development of aging biomarkers, assessing interventions, and studying reversibility of age-associated changes.
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Affiliation(s)
- Kejun Ying
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- T. H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Hanna Liu
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Massachusetts College of Pharmacy and Health Sciences, Boston, MA, USA
- Department of Pharmacy, Massachusetts General Hospital, Boston, MA, USA
| | - Andrei E Tarkhov
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Marie C Sadler
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ake T Lu
- Altos Labs, San Diego, CA, USA
- Departments of Human Genetics and Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Mahdi Moqri
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Genetics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Steve Horvath
- Altos Labs, San Diego, CA, USA
- Departments of Human Genetics and Biostatistics, University of California, Los Angeles, Los Angeles, CA, USA
| | - Zoltán Kutalik
- University Center for Primary Care and Public Health, University of Lausanne, Lausanne, Switzerland
- Department of Computational Biology, University of Lausanne, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Xia Shen
- Center for Intelligent Medicine Research, Greater Bay Area Institute of Precision Medicine (Guangzhou), Fudan University, Guangzhou, China
- State Key Laboratory of Genetic Engineering, Center for Evolutionary Biology, School of Life Sciences, Fudan University, Shanghai, China
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden
- Centre for Global Health Research, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Vadim N Gladyshev
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
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8
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Rao NR, Upadhyay A, Savas JN. Derailed protein turnover in the aging mammalian brain. Mol Syst Biol 2024; 20:120-139. [PMID: 38182797 PMCID: PMC10897147 DOI: 10.1038/s44320-023-00009-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2023] [Revised: 12/11/2023] [Accepted: 12/13/2023] [Indexed: 01/07/2024] Open
Abstract
Efficient protein turnover is essential for cellular homeostasis and organ function. Loss of proteostasis is a hallmark of aging culminating in severe dysfunction of protein turnover. To investigate protein turnover dynamics as a function of age, we performed continuous in vivo metabolic stable isotope labeling in mice along the aging continuum. First, we discovered that the brain proteome uniquely undergoes dynamic turnover fluctuations during aging compared to heart and liver tissue. Second, trends in protein turnover in the brain proteome during aging showed sex-specific differences that were tightly tied to cellular compartments. Next, parallel analyses of the insoluble proteome revealed that several cellular compartments experience hampered turnover, in part due to misfolding. Finally, we found that age-associated fluctuations in proteasome activity were associated with the turnover of core proteolytic subunits, which was recapitulated by pharmacological suppression of proteasome activity. Taken together, our study provides a proteome-wide atlas of protein turnover across the aging continuum and reveals a link between the turnover of individual proteasome subunits and the age-associated decline in proteasome activity.
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Affiliation(s)
- Nalini R Rao
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Arun Upadhyay
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Jeffrey N Savas
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, IL, 60611, USA.
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9
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Rastin F, Oryani MA, Iranpour S, Javid H, Hashemzadeh A, Karimi-Shahri M. A new era in cancer treatment: harnessing ZIF-8 nanoparticles for PD-1 inhibitor delivery. J Mater Chem B 2024; 12:872-894. [PMID: 38193564 DOI: 10.1039/d3tb02471g] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
This review delves into the potential of zeolitic imidazolate framework-8 (ZIF-8) nanoparticles in augmenting the efficacy of cancer immunotherapy, with a special focus on the delivery of programmed cell death receptor 1 (PD-1) inhibitors. The multifunctional nature of ZIF-8 nanoparticles as drug carriers is emphasized, with their ability to encapsulate a range of therapeutic agents, including PD-1 inhibitors, and facilitate their targeted delivery to tumor locations. By manipulating the pore size and surface characteristics of ZIF-8 nanoparticles, controlled drug release can be realized. The strategic use of ZIF-8 nanoparticles to deliver PD-1 inhibitors presents a precise and targeted modality for cancer treatment, reducing off-target impacts and enhancing therapeutic effectiveness. This combined strategy addresses the existing challenges and constraints of current immunotherapy techniques, with the ultimate goal of enhancing patient outcomes in cancer therapy.
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Affiliation(s)
- Farangis Rastin
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Mahsa Akbari Oryani
- Department of Pathology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Sonia Iranpour
- Department of Chemistry, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
| | - Hossein Javid
- Department of Medical Laboratory Sciences, Varastegan Institute for Medical Sciences, Mashhad, Iran
- Surgical Oncology Research Center, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Alireza Hashemzadeh
- Department of Clinical Biochemistry, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
| | - Mehdi Karimi-Shahri
- Department of Pathology, School of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran.
- Department of Pathology, School of Medicine, Gonabad University of Medical Sciences, Gonabad, Iran
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10
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Kalyakulina A, Yusipov I, Kondakova E, Bacalini MG, Giuliani C, Sivtseva T, Semenov S, Ksenofontov A, Nikolaeva M, Khusnutdinova E, Zakharova R, Vedunova M, Franceschi C, Ivanchenko M. Epigenetics of the far northern Yakutian population. Clin Epigenetics 2023; 15:189. [PMID: 38053163 PMCID: PMC10699032 DOI: 10.1186/s13148-023-01600-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Accepted: 11/13/2023] [Indexed: 12/07/2023] Open
Abstract
BACKGROUND Yakuts are one of the indigenous populations of the subarctic and arctic territories of Siberia characterized by a continental subarctic climate with severe winters, with the regular January average temperature in the regional capital city of Yakutsk dipping below - 40 °C. The epigenetic mechanisms of adaptation to such ecologies and environments and, in particular, epigenetic age acceleration in the local population have not been studied before. RESULTS This work reports the first epigenetic study of the Yakutian population using whole-blood DNA methylation data, supplemented with the comparison to the residents of Central Russia. Gene set enrichment analysis revealed, among others, geographic region-specific differentially methylated regions associated with adaptation to climatic conditions (water consumption, digestive system regulation), aging processes (actin filament activity, cell fate), and both of them (channel activity, regulation of steroid and corticosteroid hormone secretion). Further, it is demonstrated that the epigenetic age acceleration of the Yakutian representatives is significantly higher than that of Central Russia counterparts. For both geographic regions, we showed that epigenetically males age faster than females, whereas no significant sex differences were found between the regions. CONCLUSIONS We performed the first study of the epigenetic data of the Yakutia cohort, paying special attention to region-specific features, aging processes, age acceleration, and sex specificity.
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Affiliation(s)
- Alena Kalyakulina
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia.
| | - Igor Yusipov
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Elena Kondakova
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | | | - Cristina Giuliani
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, 40126, Bologna, Italy
| | - Tatiana Sivtseva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Sergey Semenov
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Artem Ksenofontov
- State Budgetary Institution of the Republic of Sakha (Yakutia) Republican Center for Public Health and Medical Prevention, Yakutsk, 677001, Russia
| | - Maria Nikolaeva
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Federal Research Centre of the Russian Academy of Sciences, Ufa, Russia, 450054
| | - Raisa Zakharova
- Research Center of the Medical Institute of the North-Eastern Federal University M.K. Ammosova, Yakutsk, 677013, Russia
| | - Maria Vedunova
- Institute of Biology and Biomedicine, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Claudio Franceschi
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
| | - Mikhail Ivanchenko
- Institute of Information Technologies, Mathematics and Mechanics, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
- Institute of Biogerontology, Lobachevsky State University, Nizhny Novgorod, 603022, Russia
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11
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Wackers P, Dollé MET, van Oostrom CT, van Kerkhof LW. Exploration of genome-wide DNA methylation profiles in night shift workers. Epigenetics 2023; 18:2152637. [PMID: 36457290 PMCID: PMC9980630 DOI: 10.1080/15592294.2022.2152637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Abstract
The past decades, studies indicated that night shift work is associated with adverse health effects, however, molecular mechanisms underlying these effects are poorly understood. A few previous studies have hypothesized a role for DNA-methylation (DNAm) in this relationship. We performed a cross-sectional epigenome-wide association study, to investigate if night shift work is associated with genome-wide DNAm changes and DNAm-based biological age acceleration, based on previously developed so-called 'epigenetic clocks.' Short term (2-6 years) and intermediate term (10-16 years) night shift workers, along with age and sex matched dayworkers (non-shift workers) were selected from the Lifelines Cohort Study. For genome-wide methylation analysis the Infinium Methylation EPIC array (Ilumina) was used. Linear regression analyses were used to detect differences in methylation at individual CpG-sites associated with night shift work. Pathway analysis was performed based on KEGG pathways and predictions of age acceleration in night shift workers were performed based on four previously developed epigenetic age calculators. Only in women, differences in methylation at individual CpG-sites were observed between night shift workers and non-shift workers. Most of these differentially methylated positions (DMPs) were observed in intermediate term night shift workers. Pathway analysis shows involvement of pathways related to circadian rhythm and cellular senescence. Increased age acceleration was observed only in short-term night shift workers (men and women). This might be indicative of adaptation to night shift work or a so-called healthy worker effect. In conclusion, these results show that DNA methylation changes are associated with night shift work, specifically in women.
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Affiliation(s)
- Paul Wackers
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Martijn E. T. Dollé
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Conny T.M. van Oostrom
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Linda W.M. van Kerkhof
- Center for Health Protection, National Institute for Public Health and the Environment, Bilthoven, The Netherlands,CONTACT Linda W.M. van Kerkhof Centre for Health Protection; National Institute for Public Health and the Environment, P.O. Box 1, 3720 BA; Bilthoven, The Netherlands
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12
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Hecker J, Lee S, Kachroo P, Prokopenko D, Maaser-Hecker A, Lutz SM, Hahn G, Irizarry R, Weiss ST, DeMeo DL, Lange C. A consistent pattern of slide effects in Illumina DNA methylation BeadChip array data. Epigenetics 2023; 18:2257437. [PMID: 37731367 PMCID: PMC11062373 DOI: 10.1080/15592294.2023.2257437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 09/01/2023] [Indexed: 09/22/2023] Open
Abstract
Background: Recent studies have identified thousands of associations between DNA methylation CpGs and complex diseases/traits, emphasizing the critical role of epigenetics in understanding disease aetiology and identifying biomarkers. However, association analyses based on methylation array data are susceptible to batch/slide effects, which can lead to inflated false positive rates or reduced statistical powerResults: We use multiple DNA methylation datasets based on the popular Illumina Infinium MethylationEPIC BeadChip array to describe consistent patterns and the joint distribution of slide effects across CpGs, confirming and extending previous results. The susceptible CpGs overlap with the Illumina Infinium HumanMethylation450 BeadChip array content.Conclusions: Our findings reveal systematic patterns in slide effects. The observations provide further insights into the characteristics of these effects and can improve existing adjustment approaches.
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Affiliation(s)
- Julian Hecker
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Sanghun Lee
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Medical Consilience, Division of Medicine, Graduate School, Dankook University, Yongin-si, South Korea
| | - Priyadarshini Kachroo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dmitry Prokopenko
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Anna Maaser-Hecker
- Genetics and Aging Unit and McCance Center for Brain Health, Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Sharon M. Lutz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Population Medicine, PRecisiOn Medicine Translational Research (PROMoTeR) Center, Harvard Pilgrim Health Care and Harvard Medical School, Boston, MA, USA
| | - Georg Hahn
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Rafael Irizarry
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Scott T. Weiss
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Dawn L. DeMeo
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
| | - Christoph Lange
- Channing Division of Network Medicine, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
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13
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Potabattula R, Prell A, Dittrich M, Nava C, Depienne C, Bejaoui Y, El Hajj N, Hahn T, Schorsch M, Haaf T. Effects of paternal and chronological age on BEGAIN methylation and its possible role in autism. Aging (Albany NY) 2023; 15:12763-12779. [PMID: 38019471 DOI: 10.18632/aging.205275] [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: 07/05/2023] [Accepted: 10/23/2023] [Indexed: 11/30/2023]
Abstract
Children from old fathers carry an increased risk for autism spectrum (ASD) and other neurodevelopmental disorders, which may at least partially be mediated by paternal age effects on the sperm epigenome. The brain enriched guanylate kinase associated (BEGAIN) protein is involved in protein-protein interactions at and transmission across synapses. Since several epigenome-wide methylation screens reported a paternal age effect on sperm BEGAIN methylation, here we confirmed a significant negative correlation between BEGAIN promoter methylation and paternal age, using more sensitive bisulfite pyrosequencing and a larger number of sperm samples. Paternal age-associated BEGAIN hypomethylation was also observed in fetal cord blood (FCB) of male but not of female offspring. There was no comparable maternal age effect on FCB methylation. In addition, we found a significant negative correlation between BEGAIN methylation and chronological age (ranging from 1 to 70 years) in peripheral blood samples of male but not of female donors. BEGAIN hypomethylation was more pronounced in male children, adolescents and adults suffering from ASD compared to controls. Both genetic variation (CC genotype of SNP rs7141087) and epigenetic factors may contribute to BEGAIN promoter hypomethylation. The age- and sex-specific BEGAIN methylation trajectories in the male germ line and somatic tissues, in particular the brain, support a role of this gene in ASD development.
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Affiliation(s)
- Ramya Potabattula
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Andreas Prell
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
| | - Marcus Dittrich
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
- Department of Bioinformatics, Julius Maximilians University, Würzburg, Germany
| | - Caroline Nava
- U.F. de Neurogénétique Moléculaire et Cellulaire, Dpt. de Génétique et Cytogénétique, Groupe Hospitalier Pitié-Salpêtrière, Paris, France
| | - Christel Depienne
- Institute of Human Genetics, University Hospital Essen, Essen, Germany
| | - Yosra Bejaoui
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | - Nady El Hajj
- College of Health and Life Sciences and College of Science and Engineering, Hamad Bin Khalifa University, Doha, Qatar
| | | | | | - Thomas Haaf
- Institute of Human Genetics, Julius Maximilians University, Würzburg, Germany
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14
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Peeters SB, Posynick BJ, Brown CJ. Out of the Silence: Insights into How Genes Escape X-Chromosome Inactivation. EPIGENOMES 2023; 7:29. [PMID: 38131901 PMCID: PMC10742877 DOI: 10.3390/epigenomes7040029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 12/23/2023] Open
Abstract
The silencing of all but one X chromosome in mammalian cells is a remarkable epigenetic process leading to near dosage equivalence in X-linked gene products between the sexes. However, equally remarkable is the ability of a subset of genes to continue to be expressed from the otherwise inactive X chromosome-in some cases constitutively, while other genes are variable between individuals, tissues or cells. In this review we discuss the advantages and disadvantages of the approaches that have been used to identify escapees. The identity of escapees provides important clues to mechanisms underlying escape from XCI, an arena of study now moving from correlation to functional studies. As most escapees show greater expression in females, the not-so-inactive X chromosome is a substantial contributor to sex differences in humans, and we highlight some examples of such impact.
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Affiliation(s)
| | | | - Carolyn J. Brown
- Molecular Epigenetics Group, Department of Medical Genetics, Life Sciences Institute, University of British Columbia, 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada
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15
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Liu Y, Sinke L, Jonkman TH, Slieker RC, van Zwet EW, Daxinger L, Heijmans BT. The inactive X chromosome accumulates widespread epigenetic variability with age. Clin Epigenetics 2023; 15:135. [PMID: 37626340 PMCID: PMC10464315 DOI: 10.1186/s13148-023-01549-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Loss of epigenetic control is a hallmark of aging. Among the most prominent roles of epigenetic mechanisms is the inactivation of one of two copies of the X chromosome in females through DNA methylation. Hence, age-related disruption of X-chromosome inactivation (XCI) may contribute to the aging process in women. METHODS We analyzed 9,777 CpGs on the X chromosome in whole blood samples from 2343 females and 1688 males (Illumina 450k methylation array) and replicated findings in duplicate using one whole blood and one purified monocyte data set (in total, 991/924 females/males). We used double generalized linear models to detect age-related differentially methylated CpGs (aDMCs), whose mean methylation level differs with age, and age-related variably methylated CpGs (aVMCs), whose methylation level becomes more variable with age. RESULTS In females, aDMCs were relatively uncommon (n = 33) and preferentially occurred in regions known to escape XCI. In contrast, many CpGs (n = 987) were found to display an increased variance with age (aVMCs). Of note, the replication rate of aVMCs was also high in purified monocytes (94%), indicating an independence of cell composition. aVMCs accumulated in CpG islands and regions subject to XCI suggesting that they stemmed from the inactive X. In males, carrying an active copy of the X chromosome only, aDMCs (n = 316) were primarily driven by cell composition, while aVMCs replicated well (95%) but were infrequent (n = 37). CONCLUSIONS Our results imply that age-related DNA methylation differences at the inactive X chromosome are dominated by the accumulation of variability.
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Affiliation(s)
- Yunfeng Liu
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Postzone S-5-P, 2333 ZC, Leiden, The Netherlands
| | - Lucy Sinke
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Postzone S-5-P, 2333 ZC, Leiden, The Netherlands
| | - Thomas H Jonkman
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Postzone S-5-P, 2333 ZC, Leiden, The Netherlands
| | - Roderick C Slieker
- Department of Cell and Chemical Biology, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Erik W van Zwet
- Medical Statistics, Department of Biomedical Data Sciences, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Lucia Daxinger
- Department of Human Genetics, Leiden University Medical Center, 2333 ZC, Leiden, The Netherlands
| | - Bastiaan T Heijmans
- Molecular Epidemiology, Department of Biomedical Data Sciences, Leiden University Medical Center, Postzone S-5-P, 2333 ZC, Leiden, The Netherlands.
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16
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Lin Q, Tam PKH, Tang CSM. Artificial intelligence-based approaches for the detection and prioritization of genomic mutations in congenital surgical diseases. Front Pediatr 2023; 11:1203289. [PMID: 37593442 PMCID: PMC10429173 DOI: 10.3389/fped.2023.1203289] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Accepted: 07/17/2023] [Indexed: 08/19/2023] Open
Abstract
Genetic mutations are critical factors leading to congenital surgical diseases and can be identified through genomic analysis. Early and accurate identification of genetic mutations underlying these conditions is vital for clinical diagnosis and effective treatment. In recent years, artificial intelligence (AI) has been widely applied for analyzing genomic data in various clinical settings, including congenital surgical diseases. This review paper summarizes current state-of-the-art AI-based approaches used in genomic analysis and highlighted some successful applications that deepen our understanding of the etiology of several congenital surgical diseases. We focus on the AI methods designed for the detection of different variant types and the prioritization of deleterious variants located in different genomic regions, aiming to uncover susceptibility genomic mutations contributed to congenital surgical disorders.
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Affiliation(s)
- Qiongfen Lin
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
| | - Paul Kwong-Hang Tam
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Faculty of Medicine, Macau University of Science and Technology, Macau, Macau SAR, China
| | - Clara Sze-Man Tang
- Department of Surgery, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR, China
- Dr Li Dak-Sum Research Centree, The University of Hong Kong - Karolinska Institutet Collaboration in Regenerative Medicine, Hong Kong, Hong Kong SAR, China
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17
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Maina JG, Pascat V, Zudina L, Ulrich A, Pupko I, Bonnefond A, Balkhiyarova Z, Kaakinen M, Froguel P, Prokopenko I. Abdominal obesity is a more important causal risk factor for pancreatic cancer than overall obesity. Eur J Hum Genet 2023:10.1038/s41431-023-01301-3. [PMID: 37161092 PMCID: PMC10400602 DOI: 10.1038/s41431-023-01301-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2022] [Revised: 11/30/2022] [Accepted: 01/24/2023] [Indexed: 05/11/2023] Open
Abstract
Obesity and type 2 diabetes (T2D) are associated with increased risk of pancreatic cancer. Here we assessed the relationship between pancreatic cancer and two distinct measures of obesity, namely total adiposity, using BMI, versus abdominal adiposity, using BMI adjusted waist-to-hip ratio (WHRadjBMI) by utilising polygenic scores (PGS) and Mendelian randomisation (MR) analyses. We constructed z-score weighted PGS for BMI and WHRadjBMI using publicly available data and tested for their association with pancreatic cancer defined in UK biobank (UKBB). Using publicly available summary statistics, we then performed bi-directional MR analyses between the two obesity traits and pancreatic cancer. PGSBMI was significantly (multiple testing-corrected) associated with pancreatic cancer (OR[95%CI] = 1.0804[1.025-1.14], P = 0.0037). The significance of association declined after T2D adjustment (OR[95%CI] = 1.073[1.018-1.13], P = 0.00904). PGSWHRadjBMI association with pancreatic cancer was at the margin of statistical significance (OR[95%CI] = 1.047[0.99-1.104], P = 0.086). T2D adjustment effectively lost any suggestive association of PGSWHRadjBMI with pancreatic cancer (OR[95%CI] = 1.039[0.99-1.097], P = 0.14). MR analyses showed a nominally significant causal effect of WHRadjBMI on pancreatic cancer (OR[95%CI] = 1.00095[1.00011-1.0018], P = 0.027) but not for BMI on pancreatic cancer. Overall, we show that abdominal adiposity measured using WHRadjBMI, may be a more important causal risk factor for pancreatic cancer compared to total adiposity, with T2D being a potential driver of this relationship.
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Affiliation(s)
- Jared G Maina
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, F-59000, Lille, France
- University of Lille, Lille University Hospital, Lille, F-59000, France
| | - Vincent Pascat
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, F-59000, Lille, France
- University of Lille, Lille University Hospital, Lille, F-59000, France
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Liudmila Zudina
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Anna Ulrich
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Igor Pupko
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK
| | - Amélie Bonnefond
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, F-59000, Lille, France
- University of Lille, Lille University Hospital, Lille, F-59000, France
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
| | - Zhanna Balkhiyarova
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
| | - Marika Kaakinen
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK
| | - Philippe Froguel
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, F-59000, Lille, France.
- University of Lille, Lille University Hospital, Lille, F-59000, France.
- Department of Metabolism, Digestion and Reproduction, Imperial College London, London, UK.
| | - Inga Prokopenko
- INSERM UMR 1283, CNRS UMR 8199, European Genomic Institute for Diabetes (EGID), Institut Pasteur de Lille, F-59000, Lille, France.
- University of Lille, Lille University Hospital, Lille, F-59000, France.
- Section of Statistical Multi-Omics, Department of Clinical and Experimental Medicine, School of Biosciences and Medicine, University of Surrey, Guildford, UK.
- People-Centred Artificial Intelligence Institute, University of Surrey, Guildford, UK.
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18
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Xiao X, Miao X, Duan S, Liu S, Cao Q, Wu R, Tao C, Zhao J, Qu Q, Markiewicz A, Peng R, Chen Y, Żaczek A, Liu J. Single-Cell Enzymatic Screening for Epithelial Mesenchymal Transition with an Ultrasensitive Superwetting Droplet-Array Microchip. SMALL METHODS 2023:e2300096. [PMID: 37086121 DOI: 10.1002/smtd.202300096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/16/2023] [Indexed: 05/03/2023]
Abstract
The phenotypic changes of circulating tumor cells (CTCs) during the epithelial-mesenchymal transition (EMT) have been a hot topic in tumor biology and cancer therapeutic development. Here, an integrated platform of single-cell fluorescent enzymatic assays with superwetting droplet-array microchips (SDAM) for ultrasensitive functional screening of epithelial-mesenchymal sub-phenotypes of CTCs is reported. The SDAM can generate high-density, volume well-defined droplet (0.66 nL per droplet) arrays isolating single tumor cells via a discontinuous dewetting effect. It enables sensitive detection of MMP9 enzyme activities secreted by single tumor cells, correlating to their epithelial-mesenchymal sub-phenotypes. In the pilot clinical double-blind tests, the authors have demonstrated that SDAM assays allow for rapid identification and functional screening of CTCs with different epithelial-mesenchymal properties. The consistency with the clinical outcomes validates the usefulness of single-cell secreted MMP9 as a biomarker for selective CTC screening and tumor metastasis monitoring. Convenient addressing and recovery of individual CTCs from SDAM have been demonstrated for gene mutation sequencing, immunostaining, and transcriptome analysis, revealing new understandings of the signaling pathways between MMP9 secretion and the EMT regulation of CTCs. The SDAM approach combined with sequencing technologies promises to explore the dynamic EMT plasticity of tumors at the single-cell level.
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Affiliation(s)
- Xiang Xiao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Xinxing Miao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Shanzhou Duan
- Department of thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, P. R. China
| | - Sidi Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Qinghua Cao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Renfei Wu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Chengcheng Tao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Jian Zhao
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Qing Qu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Aleksandra Markiewicz
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, Gdańsk, 80-211, Poland
| | - Rui Peng
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
| | - Yongbing Chen
- Department of thoracic Surgery, The Second Affiliated Hospital of Soochow University, Suzhou, 215123, P. R. China
| | - Anna Żaczek
- Laboratory of Translational Oncology, Intercollegiate Faculty of Biotechnology, Medical University of Gdansk, Gdańsk, 80-211, Poland
| | - Jian Liu
- Institute of Functional Nano & Soft Materials (FUNSOM), Jiangsu Key Laboratory for Carbon-Based Functional Materials & Devices, Joint International Research Laboratory of Carbon-Based Functional Materials and Devices, Soochow University, Suzhou, 215123, P. R. China
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19
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Romanowska J, Nustad HE, Page CM, Denault WRP, Lee Y, Magnus MC, Haftorn KL, Gjerdevik M, Novakovic B, Saffery R, Gjessing HK, Lyle R, Magnus P, Håberg SE, Jugessur A. The X-factor in ART: does the use of assisted reproductive technologies influence DNA methylation on the X chromosome? Hum Genomics 2023; 17:35. [PMID: 37085889 PMCID: PMC10122315 DOI: 10.1186/s40246-023-00484-6] [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: 01/09/2023] [Accepted: 04/10/2023] [Indexed: 04/23/2023] Open
Abstract
BACKGROUND Assisted reproductive technologies (ART) may perturb DNA methylation (DNAm) in early embryonic development. Although a handful of epigenome-wide association studies of ART have been published, none have investigated CpGs on the X chromosome. To bridge this knowledge gap, we leveraged one of the largest collections of mother-father-newborn trios of ART and non-ART (natural) conceptions to date to investigate sex-specific DNAm differences on the X chromosome. The discovery cohort consisted of 982 ART and 963 non-ART trios from the Norwegian Mother, Father, and Child Cohort Study (MoBa). To verify our results from the MoBa cohort, we used an external cohort of 149 ART and 58 non-ART neonates from the Australian 'Clinical review of the Health of adults conceived following Assisted Reproductive Technologies' (CHART) study. The Illumina EPIC array was used to measure DNAm in both datasets. In the MoBa cohort, we performed a set of X-chromosome-wide association studies ('XWASs' hereafter) to search for sex-specific DNAm differences between ART and non-ART newborns. We tested several models to investigate the influence of various confounders, including parental DNAm. We also searched for differentially methylated regions (DMRs) and regions of co-methylation flanking the most significant CpGs. Additionally, we ran an analogous model to our main model on the external CHART dataset. RESULTS In the MoBa cohort, we found more differentially methylated CpGs and DMRs in girls than boys. Most of the associations persisted after controlling for parental DNAm and other confounders. Many of the significant CpGs and DMRs were in gene-promoter regions, and several of the genes linked to these CpGs are expressed in tissues relevant for both ART and sex (testis, placenta, and fallopian tube). We found no support for parental DNAm-dependent features as an explanation for the observed associations in the newborns. The most significant CpG in the boys-only analysis was in UBE2DNL, which is expressed in testes but with unknown function. The most significant CpGs in the girls-only analysis were in EIF2S3 and AMOT. These three loci also displayed differential DNAm in the CHART cohort. CONCLUSIONS Genes that co-localized with the significant CpGs and DMRs associated with ART are implicated in several key biological processes (e.g., neurodevelopment) and disorders (e.g., intellectual disability and autism). These connections are particularly compelling in light of previous findings indicating that neurodevelopmental outcomes differ in ART-conceived children compared to those naturally conceived.
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Affiliation(s)
- Julia Romanowska
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway.
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway.
| | - Haakon E Nustad
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- DeepInsight, 0154, Oslo, Norway
| | - Christian M Page
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Mathematics, Faculty of Mathematics and Natural Sciences, University of Oslo, Oslo, Norway
| | - William R P Denault
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yunsung Lee
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Maria C Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Kristine L Haftorn
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Miriam Gjerdevik
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Computer Science, Electrical Engineering and Mathematical Sciences, Western Norway University of Applied Sciences, Bergen, Norway
| | - Boris Novakovic
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Melbourne, Australia
- Department of Paediatrics, University of Melbourne, Melbourne, Australia
| | - Håkon K Gjessing
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
| | - Robert Lyle
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Medical Genetics, Oslo University Hospital and University of Oslo, Oslo, Norway
| | - Per Magnus
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Siri E Håberg
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
| | - Astanand Jugessur
- Centre for Fertility and Health, Norwegian Institute of Public Health, Oslo, Norway
- Department of Global Public Health and Primary Care, University of Bergen, Bergen, Norway
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20
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Bernabeu E, McCartney DL, Gadd DA, Hillary RF, Lu AT, Murphy L, Wrobel N, Campbell A, Harris SE, Liewald D, Hayward C, Sudlow C, Cox SR, Evans KL, Horvath S, McIntosh AM, Robinson MR, Vallejos CA, Marioni RE. Refining epigenetic prediction of chronological and biological age. Genome Med 2023; 15:12. [PMID: 36855161 PMCID: PMC9976489 DOI: 10.1186/s13073-023-01161-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Accepted: 02/06/2023] [Indexed: 03/02/2023] Open
Abstract
BACKGROUND Epigenetic clocks can track both chronological age (cAge) and biological age (bAge). The latter is typically defined by physiological biomarkers and risk of adverse health outcomes, including all-cause mortality. As cohort sample sizes increase, estimates of cAge and bAge become more precise. Here, we aim to develop accurate epigenetic predictors of cAge and bAge, whilst improving our understanding of their epigenomic architecture. METHODS First, we perform large-scale (N = 18,413) epigenome-wide association studies (EWAS) of chronological age and all-cause mortality. Next, to create a cAge predictor, we use methylation data from 24,674 participants from the Generation Scotland study, the Lothian Birth Cohorts (LBC) of 1921 and 1936, and 8 other cohorts with publicly available data. In addition, we train a predictor of time to all-cause mortality as a proxy for bAge using the Generation Scotland cohort (1214 observed deaths). For this purpose, we use epigenetic surrogates (EpiScores) for 109 plasma proteins and the 8 component parts of GrimAge, one of the current best epigenetic predictors of survival. We test this bAge predictor in four external cohorts (LBC1921, LBC1936, the Framingham Heart Study and the Women's Health Initiative study). RESULTS Through the inclusion of linear and non-linear age-CpG associations from the EWAS, feature pre-selection in advance of elastic net regression, and a leave-one-cohort-out (LOCO) cross-validation framework, we obtain cAge prediction with a median absolute error equal to 2.3 years. Our bAge predictor was found to slightly outperform GrimAge in terms of the strength of its association to survival (HRGrimAge = 1.47 [1.40, 1.54] with p = 1.08 × 10-52, and HRbAge = 1.52 [1.44, 1.59] with p = 2.20 × 10-60). Finally, we introduce MethylBrowsR, an online tool to visualise epigenome-wide CpG-age associations. CONCLUSIONS The integration of multiple large datasets, EpiScores, non-linear DNAm effects, and new approaches to feature selection has facilitated improvements to the blood-based epigenetic prediction of biological and chronological age.
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Affiliation(s)
- Elena Bernabeu
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Daniel L McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Danni A Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Robert F Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, USA
| | - Lee Murphy
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Nicola Wrobel
- Edinburgh Clinical Research Facility, University of Edinburgh, Edinburgh, UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
| | - David Liewald
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
| | - Caroline Hayward
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Cathie Sudlow
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
- BHF Data Science Centre, Health Data Research UK, London, UK
- Edinburgh Medical School, Usher Institute, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts, University of Edinburgh, Edinburgh, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA, USA
- Altos Labs, San Diego, USA
| | - Andrew M McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | | | - Catalina A Vallejos
- Medical Research Council Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- The Alan Turing Institute, London, UK
| | - Riccardo E Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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21
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Yu N, Hwang M, Lee Y, Song BR, Kang EH, Sim H, Ahn BC, Hwang KH, Kim J, Hong S, Kim S, Park C, Han JY. Patient-derived cell-based pharmacogenomic assessment to unveil underlying resistance mechanisms and novel therapeutics for advanced lung cancer. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2023; 42:37. [PMID: 36717865 PMCID: PMC9885631 DOI: 10.1186/s13046-023-02606-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 01/19/2023] [Indexed: 02/01/2023]
Abstract
BACKGROUND A pharmacogenomic platform using patient-derived cells (PDCs) was established to identify the underlying resistance mechanisms and tailored treatment for patients with advanced or refractory lung cancer. METHODS Drug sensitivity screening and multi-omics datasets were acquired from lung cancer PDCs (n = 102). Integrative analysis was performed to explore drug candidates according to genetic variants, gene expression, and clinical profiles. RESULTS PDCs had genomic characteristics resembled with those of solid lung cancer tissues. PDC molecular subtyping classified patients into four groups: (1) inflammatory, (2) epithelial-to-mesenchymal transition (EMT)-like, (3) stemness, and (4) epithelial growth factor receptor (EGFR)-dominant. EGFR mutations of the EMT-like subtype were associated with a reduced response to EGFR-tyrosine kinase inhibitor therapy. Moreover, although RB1/TP53 mutations were significantly enriched in small-cell lung cancer (SCLC) PDCs, they were also present in non-SCLC PDCs. In contrast to its effect in the cell lines, alpelisib (a PI3K-AKT inhibitor) significantly inhibited both RB1/TP53 expression and SCLC cell growth in our PDC model. Furthermore, cell cycle inhibitors could effectively target SCLC cells. Finally, the upregulation of transforming growth factor-β expression and the YAP/TAZ pathway was observed in osimertinib-resistant PDCs, predisposing them to the EMT-like subtype. Our platform selected XAV939 (a WNT-TNKS-β-catenin inhibitor) for the treatment of osimertinib-resistant PDCs. Using an in vitro model, we further demonstrated that acquisition of osimertinib resistance enhances invasive characteristics and EMT, upregulates the YAP/TAZ-AXL axis, and increases the sensitivity of cancer cells to XAV939. CONCLUSIONS Our PDC models recapitulated the molecular characteristics of lung cancer, and pharmacogenomics analysis provided plausible therapeutic candidates.
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Affiliation(s)
- Namhee Yu
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Mihwa Hwang
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Youngjoo Lee
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Bo Ram Song
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Eun Hye Kang
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Hanna Sim
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Beung-Chul Ahn
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Kum Hui Hwang
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Jihyun Kim
- Department of Precision Medicine, National Institute of Health, Korea Disease Control and Prevention Agency, Cheongju, 28159 Republic of Korea
| | - Sehwa Hong
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Sunshin Kim
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Charny Park
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
| | - Ji-Youn Han
- grid.410914.90000 0004 0628 9810Research Institute, National Cancer Center, Goyang-si, Gyeonggi-do 10408 Republic of Korea
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22
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Iannuzzi V, Bacalini MG, Franceschi C, Giuliani C. The role of genetics and epigenetics in sex differences in human survival. GENUS 2023. [DOI: 10.1186/s41118-023-00181-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
AbstractSex differences in human survival have been extensively investigated in many studies that have in part uncovered the biological determinants that promote a longer life in females with respect to males. Moreover, researches performed in the past years have prompted increased awareness about the biological effects of environmental factors that can modulate the magnitude of the sex gap in survival. Besides the genetic background, epigenetic modifications like DNA methylation, that can modulate cell function, have been particularly studied in this framework. In this review, we aim to summarize the role of the genetic and epigenetic mechanisms in promoting female advantage from the early in life (“INNATE” features), and in influencing the magnitude of the gap in sex differences in survival and ageing (“VARIABLE” features). After briefly discussing the biological bases of sex determination in humans, we will provide much evidence showing that (i) “innate” mechanisms common to all males and to all females (both genetic and epigenetic) play a major role in sex differences in lifespan; (ii) “variable” genetic and epigenetic patterns, that vary according to context, populations and exposures to different environments, can affect the magnitude of the gap in sex differences in survival. Then we will describe recent findings in the use of epigenetic clocks to uncover sex differences in biological age and thus potentially in mortality. In conclusion, we will discuss how environmental factors cannot be kept apart from the biological factors providing evidence from the field of human ecology.
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23
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McLaughlin RT, Asthana M, Di Meo M, Ceccarelli M, Jacob HJ, Masica DL. Fast, accurate, and racially unbiased pan-cancer tumor-only variant calling with tabular machine learning. NPJ Precis Oncol 2023; 7:4. [PMID: 36611079 PMCID: PMC9825621 DOI: 10.1038/s41698-022-00340-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 12/12/2022] [Indexed: 01/08/2023] Open
Abstract
Accurately identifying somatic mutations is essential for precision oncology and crucial for calculating tumor-mutational burden (TMB), an important predictor of response to immunotherapy. For tumor-only variant calling (i.e., when the cancer biopsy but not the patient's normal tissue sample is sequenced), accurately distinguishing somatic mutations from germline variants is a challenging problem that, when unaddressed, results in unreliable, biased, and inflated TMB estimates. Here, we apply machine learning to the task of somatic vs germline classification in tumor-only solid tumor samples using TabNet, XGBoost, and LightGBM, three machine-learning models for tabular data. We constructed a training set for supervised classification using features derived exclusively from tumor-only variant calling and drawing somatic and germline truth labels from an independent pipeline using the patient-matched normal samples. All three trained models achieved state-of-the-art performance on two holdout test datasets: a TCGA dataset including sarcoma, breast adenocarcinoma, and endometrial carcinoma samples (AUC > 94%), and a metastatic melanoma dataset (AUC > 85%). Concordance between matched-normal and tumor-only TMB improves from R2 = 0.006 to 0.71-0.76 with the addition of a machine-learning classifier, with LightGBM performing best. Notably, these machine-learning models generalize across cancer subtypes and capture kits with a call rate of 100%. We reproduce the recent finding that tumor-only TMB estimates for Black patients are extremely inflated relative to that of white patients due to the racial biases of germline databases. We show that our approach with XGBoost and LightGBM eliminates this significant racial bias in tumor-only variant calling.
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Affiliation(s)
| | - Maansi Asthana
- Agricultural and Biological Engineering at Purdue University, West Lafayette, IN, USA
| | - Marc Di Meo
- Johns Hopkins University, Baltimore, MD, USA
| | - Michele Ceccarelli
- Department of Electrical Engineering and Information Technology, University of Naples "Federico II", Naples, Italy
- Biogem, Instituto di Biologia e Genetica Molecolare, Ariano Irpino, Italy
| | | | - David L Masica
- Genomics Research Center, AbbVie, Redwood City, CA, USA.
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24
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Ma S, Li H. Statistical and Computational Methods for Microbial Strain Analysis. Methods Mol Biol 2023; 2629:231-245. [PMID: 36929080 DOI: 10.1007/978-1-0716-2986-4_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Microbial strains are interpreted as a lineage derived from a recent ancestor that have not experienced "too many" recombination events and can be successfully retrieved with culture-independent techniques using metagenomic sequencing. Such a strain variability has been increasingly shown to display additional phenotypic heterogeneities that affect host health, such as virulence, transmissibility, and antibiotics resistance. New statistical and computational methods have recently been developed to track the strains in samples based on shotgun metagenomics data either based on reference genome sequences or Metagenome-assembled genomes (MAGs). In this paper, we review some recent statistical methods for strain identifications based on frequency counts at a set of single nucleotide variants (SNVs) within a set of single-copy marker genes. These methods differ in terms of whether reference genome sequences are needed, how SNVs are called, what methods of deconvolution are used and whether the methods can be applied to multiple samples. We conclude our review with areas that require further research.
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Affiliation(s)
- Siyuan Ma
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Hongzhe Li
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA.
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25
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Ramaker ME, Corcoran DL, Apsley AT, Kobor MS, Kraus VB, Kraus WE, Lin DTS, Orenduff MC, Pieper CF, Waziry R, Huffman KM, Belsky DW. Epigenome-wide Association Study Analysis of Calorie Restriction in Humans, CALERIETM Trial Analysis. J Gerontol A Biol Sci Med Sci 2022; 77:2395-2401. [PMID: 35965483 PMCID: PMC9799188 DOI: 10.1093/gerona/glac168] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Indexed: 01/20/2023] Open
Abstract
Calorie restriction (CR) increases healthy life span and is accompanied by slowing or reversal of aging-associated DNA methylation (DNAm) changes in animal models. In the Comprehensive Assessment of Long-term Effects of Reducing Intake of Energy (CALERIETM) human trial, we evaluated associations of CR and changes in whole-blood DNAm. CALERIETM randomized 220 healthy, nonobese adults in a 2:1 allocation to 2 years of CR or ad libitum (AL) diet. The average CR in the treatment group through 24 months of follow-up was 12%. Whole blood (baseline, 12, and 24 months) DNAm profiles were measured. Epigenome-wide association study (EWAS) analysis tested CR-induced changes from baseline to 12 and 24 months in the n = 197 participants with available DNAm data. CR treatment was not associated with epigenome-wide significant (false discovery rate [FDR] < 0.05) DNAm changes at the individual-CpG-site level. Secondary analysis of sets of CpG sites identified in published EWAS revealed that CR induced DNAm changes opposite to those associated with higher body mass index and cigarette smoking (p < .003 at 12- and 24-month follow-ups). In contrast, CR altered DNAm at chronological-age-associated CpG sites in the direction of older age (p < .003 at 12- and 24-month follow-ups). Although individual CpG site DNAm changes in response to CR were not identified, analyses of sets CpGs identified in prior EWAS revealed CR-induced changes to blood DNAm. Altered CpG sets were enriched for insulin production, glucose tolerance, inflammation, and DNA-binding and DNA-regulation pathways, several of which are known to be modified by CR. DNAm changes may contribute to CR effects on aging.
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Affiliation(s)
- Megan E Ramaker
- Duke University Molecular Physiology Institute, Durham, North Carolina, USA
| | - David L Corcoran
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Abner T Apsley
- Behavioral Health Department, The Pennsylvania State University, University Park, Pennsylvania, USA
- Department of Biobehavioral Health, Molecular, Cellular, and Integrative Biosciences Program, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Michael S Kobor
- BC Children’s Hopsital Research Institute (BCCHR), Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
- Program in Child and Brain Development, CIFA, MaRS Centre, Vancouver, British Columbia, Canada
- The Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Virginia B Kraus
- Duke University Molecular Physiology Institute, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - William E Kraus
- Duke University Molecular Physiology Institute, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - David T S Lin
- BC Children’s Hopsital Research Institute (BCCHR), Vancouver, British Columbia, Canada
- Centre for Molecular Medicine and Therapeutics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melissa C Orenduff
- Duke University Molecular Physiology Institute, Durham, North Carolina, USA
| | - Carl F Pieper
- Center for Aging and Human Development, Duke University Medical Center, Durham, North Carolina, USA
- Department of Biostatistics and Bioinformatics, Duke University Medical Center, Durham, North Carolina, USA
| | - Reem Waziry
- Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, New York, USA
| | - Kim M Huffman
- Duke University Molecular Physiology Institute, Durham, North Carolina, USA
- Department of Medicine, Duke University School of Medicine, Durham, North Carolina, USA
| | - Daniel W Belsky
- Butler Columbia Aging Center, Columbia University Mailman School of Public Health, New York, New York, USA
- Department of Epidemiology, Columbia University Mailman School of Public Health, New York, New York, USA
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26
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Juříčková I, Hudec M, Votava F, Vosáhlo J, Ovsepian SV, Černá M, O’Leary VB. The Immunological Epigenetic Landscape of the Human Life Trajectory. Biomedicines 2022; 10:biomedicines10112894. [PMID: 36428462 PMCID: PMC9687906 DOI: 10.3390/biomedicines10112894] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/26/2022] [Accepted: 11/08/2022] [Indexed: 11/16/2022] Open
Abstract
Adaptive immunity changes over an individual’s lifetime, maturing by adulthood and diminishing with old age. Epigenetic mechanisms involving DNA and histone methylation form the molecular basis of immunological memory during lymphocyte development. Monocytes alter their function to convey immune tolerance, yet the epigenetic influences at play remain to be fully understood in the context of lifespan. This study of a healthy genetically homogenous cohort of children, adults and seniors sought to decipher the epigenetic dynamics in B-lymphocytes and monocytes. Variable global cytosine methylation within retro-transposable LINE-1 repeats was noted in monocytes compared to B-lymphocytes across age groups. The expression of the human leukocyte antigen (HLA)-DQ alpha chain gene HLA-DQA1*01 revealed significantly reduced levels in monocytes in all ages relative to B-lymphocytes, as well as between lifespan groups. High melting point analysis and bisulfite sequencing of the HLA-DQA1*01 promoter in monocytes highlighted variable cytosine methylation in children and seniors but greater stability at this locus in adults. Further epigenetic evaluation revealed higher histone lysine 27 trimethylation in monocytes from this adult group. Chromatin immunoprecipitation and RNA pulldown demonstrated association with a novel lncRNA TINA with structurally conserved similarities to the previously recognized epigenetic modifier PARTICLE. Seeking to interpret the epigenetic immunological landscape across three representative age groups, this study focused on HLA-DQA1*01 to expose cytosine and histone methylation alterations and their association with the non-coding transcriptome. Such insights unveil previously unknown complex epigenetic layers, orchestrating the strength and weakening of adaptive immunity with the progression of life.
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Affiliation(s)
- Iva Juříčková
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Vinohrady, 10000 Prague, Czech Republic
- Correspondence: (I.J.); (V.B.O.)
| | - Michael Hudec
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Vinohrady, 10000 Prague, Czech Republic
| | - Felix Votava
- Department of Children and Adolescents, Third Faculty of Medicine, Charles University, Vinohrady, 10000 Prague, Czech Republic
- Královské Vinohrady University Hospital, Vinohrady, 10034 Prague, Czech Republic
| | - Jan Vosáhlo
- Department of Children and Adolescents, Third Faculty of Medicine, Charles University, Vinohrady, 10000 Prague, Czech Republic
- Královské Vinohrady University Hospital, Vinohrady, 10034 Prague, Czech Republic
| | - Saak Victor Ovsepian
- Faculty of Engineering and Science, University of Greenwich London, Chatham Maritime, Kent ME4 4TB, UK
| | - Marie Černá
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Vinohrady, 10000 Prague, Czech Republic
| | - Valerie Bríd O’Leary
- Department of Medical Genetics, Third Faculty of Medicine, Charles University, Vinohrady, 10000 Prague, Czech Republic
- Correspondence: (I.J.); (V.B.O.)
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27
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Higham J, Kerr L, Zhang Q, Walker RM, Harris SE, Howard DM, Hawkins EL, Sandu AL, Steele JD, Waiter GD, Murray AD, Evans KL, McIntosh AM, Visscher PM, Deary IJ, Cox SR, Sproul D. Local CpG density affects the trajectory and variance of age-associated DNA methylation changes. Genome Biol 2022; 23:216. [PMID: 36253871 PMCID: PMC9575273 DOI: 10.1186/s13059-022-02787-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND DNA methylation is an epigenetic mark associated with the repression of gene promoters. Its pattern in the genome is disrupted with age and these changes can be used to statistically predict age with epigenetic clocks. Altered rates of aging inferred from these clocks are observed in human disease. However, the molecular mechanisms underpinning age-associated DNA methylation changes remain unknown. Local DNA sequence can program steady-state DNA methylation levels, but how it influences age-associated methylation changes is unknown. RESULTS We analyze longitudinal human DNA methylation trajectories at 345,895 CpGs from 600 individuals aged between 67 and 80 to understand the factors responsible for age-associated epigenetic changes at individual CpGs. We show that changes in methylation with age occur at 182,760 loci largely independently of variation in cell type proportions. These changes are especially apparent at 8322 low CpG density loci. Using SNP data from the same individuals, we demonstrate that methylation trajectories are affected by local sequence polymorphisms at 1487 low CpG density loci. More generally, we find that low CpG density regions are particularly prone to change and do so variably between individuals in people aged over 65. This differs from the behavior of these regions in younger individuals where they predominantly lose methylation. CONCLUSIONS Our results, which we reproduce in two independent groups of individuals, demonstrate that local DNA sequence influences age-associated DNA methylation changes in humans in vivo. We suggest that this occurs because interactions between CpGs reinforce maintenance of methylation patterns in CpG dense regions.
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Affiliation(s)
- Jonathan Higham
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Lyndsay Kerr
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Qian Zhang
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
- Present address: Wellcome Sanger Institute, Hinxton, Cambridgeshire, UK
| | - Rosie M Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
- Present address: School of Psychology, University of Exeter, Edinburgh, UK
| | - Sarah E Harris
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - David M Howard
- Social, Genetic and Developmental Psychiatry Centre, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Emma L Hawkins
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Anca-Larisa Sandu
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - J Douglas Steele
- Division of Imaging Science and Technology, Medical School, University of Dundee, Dundee, UK
| | - Gordon D Waiter
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Alison D Murray
- Aberdeen Biomedical Imaging Centre, Institute of Medical Sciences, University of Aberdeen, Aberdeen, UK
| | - Kathryn L Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK
| | - Andrew M McIntosh
- Division of Psychiatry, University of Edinburgh, Royal Edinburgh Hospital, Edinburgh, UK
| | - Peter M Visscher
- Institute for Molecular Bioscience, University of Queensland, Brisbane, QLD, Australia
| | - Ian J Deary
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Simon R Cox
- Department of Psychology, Lothian Birth Cohorts Group, University of Edinburgh, Edinburgh, UK
| | - Duncan Sproul
- MRC Human Genetics Unit, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
- CRUK Edinburgh Centre, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
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The immune factors driving DNA methylation variation in human blood. Nat Commun 2022; 13:5895. [PMID: 36202838 PMCID: PMC9537159 DOI: 10.1038/s41467-022-33511-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 09/21/2022] [Indexed: 11/08/2022] Open
Abstract
Epigenetic changes are required for normal development, yet the nature and respective contribution of factors that drive epigenetic variation in humans remain to be fully characterized. Here, we assessed how the blood DNA methylome of 884 adults is affected by DNA sequence variation, age, sex and 139 factors relating to life habits and immunity. Furthermore, we investigated whether these effects are mediated or not by changes in cellular composition, measured by deep immunophenotyping. We show that DNA methylation differs substantially between naïve and memory T cells, supporting the need for adjustment on these cell-types. By doing so, we find that latent cytomegalovirus infection drives DNA methylation variation and provide further support that the increased dispersion of DNA methylation with aging is due to epigenetic drift. Finally, our results indicate that cellular composition and DNA sequence variation are the strongest predictors of DNA methylation, highlighting critical factors for medical epigenomics studies.
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29
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C. Silva T, Zhang W, Young JI, Gomez L, Schmidt MA, Varma A, Chen XS, Martin ER, Wang L. Distinct sex-specific DNA methylation differences in Alzheimer's disease. Alzheimers Res Ther 2022; 14:133. [PMID: 36109771 PMCID: PMC9479371 DOI: 10.1186/s13195-022-01070-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 08/30/2022] [Indexed: 01/17/2023]
Abstract
BACKGROUND Sex is increasingly recognized as a significant factor contributing to the biological and clinical heterogeneity in AD. There is also growing evidence for the prominent role of DNA methylation (DNAm) in Alzheimer's disease (AD). METHODS We studied sex-specific DNA methylation differences in the blood samples of AD subjects compared to cognitively normal subjects, by performing sex-specific meta-analyses of two large blood-based epigenome-wide association studies (ADNI and AIBL), which included DNA methylation data for a total of 1284 whole blood samples (632 females and 652 males). Within each dataset, we used two complementary analytical strategies, a sex-stratified analysis that examined methylation to AD associations in male and female samples separately, and a methylation-by-sex interaction analysis that compared the magnitude of these associations between different sexes. After adjusting for age, estimated immune cell type proportions, batch effects, and correcting for inflation, the inverse-variance fixed-effects meta-analysis model was used to identify the most consistent DNAm differences across datasets. In addition, we also evaluated the performance of the sex-specific methylation-based risk prediction models for AD diagnosis using an independent external dataset. RESULTS In the sex-stratified analysis, we identified 2 CpGs, mapped to the PRRC2A and RPS8 genes, significantly associated with AD in females at a 5% false discovery rate, and an additional 25 significant CpGs (21 in females, 4 in males) at P-value < 1×10-5. In methylation-by-sex interaction analysis, we identified 5 significant CpGs at P-value < 10-5. Out-of-sample validations using the AddNeuroMed dataset showed in females, the best logistic prediction model included age, estimated immune cell-type proportions, and methylation risk scores (MRS) computed from 9 of the 23 CpGs identified in AD vs. CN analysis that are also available in AddNeuroMed dataset (AUC = 0.74, 95% CI: 0.65-0.83). In males, the best logistic prediction model included only age and MRS computed from 2 of the 5 CpGs identified in methylation-by-sex interaction analysis that are also available in the AddNeuroMed dataset (AUC = 0.70, 95% CI: 0.56-0.82). CONCLUSIONS Overall, our results show that the DNA methylation differences in AD are largely distinct between males and females. Our best-performing sex-specific methylation-based prediction model in females performed better than that for males and additionally included estimated cell-type proportions. The significant discriminatory classification of AD samples with our methylation-based prediction models demonstrates that sex-specific DNA methylation could be a predictive biomarker for AD. As sex is a strong factor underlying phenotypic variability in AD, the results of our study are particularly relevant for a better understanding of the epigenetic architecture that underlie AD and for promoting precision medicine in AD.
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Affiliation(s)
- Tiago C. Silva
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Wei Zhang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA
| | - Juan I. Young
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lissette Gomez
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Michael A. Schmidt
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Achintya Varma
- grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - X. Steven Chen
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
| | - Eden R. Martin
- grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA
| | - Lily Wang
- grid.26790.3a0000 0004 1936 8606Division of Biostatistics, Department of Public Health Sciences, University of Miami, Miller School of Medicine, 1120 NW 14th Street, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Dr. John T Macdonald Foundation Department of Human Genetics, University of Miami, Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606John P. Hussman Institute for Human Genomics, University of Miami Miller School of Medicine, Miami, FL 33136 USA ,grid.26790.3a0000 0004 1936 8606Sylvester Comprehensive Cancer Center, University of Miami, Miller School of Medicine, Miami, FL 33136 USA
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30
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Tan Q, Mengel-From J, Christensen K. Sex difference in epigenomic instability during human aging. Aging (Albany NY) 2022; 14:5960-5961. [PMID: 35929839 PMCID: PMC9417232 DOI: 10.18632/aging.204199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Accepted: 07/20/2022] [Indexed: 11/25/2022]
Affiliation(s)
- Qihua Tan
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Jonas Mengel-From
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
| | - Kaare Christensen
- Epidemiology and Biostatistics, Department of Public Health, University of Southern Denmark, Odense, Denmark
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31
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Winek K, Tzur Y, Soreq H. Biological underpinnings of sex differences in neurological disorders. INTERNATIONAL REVIEW OF NEUROBIOLOGY 2022; 164:27-67. [PMID: 36038206 DOI: 10.1016/bs.irn.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The importance of sex differences in neurological disorders has been increasingly acknowledged in recent clinical and basic research studies, but the complex biology and genetics underlying sex-linked biological heterogeneity and its brain-to-body impact remained incompletely understood. Men and women differ substantially in their susceptibility to certain neurological diseases, in the severity of symptoms, prognosis as well as the nature and efficacy of their response to treatments. The detailed mechanisms underlying these differences, especially at the molecular level, are being addressed in many studies but leave a lot to be further revealed. Here, we provide an overview of recent advances in our understanding of how sex differences in the brain and brain-body signaling contribute to neurological disorders and further present some future prospects entailed in terms of diagnostics and therapeutics.
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Affiliation(s)
- Katarzyna Winek
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yonat Tzur
- The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Hermona Soreq
- The Edmond & Lily Safra Center for Brain Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel; The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel.
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32
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Oxidative stress, aging, antioxidant supplementation and their impact on human health: An overview. Mech Ageing Dev 2022; 206:111707. [PMID: 35839856 DOI: 10.1016/j.mad.2022.111707] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 07/06/2022] [Accepted: 07/10/2022] [Indexed: 12/12/2022]
Abstract
Aging is characterized by a progressive loss of tissue and organ function due to genetic and environmental factors, nutrition, and lifestyle. Oxidative stress is one the most important mechanisms of cellular senescence and increased frailty, resulting in several age-linked, noncommunicable diseases. Contributing events include genomic instability, telomere shortening, epigenetic mechanisms, reduced proteome homeostasis, altered stem-cell function, defective intercellular communication, progressive deregulation of nutrient sensing, mitochondrial dysfunction, and metabolic unbalance. These complex events and their interplay can be modulated by dietary habits and the ageing process, acting as potential measures of primary and secondary prevention. Promising nutritional approaches include the Mediterranean diet, the intake of dietary antioxidants, and the restriction of caloric intake. A comprehensive understanding of the ageing processes should promote new biomarkers of risk or diagnosis, but also beneficial treatments oriented to increase lifespan.
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33
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Novel brown adipose tissue candidate genes predicted by the human gene connectome. Sci Rep 2022; 12:7614. [PMID: 35534514 PMCID: PMC9085833 DOI: 10.1038/s41598-022-11317-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/06/2022] [Indexed: 11/08/2022] Open
Abstract
Brown adipose tissue (BAT) is a promising therapeutic target against obesity. Therefore, research on the genetic architecture of BAT could be key for the development of successful therapies against this complex phenotype. Hypothesis-driven candidate gene association studies are useful for studying genetic determinants of complex traits, but they are dependent upon the previous knowledge to select candidate genes. Here, we predicted 107 novel-BAT candidate genes in silico using the uncoupling protein one (UCP1) as the hallmark of BAT activity. We first identified the top 1% of human genes predicted by the human gene connectome to be biologically closest to the UCP1, estimating 167 additional pathway genes (BAT connectome). We validated this prediction by showing that 60 genes already associated with BAT were included in the connectome and they were biologically closer to each other than expected by chance (p < 2.2 × 10-16). The rest of genes (107) are potential candidates for BAT, being also closer to known BAT genes and more expressed in BAT biopsies than expected by chance (p < 2.2 × 10-16; p = 4.39 × 10-02). The resulting new list of predicted human BAT genes should be useful for the discovery of novel BAT genes and metabolic pathways.
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34
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Alanazi IO, Alamery SF, Ebrahimie E, Mohammadi-Dehcheshmeh M. Splice-disrupt genomic variants in prostate cancer. Mol Biol Rep 2022; 49:4237-4246. [PMID: 35286517 PMCID: PMC9262760 DOI: 10.1007/s11033-022-07257-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 02/08/2022] [Indexed: 12/11/2022]
Abstract
Background Splice-disrupt genomic variants are one of the causes of cancer-causing errors in gene expression. Little is known about splice-disrupt genomic variants. Methods and results Here, pattern of splice-disrupt variants was investigated using 21,842,764 genomic variants in different types of prostate cancer. A particular attention was paid to genomic locations of splice-disrupt variants on target genes. HLA-A in prostate cancer, MSR1 in familial prostate cancer, and EGFR in both castration-resistant prostate cancer and metastatic castration-resistant had the highest allele frequencies of splice-disrupt variations. Some splice-disrupt variants, located on coding sequences of NCOR2, PTPRC, and CRP, were solely present in the advanced metastatic castration-resistant prostate cancer. High-risk splice-disrupt variants were identified based on computationally calculated Polymorphism Phenotyping (PolyPhen), Sorting Intolerant From Tolerant (SIFT), and Genomic Evolutionary Rate Profiling (GERP) + + scores as well as the recorded clinical significance in dbSNP database of NCBI. Functional annotation of damaging splice-disrupt variants highlighted important cancer-associated functions, including endocrine resistance, lipid metabolic process, steroid metabolic process, regulation of mitotic cell cycle, and regulation of metabolic process. This is the first study that profiles the splice-disrupt genomic variants and their target genes in prostate cancer. Literature mining based variant analysis highlighted the importance of rs1800716 variant, located on the CYP2D6 gene, involved in a range of important functions, such as RNA spicing, drug interaction, death, and urotoxicity. Conclusions This is the first study that profiles the splice-disrupt genomic variants and their target genes in different types of prostate cancer. Unravelling alternative splicing opens a new avenue towards the establishment of new diagnostic and prognostic markers for prostate cancer progression and metastasis. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-022-07257-9.
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Affiliation(s)
- Ibrahim O. Alanazi
- National Center for Biotechnology, Life Science and Environment Research Institute, King Abdulaziz City for Science and Technology (KACST), Riyadh, Saudi Arabia
| | - Salman F. Alamery
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Esmaeil Ebrahimie
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, VIC 3086 Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, 5371 Australia
- School of BioSciences, The University of Melbourne, Melbourne, VIC 3010 Australia
| | - Manijeh Mohammadi-Dehcheshmeh
- Genomics Research Platform, School of Life Sciences, La Trobe University, Melbourne, VIC 3086 Australia
- School of Animal and Veterinary Sciences, The University of Adelaide, Adelaide, 5371 Australia
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35
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Li G, Wang C, Guan X, Bai Y, Feng Y, Wei W, Meng H, Fu M, He M, Zhang X, Lu Y, Lin Y, Guo H. Age-related DNA methylation on Y chromosome and their associations with total mortality among Chinese males. Aging Cell 2022; 21:e13563. [PMID: 35120273 PMCID: PMC8920452 DOI: 10.1111/acel.13563] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/10/2022] [Accepted: 01/24/2022] [Indexed: 11/28/2022] Open
Abstract
In view of the sex differences in aging‐related diseases, sex chromosomes may play a critical role during aging process. This study aimed to identify age‐related DNA methylation changes on Y chromosome (ChrY). A two‐stage study design was conducted in this study. The discovery stage contained 419 Chinese males, including 205 from the Wuhan‐Zhuhai cohort panel, 107 from the coke oven workers panel, and 107 from the Shiyan panel. The validation stage contained 587 Chinese males from the Dongfeng‐Tongji sub‐cohort. We used the Illumina HumanMethylation BeadChip to determine genome‐wide DNA methylation in peripheral blood of the study participants. The associations between age and methylation levels of ChrY CpGs were investigated by using linear regression models with adjustment for potential confounders. Further, associations of age‐related ChrY CpGs with all‐cause mortality were tested in the validation stage. We identified the significant associations of 41 ChrY CpGs with age at false discovery rate (FDR) <0.05 in the discovery stage, and 18 of them were validated in the validation stage (p < 0.05). Meta‐analysis of both stages confirmed the robust positive associations of 14 CpGs and negative associations of 4 CpGs with age (FDR<0.05). Among them, cg03441493 and cg17816615 were significantly associated with all‐cause mortality risk [HR(95% CI) = 1.37 (1.04, 1.79) and 0.70 (0.54, 0.93), respectively]. Our results highlighted the importance of ChrY CpGs on male aging.
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Affiliation(s)
- 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 China
- Department of Clinical Laboratory Medicine Shanghai Fifth People's Hospital Fudan University Shanghai 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 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 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 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 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 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 Wuhan China
| | - Ming Fu
- Department of Occupational and Environmental Health State Key Laboratory of Environmental Health (Incubating) School of Public Health Tongji Medical College Huazhong University of Science and Technology 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 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 Wuhan China
| | - Yanjun Lu
- Department of Laboratory Medicine Tongji Hospital Tongji Medical College Huazhong University of Science and Technology Wuhan China
| | - Yong Lin
- Department of Clinical Laboratory Medicine Shanghai Fifth People's Hospital Fudan University Shanghai China
- Department of Laboratory Medicine Huashan Hospital Fudan University Shanghai China
- National Clinical Research Center for Aging and Medicine Huashan Hospital Fudan University Shanghai 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 China
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36
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Lo T, Kushima I, Aleksic B, Kato H, Nawa Y, Hayashi Y, Otgonbayar G, Kimura H, Arioka Y, Mori D, Ozaki N. Sequencing of selected chromatin remodelling genes reveals increased burden of rare missense variants in ASD patients from the Japanese population. Int Rev Psychiatry 2022; 34:154-167. [PMID: 35699097 DOI: 10.1080/09540261.2022.2072193] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Chromatin remodelling is an important process in neural development and is related to autism spectrum disorder (ASD) and schizophrenia (SCZ) aetiology. To further elucidate the involvement of chromatin remodelling genes in the genetic aetiology of ASD and SCZ in the Japanese population, we performed a case-control study. Targeted sequencing was conducted on coding regions of four BAF chromatin remodelling complex genes: SMARCA2, SMARCA4, SMARCC2, and ARID1B in 185 ASD, 432 SCZ patients, and 517 controls. 27 rare non-synonymous variants were identified in ASD and SCZ patients, including 25 missense, one in-frame deletion in SMRACA4, and one frame-shift variant in SMARCC2. Association analysis was conducted to investigate the burden of rare variants in BAF genes in ASD and SCZ patients. Significant enrichment of rare missense variants in BAF genes, but not synonymous variants, was found in ASD compared to controls. Rare pathogenic variants indicated by in silico tools were significantly enriched in ASD, but not statistically significant in SCZ. Pathogenic-predicted variants were located in disordered binding regions and may confer risk for ASD and SCZ by disrupting protein-protein interactions. Our study supports the involvement of rare missense variants of BAF genes in ASD and SCZ susceptibility.
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Affiliation(s)
- Tzuyao Lo
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Itaru Kushima
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan
| | - Branko Aleksic
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hidekazu Kato
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yoshihiro Nawa
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yu Hayashi
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Gantsooj Otgonbayar
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hiroki Kimura
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Yuko Arioka
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Medical Genomics Center, Nagoya University Hospital, Nagoya, Japan.,Center for Advanced Medicine and Clinical Research, Nagoya University Hospital, Nagoya, Japan
| | - Daisuke Mori
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan.,Brain and Mind Research Center, Nagoya University, Nagoya, Japan
| | - Norio Ozaki
- Department of Psychiatry, Nagoya University Graduate School of Medicine, Nagoya, Japan
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Shepherd R, Bretherton I, Pang K, Mansell T, Czajko A, Kim B, Vlahos A, Zajac JD, Saffery R, Cheung A, Novakovic B. Gender-affirming hormone therapy induces specific DNA methylation changes in blood. Clin Epigenetics 2022; 14:24. [PMID: 35177097 PMCID: PMC8851870 DOI: 10.1186/s13148-022-01236-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Accepted: 01/13/2022] [Indexed: 11/10/2022] Open
Abstract
Background DNA methylation is an epigenetic mark that is influenced by underlying genetic profile, environment, and ageing. In addition to X-linked DNA methylation, sex-specific methylation patterns are widespread across autosomal chromosomes and can be present from birth or arise over time. In individuals where gender identity and sex assigned at birth are markedly incongruent, as in the case of transgender people, feminization or masculinization may be sought through gender-affirming hormone therapy (GAHT). GAHT is a cornerstone of transgender care, yet no studies to date have investigated its effect on genome-wide methylation. We profiled genome-wide DNA methylation in blood of transgender women (n = 13) and transgender men (n = 13) before and during GAHT (6 months and 12 months into feminizing or masculinizing hormone therapy). Results We identified several thousand differentially methylated CpG sites (DMPs) (Δβ ≥ 0.02, unadjusted p value < 0.05) and several differentially methylated regions (DMRs) in both people undergoing feminizing and masculinizing GAHT, the vast majority of which were progressive changes over time. X chromosome and sex-specific autosomal DNA methylation patterns established in early development are largely refractory to change in association with GAHT, with only 3% affected (Δβ ≥ 0.02, unadjusted p value < 0.05). The small number of sex-specific DMPs that were affected by GAHT were those that become sex-specific during the lifetime, known as sex-and-age DMPs, including DMRs in PRR4 and VMP1 genes. The GAHT-induced changes at these sex-associated probes consistently demonstrated a shift towards the methylation signature of the GAHT-naïve opposite sex, and we observed enrichment of previously reported adolescence-associated methylation changes. Conclusion We provide evidence for GAHT inducing a unique blood methylation signature in transgender people. This study advances our understanding of the complex interplay between sex hormones, sex chromosomes, and DNA methylation in the context of immunity. We highlight the need to broaden the field of ‘sex-specific’ immunity beyond cisgender males and cisgender females, as transgender people on GAHT exhibit a unique molecular profile. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-022-01236-4.
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Affiliation(s)
- Rebecca Shepherd
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Ingrid Bretherton
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Ken Pang
- Brain and Mitochondrial Research, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Inflammation Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC, Australia.,Department of Adolescent Medicine, Royal Children's Hospital, Parkville, VIC, Australia
| | - Toby Mansell
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Anna Czajko
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Bowon Kim
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Amanda Vlahos
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia
| | - Jeffrey D Zajac
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Richard Saffery
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia.,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia
| | - Ada Cheung
- Department of Medicine (Austin Health), The University of Melbourne, Parkville, VIC, Australia.,Department of Endocrinology, Austin Health, Heidelberg, VIC, Australia
| | - Boris Novakovic
- Molecular Immunity, Infection and Immunity Theme, Murdoch Children's Research Institute, Royal Children's Hospital, Parkville, VIC, Australia. .,Department of Paediatrics, The University of Melbourne, Parkville, VIC, Australia.
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38
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McCartney DL, Hillary RF, Conole ELS, Banos DT, Gadd DA, Walker RM, Nangle C, Flaig R, Campbell A, Murray AD, Maniega SM, Valdés-Hernández MDC, Harris MA, Bastin ME, Wardlaw JM, Harris SE, Porteous DJ, Tucker-Drob EM, McIntosh AM, Evans KL, Deary IJ, Cox SR, Robinson MR, Marioni RE. Blood-based epigenome-wide analyses of cognitive abilities. Genome Biol 2022; 23:26. [PMID: 35039062 PMCID: PMC8762878 DOI: 10.1186/s13059-021-02596-5] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 12/29/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Blood-based markers of cognitive functioning might provide an accessible way to track neurodegeneration years prior to clinical manifestation of cognitive impairment and dementia. RESULTS Using blood-based epigenome-wide analyses of general cognitive function, we show that individual differences in DNA methylation (DNAm) explain 35.0% of the variance in general cognitive function (g). A DNAm predictor explains ~4% of the variance, independently of a polygenic score, in two external cohorts. It also associates with circulating levels of neurology- and inflammation-related proteins, global brain imaging metrics, and regional cortical volumes. CONCLUSIONS As sample sizes increase, the ability to assess cognitive function from DNAm data may be informative in settings where cognitive testing is unreliable or unavailable.
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Affiliation(s)
- Daniel L. McCartney
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Robert F. Hillary
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Eleanor L. S. Conole
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Daniel Trejo Banos
- Department of Quantitative Biomedicine, University of Zurich, Zurich, Switzerland
- Biomedical Informatics, University Hospital of Zurich, Zurich, Switzerland
| | - Danni A. Gadd
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Rosie M. Walker
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Cliff Nangle
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Robin Flaig
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Archie Campbell
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Alison D. Murray
- Aberdeen Biomedical Imaging Centre, University of Aberdeen, Aberdeen, Scotland, UK
| | - Susana Muñoz Maniega
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - María del C. Valdés-Hernández
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Mathew A. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Mark E. Bastin
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Joanna M. Wardlaw
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
- Centre for Clinical Brain Sciences, UK Dementia Research Institute at the University of Edinburgh, Chancellor’s Building, 49 Little France Crescent, Edinburgh BioQuarter, Edinburgh, EH16 4SB UK
| | - Sarah E. Harris
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - David J. Porteous
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Elliot M. Tucker-Drob
- Department of Psychology, University of Texas, Austin, TX USA
- Population Research Center and Center on Aging and Population Sciences, University of Texas, Austin, TX USA
| | - Andrew M. McIntosh
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
- Division of Psychiatry, Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh, UK
| | - Kathryn L. Evans
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
| | - Ian J. Deary
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | - Simon R. Cox
- Lothian Birth Cohorts, Department of Psychology, University of Edinburgh, Edinburgh, EH8 9JZ UK
| | | | - Riccardo E. Marioni
- Centre for Genomic and Experimental Medicine, Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, EH4 2XU UK
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Bhat B, Jones GT. Data Analysis of DNA Methylation Epigenome-Wide Association Studies (EWAS): A Guide to the Principles of Best Practice. Methods Mol Biol 2022; 2458:23-45. [PMID: 35103960 DOI: 10.1007/978-1-0716-2140-0_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Array-based EWAS have become an increasingly popular technique to identify population epigenetic effects, particularly in humans. With the arrival of nonhuman species arrays, such as the mouse, this is likely to become an even more widely used technology. This chapter provides the less experienced researcher a guide to the analysis of data from the most widely used platform, the Illumina Infinium Methylation assay. This includes an overview of quality filtering, data normalization, analysis options, and techniques to improve the interpretation of results.
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Affiliation(s)
- Basharat Bhat
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand
| | - Gregory T Jones
- Department of Surgical Sciences, Dunedin School of Medicine, University of Otago, Dunedin, New Zealand.
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40
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Ruscheinski A, Reimler AL, Ewald R, Uhrmacher AM. VPMBench: a test bench for variant prioritization methods. BMC Bioinformatics 2021; 22:543. [PMID: 34749640 PMCID: PMC8576923 DOI: 10.1186/s12859-021-04458-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 10/23/2021] [Indexed: 11/18/2022] Open
Abstract
Background Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causing. Each time a new method is developed, its effectiveness must be evaluated and compared to other approaches based on the most recently available evaluation data. Doing so in an unbiased, systematic, and replicable manner requires significant effort. Results The open-source test bench “VPMBench” automates the evaluation of variant prioritization methods. VPMBench introduces a standardized interface for prioritization methods and provides a plugin system that makes it easy to evaluate new methods. It supports different input data formats and custom output data preparation. VPMBench exploits declaratively specified information about the methods, e.g., the variants supported by the methods. Plugins may also be provided in a technology-agnostic manner via containerization. Conclusions VPMBench significantly simplifies the evaluation of both custom and published variant prioritization methods. As we expect variant prioritization methods to become ever more critical with the advent of whole-genome sequencing in clinical diagnostics, such tool support is crucial to facilitate methodological research.
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Affiliation(s)
- Andreas Ruscheinski
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, University of Rostock, Albert-Einstein-Straße 22, 18051, Rostock, Germany.
| | - Anna Lena Reimler
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, University of Rostock, Albert-Einstein-Straße 22, 18051, Rostock, Germany
| | - Roland Ewald
- Limbus Medical Technologies GmbH, Lindenstraße 2, 18055, Rostock, Germany
| | - Adelinde M Uhrmacher
- Modeling and Simulation Group, Institute for Visual and Analytic Computing, University of Rostock, Albert-Einstein-Straße 22, 18051, Rostock, Germany
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41
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Kim HY, Jeon W, Kim D. An enhanced variant effect predictor based on a deep generative model and the Born-Again Networks. Sci Rep 2021; 11:19127. [PMID: 34580383 PMCID: PMC8476491 DOI: 10.1038/s41598-021-98693-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 09/07/2021] [Indexed: 11/09/2022] Open
Abstract
The development of an accurate and reliable variant effect prediction tool is important for research in human genetic diseases. A large number of predictors have been developed towards this goal, yet many of these predictors suffer from the problem of data circularity. Here we present MTBAN (Mutation effect predictor using the Temporal convolutional network and the Born-Again Networks), a method for predicting the deleteriousness of variants. We apply a form of knowledge distillation technique known as the Born-Again Networks (BAN) to a previously developed deep autoregressive generative model, mutationTCN, to achieve an improved performance in variant effect prediction. As the model is fully unsupervised and trained only on the evolutionarily related sequences of a protein, it does not suffer from the problem of data circularity which is common across supervised predictors. When evaluated on a test dataset consisting of deleterious and benign human protein variants, MTBAN shows an outstanding predictive ability compared to other well-known variant effect predictors. We also offer a user-friendly web server to predict variant effects using MTBAN, freely accessible at http://mtban.kaist.ac.kr . To our knowledge, MTBAN is the first variant effect prediction tool based on a deep generative model that provides a user-friendly web server for the prediction of deleteriousness of variants.
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Affiliation(s)
- Ha Young Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Woosung Jeon
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea
| | - Dongsup Kim
- Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology, Daejeon, 34141, Republic of Korea.
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42
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Suhre K, Zaghlool S. Connecting the epigenome, metabolome and proteome for a deeper understanding of disease. J Intern Med 2021; 290:527-548. [PMID: 33904619 DOI: 10.1111/joim.13306] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/18/2021] [Accepted: 03/22/2021] [Indexed: 12/26/2022]
Abstract
Epigenome-wide association studies (EWAS) identify genes that are dysregulated by the studied clinical endpoints, thereby indicating potential new diagnostic biomarkers, drug targets and therapy options. Combining EWAS with deep molecular phenotyping, such as approaches enabled by metabolomics and proteomics, allows further probing of the underlying disease-associated pathways. For instance, methylation of the TXNIP gene is associated robustly with prevalent type 2 diabetes and further with metabolites that are short-term markers of glycaemic control. These associations reflect TXNIP's function as a glucose uptake regulator by interaction with the major glucose transporter GLUT1 and suggest that TXNIP methylation can be used as a read-out for the organism's exposure to glucose stress. Another case is the association between DNA methylation of the AHRR and F2RL3 genes with smoking and a protein that is involved in the reprogramming of the bronchial epithelium. These examples show that associations between DNA methylation and intermediate molecular traits can open new windows into how the body copes with physiological challenges. This knowledge, if carefully interpreted, may indicate novel therapy options and, together with monitoring of the methylation state of specific methylation sites, may in the future allow the early diagnosis of impending disease. It is essential for medical practitioners to recognize the potential that this field holds in translating basic research findings to clinical practice. In this review, we present recent advances in the field of EWAS with metabolomics and proteomics and discuss both the potential and the challenges of translating epigenetic associations, with deep molecular phenotypes, to biomedical applications.
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Affiliation(s)
- K Suhre
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
| | - S Zaghlool
- From the, Bioinformatics Core, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar.,Department of Biophysics and Physiology, Weill Cornell Medicine, New York, USA
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43
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Simpson DJ, Chandra T. Epigenetic age prediction. Aging Cell 2021; 20:e13452. [PMID: 34415665 PMCID: PMC8441394 DOI: 10.1111/acel.13452] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 07/21/2021] [Accepted: 07/27/2021] [Indexed: 12/14/2022] Open
Abstract
Advanced age is the main common risk factor for cancer, cardiovascular disease and neurodegeneration. Yet, more is known about the molecular basis of any of these groups of diseases than the changes that accompany ageing itself. Progress in molecular ageing research was slow because the tools predicting whether someone aged slowly or fast (biological age) were unreliable. To understand ageing as a risk factor for disease and to develop interventions, the molecular ageing field needed a quantitative measure; a clock for biological age. Over the past decade, a number of age predictors utilising DNA methylation have been developed, referred to as epigenetic clocks. While they appear to estimate biological age, it remains unclear whether the methylation changes used to train the clocks are a reflection of other underlying cellular or molecular processes, or whether methylation itself is involved in the ageing process. The precise aspects of ageing that the epigenetic clocks capture remain hidden and seem to vary between predictors. Nonetheless, the use of epigenetic clocks has opened the door towards studying biological ageing quantitatively, and new clocks and applications, such as forensics, appear frequently. In this review, we will discuss the range of epigenetic clocks available, their strengths and weaknesses, and their applicability to various scientific queries.
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Affiliation(s)
- Daniel J. Simpson
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
| | - Tamir Chandra
- MRC Human Genetics UnitMRC Institute of Genetics and Molecular MedicineUniversity of EdinburghEdinburghUK
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44
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Checknita D, Tiihonen J, Hodgins S, Nilsson KW. Associations of age, sex, sexual abuse, and genotype with monoamine oxidase a gene methylation. J Neural Transm (Vienna) 2021; 128:1721-1739. [PMID: 34424394 PMCID: PMC8536631 DOI: 10.1007/s00702-021-02403-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 08/06/2021] [Indexed: 12/16/2022]
Abstract
Epigenome-wide studies report higher methylation among women than men with decreasing levels with age. Little is known about associations of sex and age with methylation of monoamine oxidase A (MAOA). Methylation of the first exonic and partial first intronic region of MAOA has been shown to strengthen associations of interactions of MAOA-uVNTR genotypes and adversity with aggression and substance misuse. Our study examined associations of sex and age with MAOA first exon and intron methylation levels in 252 women and 157 men aged 14–73 years. Participants included adolescents recruited at a substance misuse clinic, their siblings and parents, and healthy women. Women showed ~ 50% higher levels of exonic, and ~ 15% higher intronic, methylation than men. Methylation levels were similar between younger (M = 22.7 years) and older (M = 46.1 years) participants, and stable across age. Age modified few associations of methylation levels with sex. MAOA genotypes modified few associations of methylation with sex and age. Higher methylation levels among women were not explained by genotype, nor interaction of genotype and sexual abuse. Findings were similar after adjusting for lifetime diagnoses of substance dependence (women = 24.3%; men = 34.2%). Methylation levels were higher among women who experienced sexual abuse than women who did not. Results extend on prior studies by showing that women display higher levels of methylation than men within first intronic/exonic regions of MAOA, which did not decrease with age in either sex. Findings were not conditioned by genotype nor interactions of genotype and trauma, and indicate X-chromosome inactivation.
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Affiliation(s)
- David Checknita
- Department of Neuroscience, Uppsala University, Uppsala, Sweden. .,Department of Clinical Neuroscience, Karolinska Institutet, Psychiatry Building R5:00 c/o Jari Tiihonen, Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden. .,Centre for Clinical Research, Västmanland County Council, Uppsala University, Uppsala, Sweden.
| | - Jari Tiihonen
- Department of Clinical Neuroscience, Karolinska Institutet, Psychiatry Building R5:00 c/o Jari Tiihonen, Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden.,Center for Psychiatry Research, Stockholm City Council, Stockholm, Sweden.,Department of Forensic Psychiatry, Niuvanniemi Hospital, University of Eastern Finland, Kuopio, Finland
| | - Sheilagh Hodgins
- Department of Clinical Neuroscience, Karolinska Institutet, Psychiatry Building R5:00 c/o Jari Tiihonen, Karolinska Universitetssjukhuset, 171 76, Stockholm, Sweden.,Département de Psychiatrie et Addictologie, Centre de Recherche de l'Institut Universitaire en Santé Mentale de Montréal, Université de Montréal, Montréal, QC, Canada
| | - Kent W Nilsson
- Department of Neuroscience, Uppsala University, Uppsala, Sweden.,Centre for Clinical Research, Västmanland County Council, Uppsala University, Uppsala, Sweden
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45
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Tang D, Lv M, Gao Y, Cheng H, Li K, Xu C, Geng H, Li G, Shen Q, Wang C, He X, Cao Y. Novel variants in helicase for meiosis 1 lead to male infertility due to non-obstructive azoospermia. Reprod Biol Endocrinol 2021; 19:129. [PMID: 34429122 PMCID: PMC8383409 DOI: 10.1186/s12958-021-00815-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Accepted: 08/12/2021] [Indexed: 11/30/2022] Open
Abstract
BACKGROUND Non-obstructive azoospermia (NOA) is the most severe form of male infertility; more than half of the NOA patients are idiopathic. Although many NOA risk genes have been detected, the genetic factors for NOA in majority of the patients are unknown. In addition, it is difficult to retrieve sperm from these patients despite using the microsurgical testicular sperm extraction (microTESE) method. Therefore, we conducted this genetic study to identify the potential genetic factors responsible for NOA and investigate the sperm retrieval rate of microTESE for genetically deficient NOA patients. METHODS Semen analyses, sex hormone testing, and testicular biopsy were performed to categorize the patients with NOA. The chromosome karyotypes and Y chromosome microdeletion analyses were used to exclude general genetic factors. Whole exome sequencing and Sanger sequencing were performed to identify potential genetic variants in 51 patients with NOA. Hematoxylin and eosin staining (H&E) and anti-phosphorylated H2AX were used to assess the histopathology of spermatogenesis. Quantitative real time-polymerase chain reaction, western blotting, and immunofluorescence were performed to verify the effects of gene variation on expression. RESULTS We performed whole exome sequencing in 51 NOA patients and identified homozygous helicase for meiosis 1(HFM1) variants (NM_001017975: c.3490C > T: p.Q1164X; c.3470G > A: p.C1157Y) in two patients (3.9%, 2/51). Histopathology of the testis showed that spermatogenesis was completely blocked at metaphase in these two patients carrying the HFM1 homozygous variants. In comparison with unaffected controls, we found a significant reduction in the levels of HFM1 mRNA and protein expression in the testicular tissues from these two patients. The patients were also subjected to microTESE treatment, but the sperms could not be retrieved. CONCLUSIONS This study identified novel homozygous variants of HFM1 that are responsible for spermatogenic failure and NOA, and microTESE did not aid in retrieving sperms from these patients.
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Affiliation(s)
- Dongdong Tang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Mingrong Lv
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Yang Gao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Huiru Cheng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Kuokuo Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chuan Xu
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Hao Geng
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Guanjian Li
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Qunshan Shen
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Chao Wang
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Xiaojin He
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China.
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
| | - Yunxia Cao
- Reproductive Medicine Center, Department of Obstetrics and Gynecology, the First Affiliated Hospital of Anhui Medical University, No 218 Jixi Road, Hefei, 230022, Anhui, China.
- NHC Key Laboratory of Study On Abnormal Gametes and Reproductive Tract, Anhui Medical University, No 81 Meishan Road, Hefei, 230032, Anhui, China.
- Key Laboratory of Population Health Across Life Cycle, Anhui Medical University, Ministry of Education of the People's Republic of China, No 81 Meishan Road, Hefei, 230032, Anhui, China.
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Zhao Y, Bai X, Jia X, Lu Y, Cheng W, Shu M, Zhu Y, Zhu L, Wang L, Shu Y, Song Y, Jin S. Age-related changes of human serum Sirtuin6 in adults. BMC Geriatr 2021; 21:452. [PMID: 34348649 PMCID: PMC8335874 DOI: 10.1186/s12877-021-02399-0] [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: 03/16/2021] [Accepted: 07/23/2021] [Indexed: 01/02/2023] Open
Abstract
Background Aging is a natural life process and with an aging population, age-related diseases (e.g. type 2 diabetes mellitus (T2DM), atherosclerosis-based cardiovascular diseases) are the primary mortality cause in older adults. Telomerase is often used as an aging biomarker. Detection and characterization of novel biomarkers can help in a more specific and sensitive identification of a person’s aging status. Also, this could help in age-related diseases early prevent, ultimately prolonging the population’s life span. Sirtuin 6 (Sirt6) - a member of the Sirtuins NAD+-dependent histone deacetylases family - is mainly intracellularly expressed, and is reported to be involved in the regulation of aging and aging-related diseases. Whether serum Sirt6 is correlated with aging and could be used as an aging biomarker is unknown. In the present study, we aimed to investigate the age-related Sirt6 changes in the serum of human adults. Methods Participants were divided into three groups according to age: 20–30 years (Young); 45–55 years (Middle-aged); and ≥ 70 years (Old). The Sirt6 and telomerase serum concentrations were determined by ELISA. The Sirt6 and human telomerase reverse transcriptase (hTERT) expression in vessels from amputated human lower limbs were analyzed using real-time quantitative PCR (RT-qPCR) and immunohistochemical staining. The relationships between variables were evaluated by Pearson correlation analysis. Results The Sirt6 and telomerase serum levels reduced with an increase in age. A similar tendency was observed for Sirt6 and hTERT in the vessel. Serum levels of Sirt6 were higher in females compared with males. Pearson’s regression analysis revealed that the Sirt6 serum level positively correlated with telomerase (r = 0.5743) and both were significantly negatively correlated with age (r = − 0.5830 and r = − 0.5993, respectively). Conclusions We reported a negative correlation between serum Sirt6 concentration and aging in human beings. Therefore, the Sirt6 serum level is a potential sex-specific aging marker.
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Affiliation(s)
- Ying Zhao
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Xiangli Bai
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Xiong Jia
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Yajing Lu
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Wenzhuo Cheng
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Meng Shu
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Yan Zhu
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Lin Zhu
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Li Wang
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Yan Shu
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Yi Song
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China
| | - Si Jin
- Department of Endocrinology, Institute of geriatric medicine, Liyuan Hospital, Tongji Medical College, Huazhong University of Science and Technology, 39 Lake Road, East Lake Ecological Scenic, Wuhan, 430077, Hubei Province, China.
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Salekeen R, Diaconeasa AG, Billah MM, Islam KMD. Energy Metabolism Focused Analysis of Sexual Dimorphism in Biological Aging and Hypothesized Sex-specificity in Sirtuin Dependency. Mitochondrion 2021; 60:85-100. [PMID: 34332101 DOI: 10.1016/j.mito.2021.07.007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 07/09/2021] [Accepted: 07/26/2021] [Indexed: 01/09/2023]
Abstract
The process of biological aging or senescence refers to the gradual loss of homeostasis and subsequent loss of function - leading to higher chances of mortality. Many mechanisms and driving forces have been suggested to facilitate the evolution of a molecular circuit acting as a trade-off between survival and proliferation, resulting in senescence. A major observation on biological aging and longevity in humans and model organisms is the prevalence of significant sexual divergence in the onset, mechanisms and effects of aging associated processes. In the current account, we describe possible mechanisms by which aging, sex and reproduction are evolutionarily intertwined in order to maintain systemic energy homeostasis. We also interrogate existing literature on the sexual dimorphism of genetic, cellular, metabolic, endocrine and epigenetic processes driving cellular and systemic aging. Subsequently, based on available evidence, we propose a hypothetic model of sex-limited decoupling of female longevity from sirtuins, a major family of regulator proteins of the survival-proliferation trade-off. We also provide necessary considerations to be made in order to test the hypothesis and explore the physiological and therapeutic implications of this decoupling event in male and female longevity after reaching reproductive maturity. HYPOTHESIS STATEMENT: Sirtuins provide survival benefits in a sex-nonspecific manner but the dependency on sirtuins in driving metabolic networks after reaching reproductive maturity is evolutionarily decoupled from female longevity.
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Affiliation(s)
- Rahagir Salekeen
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
| | - Amalia Gabriela Diaconeasa
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, Bucharest, Romania.
| | - Md Morsaline Billah
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
| | - Kazi Mohammed Didarul Islam
- Biotechnology and Genetic Engineering Discipline, Life Science School, Khulna University, Khulna, Bangladesh.
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Olbrecht S, Busschaert P, Qian J, Vanderstichele A, Loverix L, Van Gorp T, Van Nieuwenhuysen E, Han S, Van den Broeck A, Coosemans A, Van Rompuy AS, Lambrechts D, Vergote I. High-grade serous tubo-ovarian cancer refined with single-cell RNA sequencing: specific cell subtypes influence survival and determine molecular subtype classification. Genome Med 2021; 13:111. [PMID: 34238352 PMCID: PMC8268616 DOI: 10.1186/s13073-021-00922-x] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 06/08/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND High-grade serous tubo-ovarian cancer (HGSTOC) is characterised by extensive inter- and intratumour heterogeneity, resulting in persistent therapeutic resistance and poor disease outcome. Molecular subtype classification based on bulk RNA sequencing facilitates a more accurate characterisation of this heterogeneity, but the lack of strong prognostic or predictive correlations with these subtypes currently hinders their clinical implementation. Stromal admixture profoundly affects the prognostic impact of the molecular subtypes, but the contribution of stromal cells to each subtype has poorly been characterised. Increasing the transcriptomic resolution of the molecular subtypes based on single-cell RNA sequencing (scRNA-seq) may provide insights in the prognostic and predictive relevance of these subtypes. METHODS We performed scRNA-seq of 18,403 cells unbiasedly collected from 7 treatment-naive HGSTOC tumours. For each phenotypic cluster of tumour or stromal cells, we identified specific transcriptomic markers. We explored which phenotypic clusters correlated with overall survival based on expression of these transcriptomic markers in microarray data of 1467 tumours. By evaluating molecular subtype signatures in single cells, we assessed to what extent a phenotypic cluster of tumour or stromal cells contributes to each molecular subtype. RESULTS We identified 11 cancer and 32 stromal cell phenotypes in HGSTOC tumours. Of these, the relative frequency of myofibroblasts, TGF-β-driven cancer-associated fibroblasts, mesothelial cells and lymphatic endothelial cells predicted poor outcome, while plasma cells correlated with more favourable outcome. Moreover, we identified a clear cell-like transcriptomic signature in cancer cells, which correlated with worse overall survival in HGSTOC patients. Stromal cell phenotypes differed substantially between molecular subtypes. For instance, the mesenchymal, immunoreactive and differentiated signatures were characterised by specific fibroblast, immune cell and myofibroblast/mesothelial cell phenotypes, respectively. Cell phenotypes correlating with poor outcome were enriched in molecular subtypes associated with poor outcome. CONCLUSIONS We used scRNA-seq to identify stromal cell phenotypes predicting overall survival in HGSTOC patients. These stromal features explain the association of the molecular subtypes with outcome but also the latter's weakness of clinical implementation. Stratifying patients based on marker genes specific for these phenotypes represents a promising approach to predict prognosis or response to therapy.
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Affiliation(s)
- Siel Olbrecht
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium.
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium.
- VIB Centre for Cancer Biology, Leuven, Belgium.
| | - Pieter Busschaert
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
| | - Junbin Qian
- VIB Centre for Cancer Biology, Leuven, Belgium
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Adriaan Vanderstichele
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
| | - Liselore Loverix
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
- VIB Centre for Cancer Biology, Leuven, Belgium
| | - Toon Van Gorp
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
| | - Els Van Nieuwenhuysen
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
| | - Sileny Han
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
| | - Annick Van den Broeck
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
| | - An Coosemans
- Department of Oncology, Laboratory of Tumour Immunology and Immunotherapy, KU Leuven, Leuven, Belgium
| | - Anne-Sophie Van Rompuy
- Department of Imaging and Pathology, University Hospitals Leuven, Leuven, Belgium
- Department of Translational Cell and Tissue Research, KU Leuven, Leuven, Belgium
| | - Diether Lambrechts
- VIB Centre for Cancer Biology, Leuven, Belgium.
- Laboratory for Translational Genetics, Department of Human Genetics, KU Leuven, Leuven, Belgium.
| | - Ignace Vergote
- Department of Obstetrics and Gynaecology, Division of Gynaecological Oncology, University Hospitals Leuven, Leuven, Belgium
- Department of Oncology, Laboratory of Gynaecologic Oncology, KU Leuven, Leuven, Belgium
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Sugrue VJ, Zoller JA, Narayan P, Lu AT, Ortega-Recalde OJ, Grant MJ, Bawden CS, Rudiger SR, Haghani A, Bond DM, Hore RR, Garratt M, Sears KE, Wang N, Yang XW, Snell RG, Hore TA, Horvath S. Castration delays epigenetic aging and feminizes DNA methylation at androgen-regulated loci. eLife 2021; 10:e64932. [PMID: 34227937 PMCID: PMC8260231 DOI: 10.7554/elife.64932] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
In mammals, females generally live longer than males. Nevertheless, the mechanisms underpinning sex-dependent longevity are currently unclear. Epigenetic clocks are powerful biological biomarkers capable of precisely estimating chronological age and identifying novel factors influencing the aging rate using only DNA methylation data. In this study, we developed the first epigenetic clock for domesticated sheep (Ovis aries), which can predict chronological age with a median absolute error of 5.1 months. We have discovered that castrated male sheep have a decelerated aging rate compared to intact males, mediated at least in part by the removal of androgens. Furthermore, we identified several androgen-sensitive CpG dinucleotides that become progressively hypomethylated with age in intact males, but remain stable in castrated males and females. Comparable sex-specific methylation differences in MKLN1 also exist in bat skin and a range of mouse tissues that have high androgen receptor expression, indicating that it may drive androgen-dependent hypomethylation in divergent mammalian species. In characterizing these sites, we identify biologically plausible mechanisms explaining how androgens drive male-accelerated aging.
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Affiliation(s)
| | - Joseph Alan Zoller
- Department of Biostatistics, Fielding School of Public Health, University of California, Los AngelesLos AngelesUnited States
| | - Pritika Narayan
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - Ake T Lu
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | | | - Matthew J Grant
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - C Simon Bawden
- Livestock and Farming Systems, South Australian Research and Development InstituteRoseworthyAustralia
| | - Skye R Rudiger
- Livestock and Farming Systems, South Australian Research and Development InstituteRoseworthyAustralia
| | - Amin Haghani
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
| | - Donna M Bond
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Reuben R Hore
- Blackstone Hill Station, Becks, RD2OmakauNew Zealand
| | - Michael Garratt
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Karen E Sears
- Department of Ecology and Evolutionary Biology, UCLALos AngelesUnited States
| | - Nan Wang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (UCLA)Los AngelesUnited States
| | - Xiangdong William Yang
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California, Los Angeles (UCLA)Los AngelesUnited States
- Department of Psychiatry and Biobehavioral Sciences, David Geffen School of Medicine at UCLALos AngelesUnited States
| | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, Centre for Brain Research, The University of AucklandAucklandNew Zealand
| | - Timothy A Hore
- Department of Anatomy, University of OtagoDunedinNew Zealand
| | - Steve Horvath
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los AngelesLos AngelesUnited States
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50
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Kananen L, Marttila S. Ageing-associated changes in DNA methylation in X and Y chromosomes. Epigenetics Chromatin 2021; 14:33. [PMID: 34215292 PMCID: PMC8254238 DOI: 10.1186/s13072-021-00407-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Accepted: 06/23/2021] [Indexed: 12/24/2022] Open
Abstract
Background Ageing displays clear sexual dimorphism, evident in both morbidity and mortality. Ageing is also associated with changes in DNA methylation, but very little focus has been on the sex chromosomes, potential biological contributors to the observed sexual dimorphism. Here, we sought to identify DNA methylation changes associated with ageing in the Y and X chromosomes, by utilizing datasets available in data repositories, comprising in total of 1240 males and 1191 females, aged 14–92 years. Results In total, we identified 46 age-associated CpG sites in the male Y, 1327 age-associated CpG sites in the male X, and 325 age-associated CpG sites in the female X. The X chromosomal age-associated CpGs showed significant overlap between females and males, with 122 CpGs identified as age-associated in both sexes. Age-associated X chromosomal CpGs in both sexes were enriched in CpG islands and depleted from gene bodies and showed no strong trend towards hypermethylation nor hypomethylation. In contrast, the Y chromosomal age-associated CpGs were enriched in gene bodies, and showed a clear trend towards hypermethylation with age. Conclusions Significant overlap in X chromosomal age-associated CpGs identified in males and females and their shared features suggest that despite the uneven chromosomal dosage, differences in ageing-associated DNA methylation changes in the X chromosome are unlikely to be a major contributor of sex dimorphism in ageing. While age-associated CpGs showed good replication across datasets in the present study, only a limited set of previously reported age-associated CpGs were replicated. One contributor to the limited overlap are differences in the age range of individuals included in each data set. Further study is needed to identify biologically significant age-associated CpGs in the sex chromosomes. Supplementary Information The online version contains supplementary material available at 10.1186/s13072-021-00407-6.
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Affiliation(s)
- Laura Kananen
- Faculty of Social Sciences (Health Sciences), Tampere University, Tampere, Finland. .,Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland. .,Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm, Sweden. .,Gerontology Research Center, Tampere University, Tampere, Finland.
| | - Saara Marttila
- Gerontology Research Center, Tampere University, Tampere, Finland. .,Department of Clinical Chemistry, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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