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Landen S, Hiam D, Voisin S, Jacques M, Lamon S, Eynon N. Physiological and molecular sex differences in human skeletal muscle in response to exercise training. J Physiol 2023; 601:419-434. [PMID: 34762308 DOI: 10.1113/jp279499] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 11/01/2021] [Indexed: 02/04/2023] Open
Abstract
Sex differences in exercise physiology, such as substrate metabolism and skeletal muscle fatigability, stem from inherent biological factors, including endogenous hormones and genetics. Studies investigating exercise physiology frequently include only males or do not take sex differences into consideration. Although there is still an underrepresentation of female participants in exercise research, existing studies have identified sex differences in physiological and molecular responses to exercise training. The observed sex differences in exercise physiology are underpinned by the sex chromosome complement, sex hormones and, on a molecular level, the epigenome and transcriptome. Future research in the field should aim to include both sexes, control for menstrual cycle factors, conduct large-scale and ethnically diverse studies, conduct meta-analyses to consolidate findings from various studies, leverage unique cohorts (such as post-menopausal, transgender, and those with sex chromosome abnormalities), as well as integrate tissue and cell-specific -omics data. This knowledge is essential for developing deeper insight into sex-specific physiological responses to exercise training, thus directing future exercise physiology studies and practical application.
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Affiliation(s)
- Shanie Landen
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Danielle Hiam
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia.,Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Sarah Voisin
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Macsue Jacques
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
| | - Séverine Lamon
- Institute for Physical Activity and Nutrition, School of Exercise and Nutrition Sciences, Deakin University, Geelong, Australia
| | - Nir Eynon
- Institute for Health and Sport (iHeS), Victoria University, Melbourne, Australia
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2
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Gene regulation in time and space during X-chromosome inactivation. Nat Rev Mol Cell Biol 2022; 23:231-249. [PMID: 35013589 DOI: 10.1038/s41580-021-00438-7] [Citation(s) in RCA: 65] [Impact Index Per Article: 32.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/21/2022]
Abstract
X-chromosome inactivation (XCI) is the epigenetic mechanism that ensures X-linked dosage compensation between cells of females (XX karyotype) and males (XY). XCI is essential for female embryos to survive through development and requires the accurate spatiotemporal regulation of many different factors to achieve remarkable chromosome-wide gene silencing. As a result of XCI, the active and inactive X chromosomes are functionally and structurally different, with the inactive X chromosome undergoing a major conformational reorganization within the nucleus. In this Review, we discuss the multiple layers of genetic and epigenetic regulation that underlie initiation of XCI during development and then maintain it throughout life, in light of the most recent findings in this rapidly advancing field. We discuss exciting new insights into the regulation of X inactive-specific transcript (XIST), the trigger and master regulator of XCI, and into the mechanisms and dynamics that underlie the silencing of nearly all X-linked genes. Finally, given the increasing interest in understanding the impact of chromosome organization on gene regulation, we provide an overview of the factors that are thought to reshape the 3D structure of the inactive X chromosome and of the relevance of such structural changes for XCI establishment and maintenance.
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3
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Golden Syrian Hamsters as a Model for Revisiting the Role of Biological Sex Differences in SARS-CoV-2 Infection. mBio 2021; 12:e0184821. [PMID: 34809458 PMCID: PMC8609349 DOI: 10.1128/mbio.01848-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
There is growing evidence that coronavirus disease 2019 (COVID-19) affects males more severely than females, including compelling evidence indicating that biological sex is an important clinical factor influencing disease pathology and outcomes. In their recent article in mBio, S. Dhakal, C. A. Ruiz-Bedoya, R. Zhou, P. S. Creisher, et al. (mBio 12:e00974-21, 2021, https://doi.org/10.1128/mBio.00974-21) find further evidence to support this hypothesis as they interrogate biological sex differences in the pathogenesis and clinical features of COVID-19 in the golden Syrian hamster model. Their study probes SARS-CoV-2 infection in terms of loss of body mass, recovery, lung compromise, viral replication, inflammatory response, immune response, and, most importantly, the role of estrogen. They also demonstrate the value of a novel unbiased, quantitative chest computed tomography (CT) imaging approach. The golden Syrian hamster model holds a promising opportunity to further investigate how biological sex acts as a primary determinant in SARS-CoV-2 pathogenesis, as also demonstrated in this study.
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4
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Shi W, Sheng X, Dorr KM, Hutton JE, Emerson JI, Davies HA, Andrade TD, Wasson LK, Greco TM, Hashimoto Y, Federspiel JD, Robbe ZL, Chen X, Arnold AP, Cristea IM, Conlon FL. Cardiac proteomics reveals sex chromosome-dependent differences between males and females that arise prior to gonad formation. Dev Cell 2021; 56:3019-3034.e7. [PMID: 34655525 PMCID: PMC9290207 DOI: 10.1016/j.devcel.2021.09.022] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/22/2021] [Accepted: 09/23/2021] [Indexed: 01/03/2023]
Abstract
Sex disparities in cardiac homeostasis and heart disease are well documented, with differences attributed to actions of sex hormones. However, studies have indicated sex chromosomes act outside of the gonads to function without mediation by gonadal hormones. Here, we performed transcriptional and proteomics profiling to define differences between male and female mouse hearts. We demonstrate, contrary to current dogma, cardiac sex disparities are controlled not only by sex hormones but also through a sex-chromosome mechanism. Using Turner syndrome (XO) and Klinefelter (XXY) models, we find the sex-chromosome pathway is established by X-linked gene dosage. We demonstrate cardiac sex disparities occur at the earliest stages of heart formation, a period before gonad formation. Using these datasets, we identify and define a role for alpha-1B-glycoprotein (A1BG), showing loss of A1BG leads to cardiac defects in females, but not males. These studies provide resources for studying sex-biased cardiac disease states.
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Affiliation(s)
- Wei Shi
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinlei Sheng
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Kerry M Dorr
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Josiah E Hutton
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - James I Emerson
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Haley A Davies
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tia D Andrade
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lauren K Wasson
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Todd M Greco
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Yutaka Hashimoto
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Joel D Federspiel
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA
| | - Zachary L Robbe
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xuqi Chen
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Arthur P Arnold
- Department of Integrative Biology & Physiology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Ileana M Cristea
- Department of Molecular Biology, Princeton University, Lewis Thomas Laboratory, Washington Road, Princeton, NJ 08544, USA.
| | - Frank L Conlon
- Department of Biology and Genetics, McAllister Heart Institute, UNC-Chapel Hill, Chapel Hill, NC 27599, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA.
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5
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Olney KC, Brotman SM, Andrews JP, Valverde-Vesling VA, Wilson MA. Reference genome and transcriptome informed by the sex chromosome complement of the sample increase ability to detect sex differences in gene expression from RNA-Seq data. Biol Sex Differ 2020; 11:42. [PMID: 32693839 PMCID: PMC7374973 DOI: 10.1186/s13293-020-00312-9] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Human X and Y chromosomes share an evolutionary origin and, as a consequence, sequence similarity. We investigated whether the sequence homology between the X and Y chromosomes affects the alignment of RNA-Seq reads and estimates of differential expression. We tested the effects of using reference genomes and reference transcriptomes informed by the sex chromosome complement of the sample's genome on the measurements of RNA-Seq abundance and sex differences in expression. RESULTS The default genome includes the entire human reference genome (GRCh38), including the entire sequence of the X and Y chromosomes. We created two sex chromosome complement informed reference genomes. One sex chromosome complement informed reference genome was used for samples that lacked a Y chromosome; for this reference genome version, we hard-masked the entire Y chromosome. For the other sex chromosome complement informed reference genome, to be used for samples with a Y chromosome, we hard-masked only the pseudoautosomal regions of the Y chromosome, because these regions are duplicated identically in the reference genome on the X chromosome. We analyzed the transcript abundance in the whole blood, brain cortex, breast, liver, and thyroid tissues from 20 genetic female (46, XX) and 20 genetic male (46, XY) samples. Each sample was aligned twice: once to the default reference genome and then independently aligned to a reference genome informed by the sex chromosome complement of the sample, repeated using two different read aligners, HISAT and STAR. We then quantified sex differences in gene expression using featureCounts to get the raw count estimates followed by Limma/Voom for normalization and differential expression. We additionally created sex chromosome complement informed transcriptome references for use in pseudo-alignment using Salmon. Transcript abundance was quantified twice for each sample: once to the default target transcripts and then independently to target transcripts informed by the sex chromosome complement of the sample. CONCLUSIONS We show that regardless of the choice of the read aligner, using an alignment protocol informed by the sex chromosome complement of the sample results in higher expression estimates on the pseudoautosomal regions of the X chromosome in both genetic male and genetic female samples, as well as an increased number of unique genes being called as differentially expressed between the sexes. We additionally show that using a pseudo-alignment approach informed on the sex chromosome complement of the sample eliminates Y-linked expression in female XX samples.
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Affiliation(s)
- Kimberly C Olney
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA.,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA
| | - Sarah M Brotman
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA.,Department of Genetics, University of North Carolina, Chapel Hill, NC, 27599, USA
| | - Jocelyn P Andrews
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA.,College of Osteopathic Medicine of the Pacific, Western University of Health Sciences, Pomona, CA, 91766, USA
| | | | - Melissa A Wilson
- School of Life Sciences, Arizona State University, PO Box 874501, Tempe, AZ, 85287-4501, USA. .,Center for Evolution and Medicine, Arizona State University, Tempe, AZ, 85282, USA. .,Center for Mechanisms of Evolution, The Biodesign Institute, Arizona State University, Tempe, AZ, 85282, USA.
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Jackson MR, Loring KE, Homan CC, Thai MH, Määttänen L, Arvio M, Jarvela I, Shaw M, Gardner A, Gecz J, Shoubridge C. Heterozygous loss of function of IQSEC2/ Iqsec2 leads to increased activated Arf6 and severe neurocognitive seizure phenotype in females. Life Sci Alliance 2019; 2:2/4/e201900386. [PMID: 31439632 PMCID: PMC6706959 DOI: 10.26508/lsa.201900386] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Revised: 07/25/2019] [Accepted: 08/15/2019] [Indexed: 12/30/2022] Open
Abstract
Clinical presentations of mutations in the IQSEC2 gene on the X-chromosome initially implicated to cause non-syndromic intellectual disability (ID) in males have expanded to include early onset seizures in males as well as in females. The molecular pathogenesis is not well understood, nor the mechanisms driving disease expression in heterozygous females. Using a CRISPR/Cas9-edited Iqsec2 KO mouse model, we confirm the loss of Iqsec2 mRNA expression and lack of Iqsec2 protein within the brain of both founder and progeny mice. Both male (52%) and female (46%) Iqsec2 KO mice present with frequent and recurrent seizures. Focusing on Iqsec2 KO heterozygous female mice, we demonstrate increased hyperactivity, altered anxiety and fear responses, decreased social interactions, delayed learning capacity and decreased memory retention/novel recognition, recapitulating psychiatric issues, autistic-like features, and cognitive deficits present in female patients with loss-of-function IQSEC2 variants. Despite Iqsec2 normally acting to activate Arf6 substrate, we demonstrate that mice modelling the loss of Iqsec2 function present with increased levels of activated Arf6. We contend that loss of Iqsec2 function leads to altered regulation of activated Arf6-mediated responses to synaptic signalling and immature synaptic networks. We highlight the importance of IQSEC2 function for females by reporting a novel nonsense variant c.566C > A, p.(S189*) in an elderly female patient with profound intellectual disability, generalised seizures, and behavioural disturbances. Our human and mouse data reaffirm IQSEC2 as another disease gene with an unexpected X-chromosome heterozygous female phenotype. Our Iqsec2 mouse model recapitulates the phenotypes observed in human patients despite the differences in the IQSEC2/Iqsec2 gene X-chromosome inactivation between the species.
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Affiliation(s)
- Matilda R Jackson
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Karagh E Loring
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia.,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Claire C Homan
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Monica Hn Thai
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia
| | - Laura Määttänen
- Department of Child Neurology, Turku University Hospital, Turku, Finland
| | - Maria Arvio
- Department of Child Neurology, Turku University Hospital, Turku, Finland.,Joint Authority for Päijät-Häme Social and Health Care, Lahti, Finland.,PEDEGO, Oulu University Hospital, Oulu, Finland
| | - Irma Jarvela
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Marie Shaw
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Alison Gardner
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
| | - Jozef Gecz
- Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia.,South Australian Health and Medical Research Institute, Adelaide, Australia
| | - Cheryl Shoubridge
- Intellectual Disability Research, Adelaide Medical School, The University of Adelaide, Adelaide, Australia .,Department of Paediatrics, Robinson Research Institute, University of Adelaide, Adelaide, Australia
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7
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Larson NB, Fogarty ZC, Larson MC, Kalli KR, Lawrenson K, Gayther S, Fridley BL, Goode EL, Winham SJ. An integrative approach to assess X-chromosome inactivation using allele-specific expression with applications to epithelial ovarian cancer. Genet Epidemiol 2017; 41:898-914. [PMID: 29119601 PMCID: PMC5726546 DOI: 10.1002/gepi.22091] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2017] [Revised: 09/06/2017] [Accepted: 09/27/2017] [Indexed: 01/05/2023]
Abstract
X-chromosome inactivation (XCI) epigenetically silences transcription of an X chromosome in females; patterns of XCI are thought to be aberrant in women's cancers, but are understudied due to statistical challenges. We develop a two-stage statistical framework to assess skewed XCI and evaluate gene-level patterns of XCI for an individual sample by integration of RNA sequence, copy number alteration, and genotype data. Our method relies on allele-specific expression (ASE) to directly measure XCI and does not rely on male samples or paired normal tissue for comparison. We model ASE using a two-component mixture of beta distributions, allowing estimation for a given sample of the degree of skewness (based on a composite likelihood ratio test) and the posterior probability that a given gene escapes XCI (using a Bayesian beta-binomial mixture model). To illustrate the utility of our approach, we applied these methods to data from tumors of ovarian cancer patients. Among 99 patients, 45 tumors were informative for analysis and showed evidence of XCI skewed toward a particular parental chromosome. For 397 X-linked genes, we observed tumor XCI patterns largely consistent with previously identified consensus states based on multiple normal tissue types. However, 37 genes differed in XCI state between ovarian tumors and the consensus state; 17 genes aberrantly escaped XCI in ovarian tumors (including many oncogenes), whereas 20 genes were unexpectedly inactivated in ovarian tumors (including many tumor suppressor genes). These results provide evidence of the importance of XCI in ovarian cancer and demonstrate the utility of our two-stage analysis.
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MESH Headings
- Adult
- Alleles
- Bayes Theorem
- Carcinoma, Ovarian Epithelial
- Chromosomes, Human, X
- Female
- Genes, X-Linked
- Genotype
- Humans
- Models, Genetic
- Neoplasms, Glandular and Epithelial/genetics
- Neoplasms, Glandular and Epithelial/pathology
- Ovarian Neoplasms/genetics
- Ovarian Neoplasms/pathology
- Polymorphism, Single Nucleotide
- RNA, Neoplasm/chemistry
- RNA, Neoplasm/isolation & purification
- RNA, Neoplasm/metabolism
- Sequence Analysis, RNA
- X Chromosome Inactivation
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Affiliation(s)
- Nicholas B. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Zachary C. Fogarty
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Melissa C. Larson
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | | | - Kate Lawrenson
- Women’s Cancer Program, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Simon Gayther
- Center for Bioinformatics and Functional Genomics, Samuel Oschin Comprehensive Cancer Institute, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Brooke L. Fridley
- Department of Biostatistics and Bioinformatics, Moffitt Cancer Center, Tampa, FL, USA
| | - Ellen L. Goode
- Division of Epidemiology, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Stacey J. Winham
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
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