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Miranda Furtado CL, Hansen M, Kogure GS, Ribeiro VB, Taylor N, Racy Soares M, Ferriani RA, Aston KI, Jenkins T, dos Reis RM. Resistance and aerobic training increases genome-wide DNA methylation in women with polycystic ovary syndrome. Epigenetics 2024; 19:2305082. [PMID: 38245873 PMCID: PMC10802204 DOI: 10.1080/15592294.2024.2305082] [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: 07/21/2023] [Accepted: 01/09/2024] [Indexed: 01/23/2024] Open
Abstract
Physical activity is a first-line treatment for polycystic ovary syndrome (PCOS). Resistance or aerobic exercise improves metabolic complications, reproductive outcomes, and quality of life in PCOS. DNA methylation reprogramming during exercise may be the major modifier behind these changes. We sought to evaluate genome-wide DNA methylation changes after supervised resistance and aerobic exercise in women with PCOS. Exercises were performed in 56 women with PCOS (resistance, n = 30; aerobic, n = 26), for 16 weeks (wks), three times per week, in 50-minute to one-hour sessions. Anthropometric indices and hormonal and metabolic parameters were measured before and after training. Genome-wide leukocyte DNA methylation was analysed by Infinium Human MethylationEPIC 850K BeadChip microarrays (Illumina). Both resistance and aerobic exercise improved anthropometric indices, metabolic dysfunction, and hyperandrogenism in PCOS after the training programme, but no differences were observed between the two exercises. Resistance and aerobic exercise increased genome-wide DNA methylation, although resistance changed every category in the CpG island context (islands, shores, shelve, and open sea), whereas aerobic exercise altered CpG shores and the open sea. Using a stringent FDR (>40), 6 significantly differentially methylated regions (DMRs) were observed in the resistance exercise cohort and 14 DRMs in the aerobic cohort, all of which were hypermethylated. The increase in genome-wide DNA methylation may be related to the metabolic and hormonal changes observed in PCOS after resistance and aerobic exercise. Since the mammalian genome is hypermethylated globally to prevent genomic instability and ageing, resistance and aerobic exercise may promote health and longevity through environmentally induced epigenetic changes.
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Affiliation(s)
- Cristiana Libardi Miranda Furtado
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
- Experimental Biology Center, Graduate Program in Medical Sciences, University of Fortaleza, Fortaleza, Ceará, Brazil
- Drug Research and Development Center, Postgraduate Program in Translational Medicine, Federal University of Ceará, Fortaleza, Brazil
| | - Megan Hansen
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Gislaine Satyko Kogure
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Victor Barbosa Ribeiro
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Nathanael Taylor
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Murilo Racy Soares
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Rui Alberto Ferriani
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
| | - Kenneth Ivan Aston
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Timothy Jenkins
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
- Department of Surgery, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Rosana Maria dos Reis
- Department of Gynecology and Obstetrics, Ribeirao Preto Medical School, University of Sao Paulo, Ribeirao Preto, Brazil
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2
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Woo SJ, Han JY. Epigenetic programming of chicken germ cells: a comparative review. Poult Sci 2024; 103:103977. [PMID: 38970845 PMCID: PMC11269908 DOI: 10.1016/j.psj.2024.103977] [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: 03/12/2024] [Revised: 05/26/2024] [Accepted: 06/10/2024] [Indexed: 07/08/2024] Open
Abstract
Chicken embryos serve as an important model for investigating germ cells due to their ease of accessibility and manipulation within the egg. Understanding the development of germ cells is particularly crucial, as they are the only cell types capable of transmitting genetic information to the next generation. Therefore, gene expression regulation in germ cells is important for genomic function. Epigenetic programming is a crucial biological process for the regulation of gene expression without altering the genome sequence. Although epigenetic programming is evolutionarily conserved, several differences between chickens and mammals have been revealed. In this review, we compared the epigenetic regulation of germ cells in chickens and mammals (mainly mice as a representative species). In mammals, migrating primordial germ cells (precursors for germ cells [PGCs]) undergo global DNA demethylation and persist until sexual differentiation, while in chickens, DNA is demethylated until reaching the gonad but remethylated when sexually differentiated. Prospermatogonia is methylated at the onset of mitotic arrest in mammals, while DNA is demethylated at mitotic arrest in chickens. Furthermore, genomic imprinting and inactivation of sex chromosomes are differentially regulated through DNA methylation in chickens and mammals. Chickens and mammals exhibit different patterns of histone modifications during germ cell development, and non-coding RNA, which is not involved in PGC differentiation in mice, plays an important role in chicken PGC development. Additionally, several chicken-specific non-coding RNAs have been identified. In conclusion, we summarized current knowledge of epigenetic gene regulation of chicken germ cells, comparing that of mammals, and highlighted notable differences between them.
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Affiliation(s)
- Seung Je Woo
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jae Yong Han
- Department of Agricultural Biotechnology and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.
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3
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Blanton LV, San Roman AK, Wood G, Buscetta A, Banks N, Skaletsky H, Godfrey AK, Pham TT, Hughes JF, Brown LG, Kruszka P, Lin AE, Kastner DL, Muenke M, Page DC. Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types. CELL GENOMICS 2024:100628. [PMID: 39111319 DOI: 10.1016/j.xgen.2024.100628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2024] [Revised: 05/11/2024] [Accepted: 07/12/2024] [Indexed: 08/10/2024]
Abstract
Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression. We tested these findings in vivo. Linear modeling of CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes revealed 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo. Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro; autosomal responses to Xi and/or Y dosage were largely cell-type specific (∼2.6-fold more variation than sex-chromosomal responses). Targets of the sex-chromosomal transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro. We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable, yet they modulate autosomal and Xa genes in a cell-type-specific fashion.
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Affiliation(s)
| | | | - Geryl Wood
- Inflammatory Disease Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ashley Buscetta
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Nicole Banks
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA; Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD 20892, USA
| | - Helen Skaletsky
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | | | - Thao T Pham
- Whitehead Institute, Cambridge, MA 02142, USA
| | | | - Laura G Brown
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA
| | - Paul Kruszka
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Angela E Lin
- Genetics Unit, MassGeneral for Children, Boston, MA 02114, USA
| | - Daniel L Kastner
- Inflammatory Disease Section, Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Maximilian Muenke
- Medical Genetics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David C Page
- Whitehead Institute, Cambridge, MA 02142, USA; Howard Hughes Medical Institute, Whitehead Institute, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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4
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Stanojević D, Li Z, Bakić S, Foo R, Šikić M. Rockfish: A transformer-based model for accurate 5-methylcytosine prediction from nanopore sequencing. Nat Commun 2024; 15:5580. [PMID: 38961062 PMCID: PMC11222435 DOI: 10.1038/s41467-024-49847-0] [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: 09/24/2023] [Accepted: 06/19/2024] [Indexed: 07/05/2024] Open
Abstract
DNA methylation plays an important role in various biological processes, including cell differentiation, ageing, and cancer development. The most important methylation in mammals is 5-methylcytosine mostly occurring in the context of CpG dinucleotides. Sequencing methods such as whole-genome bisulfite sequencing successfully detect 5-methylcytosine DNA modifications. However, they suffer from the serious drawbacks of short read lengths and might introduce an amplification bias. Here we present Rockfish, a deep learning algorithm that significantly improves read-level 5-methylcytosine detection by using Nanopore sequencing. Rockfish is compared with other methods based on Nanopore sequencing on R9.4.1 and R10.4.1 datasets. There is an increase in the single-base accuracy and the F1 measure of up to 5 percentage points on R.9.4.1 datasets, and up to 0.82 percentage points on R10.4.1 datasets. Moreover, Rockfish shows a high correlation with whole-genome bisulfite sequencing, requires lower read depth, and achieves higher confidence in biologically important regions such as CpG-rich promoters while being computationally efficient. Its superior performance in human and mouse samples highlights its versatility for studying 5-methylcytosine methylation across varied organisms and diseases. Finally, its adaptable architecture ensures compatibility with new versions of pores and chemistry as well as modification types.
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Affiliation(s)
- Dominik Stanojević
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia
| | - Zhe Li
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
| | - Sara Bakić
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore
- School of Computing, National University of Singapore, Singapore, Singapore
| | - Roger Foo
- Yong Loo Lin School of Medicine, National University of Singapore, Singapore, Singapore
| | - Mile Šikić
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore, Singapore.
- Faculty of Electrical Engineering and Computing, University of Zagreb, Zagreb, Croatia.
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5
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Forsyth KS, Jiwrajka N, Lovell CD, Toothacre NE, Anguera MC. The conneXion between sex and immune responses. Nat Rev Immunol 2024; 24:487-502. [PMID: 38383754 PMCID: PMC11216897 DOI: 10.1038/s41577-024-00996-9] [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] [Accepted: 01/18/2024] [Indexed: 02/23/2024]
Abstract
There are notable sex-based differences in immune responses to pathogens and self-antigens, with female individuals exhibiting increased susceptibility to various autoimmune diseases, and male individuals displaying preferential susceptibility to some viral, bacterial, parasitic and fungal infections. Although sex hormones clearly contribute to sex differences in immune cell composition and function, the presence of two X chromosomes in female individuals suggests that differential gene expression of numerous X chromosome-linked immune-related genes may also influence sex-biased innate and adaptive immune cell function in health and disease. Here, we review the sex differences in immune system composition and function, examining how hormones and genetics influence the immune system. We focus on the genetic and epigenetic contributions responsible for altered X chromosome-linked gene expression, and how this impacts sex-biased immune responses in the context of pathogen infection and systemic autoimmunity.
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Affiliation(s)
- Katherine S Forsyth
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Nikhil Jiwrajka
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
- Division of Rheumatology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Claudia D Lovell
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Natalie E Toothacre
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Montserrat C Anguera
- Department of Biomedical Sciences, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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6
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Ko YK, Chi S, Nam GH, Baek KW, Ahn K, Ahn Y, Kang J, Lee MS, Gim JA. Epigenome-wide Association Study for Tic Disorders in Children: A Preliminary Study in Korean Population. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE : THE OFFICIAL SCIENTIFIC JOURNAL OF THE KOREAN COLLEGE OF NEUROPSYCHOPHARMACOLOGY 2024; 22:295-305. [PMID: 38627076 PMCID: PMC11024688 DOI: 10.9758/cpn.23.1099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/24/2023] [Accepted: 11/24/2023] [Indexed: 04/20/2024]
Abstract
Objective : Tic disorders can affect the quality of life in both childhood and adolescence. Many factors are involved in the etiology of tic disorders, and the genetic and epigenetic factors of tic disorders are considered complex and heterogeneous. Methods : In this study, the differentially methylated regions (DMRs) between normal controls (n = 24; aged 6-15; 7 females) and patients with tic disorders (n = 16; aged 6-15; 5 females) were analyzed. We performed an epigenome-wide association study of tic disorders in Korean children. The tics were assessed using Yale Global Tic Severity Scale. The DNA methylation data consisted of 726,945 cytosine phosphate guanine (CpG) sites, assessed using the Illumina Infinium MethylationEPIC (850k) BeadChip. The DNA methylation data of the 40 participants were retrieved, and DMRs between the four groups based on sex and tic disorder were identified. From 28 male and 16 female samples, 37 and 38 DMRs were identified, respectively. We analyzed the enriched terms and visualized the network, heatmap, and upset plot. Results : In male, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed hypomethylated patterns in the ligand, receptor, and second signal transductors of the PI3K-Akt and MAPK signaling pathway (most cells were indicated as green color), and in female, the opposite patterns were revealed (most cells were indicated as red color). Five mental disorder-related enriched terms were identified in the network analysis. Conclusion : Here, we provide insights into the epigenetic mechanisms of tic disorders. Abnormal DNA methylation patterns are associated with mental disorder-related symptoms.
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Affiliation(s)
- Young Kyung Ko
- Division of Pulmonary, Allergy and Critical Care Medicine, Department of Internal Medicine, Korea University Guro Hospital, Seoul, Korea
| | - Suhyuk Chi
- Department of Psychiatry, Korea University Guro Hospital, Seoul, Korea
| | - Gyu-Hwi Nam
- PhileKorea Technology Co. Ltd., Daejeon, Korea
| | - Kyung-Wan Baek
- Department of Physical Education, Gyeongsang National University, Jinju, Korea
| | | | | | - June Kang
- Department of Brain and Cognitive Engineering, Korea University, Seoul, Korea
| | - Moon-Soo Lee
- Department of Psychiatry, Korea University Guro Hospital, Seoul, Korea
| | - Jeong-An Gim
- Department of Medical Science, Soonchunhyang University, Asan, Korea
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7
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Nagata N, Kurosaka H, Higashi K, Yamaguchi M, Yamamoto S, Inubushi T, Nagata M, Ishihara Y, Yonei A, Miyashita Y, Asano Y, Sakai N, Sakata Y, Kawabata S, Yamashiro T. Characteristic craniofacial defects associated with a novel USP9X truncation mutation. Hum Genome Var 2024; 11:21. [PMID: 38755172 PMCID: PMC11099082 DOI: 10.1038/s41439-024-00277-w] [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: 01/29/2024] [Revised: 03/12/2024] [Accepted: 03/25/2024] [Indexed: 05/18/2024] Open
Abstract
Germline loss-of-function mutations in USP9X have been reported to cause a wide spectrum of congenital anomalies. Here, we report a Japanese girl with a novel heterozygous nonsense mutation in USP9X who exhibited intellectual disability with characteristic craniofacial abnormalities, including hypotelorism, brachycephaly, hypodontia, micrognathia, severe dental crowding, and an isolated submucous cleft palate. Our findings provide further evidence that disruptions in USP9X contribute to a broad range of congenital craniofacial abnormalities.
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Affiliation(s)
- Namiki Nagata
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Hiroshi Kurosaka
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan.
| | - Kotaro Higashi
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
- Department of Removable Prosthodontics and Gerodontology, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Masaya Yamaguchi
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
- Bioinformatics Research Unit, Osaka University Graduate School of Dentistry, Suita, Japan
- Bioinformatics Center, Research Institute for Microbial Diseases, Osaka University, Suita, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Suita, Japan
| | - Sayuri Yamamoto
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Toshihiro Inubushi
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
| | - Miho Nagata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yasuki Ishihara
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Ayumi Yonei
- Department of Genetic Counseling, Osaka University Hospital, Osaka, Japan
| | - Yohei Miyashita
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Yoshihiro Asano
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Norio Sakai
- Child Healthcare and Genetic Science Laboratory, Division of Health Sciences, Osaka University Graduate School of Medicine, Suita, Osaka, Japan
| | - Yasushi Sakata
- Department of Cardiovascular Medicine, Osaka University Graduate School of Medicine, Suita, Japan
| | - Shigetada Kawabata
- Department of Microbiology, Osaka University Graduate School of Dentistry, Suita, Japan
- Center for Infectious Diseases Education and Research, Osaka University, Suita, Japan
| | - Takashi Yamashiro
- Department of Orthodontics and Dentofacial Orthopedics, Osaka University Graduate School of Dentistry, Suita, Japan
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8
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Ocaña-Paredes B, Rivera-Orellana S, Ramírez-Sánchez D, Montalvo-Guerrero J, Freire MP, Espinoza-Ferrao S, Altamirano-Colina A, Echeverría-Espinoza P, Ramos-Medina MJ, Echeverría-Garcés G, Granda-Moncayo D, Jácome-Alvarado A, Andrade MG, López-Cortés A. The pharmacoepigenetic paradigm in cancer treatment. Front Pharmacol 2024; 15:1381168. [PMID: 38720770 PMCID: PMC11076712 DOI: 10.3389/fphar.2024.1381168] [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: 02/02/2024] [Accepted: 04/11/2024] [Indexed: 05/12/2024] Open
Abstract
Epigenetic modifications, characterized by changes in gene expression without altering the DNA sequence, play a crucial role in the development and progression of cancer by significantly influencing gene activity and cellular function. This insight has led to the development of a novel class of therapeutic agents, known as epigenetic drugs. These drugs, including histone deacetylase inhibitors, histone acetyltransferase inhibitors, histone methyltransferase inhibitors, and DNA methyltransferase inhibitors, aim to modulate gene expression to curb cancer growth by uniquely altering the epigenetic landscape of cancer cells. Ongoing research and clinical trials are rigorously evaluating the efficacy of these drugs, particularly their ability to improve therapeutic outcomes when used in combination with other treatments. Such combination therapies may more effectively target cancer and potentially overcome the challenge of drug resistance, a significant hurdle in cancer therapy. Additionally, the importance of nutrition, inflammation control, and circadian rhythm regulation in modulating drug responses has been increasingly recognized, highlighting their role as critical modifiers of the epigenetic landscape and thereby influencing the effectiveness of pharmacological interventions and patient outcomes. Epigenetic drugs represent a paradigm shift in cancer treatment, offering targeted therapies that promise a more precise approach to treating a wide spectrum of tumors, potentially with fewer side effects compared to traditional chemotherapy. This progress marks a step towards more personalized and precise interventions, leveraging the unique epigenetic profiles of individual tumors to optimize treatment strategies.
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Affiliation(s)
- Belén Ocaña-Paredes
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - David Ramírez-Sánchez
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | - María Paula Freire
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - María José Ramos-Medina
- German Cancer Research Center (DKFZ), Faculty of Biosciences, Heidelberg University, Heidelberg, Germany
| | - Gabriela Echeverría-Garcés
- Centro de Referencia Nacional de Genómica, Secuenciación y Bioinformática, Instituto Nacional de Investigación en Salud Pública “Leopoldo Izquieta Pérez”, Quito, Ecuador
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Santiago, Chile
| | | | - Andrea Jácome-Alvarado
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - María Gabriela Andrade
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Andrés López-Cortés
- Cancer Research Group (CRG), Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
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9
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Morgan R, Loh E, Singh D, Mendizabal I, Yi SV. DNA methylation differences between the female and male X chromosomes in human brain. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.04.16.589778. [PMID: 38659923 PMCID: PMC11042362 DOI: 10.1101/2024.04.16.589778] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/26/2024]
Abstract
The mechanisms of X chromosome inactivation suggest fundamental epigenetic differences between the female and male X chromosomes. However, DNA methylation studies often exclude the X chromosomes. In addition, many previous studies relied on techniques that examine non-randomly selected subsets of positions such as array-based methods, rather than assessing the whole X chromosome. Consequently, our understanding of X chromosome DNA methylation lags behind that of autosomes. Here we addressed this gap of knowledge by studying X chromosome DNA methylation using 89 whole genome bisulfite sequencing (WGBS) maps from neurons and oligodendrocytes. Using this unbiased and comprehensive data, we show that DNA methylation of the female X chromosomes is globally reduced (hypomethylated) across the entire chromosome compared to the male X chromosomes and autosomes. On the other hand, the majority of X-linked promoters were more highly methylated (hypermethylated) in females compared to males, consistent with the role of DNA methylation in X chromosome inactivation and dosage compensation. Remarkably, hypermethylation of female X promoters was limited to a group of previously lowly methylated promoters. The other group of highly methylated promoters were both hyper- and hypo-methylated in females with no obvious association with gene expression. Therefore, X chromosome inactivation by DNA methylation was exclusive to a subset of promoters with distinctive epigenetic feature. Apart from this group of promoters, differentially methylated regions in the female and male X chromosomes were dominated by female hypomethylation. Our study furthers the understanding of X-chromosome dosage regulation by DNA methylation on the chromosomal level as well as on individual gene level.
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Affiliation(s)
- Robert Morgan
- College of Computing, Georgia Institute of Technology, Atlanta, GA 30332
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Current address: Arbor Biotechnologies, Cambridge, MA, 02140
| | - Eddie Loh
- Department of Ecology and Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara
| | - Devika Singh
- School of Biological Sciences, Institute for Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA 30332
- Current address: Foundation Medicine, Inc., Boston, MA, 02210
| | - Isabel Mendizabal
- Center for Cooperative Research in Biosciences (CIC bioGUNE), Basque Research and Technology Alliance (BRTA), Bizkaia Technology Park, Building 801A, 48160, Derio, Spain
- Ikerbasque, Basque Foundation for Science, Bilbao, Spain
- Translational prostate cancer Research lab, CIC bioGUNE-Basurto, Biocruces Bizkaia Health Research Institute, Derio, Spain
| | - Soojin V Yi
- Department of Ecology and Evolution and Marine Biology, Department of Molecular, Cellular and Developmental Biology, Neuroscience Research Institute, University of California, Santa Barbara
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10
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Hattori A, Seki A, Inaba N, Nakabayashi K, Takeda K, Tatsusmi K, Naiki Y, Nakamura A, Ishiwata K, Matsumoto K, Nasu M, Okamura K, Michigami T, Katoh-Fukui Y, Umezawa A, Ogata T, Kagami M, Fukami M. Expression levels and DNA methylation profiles of the growth gene SHOX in cartilage tissues and chondrocytes. Sci Rep 2024; 14:8069. [PMID: 38580675 PMCID: PMC10997625 DOI: 10.1038/s41598-024-58530-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 04/01/2024] [Indexed: 04/07/2024] Open
Abstract
All attempts to identify male-specific growth genes in humans have failed. This study aimed to clarify why men are taller than women. Microarray-based transcriptome analysis of the cartilage tissues of four adults and chondrocytes of 12 children showed that the median expression levels of SHOX, a growth gene in the pseudoautosomal region (PAR), were higher in male samples than in female samples. Male-dominant SHOX expression was confirmed by quantitative RT-PCR for 36 cartilage samples. Reduced representation bisulfite sequencing of four cartilage samples revealed sex-biased DNA methylation in the SHOX-flanking regions, and pyrosequencing of 22 cartilage samples confirmed male-dominant DNA methylation at the CpG sites in the SHOX upstream region and exon 6a. DNA methylation indexes of these regions were positively correlated with SHOX expression levels. These results, together with prior findings that PAR genes often exhibit male-dominant expression, imply that the relatively low SHOX expression in female cartilage tissues reflects the partial spread of X chromosome inactivation into PAR. Altogether, this study provides the first indication that sex differences in height are ascribed, at least in part, to the sex-dependent epigenetic regulation of SHOX. Our findings deserve further validation.
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Affiliation(s)
- Atsushi Hattori
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Atsuhito Seki
- Department of Orthopaedic Surgery, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Naoto Inaba
- Department of Orthopaedic Surgery, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Kazuhiko Nakabayashi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kazue Takeda
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kuniko Tatsusmi
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Yasuhiro Naiki
- Division of Endocrinology and Metabolism, National Medical Center for Children and Mothers, Tokyo, 157-8535, Japan
| | - Akie Nakamura
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Keisuke Ishiwata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Michiyo Nasu
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Kohji Okamura
- Department of Systems BioMedicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Toshimi Michigami
- Department of Bone and Mineral Research, Research Institute, Osaka Women's and Children's Hospital, Osaka Prefectural Hospital Organization, Izumi, 594-1101, Japan
| | - Yuko Katoh-Fukui
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Akihiro Umezawa
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Tsutomu Ogata
- Department of Pediatrics, Hamamatsu University School of Medicine, Hamamatsu, 431-3192, Japan
- Department of Pediatrics, Hamamatsu Medical Center, Hamamatsu, 432-8580, Japan
| | - Masayo Kagami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan
| | - Maki Fukami
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
- Division of Diversity Research, National Research Institute for Child Health and Development, Tokyo, 157-8535, Japan.
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11
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Roussos P, Ma Y, Girdhar K, Hoffman G, Fullard J, Bendl J. Sex differences in brain cell-type specific chromatin accessibility in schizophrenia. RESEARCH SQUARE 2024:rs.3.rs-4158509. [PMID: 38645177 PMCID: PMC11030506 DOI: 10.21203/rs.3.rs-4158509/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
Our understanding of the sex-specific role of the non-coding genome in serious mental illness remains largely incomplete. To address this gap, we explored sex differences in 1,393 chromatin accessibility profiles, derived from neuronal and non-neuronal nuclei of two distinct cortical regions from 234 cases with serious mental illness and 235 controls. We identified sex-specific enhancer-promoter interactions and showed that they regulate genes involved in X-chromosome inactivation (XCI). Examining chromosomal conformation allowed us to identify sex-specific cis- and trans-regulatory domains (CRDs and TRDs). Co-localization of sex-specific TRDs with schizophrenia common risk variants pinpointed male-specific regulatory regions controlling a number of metabolic pathways. Additionally, enhancers from female-specific TRDs were found to regulate two genes known to escape XCI, (XIST and JPX), underlying the importance of TRDs in deciphering sex differences in schizophrenia. Overall, these findings provide extensive characterization of sex differences in the brain epigenome and disease-associated regulomes.
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Affiliation(s)
| | - Yixuan Ma
- Icahn School of Medicine at Mount Sinai
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12
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Blanton LV, San Roman AK, Wood G, Buscetta A, Banks N, Skaletsky H, Godfrey AK, Pham TT, Hughes JF, Brown LG, Kruszka P, Lin AE, Kastner DL, Muenke M, Page DC. Stable and robust Xi and Y transcriptomes drive cell-type-specific autosomal and Xa responses in vivo and in vitro in four human cell types. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.18.585578. [PMID: 38562807 PMCID: PMC10983990 DOI: 10.1101/2024.03.18.585578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Recent in vitro studies of human sex chromosome aneuploidy showed that the Xi ("inactive" X) and Y chromosomes broadly modulate autosomal and Xa ("active" X) gene expression in two cell types. We tested these findings in vivo in two additional cell types. Using linear modeling in CD4+ T cells and monocytes from individuals with one to three X chromosomes and zero to two Y chromosomes, we identified 82 sex-chromosomal and 344 autosomal genes whose expression changed significantly with Xi and/or Y dosage in vivo . Changes in sex-chromosomal expression were remarkably constant in vivo and in vitro across all four cell types examined. In contrast, autosomal responses to Xi and/or Y dosage were largely cell-type-specific, with up to 2.6-fold more variation than sex-chromosomal responses. Targets of the X- and Y-encoded transcription factors ZFX and ZFY accounted for a significant fraction of these autosomal responses both in vivo and in vitro . We conclude that the human Xi and Y transcriptomes are surprisingly robust and stable across the four cell types examined, yet they modulate autosomal and Xa genes - and cell function - in a cell-type-specific fashion. These emerging principles offer a foundation for exploring the wide-ranging regulatory roles of the sex chromosomes across the human body.
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13
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Hauth A, Panten J, Kneuss E, Picard C, Servant N, Rall I, Pérez-Rico YA, Clerquin L, Servaas N, Villacorta L, Jung F, Luong C, Chang HY, Zaugg JB, Stegle O, Odom DT, Loda A, Heard E. Escape from X inactivation is directly modulated by levels of Xist non-coding RNA. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.02.22.581559. [PMID: 38559194 PMCID: PMC10979913 DOI: 10.1101/2024.02.22.581559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
In placental females, one copy of the two X chromosomes is largely silenced during a narrow developmental time window, in a process mediated by the non-coding RNA Xist1. Here, we demonstrate that Xist can initiate X-chromosome inactivation (XCI) well beyond early embryogenesis. By modifying its endogenous level, we show that Xist has the capacity to actively silence genes that escape XCI both in neuronal progenitor cells (NPCs) and in vivo, in mouse embryos. We also show that Xist plays a direct role in eliminating TAD-like structures associated with clusters of escapee genes on the inactive X chromosome, and that this is dependent on Xist's XCI initiation partner, SPEN2. We further demonstrate that Xist's function in suppressing gene expression of escapees and topological domain formation is reversible for up to seven days post-induction, but that sustained Xist up-regulation leads to progressively irreversible silencing and CpG island DNA methylation of facultative escapees. Thus, the distinctive transcriptional and regulatory topologies of the silenced X chromosome is actively, directly - and reversibly - controlled by Xist RNA throughout life.
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Affiliation(s)
- Antonia Hauth
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Collaboration for joint PhD degree between EMBL and Heidelberg University, Germany
| | - Jasper Panten
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
| | - Emma Kneuss
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Christel Picard
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Present address: Institute of Molecular Genetics of Montpellier University of Montpellier, CNRS, 34090 Montpellier, France
| | - Nicolas Servant
- Bioinformatics and Computational Systems Biology of Cancer, INSERM U900, Paris 75005, France
| | - Isabell Rall
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Present address: Institute of Human Biology (IHB), Roche Innovation Center Basel, 4070 Basel, Switzerland
| | - Yuvia A Pérez-Rico
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Lena Clerquin
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Nila Servaas
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
| | - Laura Villacorta
- European Molecular Biology Laboratory, Genomics Core Facility, 69117 Heidelberg, Germany
| | - Ferris Jung
- European Molecular Biology Laboratory, Genomics Core Facility, 69117 Heidelberg, Germany
| | - Christy Luong
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University, Stanford, CA 94305, USA
- Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Judith B Zaugg
- European Molecular Biology Laboratory, Structural and Computational Biology Unit, 69117 Heidelberg, Germany
- Molecular Medicine Partnership Unit, EMBL-University of Heidelberg, Heidelberg, Germany
| | - Oliver Stegle
- European Molecular Biology Laboratory, Genome Biology Unit, 69117 Heidelberg, Germany
- Division of Computational Genomics and Systems Genetics, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
| | - Duncan T Odom
- Division of Regulatory Genomics and Cancer Evolution, German Cancer Research Centre (DKFZ), 69120, Heidelberg, Germany
- Faculty of Biosciences, Heidelberg University, 69117, Heidelberg, Germany
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge, UK
| | - Agnese Loda
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
| | - Edith Heard
- European Molecular Biology Laboratory, Directors' Research, 69117 Heidelberg, Germany
- Collège de France, Paris 75005, France
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14
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Zhang H, Mañán-Mejías PM, Miles HN, Putnam AA, MacGillivray LR, Ricke WA. DDX3X and Stress Granules: Emerging Players in Cancer and Drug Resistance. Cancers (Basel) 2024; 16:1131. [PMID: 38539466 PMCID: PMC10968774 DOI: 10.3390/cancers16061131] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2024] [Revised: 03/09/2024] [Accepted: 03/11/2024] [Indexed: 05/02/2024] Open
Abstract
The DEAD (Asp-Glu-Ala-Asp)-box helicase 3 X-linked (DDX3X) protein participates in many aspects of mRNA metabolism and stress granule (SG) formation. DDX3X has also been associated with signal transduction and cell cycle regulation that are important in maintaining cellular homeostasis. Malfunctions of DDX3X have been implicated in multiple cancers, including brain cancer, leukemia, prostate cancer, and head and neck cancer. Recently, literature has reported SG-associated cancer drug resistance, which correlates with a negative disease prognosis. Based on the connections between DDX3X, SG formation, and cancer pathology, targeting DDX3X may be a promising direction for cancer therapeutics development. In this review, we describe the biological functions of DDX3X in terms of mRNA metabolism, signal transduction, and cell cycle regulation. Furthermore, we summarize the contributions of DDX3X in SG formation and cellular stress adaptation. Finally, we discuss the relationships of DDX3X, SG, and cancer drug resistance, and discuss the current research progress of several DDX3X inhibitors for cancer treatment.
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Affiliation(s)
- Han Zhang
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Paula M. Mañán-Mejías
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Hannah N. Miles
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
| | - Andrea A. Putnam
- Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
| | | | - William A. Ricke
- Division of Pharmaceutical Sciences, School of Pharmacy, University of Wisconsin-Madison, Madison, WI 53705, USA
- Department of Urology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
- George M. O’Brien Urology Research Center of Excellence, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI 53705, USA
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15
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Rosa E Silva I, Smetana JHC, de Oliveira JF. A comprehensive review on DDX3X liquid phase condensation in health and neurodevelopmental disorders. Int J Biol Macromol 2024; 259:129330. [PMID: 38218270 DOI: 10.1016/j.ijbiomac.2024.129330] [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: 11/22/2023] [Revised: 12/22/2023] [Accepted: 01/06/2024] [Indexed: 01/15/2024]
Abstract
DEAD-box helicases are global regulators of liquid-liquid phase separation (LLPS), a process that assembles membraneless organelles inside cells. An outstanding member of the DEAD-box family is DDX3X, a multi-functional protein that plays critical roles in RNA metabolism, including RNA transcription, splicing, nucleocytoplasmic export, and translation. The diverse functions of DDX3X result from its ability to bind and remodel RNA in an ATP-dependent manner. This capacity enables the protein to act as an RNA chaperone and an RNA helicase, regulating ribonucleoprotein complex assembly. DDX3X and its orthologs from mouse, yeast (Ded1), and C. elegans (LAF-1) can undergo LLPS, driving the formation of neuronal granules, stress granules, processing bodies or P-granules. DDX3X has been related to several human conditions, including neurodevelopmental disorders, such as intellectual disability and autism spectrum disorder. Although the research into the pathogenesis of aberrant biomolecular condensation in neurodegenerative diseases is increasing rapidly, the role of LLPS in neurodevelopmental disorders is underexplored. This review summarizes current findings relevant for DDX3X phase separation in neurodevelopment and examines how disturbances in the LLPS process can be related to neurodevelopmental disorders.
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Affiliation(s)
- Ivan Rosa E Silva
- Brazilian Biosciences National Laboratory, Center for Research in Energy and Materials, Campinas, SP, Brazil
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16
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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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17
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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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18
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Achom M, Sadagopan A, Bao C, McBride F, Xu Q, Konda P, Tourdot RW, Li J, Nakhoul M, Gallant DS, Ahmed UA, O’Toole J, Freeman D, Mary Lee GS, Hecht JL, Kauffman EC, Einstein DJ, Choueiri TK, Zhang CZ, Viswanathan SR. A genetic basis for cancer sex differences revealed in Xp11 translocation renal cell carcinoma. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.04.552029. [PMID: 37577497 PMCID: PMC10418269 DOI: 10.1101/2023.08.04.552029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Xp11 translocation renal cell carcinoma (tRCC) is a female-predominant kidney cancer driven by translocations between the TFE3 gene on chromosome Xp11.2 and partner genes located on either chrX or on autosomes. The rearrangement processes that underlie TFE3 fusions, and whether they are linked to the female sex bias of this cancer, are largely unexplored. Moreover, whether oncogenic TFE3 fusions arise from both the active and inactive X chromosomes in females remains unknown. Here we address these questions by haplotype-specific analyses of whole-genome sequences of 29 tRCC samples from 15 patients and by re-analysis of 145 published tRCC whole-exome sequences. We show that TFE3 fusions universally arise as reciprocal translocations with minimal DNA loss or insertion at paired break ends. Strikingly, we observe a near exact 2:1 female:male ratio in TFE3 fusions arising via X:autosomal translocation (but not via X inversion), which accounts for the female predominance of tRCC. This 2:1 ratio is at least partially attributable to oncogenic fusions involving the inactive X chromosome and is accompanied by partial re-activation of silenced chrX genes on the rearranged chromosome. Our results highlight how somatic alterations involving the X chromosome place unique constraints on tumor initiation and exemplify how genetic rearrangements of the sex chromosomes can underlie cancer sex differences.
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Affiliation(s)
- Mingkee Achom
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Ananthan Sadagopan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Chunyang Bao
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Fiona McBride
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Qingru Xu
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Prathyusha Konda
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Richard W. Tourdot
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Biomedical Informatics, Blavatnik Institute, Harvard Medical School; Boston, MA, USA
| | - Jiao Li
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
| | - Maria Nakhoul
- Department of Informatics & Analytics, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Daniel S. Gallant
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Usman Ali Ahmed
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jillian O’Toole
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Dory Freeman
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Gwo-Shu Mary Lee
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
| | - Jonathan L. Hecht
- Department of Pathology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Eric C Kauffman
- Department of Urology, Roswell Park Comprehensive Cancer Center; Buffalo, New York, USA
| | - David J Einstein
- Division of Medical Oncology, Beth Israel Deaconess Medical Center; Boston, MA, USA
| | - Toni K. Choueiri
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
| | - Cheng-Zhong Zhang
- Department of Data Science, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Pathology, Brigham and Women’s Hospital; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
| | - Srinivas R. Viswanathan
- Department of Medical Oncology, Dana-Farber Cancer Institute; Boston, MA, USA
- Department of Medicine, Harvard Medical School; Boston, MA, USA
- Cancer Program, Broad Institute of MIT and Harvard; Cambridge, MA, USA
- Department of Medicine, Brigham and Women’s Hospital; Boston, MA, USA
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19
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Khramtsova EA, Wilson MA, Martin J, Winham SJ, He KY, Davis LK, Stranger BE. Quality control and analytic best practices for testing genetic models of sex differences in large populations. Cell 2023; 186:2044-2061. [PMID: 37172561 PMCID: PMC10266536 DOI: 10.1016/j.cell.2023.04.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Revised: 01/31/2023] [Accepted: 04/07/2023] [Indexed: 05/15/2023]
Abstract
Phenotypic sex-based differences exist for many complex traits. In other cases, phenotypes may be similar, but underlying biology may vary. Thus, sex-aware genetic analyses are becoming increasingly important for understanding the mechanisms driving these differences. To this end, we provide a guide outlining the current best practices for testing various models of sex-dependent genetic effects in complex traits and disease conditions, noting that this is an evolving field. Insights from sex-aware analyses will not only teach us about the biology of complex traits but also aid in achieving the goals of precision medicine and health equity for all.
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Affiliation(s)
- Ekaterina A Khramtsova
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA.
| | - Melissa A Wilson
- School of Life Sciences, Center for Evolution and Medicine, Biodesign Center for Mechanisms of Evolution, Arizona State University, Tempe, AZ 85282, USA
| | - Joanna Martin
- Centre for Neuropsychiatric Genetics and Genomics, Division of Psychological Medicine and Clinical Neurosciences, Cardiff University, Cardiff, UK
| | - Stacey J Winham
- Department of Quantitative Health Sciences, Division of Computational Biology, Mayo Clinic, Rochester, MN, USA
| | - Karen Y He
- Population Analytics and Insights, Data Science Analytics & Insights, Janssen R&D, Lower Gwynedd Township, PA, USA
| | - Lea K Davis
- Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Psychiatry and Behavioral Sciences, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Barbara E Stranger
- Center for Genetic Medicine, Department of Pharmacology, Northwestern University, Chicago, IL, USA.
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20
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Miquel CH, Faz-Lopez B, Guéry JC. Influence of X chromosome in sex-biased autoimmune diseases. J Autoimmun 2023; 137:102992. [PMID: 36641351 DOI: 10.1016/j.jaut.2023.102992] [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: 01/03/2023] [Accepted: 01/03/2023] [Indexed: 01/13/2023]
Abstract
Females have better ability to resolve infections, compared to males, but also, a greater susceptibility to develop autoimmunity. Besides the initial interest on the contribution of sex-steroid hormone signaling, the role of genetic factors linked to X chromosome has recently focused much attention. In human and mouse, the number of X chromosomes, rather than sex-steroid hormones, have been found associated with higher risk or susceptibility to develop autoimmunity, particularly rheumatic diseases, such as SLE, Sjögren's syndrome or Scleroderma. For all of these diseases, the Toll-like receptor TLR7 and TLR8, encoded on the same locus in the human Xp, have been demonstrated to be causal in disease development through gene dosage effect or gain of function mutations. During embryonic development in female mammals, one X chromosome is stochastically inactivated to balance X-linked gene expression between males and females, a process known as X chromosome inactivation (XCI). Nevertheless, some genes including immune related genes can escape XCI to variable degree and penetrance, resulting in a bi-allelic expression in some immune cells, such as TLR7. Because tight regulation of TLR expression is necessary for a healthy, self-tolerant immune environment, XCI escape has been proposed as a mechanism contributing to this sexual dimorphism. In this review, we will summarize general mechanisms of XCI, and describe the known escapee's genes in immune cells, the cellular diversity created by such mechanisms and its potential implication in autoimmune diseases, with a particular focus on the X-linked genes and immune cell populations involved in SLE. Whether dysregulated expression of X-linked genes could contribute to the enhanced susceptibility of females to develop such diseases remains to be proven. Shedding lights onto the X-linked genetic mechanisms contributing to modulation of immune cell functions will undoubtedly provide new insights into the intricate mechanisms underlying sex differences in immunity and autoimmunity.
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Affiliation(s)
- Charles-Henry Miquel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, France; Arthritis R&D, Neuilly-Sur-Seine, France
| | - Berenice Faz-Lopez
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, France
| | - Jean-Charles Guéry
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, France.
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21
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Lee J, Kim J, Zinia SS, Park J, Won S, Kim WJ. Prenatal phthalate exposure and cord blood DNA methylation. Sci Rep 2023; 13:7046. [PMID: 37120575 PMCID: PMC10148847 DOI: 10.1038/s41598-023-33002-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Accepted: 04/05/2023] [Indexed: 05/01/2023] Open
Abstract
Exposure to phthalates has been shown to impede the human endocrine system, resulting in deleterious effects on pregnant women and their children. Phthalates modify DNA methylation patterns in infant cord blood. We examined the association between prenatal phthalate exposure and DNA methylation patterns in cord blood in a Korean birth cohort. Phthalate levels were measured in 274 maternal urine samples obtained during late pregnancy and 102 neonatal urine samples obtained at birth, and DNA methylation levels were measured in cord blood samples. For each infant in the cohort, associations between CpG methylation and both maternal and neonate phthalate levels were analyzed using linear mixed models. The results were combined with those from a meta-analysis of the levels of phthalates in maternal and neonatal urine samples, which were also analyzed for MEOHP, MEHHP, MnBP, and DEHP. This meta-analysis revealed significant associations between the methylation levels of CpG sites near the CHN2 and CUL3 genes, which were also associated with MEOHP and MnBP in neonatal urine. When the data were stratified by the sex of the infant, MnBP concentration was found to be associated with one CpG site near the OR2A2 and MEGF11 genes in female infants. In contrast, the concentrations of the three maternal phthalates showed no significant association with CpG site methylation. Furthermore, the data identified distinct differentially methylated regions in maternal and neonatal urine samples following exposure to phthalates. The CpGs with methylation levels that were positively associated with phthalate levels (particularly MEOHP and MnBP) were found to be enriched genes and related pathways. These results indicate that prenatal phthalate exposure is significantly associated with DNA methylation at multiple CpG sites. These alterations in DNA methylation may serve as biomarkers of maternal exposure to phthalates in infants and are potential candidates for investigating the mechanisms by which phthalates impact maternal and neonatal health.
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Affiliation(s)
- Jooah Lee
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea
| | - Jeeyoung Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, 24341, South Korea
| | - Sabrina Shafi Zinia
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, 24341, South Korea
| | - Jaehyun Park
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, South Korea
| | - Sungho Won
- Department of Public Health Sciences, Seoul National University, Seoul, South Korea.
- Interdisciplinary Program of Bioinformatics, College of Natural Sciences, Seoul National University, Seoul, 08826, South Korea.
- Institute of Health and Environment, Seoul National University, Seoul, South Korea.
- RexSoft Corp, Seoul, South Korea.
| | - Woo Jin Kim
- Department of Internal Medicine and Environmental Health Center, School of Medicine, Kangwon National University, Chuncheon, 24341, South Korea.
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22
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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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23
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Escape from X-inactivation in twins exhibits intra- and inter-individual variability across tissues and is heritable. PLoS Genet 2023; 19:e1010556. [PMID: 36802379 PMCID: PMC9942974 DOI: 10.1371/journal.pgen.1010556] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 12/06/2022] [Indexed: 02/23/2023] Open
Abstract
X-chromosome inactivation (XCI) silences one X in female cells to balance sex-differences in X-dosage. A subset of X-linked genes escape XCI, but the extent to which this phenomenon occurs and how it varies across tissues and in a population is as yet unclear. To characterize incidence and variability of escape across individuals and tissues, we conducted a transcriptomic study of escape in adipose, skin, lymphoblastoid cell lines and immune cells in 248 healthy individuals exhibiting skewed XCI. We quantify XCI escape from a linear model of genes' allelic fold-change and XIST-based degree of XCI skewing. We identify 62 genes, including 19 lncRNAs, with previously unknown patterns of escape. We find a range of tissue-specificity, with 11% of genes escaping XCI constitutively across tissues and 23% demonstrating tissue-restricted escape, including cell type-specific escape across immune cells of the same individual. We also detect substantial inter-individual variability in escape. Monozygotic twins share more similar escape than dizygotic twins, indicating that genetic factors may underlie inter-individual differences in escape. However, discordant escape also occurs within monozygotic co-twins, suggesting environmental factors also influence escape. Altogether, these data indicate that XCI escape is an under-appreciated source of transcriptional differences, and an intricate phenotype impacting variable trait expressivity in females.
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24
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de Oliveira FM, Barros BA, Dos Santos AP, Campos NLV, Mazzola TN, Filho PL, Andrade LALDA, Guaragna MS, de Mello MP, Guerra-Junior G, Vieira TAP, Maciel-Guerra AT. SOX3 duplication in a boy with 46,XX ovotesticular disorder of sex development and his 46,XX sister with atypical genitalia: Probable germline mosaicism. Am J Med Genet A 2023; 191:592-598. [PMID: 36416214 DOI: 10.1002/ajmg.a.63051] [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: 08/08/2022] [Revised: 10/19/2022] [Accepted: 11/04/2022] [Indexed: 11/24/2022]
Abstract
Ovotesticular disorders of sex development (OT-DSD) are characterized by ovarian follicles and seminiferous tubules in the same individual, with a wide range of atypical genitalia. We report on two sibs with atypical genitalia and SRY-negative 46,XX DSD, OT-DSD was confirmed only in the boy, while the girl had bilateral ovaries. Chromosome microarray analysis (CMA) showed a 737-kb duplication at Xq27.1 including the entire SOX3 gene in both sibs, which was confirmed by quantitative real time PCR. Also, X chromosome inactivation assay showed random inactivation in both sibs. Whole exome sequencing revealed no pathogenic or likely pathogenic variant. CMA of the parents showed normal results for both, suggesting that germline mosaicism could be the reason of recurrence of this duplication in the siblings. Our results support a pathogenic role of SOX3 overexpression in 46,XX subjects leading to variable DSD phenotypes.
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Affiliation(s)
- Flávia Marcorin de Oliveira
- Department of Translational Medicine, School of Medical Sciences (FCM), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | | | - Ana Paula Dos Santos
- Department of Translational Medicine, School of Medical Sciences (FCM), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Nilma Lúcia Viguetti Campos
- Department of Translational Medicine, School of Medical Sciences (FCM), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Taís Nitsch Mazzola
- Pediatric Research Center - Ciped, FCM, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Paulo Latuf Filho
- Pediatric Research Center - Ciped, FCM, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | | | - Mara Sanches Guaragna
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Maricilda Palandi de Mello
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Gil Guerra-Junior
- Department of Pediatrics, FCM, University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Társis Antonio Paiva Vieira
- Department of Translational Medicine, School of Medical Sciences (FCM), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
| | - Andréa Trevas Maciel-Guerra
- Department of Translational Medicine, School of Medical Sciences (FCM), University of Campinas (Unicamp), Campinas, São Paulo, Brazil
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25
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Kravitz SN, Ferris E, Love MI, Thomas A, Quinlan AR, Gregg C. Random allelic expression in the adult human body. Cell Rep 2023; 42:111945. [PMID: 36640362 PMCID: PMC10484211 DOI: 10.1016/j.celrep.2022.111945] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 10/17/2022] [Accepted: 12/15/2022] [Indexed: 01/07/2023] Open
Abstract
Genes are typically assumed to express both parental alleles similarly, yet cell lines show random allelic expression (RAE) for many autosomal genes that could shape genetic effects. Thus, understanding RAE in human tissues could improve our understanding of phenotypic variation. Here, we develop a methodology to perform genome-wide profiling of RAE and biallelic expression in GTEx datasets for 832 people and 54 tissues. We report 2,762 autosomal genes with some RAE properties similar to randomly inactivated X-linked genes. We found that RAE is associated with rapidly evolving regions in the human genome, adaptive signaling processes, and genes linked to age-related diseases such as neurodegeneration and cancer. We define putative mechanistic subtypes of RAE distinguished by gene overlaps on sense and antisense DNA strands, aggregation in clusters near telomeres, and increased regulatory complexity and inputs compared with biallelic genes. We provide foundations to study RAE in human phenotypes, evolution, and disease.
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Affiliation(s)
- Stephanie N Kravitz
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Elliott Ferris
- Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Michael I Love
- Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Alun Thomas
- Department of Internal Medicine, Epidemiology, University of Utah School of Medicine, Salt Lake City, UT, USA
| | - Aaron R Quinlan
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA
| | - Christopher Gregg
- Department of Human Genetics, University of Utah, Salt Lake City, UT, USA; Neurobiology, University of Utah, Salt Lake City, UT, USA.
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26
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Lafont JE, Moustaghfir S, Durand AL, Mallein-Gerin F. The epigenetic players and the chromatin marks involved in the articular cartilage during osteoarthritis. Front Physiol 2023; 14:1070241. [PMID: 36733912 PMCID: PMC9887161 DOI: 10.3389/fphys.2023.1070241] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 01/04/2023] [Indexed: 01/18/2023] Open
Abstract
Epigenetics defines the modifications of the genome that do not involve a change in the nucleotide sequence of DNA. These modifications constitute a mechanism of gene regulation poorly explored in the context of cartilage physiology. They are now intensively studied by the scientific community working on articular cartilage and its related pathology such as osteoarthritis. Indeed, epigenetic regulations can control the expression of crucial gene in the chondrocytes, the only resident cells of cartilage. Some epigenetic changes are considered as a possible cause of the abnormal gene expression and the subsequent alteration of the chondrocyte phenotype (hypertrophy, proliferation, senescence…) as observed in osteoarthritic cartilage. Osteoarthritis is a joint pathology, which results in impaired extracellular matrix homeostasis and leads ultimately to the progressive destruction of cartilage. To date, there is no pharmacological treatment and the exact causes have yet to be defined. Given that the epigenetic modifying enzymes can be controlled by pharmacological inhibitors, it is thus crucial to describe the epigenetic marks that enable the normal expression of extracellular matrix encoding genes, and those associated with the abnormal gene expression such as degradative enzyme or inflammatory cytokines encoding genes. In this review, only the DNA methylation and histone modifications will be detailed with regard to normal and osteoarthritic cartilage. Although frequently referred as epigenetic mechanisms, the regulatory mechanisms involving microRNAs will not be discussed. Altogether, this review will show how this nascent field influences our understanding of the pathogenesis of OA in terms of diagnosis and how controlling the epigenetic marks can help defining epigenetic therapies.
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27
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Inkster AM, Wong MT, Matthews AM, Brown CJ, Robinson WP. Who's afraid of the X? Incorporating the X and Y chromosomes into the analysis of DNA methylation array data. Epigenetics Chromatin 2023; 16:1. [PMID: 36609459 PMCID: PMC9825011 DOI: 10.1186/s13072-022-00477-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 12/27/2022] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Many human disease phenotypes manifest differently by sex, making the development of methods for incorporating X and Y-chromosome data into analyses vital. Unfortunately, X and Y chromosome data are frequently excluded from large-scale analyses of the human genome and epigenome due to analytical complexity associated with sex chromosome dosage differences between XX and XY individuals, and the impact of X-chromosome inactivation (XCI) on the epigenome. As such, little attention has been given to considering the methods by which sex chromosome data may be included in analyses of DNA methylation (DNAme) array data. RESULTS With Illumina Infinium HumanMethylation450 DNAme array data from 634 placental samples, we investigated the effects of probe filtering, normalization, and batch correction on DNAme data from the X and Y chromosomes. Processing steps were evaluated in both mixed-sex and sex-stratified subsets of the analysis cohort to identify whether including both sexes impacted processing results. We found that identification of probes that have a high detection p-value, or that are non-variable, should be performed in sex-stratified data subsets to avoid over- and under-estimation of the quantity of probes eligible for removal, respectively. All normalization techniques investigated returned X and Y DNAme data that were highly correlated with the raw data from the same samples. We found no difference in batch correction results after application to mixed-sex or sex-stratified cohorts. Additionally, we identify two analytical methods suitable for XY chromosome data, the choice between which should be guided by the research question of interest, and we performed a proof-of-concept analysis studying differential DNAme on the X and Y chromosome in the context of placental acute chorioamnionitis. Finally, we provide an annotation of probe types that may be desirable to filter in X and Y chromosome analyses, including probes in repetitive elements, the X-transposed region, and cancer-testis gene promoters. CONCLUSION While there may be no single "best" approach for analyzing DNAme array data from the X and Y chromosome, analysts must consider key factors during processing and analysis of sex chromosome data to accommodate the underlying biology of these chromosomes, and the technical limitations of DNA methylation arrays.
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Affiliation(s)
- Amy M Inkster
- BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC, V6H 3N1, Canada.
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada.
| | - Martin T Wong
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada
| | - Allison M Matthews
- BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC, V6H 3N1, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, Vancouver, V6T 1Z7, Canada
| | - Carolyn J Brown
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada
| | - Wendy P Robinson
- BC Children's Hospital Research Institute, 950 W 28th Ave, Vancouver, BC, V6H 3N1, Canada
- Department of Medical Genetics, University of British Columbia, 4500 Oak St, Vancouver, V6H 3N1, Canada
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28
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Anesi N, Miquel CH, Laffont S, Guéry JC. The Influence of Sex Hormones and X Chromosome in Immune Responses. Curr Top Microbiol Immunol 2023; 441:21-59. [PMID: 37695424 DOI: 10.1007/978-3-031-35139-6_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: 09/12/2023]
Abstract
Males and females differ in their susceptibility to develop autoimmunity and allergy but also in their capacity to cope with infections and cancers. Cellular targets and molecular pathways underlying sexual dimorphism in immunity have started to emerge and appeared multifactorial. It became increasingly clear that sex-linked biological factors have important impact on the development, tissue maintenance and effector function acquisition of distinct immune cell populations, thereby regulating multiple layers of innate or adaptive immunity through distinct mechanisms. This review discusses the recent development in our understanding of the cell-intrinsic actions of biological factors linked to sex, sex hormones and sex chromosome complement, on immune cells, which may account for the sex differences in susceptibility to autoimmune diseases and allergies, and the sex-biased responses in natural immunity and cancer.
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Affiliation(s)
- Nina Anesi
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, Toulouse, France
| | - Charles-Henry Miquel
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, Toulouse, France
| | - Sophie Laffont
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, Toulouse, France
| | - Jean-Charles Guéry
- Toulouse Institute for Infectious and Inflammatory Diseases (INFINITY), Université de Toulouse, INSERM, CNRS, UPS, 31300, Toulouse, France.
- INSERM UMR1291, Centre Hospitalier Universitaire Purpan, Place du Dr. Baylac, 31024, Toulouse Cedex 3, France.
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29
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De Riso G, Sarnataro A, Scala G, Cuomo M, Della Monica R, Amente S, Chiariotti L, Miele G, Cocozza S. MC profiling: a novel approach to analyze DNA methylation heterogeneity in genome-wide bisulfite sequencing data. NAR Genom Bioinform 2022; 4:lqac096. [PMID: 36601577 PMCID: PMC9803872 DOI: 10.1093/nargab/lqac096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 11/24/2022] [Accepted: 12/08/2022] [Indexed: 01/01/2023] Open
Abstract
DNA methylation is an epigenetic mark implicated in crucial biological processes. Most of the knowledge about DNA methylation is based on bulk experiments, in which DNA methylation of genomic regions is reported as average methylation. However, average methylation does not inform on how methylated cytosines are distributed in each single DNA molecule. Here, we propose Methylation Class (MC) profiling as a genome-wide approach to the study of DNA methylation heterogeneity from bulk bisulfite sequencing experiments. The proposed approach is built on the concept of MCs, groups of DNA molecules sharing the same number of methylated cytosines. The relative abundances of MCs from sequencing reads incorporates the information on the average methylation, and directly informs on the methylation level of each molecule. By applying our approach to publicly available bisulfite-sequencing datasets, we individuated cell-to-cell differences as the prevalent contributor to methylation heterogeneity. Moreover, we individuated signatures of loci undergoing imprinting and X-inactivation, and highlighted differences between the two processes. When applying MC profiling to compare different conditions, we identified methylation changes occurring in regions with almost constant average methylation. Altogether, our results indicate that MC profiling can provide useful insights on the epigenetic status and its evolution at multiple genomic regions.
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Affiliation(s)
- Giulia De Riso
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Antonella Sarnataro
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Giovanni Scala
- Department of Biology, University of Naples Federico II, Via Vicinale Cupa Cintia 21, 80126 Naples, Italy
| | - Mariella Cuomo
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Rosa Della Monica
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Stefano Amente
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
| | - Lorenzo Chiariotti
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
- CEINGE - Biotecnologie Avanzate, Via Gaetano Salvatore, 486, 80145 Naples, Italy
| | - Gennaro Miele
- Department of Physics “E. Pancini”, University of Naples “Federico II”, Via Cinthia, 80126 Naples, Italy
- Istituto Nazionale di Fisica Nucleare (INFN), Sezione di Napoli, 80126 Naples, Italy
| | - Sergio Cocozza
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, via Sergio Pansini 5, 80131 Naples, Italy
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30
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Somatic XIST activation and features of X chromosome inactivation in male human cancers. Cell Syst 2022; 13:932-944.e5. [PMID: 36356577 DOI: 10.1016/j.cels.2022.10.002] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 05/09/2022] [Accepted: 10/04/2022] [Indexed: 11/11/2022]
Abstract
Expression of the non-coding RNA XIST is essential for initiating X chromosome inactivation (XCI) during early development in female mammals. As the main function of XCI is to enable dosage compensation of chromosome X genes between the sexes, XCI and XIST expression are generally absent in male normal tissues, except in germ cells and in individuals with supernumerary X chromosomes. Via a systematic analysis of public sequencing data of both cancerous and normal tissues, we report that XIST is somatically activated in a subset of male human cancers across diverse lineages. Some of these cancers display hallmarks of XCI, including silencing of gene expression, reduced chromatin accessibility, and increased DNA methylation across chromosome X, suggesting that the developmentally restricted, female-specific program of XCI can be somatically accessed in male cancers.
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31
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Systematic analysis and prediction of genes associated with monogenic disorders on human chromosome X. Nat Commun 2022; 13:6570. [PMID: 36323681 PMCID: PMC9630267 DOI: 10.1038/s41467-022-34264-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 10/19/2022] [Indexed: 11/06/2022] Open
Abstract
Disease gene discovery on chromosome (chr) X is challenging owing to its unique modes of inheritance. We undertook a systematic analysis of human chrX genes. We observe a higher proportion of disorder-associated genes and an enrichment of genes involved in cognition, language, and seizures on chrX compared to autosomes. We analyze gene constraints, exon and promoter conservation, expression, and paralogues, and report 127 genes sharing one or more attributes with known chrX disorder genes. Using machine learning classifiers trained to distinguish disease-associated from dispensable genes, we classify 247 genes, including 115 of the 127, as having high probability of being disease-associated. We provide evidence of an excess of variants in predicted genes in existing databases. Finally, we report damaging variants in CDK16 and TRPC5 in patients with intellectual disability or autism spectrum disorders. This study predicts large-scale gene-disease associations that could be used for prioritization of X-linked pathogenic variants.
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32
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Ryan CS, Schröder M. The human DEAD-box helicase DDX3X as a regulator of mRNA translation. Front Cell Dev Biol 2022; 10:1033684. [PMID: 36393867 PMCID: PMC9642913 DOI: 10.3389/fcell.2022.1033684] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 10/07/2022] [Indexed: 08/27/2023] Open
Abstract
The human DEAD-box protein DDX3X is an RNA remodelling enzyme that has been implicated in various aspects of RNA metabolism. In addition, like many DEAD-box proteins, it has non-conventional functions that are independent of its enzymatic activity, e.g., DDX3X acts as an adaptor molecule in innate immune signalling pathways. DDX3X has been linked to several human diseases. For example, somatic mutations in DDX3X were identified in various human cancers, and de novo germline mutations cause a neurodevelopmental condition now termed 'DDX3X syndrome'. DDX3X is also an important host factor in many different viral infections, where it can have pro-or anti-viral effects depending on the specific virus. The regulation of translation initiation for specific mRNA transcripts is likely a central cellular function of DDX3X, yet many questions regarding its exact targets and mechanisms of action remain unanswered. In this review, we explore the current knowledge about DDX3X's physiological RNA targets and summarise its interactions with the translation machinery. A role for DDX3X in translational reprogramming during cellular stress is emerging, where it may be involved in the regulation of stress granule formation and in mediating non-canonical translation initiation. Finally, we also discuss the role of DDX3X-mediated translation regulation during viral infections. Dysregulation of DDX3X's function in mRNA translation likely contributes to its involvement in disease pathophysiology. Thus, a better understanding of its exact mechanisms for regulating translation of specific mRNA targets is important, so that we can potentially develop therapeutic strategies for overcoming the negative effects of its dysregulation.
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Sun Y, Qian Y, Sun HX, Chen M, Luo Y, Xu X, Yan K, Wang L, Hu J, Dong M. Case Report: De novo DDX3X mutation caused intellectual disability in a female with skewed X-chromosome inactivation on the mutant allele. Front Genet 2022; 13:999442. [PMID: 36299587 PMCID: PMC9589230 DOI: 10.3389/fgene.2022.999442] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Accepted: 09/26/2022] [Indexed: 12/13/2023] Open
Abstract
Skewed XCI plays an important role in the phenotypic heterogeneities of many X-linked disorders, even involving in diseases caused by XCI-escaping genes. DDX3X-related intellectual disability is more common in females and less common in males, who usually inherit from unaffected heterozygous mothers. As an X inactivation (XCI) escaping gene, the role of skewed XCI in the phenotype of DDX3X mutant female is unknown. Here we reported a DDX3X: c.694_711dup18 de novo heterozygous mutation in a female with intellectual disability on the maternal X chromosome on the basis of SNPs detected by PCR-sanger sequencing. AR assay revealed that the maternal mutant X chromosome was extremely inactivated in the proband. Using RNA sequencing and whole-exome sequencing, we quantified allelic read counts and allele-specific expression, and confirmed that the mutant X chromosome was inactive. Further, we verified that the mutant DDX3X allele had a lower expression level by RNA sequencing and RT-PCR, and the normal and mutated DDX3X expression accounted for respectively 70% and 30% of total. In conclusion, we found a symptomatic female with extreme skewing XCI in the DDX3X mutant allele. It was discovered that XCI in the mutant allele was insufficient to reverse the phenotype of DDX3X-related neurodevelopmental disorder. It contributed to a better understanding of the role of skewed XCI in phenotypic differences, which can aid in the genetic counseling and prenatal diagnosis of disorders in females with DDX3X defects.
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Affiliation(s)
- Yixi Sun
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yangwen Qian
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Hai-Xi Sun
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Min Chen
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Yuqin Luo
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Xiaojing Xu
- College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China
| | - Kai Yan
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Liya Wang
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Junjie Hu
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
| | - Minyue Dong
- Department of Reproductive Genetics, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
- Key Laboratory of Reproductive Genetics, Ministry of Education (Zhejiang University), Hangzhou, Zhejiang, China
- Key Laboratory of Women’s Reproductive Health of Zhejiang Province, Women’s Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, China
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Baladron B, Mielu LM, López-Martín E, Barrero MJ, Lopez L, Alvarado JI, Monzón S, Varona S, Cuesta I, Cazorla R, Lara J, Iglesias G, Román E, Ros P, Gomez-Mariano G, Cubillo I, Miguel EHS, Rivera D, Alonso J, Bermejo-Sánchez E, Posada M, Martínez-Delgado B. Differences in Expression of IQSEC2 Transcript Isoforms in Male and Female Cases with Loss of Function Variants and Neurodevelopmental Disorder. Int J Mol Sci 2022; 23:ijms23169480. [PMID: 36012761 PMCID: PMC9409358 DOI: 10.3390/ijms23169480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Revised: 08/18/2022] [Accepted: 08/20/2022] [Indexed: 11/16/2022] Open
Abstract
Pathogenic hemizygous or heterozygous mutations in the IQSEC2 gene cause X-linked intellectual developmental disorder-1 (XLID1), characterized by a variable phenotype including developmental delay, intellectual disability, epilepsy, hypotonia, autism, microcephaly and stereotypies. It affects both males and females typically through loss of function in males and haploinsufficiency in heterozygous females. Females are generally less affected than males. Two novel unrelated cases, one male and one female, with de novo IQSEC2 variants were detected by trio-based whole exome sequencing. The female case had a previously undescribed frameshift mutation (NM_001111125:c.3300dup; p.Met1101Tyrfs*5), and the male showed an intronic variant in intron 6, with a previously unknown effect (NM_001111125:c.2459+21C>T). IQSEC2 gene expression study revealed that this intronic variant created an alternative donor splicing site and an aberrant product, with the inclusion of 19bp, confirming the pathogenic effect of the intron variant. Moreover, a strong reduction in the expression of the long, but also the short IQSEC2 isoforms, was detected in the male correlating with a more severe phenotype, while the female case showed no decreased expression of the short isoform, and milder effects of the disease. This suggests that the abnormal expression levels of the different IQSEC2 transcripts could be implicated in the severity of disease manifestations.
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Affiliation(s)
- Beatriz Baladron
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Lidia M. Mielu
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Estrella López-Martín
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Maria J. Barrero
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Lidia Lopez
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Jose I. Alvarado
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Sara Monzón
- Bioinformatics Unit, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Sarai Varona
- Bioinformatics Unit, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Isabel Cuesta
- Bioinformatics Unit, Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Rosario Cazorla
- Neuropediatrics Service, Hospital Puerta de Hierro, 28222 Madrid, Spain
| | - Julián Lara
- Neuropediatrics Service, Hospital Puerta de Hierro, 28222 Madrid, Spain
| | - Gemma Iglesias
- Neuropediatrics Service, Hospital Puerta de Hierro, 28222 Madrid, Spain
| | - Enriqueta Román
- Neuropediatrics Service, Hospital Puerta de Hierro, 28222 Madrid, Spain
| | - Purificación Ros
- Neuropediatrics Service, Hospital Puerta de Hierro, 28222 Madrid, Spain
| | - Gema Gomez-Mariano
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Isabel Cubillo
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Esther Hernandez-San Miguel
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Daniel Rivera
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Javier Alonso
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U758, 28029 Madrid, Spain
| | - Eva Bermejo-Sánchez
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Manuel Posada
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
| | - Beatriz Martínez-Delgado
- Instituto de Investigación de Enfermedades Raras (IIER), Instituto de Salud Carlos III (ISCIII), 28220 Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), U758, 28029 Madrid, Spain
- Correspondence:
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Anqi Y, Saina Y, Chujie C, Yanfei Y, Xiangwei T, Jiajia M, Jiaojiao X, Maoliang R, Bin C. Regulation of DNA methylation during the testicular development of Shaziling pigs. Genomics 2022; 114:110450. [PMID: 35995261 DOI: 10.1016/j.ygeno.2022.110450] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 07/21/2022] [Accepted: 08/16/2022] [Indexed: 11/18/2022]
Abstract
DNA methylation is one of the key epigenetic regulatory mechanisms in development and spermatogenesis. However, the dynamic regulatory mechanisms of genome-wide DNA methylation during testicular development remain largely unknown. Herein, we generated a single-base resolution DNA methylome and transcriptome atlas of precocious porcine testicular tissues across three developmental stages (1, 75, and 150 days old). The results showed that the dynamic methylation patterns were directly related to the expression of the DNMT3A gene. Conjoint analysis revealed a negative regulatory pattern between promoter methylation and the positive regulation of 3'-untranslated region (3'UTR) methylation. Mechanistically, the decrease in promoter methylation affected the upregulation of meiosis-related genes, such as HORMAD1, SPO11, and SYCE1. Demethylation in the 3'UTR induced the downregulation of the INHBA gene and knockdown of INHBA inhibited cell proliferation by reducing the synthesis of activin A. These findings contribute to exploring the regulatory mechanisms of DNA methylation in testicular development.
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Affiliation(s)
- Yang Anqi
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yan Saina
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Chen Chujie
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Yin Yanfei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Tang Xiangwei
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ma Jiajia
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Xiang Jiaojiao
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China
| | - Ran Maoliang
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
| | - Chen Bin
- College of Animal Science and Technology, Hunan Provincial Key Laboratory for Genetic Improvement of Domestic Animal, Hunan Agricultural University, Hunan, Changsha 410128, China.
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36
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González‐Olvera JC, Fiala R, Pless RC. Protonation of Guanine:5‐Methylcytosine and Guanine:Cytosine Base Pairs in Duplex Oligodeoxyribonucleotides. ChemistrySelect 2022. [DOI: 10.1002/slct.202200835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Julio C. González‐Olvera
- Universidad Politécnica de Santa Rosa Jáuregui Carretera Federal 57 QRO-SLP km 31-150, Parque Industrial Querétaro, Santa Rosa Jáuregui Querétaro 76220 Mexico
| | - Radovan Fiala
- CEITEC-Central European Institute of Technology Masaryk University Kamenice 753/5 62500 Brno Czech Republic
| | - Reynaldo C. Pless
- Centro de Investigación en Ciencia Aplicada y Tecnología Avanzada Instituto Politécnico Nacional Cerro Blanco 141 Querétaro Querétaro 76090 Mexico
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Shen H, Yanas A, Owens MC, Zhang C, Fritsch C, Fare CM, Copley KE, Shorter J, Goldman YE, Liu KF. Sexually dimorphic RNA helicases DDX3X and DDX3Y differentially regulate RNA metabolism through phase separation. Mol Cell 2022; 82:2588-2603.e9. [PMID: 35588748 PMCID: PMC9308757 DOI: 10.1016/j.molcel.2022.04.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 04/09/2022] [Accepted: 04/19/2022] [Indexed: 02/05/2023]
Abstract
Sex differences are pervasive in human health and disease. One major key to sex-biased differences lies in the sex chromosomes. Although the functions of the X chromosome proteins are well appreciated, how they compare with their Y chromosome homologs remains elusive. Herein, using ensemble and single-molecule techniques, we report that the sex chromosome-encoded RNA helicases DDX3X and DDX3Y are distinct in their propensities for liquid-liquid phase separation (LLPS), dissolution, and translation repression. We demonstrate that the N-terminal intrinsically disordered region of DDX3Y more strongly promotes LLPS than the corresponding region of DDX3X and that the weaker ATPase activity of DDX3Y, compared with DDX3X, contributes to the slower disassembly dynamics of DDX3Y-positive condensates. Interestingly, DDX3Y-dependent LLPS represses mRNA translation and enhances aggregation of FUS more strongly than DDX3X-dependent LLPS. Our study provides a platform for future comparisons of sex chromosome-encoded protein homologs, providing insights into sex differences in RNA metabolism and human disease.
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Affiliation(s)
- Hui Shen
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Amber Yanas
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Michael C Owens
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Celia Zhang
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Clark Fritsch
- Graduate Group in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Charlotte M Fare
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Katie E Copley
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - James Shorter
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Cellular and Molecular Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Neuroscience, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Yale E Goldman
- Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Physiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kathy Fange Liu
- Department of Biochemistry and Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Graduate Group in Biochemistry and Molecular Biophysics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Phung TN, Olney KC, Pinto BJ, Silasi M, Perley L, O’Bryan J, Kliman HJ, Wilson MA. X chromosome inactivation in the human placenta is patchy and distinct from adult tissues. HGG ADVANCES 2022; 3:100121. [PMID: 35712697 PMCID: PMC9194956 DOI: 10.1016/j.xhgg.2022.100121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
In humans, one of the X chromosomes in genetic females is inactivated by a process called X chromosome inactivation (XCI). Variation in XCI across the placenta may contribute to observed sex differences and variability in pregnancy outcomes. However, XCI has predominantly been studied in human adult tissues. Here, we sequenced and analyzed DNA and RNA from two locations from 30 full-term pregnancies. Implementing an allele-specific approach to examine XCI, we report evidence that XCI in the human placenta is patchy, with large patches of either maternal or paternal X chromosomes inactivated. Further, using similar measurements, we show that this is in contrast to adult tissues, which generally exhibit mosaic X inactivation, where bulk samples exhibit both maternal and paternal X chromosome expression. Further, by comparing skewed samples in placenta and adult tissues, we identify genes that are uniquely inactivated or expressed in the placenta compared with adult tissues, highlighting the need for tissue-specific maps of XCI.
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Affiliation(s)
- Tanya N. Phung
- Center for Evolution and Medicine, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
| | - Kimberly C. Olney
- Center for Evolution and Medicine, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
| | - Brendan J. Pinto
- Center for Evolution and Medicine, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
- Department of Zoology, Milwaukee Public Museum, Milwaukee, WI 53233, USA
| | - Michelle Silasi
- Department of Maternal-Fetal Medicine, Mercy Hospital St. Louis, St. Louis, MO 63141, USA
| | - Lauren Perley
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Jane O’Bryan
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Harvey J. Kliman
- Department of Obstetrics, Gynecology and Reproductive Sciences, Yale University School of Medicine, New Haven, CT 06520, USA
| | - Melissa A. Wilson
- Center for Evolution and Medicine, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
- The Biodesign Center for Mechanisms of Evolution, Arizona State University, PO Box 874501, Tempe, AZ 85282, USA
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Sex bias in systemic lupus erythematosus: a molecular insight. IMMUNOMETABOLISM (COBHAM (SURREY, ENGLAND)) 2022; 4:e00004. [PMID: 35966636 PMCID: PMC9358995 DOI: 10.1097/in9.0000000000000004] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Accepted: 05/09/2022] [Indexed: 12/24/2022]
Abstract
Acknowledging sex differences in immune response is particularly important when we consider the differences between men and women in the incidence of disease. For example, over 80% of autoimmune disease occurs in women, whereas men have a higher incidence of solid tumors compared to women. In general women have stronger innate and adaptive immune responses than men, explaining their ability to clear viral and bacterial infections faster, but also contributing to their increased susceptibility to autoimmune disease. The autoimmune disease systemic lupus erythematosus (SLE) is the archetypical sexually dimorphic disease, with 90% of patients being women. Various mechanisms have been suggested to account for the female prevalence of SLE, including sex hormones, X-linked genes, and epigenetic regulation of gene expression. Here, we will discuss how these mechanisms contribute to pathobiology of SLE and how type I interferons work with them to augment sex specific disease pathogenesis in SLE.
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40
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Wang Y, Gorrie-Stone TJ, Grant OA, Andrayas AD, Zhai X, McDonald-Maier KD, Schalkwyk LC. InterpolatedXY: a two-step strategy to normalize DNA methylation microarray data avoiding sex bias. Bioinformatics 2022; 38:3950-3957. [PMID: 35771651 PMCID: PMC9364386 DOI: 10.1093/bioinformatics/btac436] [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: 09/29/2021] [Revised: 05/31/2022] [Accepted: 06/28/2022] [Indexed: 12/24/2022] Open
Abstract
MOTIVATION Data normalization is an essential step to reduce technical variation within and between arrays. Due to the different karyotypes and the effects of X chromosome inactivation, females and males exhibit distinct methylation patterns on sex chromosomes; thus, it poses a significant challenge to normalize sex chromosome data without introducing bias. Currently, existing methods do not provide unbiased solutions to normalize sex chromosome data, usually, they just process autosomal and sex chromosomes indiscriminately. RESULTS Here, we demonstrate that ignoring this sex difference will lead to introducing artificial sex bias, especially for thousands of autosomal CpGs. We present a novel two-step strategy (interpolatedXY) to address this issue, which is applicable to all quantile-based normalization methods. By this new strategy, the autosomal CpGs are first normalized independently by conventional methods, such as funnorm or dasen; then the corrected methylation values of sex chromosome-linked CpGs are estimated as the weighted average of their nearest neighbors on autosomes. The proposed two-step strategy can also be applied to other non-quantile-based normalization methods, as well as other array-based data types. Moreover, we propose a useful concept: the sex explained fraction of variance, to quantitatively measure the normalization effect. AVAILABILITY AND IMPLEMENTATION The proposed methods are available by calling the function 'adjustedDasen' or 'adjustedFunnorm' in the latest wateRmelon package (https://github.com/schalkwyk/wateRmelon), with methods compatible with all the major workflows, including minfi. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Yucheng Wang
- School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, UK
| | | | - Olivia A Grant
- School of Life Sciences, University of Essex, Colchester CO4 3SQ, UK
| | - Alexandria D Andrayas
- Institute for Social and Economic Research, University of Essex, Colchester CO4 3SQ, UK
| | | | - Klaus D McDonald-Maier
- School of Computer Science and Electronic Engineering, University of Essex, Colchester CO4 3SQ, UK
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A lifelong duty: how Xist maintains the inactive X chromosome. Curr Opin Genet Dev 2022; 75:101927. [PMID: 35717799 PMCID: PMC9472561 DOI: 10.1016/j.gde.2022.101927] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 05/10/2022] [Accepted: 05/14/2022] [Indexed: 11/22/2022]
Abstract
Female eutherians transcriptionally silence one X chromosome to balance gene dosage between the sexes. X-chromosome inactivation (XCI) is initiated by the lncRNA Xist, which assembles many proteins within the inactive X chromosome (Xi) to trigger gene silencing and heterochromatin formation. It is well established that gene silencing on the Xi is maintained through repressive epigenetic processes, including histone deacetylation and DNA methylation. Recent studies revealed a new mechanism where RNA-binding proteins that interact directly with the RNA contribute to the maintenance of Xist localization and gene silencing. In addition, a surprising plasticity of the Xi was uncovered with many genes becoming upregulated upon experimental deletion of Xist. Intriguingly, immune cells normally lose Xist from the Xi, suggesting that thisXist dependence is utilized in vivo to dynamically regulate gene expression from the Xi. These new studies expose fundamental regulatory mechanisms for the chromatin association of RNAs, highlight the need for studying the maintenance of XCI and Xist localization in a gene- and cell-type-specific manner, and are likely to have clinical impact.
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Deshpande AS, Ulahannan N, Pendleton M, Dai X, Ly L, Behr JM, Schwenk S, Liao W, Augello MA, Tyer C, Rughani P, Kudman S, Tian H, Otis HG, Adney E, Wilkes D, Mosquera JM, Barbieri CE, Melnick A, Stoddart D, Turner DJ, Juul S, Harrington E, Imieliński M. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Nat Biotechnol 2022; 40:1488-1499. [DOI: 10.1038/s41587-022-01289-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2020] [Accepted: 03/16/2022] [Indexed: 12/28/2022]
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England-Mason G, Merrill SM, Gladish N, Moore SR, Giesbrecht GF, Letourneau N, MacIsaac JL, MacDonald AM, Kinniburgh DW, Ponsonby AL, Saffery R, Martin JW, Kobor MS, Dewey D. Prenatal exposure to phthalates and peripheral blood and buccal epithelial DNA methylation in infants: An epigenome-wide association study. ENVIRONMENT INTERNATIONAL 2022; 163:107183. [PMID: 35325772 DOI: 10.1016/j.envint.2022.107183] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/16/2022] [Accepted: 03/09/2022] [Indexed: 06/14/2023]
Abstract
BACKGROUND Prenatal exposure to phthalates has been associated with adverse health and neurodevelopmental outcomes. DNA methylation (DNAm) alterations may be a mechanism underlying these effects, but prior investigations of prenatal exposure to phthalates and neonatal DNAm profiles are limited to placental tissue and umbilical cord blood. OBJECTIVE Conduct an epigenome-wide association study (EWAS) of the associations between prenatal exposure to phthalates and DNAm in two accessible infant tissues, venous buffy coat blood and buccal epithelial cells (BECs). METHODS Participants included 152 maternal-infant pairs from the Alberta Pregnancy Outcomes and Nutrition (APrON) study. Maternal second trimester urine samples were analyzed for nine phthalate metabolites. Blood (n = 74) or BECs (n = 78) were collected from 3-month-old infants and profiled for DNAm using the Infinium HumanMethylation450 (450K) BeadChip. Robust linear regressions were used to investigate the associations between high (HMWPs) and low molecular weight phthalates (LMWPs) and change in methylation levels at variable Cytosine-phosphate-Guanine (CpG) sites in infant tissues, as well as the sensitivity of associations to potential confounders. RESULTS One candidate CpG in gene RNF39 reported by a previous study examining prenatal exposure to phthalates and cord blood DNAm was replicated. The EWAS identified 12 high-confidence CpGs in blood and another 12 in BECs associated with HMWPs and/or LMWPs. Prenatal exposure to bisphenol A (BPA) associated with two of the CpGs associated with HMWPs in BECs. DISCUSSION Prenatal exposure to phthalates was associated with DNAm variation at CpGs annotated to genes associated with endocrine hormone activity (i.e., SLCO4A1, TPO), immune pathways and DNA damage (i.e., RASGEF1B, KAZN, HLA-A, MYO18A, DIP2C, C1or109), and neurodevelopment (i.e., AMPH, NOTCH3, DNAJC5). Future studies that characterize the stability of these associations in larger samples, multiple cohorts, across tissues, and investigate the potential associations between these biomarkers and relevant health and neurodevelopmental outcomes are needed.
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Affiliation(s)
- Gillian England-Mason
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada
| | - Sarah M Merrill
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Nicole Gladish
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Sarah R Moore
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Gerald F Giesbrecht
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Psychology, Faculty of Arts, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Nicole Letourneau
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Faculty of Nursing, University of Calgary, Calgary, Alberta, Canada; Department of Psychiatry, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada
| | - Julia L MacIsaac
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada
| | - Amy M MacDonald
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada
| | - David W Kinniburgh
- Alberta Centre for Toxicology, University of Calgary, Calgary, Alberta, Canada; Department of Laboratory Medicine and Pathology, University of Alberta, Edmonton, Alberta, Canada
| | - Anne-Louise Ponsonby
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Richard Saffery
- Murdoch Children's Research Institute, Royal Children's Hospital, University of Melbourne, Melbourne, Victoria, Australia
| | - Jonathan W Martin
- Science for Life Laboratory, Department of Environmental Science, Stockholm University, Stockholm, Södermanland, Sweden
| | - Michael S Kobor
- Department of Medical Genetics, Faculty of Medicine, University of British Columbia, Vancouver, British Columbia, Canada; British Columbia Children's Hospital Research Institute, University of British Columbia, Vancouver, British Columbia, Canada; Centre for Molecular Medicine and Therapeutics, Vancouver, British Columbia, Canada; Program in Child and Brain Development, CIFAR, Toronto, Ontario, Canada
| | - Deborah Dewey
- Department of Paediatrics, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Owerko Centre, Alberta Children's Hospital Research Institute, University of Calgary, Calgary, Alberta, Canada; Department of Community Health Sciences, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada; Hotchkiss Brain Institute, Calgary, Alberta, Canada.
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Mechanistic Study on DNA Mutation of the Cytosine Methylation Reaction at C5 Position. ARAB J CHEM 2022. [DOI: 10.1016/j.arabjc.2022.103956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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45
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Chen X, Wilson KA, Schaefer N, De Hayr L, Windsor M, Scalais E, van Rijckevorsel G, Stouffs K, Villmann C, O’Mara ML, Lynch JW, Harvey RJ. Loss, Gain and Altered Function of GlyR α2 Subunit Mutations in Neurodevelopmental Disorders. Front Mol Neurosci 2022; 15:886729. [PMID: 35571374 PMCID: PMC9103196 DOI: 10.3389/fnmol.2022.886729] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/07/2022] [Indexed: 12/11/2022] Open
Abstract
Glycine receptors (GlyRs) containing the α2 subunit govern cell fate, neuronal migration and synaptogenesis in the developing cortex and spinal cord. Rare missense variants and microdeletions in the X-linked GlyR α2 subunit gene (GLRA2) have been associated with human autism spectrum disorder (ASD), where they typically cause a loss-of-function via protein truncation, reduced cell-surface trafficking and/or reduced glycine sensitivity (e.g., GLRA2Δex8-9 and extracellular domain variants p.N109S and p.R126Q). However, the GlyR α2 missense variant p.R323L in the intracellular M3-M4 domain results in a gain-of-function characterized by slower synaptic decay times, longer duration active periods and increases in channel conductance. This study reports the functional characterization of four missense variants in GLRA2 associated with ASD or developmental disorders (p.V-22L, p.N38K, p.K213E, p.T269M) using a combination of bioinformatics, molecular dynamics simulations, cellular models of GlyR trafficking and electrophysiology in artificial synapses. The GlyR α2V–22L variant resulted in altered predicted signal peptide cleavage and a reduction in cell-surface expression, suggestive of a partial loss-of-function. Similarly, GlyR α2N38K homomers showed reduced cell-surface expression, a reduced affinity for glycine and a reduced magnitude of IPSCs in artificial synapses. By contrast, GlyR α2K213E homomers showed a slight reduction in cell-surface expression, but IPSCs were larger, with faster rise/decay times, suggesting a gain-of-function. Lastly, GlyR α2T269M homomers exhibited a high glycine sensitivity accompanied by a substantial leak current, suggestive of an altered function that could dramatically enhance glycinergic signaling. These results may explain the heterogeneity of clinical phenotypes associated with GLRA2 mutations and reveal that missense variants can result in a loss, gain or alteration of GlyR α2 function. In turn, these GlyR α2 missense variants are likely to either negatively or positively deregulate cortical progenitor homeostasis and neuronal migration in the developing brain, leading to changes in cognition, learning, and memory.
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Affiliation(s)
- Xiumin Chen
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Katie A. Wilson
- Research School of Chemistry, The Australian National University, Canberra, ACT, Australia
| | - Natascha Schaefer
- Institute of Clinical Neurobiology, University Hospital, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Lachlan De Hayr
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Mark Windsor
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, QLD, Australia
| | - Emmanuel Scalais
- Neurologie Pédiatrique, Centre Hospitalier de Luxembourg, Luxembourg, Luxembourg
| | | | - Katrien Stouffs
- Center for Medical Genetics, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Carmen Villmann
- Institute of Clinical Neurobiology, University Hospital, Julius-Maximilians-University Würzburg, Würzburg, Germany
| | - Megan L. O’Mara
- Research School of Chemistry, The Australian National University, Canberra, ACT, Australia
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, Brisbane, QLD, Australia
| | - Joseph W. Lynch
- Queensland Brain Institute, The University of Queensland, Brisbane, QLD, Australia
| | - Robert J. Harvey
- School of Health and Behavioural Sciences, University of the Sunshine Coast, Maroochydore, QLD, Australia
- Sunshine Coast Health Institute, Birtinya, QLD, Australia
- *Correspondence: Robert J. Harvey,
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O’Geen H, Tomkova M, Combs JA, Tilley EK, Segal D. Determinants of heritable gene silencing for KRAB-dCas9 + DNMT3 and Ezh2-dCas9 + DNMT3 hit-and-run epigenome editing. Nucleic Acids Res 2022; 50:3239-3253. [PMID: 35234927 PMCID: PMC8989539 DOI: 10.1093/nar/gkac123] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 02/01/2022] [Accepted: 02/08/2022] [Indexed: 11/12/2022] Open
Abstract
Precision epigenome editing has gained significant attention as a method to modulate gene expression without altering genetic information. However, a major limiting factor has been that the gene expression changes are often transient, unlike the life-long epigenetic changes that occur frequently in nature. Here, we systematically interrogate the ability of CRISPR/dCas9-based epigenome editors (Epi-dCas9) to engineer persistent epigenetic silencing. We elucidated cis regulatory features that contribute to the differential stability of epigenetic reprogramming, such as the active transcription histone marks H3K36me3 and H3K27ac strongly correlating with resistance to short-term repression and resistance to long-term silencing, respectively. H3K27ac inversely correlates with increased DNA methylation. Interestingly, the dependance on H3K27ac was only observed when a combination of KRAB-dCas9 and targetable DNA methyltransferases (DNMT3A-dCas9 + DNMT3L) was used, but not when KRAB was replaced with the targetable H3K27 histone methyltransferase Ezh2. In addition, programmable Ezh2/DNMT3A + L treatment demonstrated enhanced engineering of localized DNA methylation and was not sensitive to a divergent chromatin state. Our results highlight the importance of local chromatin features for heritability of programmable silencing and the differential response to KRAB- and Ezh2-based epigenetic editing platforms. The information gained in this study provides fundamental insights into understanding contextual cues to more predictably engineer persistent silencing.
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Affiliation(s)
| | - Marketa Tomkova
- Genome Center, University of California, Davis, CA 95616, USA
| | | | - Emma K Tilley
- Genome Center, University of California, Davis, CA 95616, USA
| | - David J Segal
- Genome Center, University of California, Davis, CA 95616, USA
- Department of Biochemistry and Molecular Medicine, University of California, Davis, CA 95616, USA
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47
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Gershman A, Sauria MEG, Guitart X, Vollger MR, Hook PW, Hoyt SJ, Jain M, Shumate A, Razaghi R, Koren S, Altemose N, Caldas GV, Logsdon GA, Rhie A, Eichler EE, Schatz MC, O'Neill RJ, Phillippy AM, Miga KH, Timp W. Epigenetic patterns in a complete human genome. Science 2022; 376:eabj5089. [PMID: 35357915 PMCID: PMC9170183 DOI: 10.1126/science.abj5089] [Citation(s) in RCA: 116] [Impact Index Per Article: 58.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.
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Affiliation(s)
- Ariel Gershman
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
| | - Michael E G Sauria
- Department of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Xavi Guitart
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Mitchell R Vollger
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Paul W Hook
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Savannah J Hoyt
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Miten Jain
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Alaina Shumate
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Roham Razaghi
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
| | - Sergey Koren
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Nicolas Altemose
- Department of Bioengineering, University of California Berkeley, Berkeley, CA, USA
| | - Gina V Caldas
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley CA, USA
| | - Glennis A Logsdon
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
| | - Arang Rhie
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Michael C Schatz
- Department of Biology and Computer Science, Johns Hopkins University, Baltimore, MD, USA
| | - Rachel J O'Neill
- Institute for Systems Genomics, University of Connecticut, Storrs, CT, USA
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, USA
| | - Adam M Phillippy
- Genome Informatics Section, Computational and Statistical Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Karen H Miga
- UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Winston Timp
- Department of Molecular Biology and Genetics, Johns Hopkins University, Baltimore, MD, USA
- Department of Biomedical Engineering, Johns Hopkins University, Baltimore, MD, USA
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48
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Al Adhami H, Bardet AF, Dumas M, Cleroux E, Guibert S, Fauque P, Acloque H, Weber M. A comparative methylome analysis reveals conservation and divergence of DNA methylation patterns and functions in vertebrates. BMC Biol 2022; 20:70. [PMID: 35317801 PMCID: PMC8941758 DOI: 10.1186/s12915-022-01270-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/04/2022] [Indexed: 12/24/2022] Open
Abstract
Background Cytosine DNA methylation is a heritable epigenetic mark present in most eukaryotic groups. While the patterns and functions of DNA methylation have been extensively studied in mouse and human, their conservation in other vertebrates remains poorly explored. In this study, we interrogated the distribution and function of DNA methylation in primary fibroblasts of seven vertebrate species including bio-medical models and livestock species (human, mouse, rabbit, dog, cow, pig, and chicken). Results Our data highlight both divergence and conservation of DNA methylation patterns and functions. We show that the chicken genome is hypomethylated compared to other vertebrates. Furthermore, compared to mouse, other species show a higher frequency of methylation of CpG-rich DNA. We reveal the conservation of large unmethylated valleys and patterns of DNA methylation associated with X-chromosome inactivation through vertebrate evolution and make predictions of conserved sets of imprinted genes across mammals. Finally, using chemical inhibition of DNA methylation, we show that the silencing of germline genes and endogenous retroviruses (ERVs) are conserved functions of DNA methylation in vertebrates. Conclusions Our data highlight conserved properties of DNA methylation in vertebrate genomes but at the same time point to differences between mouse and other vertebrate species. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01270-x.
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Affiliation(s)
- Hala Al Adhami
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Anaïs Flore Bardet
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Michael Dumas
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Elouan Cleroux
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Sylvain Guibert
- University of Strasbourg, Strasbourg, France.,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France
| | - Patricia Fauque
- Université Bourgogne Franche-Comté, Equipe Génétique des Anomalies du Développement (GAD) INSERM UMR1231, 2 Rue Angélique Ducoudray, 21000, Dijon, France.,CHU Dijon Bourgogne, Laboratoire de Biologie de la Reproduction - CECOS, 14 rue Gaffarel, 21000, Dijon, France
| | - Hervé Acloque
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Michael Weber
- University of Strasbourg, Strasbourg, France. .,CNRS UMR7242, Biotechnology and Cell Signaling, 300 Bd Sébastien Brant, 67412, Illkirch Cedex, France.
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Abstract
Background: Sex dimorphism strongly impacts tumor biology, with most cancers having a male predominance. Uniquely, thyroid cancer (TC) is the only nonreproductive cancer with striking female predominance with three- to four-fold higher incidence among females, although males generally have more aggressive disease. The molecular basis for this observation is not known, and current approaches in treatment and surveillance are not sex specific. Summary: Although TC has overall good prognosis, 6-20% of patients develop regional or distant metastasis, one third of whom are not responsive to conventional treatment approaches and suffer a 10-year survival rate of only 10%. More efficacious treatment strategies are needed for these aggressive TCs, as tyrosine kinase inhibitors and immunotherapy have major toxicities without demonstrable overall survival benefit. Emerging evidence indicates a role of sex hormones, genetics, and the immune system in modulation of both risk for TC and its progression in a sex-specific manner. Conclusion: Greater understanding of the molecular mechanisms underlying sex differences in TC pathogenesis could provide insights into the development of sex-specific, targeted, and effective strategies for prevention, diagnosis, and management. This review summarizes emerging evidence for the importance of sex in the pathogenesis, progression, and response to treatment in differentiated TC with emphasis on the role of sex hormones, genetics, and the immune system.
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Affiliation(s)
- Leila Shobab
- MedStar Washington Hospital Center, Washington, District of Columbia, USA
| | - Kenneth D Burman
- MedStar Washington Hospital Center, Washington, District of Columbia, USA
| | - Leonard Wartofsky
- Medstar Health Research Institute, Washington, District of Columbia, USA
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50
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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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