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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. RESEARCH SQUARE 2024:rs.3.rs-4559581. [PMID: 38978599 PMCID: PMC11230509 DOI: 10.21203/rs.3.rs-4559581/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/10/2024]
Abstract
Background STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Results Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~ 50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). Conclusions HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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Chang TY, Waxman DJ. HDI-STARR-seq: Condition-specific enhancer discovery in mouse liver in vivo. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.06.10.598329. [PMID: 38915578 PMCID: PMC11195054 DOI: 10.1101/2024.06.10.598329] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
STARR-seq and other massively-parallel reporter assays are widely used to discover functional enhancers in transfected cell models, which can be confounded by plasmid vector-induced type-I interferon immune responses and lack the multicellular environment and endogenous chromatin state of complex mammalian tissues. Here, we describe HDI-STARR-seq, which combines STARR-seq plasmid library delivery to the liver, by hydrodynamic tail vein injection (HDI), with reporter RNA transcriptional initiation driven by a minimal Albumin promoter, which we show is essential for mouse liver STARR-seq enhancer activity assayed 7 days after HDI. Importantly, little or no vector-induced innate type-I interferon responses were observed. Comparisons of HDI-STARR-seq activity between male and female mouse livers and in livers from males treated with an activating ligand of the transcription factor CAR (Nr1i3) identified many condition-dependent enhancers linked to condition-specific gene expression. Further, thousands of active liver enhancers were identified using a high complexity STARR-seq library comprised of ~50,000 genomic regions released by DNase-I digestion of mouse liver nuclei. When compared to stringently inactive library sequences, the active enhancer sequences identified were highly enriched for liver open chromatin regions with activating histone marks (H3K27ac, H3K4me1, H3K4me3), were significantly closer to gene transcriptional start sites, and were significantly depleted of repressive (H3K27me3, H3K9me3) and transcribed region histone marks (H3K36me3). HDI-STARR-seq offers substantial improvements over current methodologies for large scale, functional profiling of enhancers, including condition-dependent enhancers, in liver tissue in vivo, and can be adapted to characterize enhancer activities in a variety of species and tissues by selecting suitable tissue- and species-specific promoter sequences.
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Affiliation(s)
- Ting-Ya Chang
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
| | - David J Waxman
- Departments of Biology and Biomedical Engineering, and Bioinformatics program, Boston University, Boston, MA 02215
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3
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Armani-Tourret M, Bone B, Tan TS, Sun W, Bellefroid M, Struyve T, Louella M, Yu XG, Lichterfeld M. Immune targeting of HIV-1 reservoir cells: a path to elimination strategies and cure. Nat Rev Microbiol 2024; 22:328-344. [PMID: 38337034 PMCID: PMC11131351 DOI: 10.1038/s41579-024-01010-8] [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] [Accepted: 01/12/2024] [Indexed: 02/12/2024]
Abstract
Successful approaches for eradication or cure of HIV-1 infection are likely to include immunological mechanisms, but remarkably little is known about how human immune responses can recognize and interact with the few HIV-1-infected cells that harbour genome-intact viral DNA, persist long term despite antiretroviral therapy and represent the main barrier to a cure. For a long time regarded as being completely shielded from host immune responses due to viral latency, these cells do, on closer examination with single-cell analytic techniques, display discrete footprints of immune selection, implying that human immune responses may be able to effectively engage and target at least some of these cells. The failure to eliminate rebound-competent virally infected cells in the majority of persons likely reflects the evolution of a highly selected pool of reservoir cells that are effectively camouflaged from immune recognition or rely on sophisticated approaches for resisting immune-mediated killing. Understanding the fine-tuned interplay between host immune responses and viral reservoir cells will help to design improved interventions that exploit the immunological vulnerabilities of HIV-1 reservoir cells.
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Affiliation(s)
- Marie Armani-Tourret
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Benjamin Bone
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Toong Seng Tan
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Weiwei Sun
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Maxime Bellefroid
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Tine Struyve
- HIV Cure Research Center, Ghent University, Ghent, Belgium
| | - Michael Louella
- Community Advisory Board, Delaney AIDS Research Enterprise (DARE), San Francisco, CA, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Xu G Yu
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
| | - Mathias Lichterfeld
- Infectious Disease Division, Brigham and Women's Hospital, Boston, MA, USA.
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA.
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4
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Wu XN, Wang MZ, Zhang N, Zhang W, Dong J, Ke MY, Xiang JX, Ma F, Xue F, Hou JJ, Ma ZJ, Wang FM, Liu XM, Wu R, Pawlik TM, Ye K, Yu J, Zhang XF, Lyu Y. Sex-determining region Y gene promotes liver fibrosis and accounts for sexual dimorphism in its pathophysiology. J Hepatol 2024; 80:928-940. [PMID: 38336346 DOI: 10.1016/j.jhep.2024.01.036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 01/13/2024] [Accepted: 01/29/2024] [Indexed: 02/12/2024]
Abstract
BACKGROUND & AIMS Men are more prone to develop and die from liver fibrosis than women. In this study, we aim to investigate how sex-determining region Y gene (SRY) in hepatocytes promotes liver fibrosis. METHODS Hepatocyte-specific Sry knock-in (KI), Sry knockout (KO), and Sry KI with platelet-derived growth factor receptor α (Pdgfrα) KO mice were generated. Liver fibrosis was induced in mice by bile duct ligation for 2 weeks or carbon tetrachloride treatment for 6 weeks. In addition, primary hepatocytes, hepatic stellate cells (HSCs), and immortalized cell lines were used for in vitro studies and mechanistic investigation. RESULTS Compared to females, the severity of toxin- or cholestasis-induced liver fibrosis is similarly increased in castrated and uncastrated male mice. Among all Y chromosome-encoded genes, SRY was the most significantly upregulated and consistently increased gene in fibrotic/cirrhotic livers in male patients and in mouse models. Sry KI mice developed exacerbated liver fibrosis, whereas Sry KO mice had alleviated liver fibrosis, compared to age- and sex-matched control mice after bile duct ligation or administration of carbon tetrachloride. Mechanistically, both our in vivo and in vitro studies illustrated that SRY in hepatocytes can transcriptionally regulate Pdgfrα expression, and promote HMGB1 (high mobility group box 1) release and subsequent HSC activation. Pdgfrα KO or treatment with the SRY inhibitor DAX1 in Sry KI mice abolished SRY-induced HMGB1 secretion and liver fibrosis. CONCLUSIONS SRY is a strong pro-fibrotic factor and accounts for the sex disparity observed in liver fibrosis, suggesting its critical role as a potentially sex-specific therapeutic target for prevention and treatment of the disease. IMPACT AND IMPLICATION We identified that a male-specific gene, sex-determining region Y gene (SRY), is a strong pro-fibrotic gene that accounts for the sex disparity observed in liver fibrosis. As such, SRY might be an appropriate target for surveillance and treatment of liver fibrosis in a sex-specific manner. Additionally, SRY might be a key player in the sexual dimorphism observed in hepatic pathophysiology more generally.
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Affiliation(s)
- Xiao-Ning Wu
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Meng-Zhou Wang
- National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Nan Zhang
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Wei Zhang
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Jian Dong
- Department of Vascular Surgery, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Meng-Yun Ke
- National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Jun-Xi Xiang
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Feng Ma
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Feng Xue
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Jing-Jing Hou
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Zhi-Jie Ma
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Fu-Min Wang
- National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Xue-Min Liu
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Rongqian Wu
- National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China
| | - Timothy M Pawlik
- Department of Surgery, Division of Surgical Oncology, The Ohio State University Wexner Medical Center and James Comprehensive Cancer Center, Columbus, Ohio, USA
| | - Kai Ye
- School of Automation Science and Engineering, Faculty of Electronic and Information Engineering, Xi'an Jiaotong University, China; Genome Institute, The First Affiliated Hospital of Xi'an Jiaotong University, China
| | - Jun Yu
- Institute of Digestive Disease and Department of Medicine and Therapeutics, State Key Laboratory of Digestive Disease, Li Ka Shing Institute of Health Sciences, The Chinese University of Hong Kong, Shatin, Hong Kong, China
| | - Xu-Feng Zhang
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China.
| | - Yi Lyu
- Department of Hepatobiliary Surgery and Institute of Advanced Surgical Technology and Engineering, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, Shaanxi Province, China; National-Local Joint Engineering Research Center for Precision Surgery & Regenerative Medicine, Xi'an Jiaotong University, Xi'an, Shaanxi Province, China.
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Sarver DC, Garcia-Diaz J, Saqib M, Riddle RC, Wong GW. Tmem263 deletion disrupts the GH/IGF-1 axis and causes dwarfism and impairs skeletal acquisition. eLife 2024; 12:RP90949. [PMID: 38241182 PMCID: PMC10945605 DOI: 10.7554/elife.90949] [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] [Indexed: 01/21/2024] Open
Abstract
Genome-wide association studies (GWAS) have identified a large number of candidate genes believed to affect longitudinal bone growth and bone mass. One of these candidate genes, TMEM263, encodes a poorly characterized plasma membrane protein. Single nucleotide polymorphisms in TMEM263 are associated with bone mineral density in humans and mutations are associated with dwarfism in chicken and severe skeletal dysplasia in at least one human fetus. Whether this genotype-phenotype relationship is causal, however, remains unclear. Here, we determine whether and how TMEM263 is required for postnatal growth. Deletion of the Tmem263 gene in mice causes severe postnatal growth failure, proportional dwarfism, and impaired skeletal acquisition. Mice lacking Tmem263 show no differences in body weight within the first 2 weeks of postnatal life. However, by P21 there is a dramatic growth deficit due to a disrupted growth hormone (GH)/insulin-like growth factor 1 (IGF-1) axis, which is critical for longitudinal bone growth. Tmem263-null mice have low circulating IGF-1 levels and pronounced reductions in bone mass and growth plate length. The low serum IGF-1 in Tmem263-null mice is associated with reduced hepatic GH receptor (GHR) expression and GH-induced JAK2/STAT5 signaling. A deficit in GH signaling dramatically alters GH-regulated genes and feminizes the liver transcriptome of Tmem263-null male mice, with their expression profile resembling wild-type female, hypophysectomized male, and Stat5b-null male mice. Collectively, our data validates the causal role for Tmem263 in regulating postnatal growth and raises the possibility that rare mutations or variants of TMEM263 may potentially cause GH insensitivity and impair linear growth.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Jean Garcia-Diaz
- Department of Orthopaedic Surgery, Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Orthopaedics, University of Maryland School of MedicineBaltimoreUnited States
- Cell and Molecular Medicine graduate program, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Muzna Saqib
- Department of Physiology, Johns Hopkins University School of MedicineBaltimoreUnited States
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of MedicineBaltimoreUnited States
- Department of Orthopaedics, University of Maryland School of MedicineBaltimoreUnited States
- Research and Development Service, Baltimore Veterans Administration Medical CenterBaltimoreUnited States
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of MedicineBaltimoreUnited States
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6
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Rampersaud A, Connerney J, Waxman DJ. Plasma growth hormone pulses induce male-biased pulsatile chromatin opening and epigenetic regulation in adult mouse liver. eLife 2023; 12:RP91367. [PMID: 38091606 PMCID: PMC10721219 DOI: 10.7554/elife.91367] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Sex differences in plasma growth hormone (GH) profiles, pulsatile in males and persistent in females, regulate sex differences in hepatic STAT5 activation linked to sex differences in gene expression and liver disease susceptibility, but little is understood about the fundamental underlying, GH pattern-dependent regulatory mechanisms. Here, DNase-I hypersensitivity site (DHS) analysis of liver chromatin accessibility in a cohort of 18 individual male mice established that the endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility. Strikingly, a single physiological replacement dose of GH given to hypophysectomized male mice restored, within 30 min, liver STAT5 activity and chromatin accessibility at 83% of the dynamic, pituitary hormone-dependent male-biased DHS. Sex-dependent transcription factor binding patterns and chromatin state analysis identified key genomic and epigenetic features distinguishing this dynamic, STAT5-driven mechanism of male-biased chromatin opening from a second GH-dependent mechanism operative at static male-biased DHS, which are constitutively open in male liver. Dynamic but not static male-biased DHS adopt a bivalent-like epigenetic state in female liver, as do static female-biased DHS in male liver, albeit using distinct repressive histone marks in each sex, namely, H3K9me3 at male-biased DHS in female liver and H3K27me3 at female-biased DHS in male liver. Moreover, sex-biased H3K36me3 marks are uniquely enriched at static sex-biased DHS, which may serve to keep these sex-dependent hepatocyte enhancers free of H3K27me3 repressive marks and thus constitutively open. Pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is thus one of two distinct GH-determined mechanisms for establishing widespread sex differences in hepatic chromatin accessibility and epigenetic regulation, both closely linked to sex-biased gene transcription and the sexual dimorphism of liver function.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston UniversityBostonUnited States
| | - Jeannette Connerney
- Department of Biology and Bioinformatics Program, Boston UniversityBostonUnited States
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston UniversityBostonUnited States
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7
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Rampersaud A, Connerney J, Waxman DJ. Plasma Growth Hormone Pulses Induce Male-biased Pulsatile Chromatin Opening and Epigenetic Regulation in Adult Mouse Liver. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554153. [PMID: 37662275 PMCID: PMC10473588 DOI: 10.1101/2023.08.21.554153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Sex-differences in plasma growth hormone (GH) profiles, pulsatile in males and persistent in females, regulate sex differences in hepatic STAT5 activation linked to sex differences in gene expression and liver disease susceptibility, but little is understood about the fundamental underlying, GH pattern-dependent regulatory mechanisms. Here, DNase hypersensitivity site (DHS) analysis of liver chromatin accessibility in a cohort of 18 individual male mice established that the endogenous male rhythm of plasma GH pulse-stimulated liver STAT5 activation induces dynamic, repeated cycles of chromatin opening and closing at several thousand liver DHS and comprises a novel mechanism conferring male bias to liver chromatin accessibility. Strikingly, a single physiological replacement dose of GH given to hypophysectomized male mice restored, within 30 min, liver STAT5 activity and chromatin accessibility at 83% of the pituitary hormone-dependent dynamic male-biased DHS. Sex-dependent transcription factor binding patterns and chromatin state analysis identified key genomic and epigenetic features distinguishing this dynamic, STAT5-driven mechanism of male-biased chromatin opening from a second GH-dependent mechanism operative at static male-biased DHS, which are constitutively open in male liver. Dynamic but not static male-biased DHS adopt a bivalent-like epigenetic state in female liver, as do static female-biased DHS in male liver, albeit using distinct repressive histone marks in each sex, namely, H3K27me3 at female-biased DHS in male liver, and H3K9me3 at male-biased DHS in female liver. Moreover, sex-biased H3K36me3 marks are uniquely enriched at static sex-biased DHS, which may serve to keep these sex-dependent hepatocyte enhancers free of H3K27me3 repressive marks and thus constitutively open. Pulsatile chromatin opening stimulated by endogenous, physiological hormone pulses is thus one of two distinct GH-determined mechanisms for establishing widespread sex differences in hepatic chromatin accessibility and epigenetic regulation, both closely linked to sex-biased gene transcription and the sexual dimorphism of liver function.
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Affiliation(s)
- Andy Rampersaud
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215 USA
| | - Jeannette Connerney
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215 USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215 USA
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8
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Sarver DC, Garcia-Diaz J, Saqib M, Riddle RC, Wong GW. Tmem263 deletion disrupts the GH/IGF-1 axis and causes dwarfism and impairs skeletal acquisition. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.02.551694. [PMID: 37577461 PMCID: PMC10418210 DOI: 10.1101/2023.08.02.551694] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
Genome-wide association studies (GWAS) have identified a large number of candidate genes believed to affect longitudinal bone growth and bone mass. One of these candidate genes, TMEM263, encodes a poorly characterized plasma membrane protein. Single nucleotide polymorphisms in TMEM263 are associated with bone mineral density in humans and mutations are associated with dwarfism in chicken and severe skeletal dysplasia in at least one human fetus. Whether this genotype-phenotype relationship is causal, however, remains unclear. Here, we determine whether and how TMEM263 is required for postnatal growth. Deletion of the Tmem263 gene in mice causes severe postnatal growth failure, proportional dwarfism, and impaired skeletal acquisition. Mice lacking Tmem263 show no differences in body weight within the first two weeks of postnatal life. However, by P21 there is a dramatic growth deficit due to a disrupted GH/IGF-1 axis, which is critical for longitudinal bone growth. Tmem263-null mice have low circulating IGF-1 levels and pronounced reductions in bone mass and growth plate length. The low serum IGF-1 in Tmem263-null mice is associated with reduced hepatic GH receptor (GHR) expression and GH-induced JAK2/STAT5 signaling. A deficit in GH signaling dramatically alters GH-regulated genes and feminizes the liver transcriptome of Tmem263-null male mice, with their expression profile resembling a wild-type female, hypophysectomized male, and Stat5b-null male mice. Collectively, our data validates the causal role for Tmem263 in regulating postnatal growth and raises the possibility that rare mutations or variants of TMEM263 may potentially cause GH insensitivity and impair linear growth.
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Affiliation(s)
- Dylan C Sarver
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Jean Garcia-Diaz
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Cell and Molecular Medicine graduate program, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Muzna Saqib
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Ryan C Riddle
- Department of Orthopaedic Surgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
- Department of Orthopaedics, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Research and Development Service, Baltimore Veterans Administration Medical Center, Baltimore, Maryland, USA
| | - G William Wong
- Department of Physiology, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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9
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Miao Z, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor control of sexually dimorphic gene expression in the mammalian kidney. Dev Cell 2023; 58:2338-2358.e5. [PMID: 37673062 PMCID: PMC10873092 DOI: 10.1016/j.devcel.2023.08.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 07/20/2023] [Accepted: 08/04/2023] [Indexed: 09/08/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility, and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA sequencing (RNA-seq) data demonstrated that sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR)-mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation, whereas analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, disease, and metabolic linkage of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Zhen Miao
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | - Ingileif B Hallgrimsdottir
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA; Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA.
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10
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Rodríguez-Montes L, Ovchinnikova S, Yuan X, Studer T, Sarropoulos I, Anders S, Kaessmann H, Cardoso-Moreira M. Sex-biased gene expression across mammalian organ development and evolution. Science 2023; 382:eadf1046. [PMID: 37917687 PMCID: PMC7615307 DOI: 10.1126/science.adf1046] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Accepted: 09/18/2023] [Indexed: 11/04/2023]
Abstract
Sexually dimorphic traits are common among mammals and are specified during development through the deployment of sex-specific genetic programs. Because little is known about these programs, we investigated them using a resource of gene expression profiles in males and females throughout the development of five organs in five mammals (human, mouse, rat, rabbit, and opossum) and a bird (chicken). We found that sex-biased gene expression varied considerably across organs and species and was often cell-type specific. Sex differences increased abruptly around sexual maturity instead of increasing gradually during organ development. Finally, sex-biased gene expression evolved rapidly at the gene level, with differences between organs in the evolutionary mechanisms used, but more slowly at the cellular level, with the same cell types being sexually dimorphic across species.
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Affiliation(s)
- Leticia Rodríguez-Montes
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | | | - Xuefei Yuan
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Tania Studer
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Ioannis Sarropoulos
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
| | - Simon Anders
- BioQuant, Heidelberg University, D-69120 Heidelberg, Germany
| | - Henrik Kaessmann
- Center for Molecular Biology of Heidelberg University (ZMBH), DKFZ-ZMBH Alliance, D-69120 Heidelberg, Germany
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11
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Wiese CB, Avetisyan R, Reue K. The impact of chromosomal sex on cardiometabolic health and disease. Trends Endocrinol Metab 2023; 34:652-665. [PMID: 37598068 PMCID: PMC11090013 DOI: 10.1016/j.tem.2023.07.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Revised: 07/14/2023] [Accepted: 07/20/2023] [Indexed: 08/21/2023]
Abstract
Many aspects of metabolism are sex-biased, from gene expression in metabolic tissues to the prevalence and presentation of cardiometabolic diseases. The influence of hormones produced by male and female gonads has been widely documented, but recent studies have begun to elucidate the impact of genetic sex (XX or XY chromosomes) on cellular and organismal metabolism. XX and XY cells have differential gene dosage conferred by specific genes that escape X chromosome inactivation or the presence of Y chromosome genes that are absent from XX cells. Studies in mouse models that dissociate chromosomal and gonadal sex have uncovered mechanisms for sex-biased epigenetic, transcriptional, and post-transcriptional regulation of gene expression in conditions such as obesity, atherosclerosis, pulmonary hypertension, autoimmune disease, and Alzheimer's disease.
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Affiliation(s)
- Carrie B Wiese
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Rozeta Avetisyan
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA
| | - Karen Reue
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, CA 90095, USA.
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12
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Vu H, Ernst J. Universal chromatin state annotation of the mouse genome. Genome Biol 2023; 24:153. [PMID: 37370147 PMCID: PMC10294404 DOI: 10.1186/s13059-023-02994-x] [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: 12/12/2022] [Accepted: 06/18/2023] [Indexed: 06/29/2023] Open
Abstract
A large-scale application of the "stacked modeling" approach for chromatin state discovery previously provides a single "universal" chromatin state annotation of the human genome based jointly on data from many cell and tissue types. Here, we produce an analogous chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 cell or tissue types. To characterize each chromatin state, we relate the states to external annotations and compare them to analogously defined human states. We expect the universal chromatin state annotation for mouse to be a useful resource for studying this key model organism's genome.
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Affiliation(s)
- Ha Vu
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Jason Ernst
- Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.
- Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Eli and Edythe Broad Center of Regenerative Medicine and Stem Cell Research at University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Computer Science Department, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
- Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, 90095, USA.
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13
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Xiong L, Liu J, Han SY, Koppitch K, Guo JJ, Rommelfanger M, Gao F, Hallgrimsdottir IB, Pachter L, Kim J, MacLean AL, McMahon AP. Direct androgen receptor regulation of sexually dimorphic gene expression in the mammalian kidney. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.06.539585. [PMID: 37205355 PMCID: PMC10187285 DOI: 10.1101/2023.05.06.539585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Mammalian organs exhibit distinct physiology, disease susceptibility and injury responses between the sexes. In the mouse kidney, sexually dimorphic gene activity maps predominantly to proximal tubule (PT) segments. Bulk RNA-seq data demonstrated sex differences were established from 4 and 8 weeks after birth under gonadal control. Hormone injection studies and genetic removal of androgen and estrogen receptors demonstrated androgen receptor (AR) mediated regulation of gene activity in PT cells as the regulatory mechanism. Interestingly, caloric restriction feminizes the male kidney. Single-nuclear multiomic analysis identified putative cis-regulatory regions and cooperating factors mediating PT responses to AR activity in the mouse kidney. In the human kidney, a limited set of genes showed conserved sex-linked regulation while analysis of the mouse liver underscored organ-specific differences in the regulation of sexually dimorphic gene expression. These findings raise interesting questions on the evolution, physiological significance, and disease and metabolic linkage, of sexually dimorphic gene activity.
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Affiliation(s)
- Lingyun Xiong
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Jing Liu
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Seung Yub Han
- Graduate Program in Genomics and Computational Biology, Biomedical Graduate Studies, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Kari Koppitch
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Jin-Jin Guo
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
| | - Megan Rommelfanger
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Fan Gao
- Caltech Bioinformatics Resource Center at Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
| | | | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
- Department of Computing and Mathematical Sciences, California Institute of Technology, Pasadena, CA 91125, USA
| | - Junhyong Kim
- Department of Biology, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Adam L. MacLean
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Andrew P. McMahon
- Department of Stem Cell Biology and Regenerative Medicine, Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research, Keck School of Medicine of the University of Southern California, Los Angeles, CA 90089, USA
- Lead Contact
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14
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Chen L, Chou CL, Yang CR, Knepper MA. Multiomics Analyses Reveal Sex Differences in Mouse Renal Proximal Subsegments. J Am Soc Nephrol 2023; 34:829-845. [PMID: 36758122 PMCID: PMC10125651 DOI: 10.1681/asn.0000000000000089] [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: 10/05/2022] [Accepted: 01/04/2023] [Indexed: 02/11/2023] Open
Abstract
SIGNIFICANCE STATEMENT Sex-dependent differences in kidney function are recognized but the underlying molecular mechanisms are largely unexplored. Advances in genomics and proteomic technologies now allow extensive characterization of differences between the same cell types of males and females. Multiomics integrating RNA-seq, ATAC-seq, and proteomics data to investigate differences in gene expression, chromatin accessibility, and protein expression in proximal tubules of male and female mice identified many sex-biased genes and proteins associated with kidney functions, including metabolic and transport processes. Sex differences may also arise from variations of the interaction between transcription factors and accessible chromatin regions. A comprehensive web resource is provided to advance understanding of sex differences in cells of the proximal tubule. BACKGROUND Sex differences have been increasingly recognized as important in kidney physiology and pathophysiology, but limited resources are available for comprehensive interrogation of sex differences. METHODS RNA-seq and ATAC-seq of microdissected mouse proximal tubules and protein mass spectrometry of homogenized perfused mouse kidneys reveal differences in proximal tubule cells of males and females. RESULTS The transcriptomic data indicated that the major differences in the proximal tubules between the sexes were in the S2/S3 segments, and most of the sex-biased transcripts mapped to autosomes rather than to the sex chromosomes. Many of the transcripts exhibiting sex-biased expression are involved in monocarboxylic acid metabolic processes, organic anion transport, and organic acid transport. The ATAC-seq method on microdissected tubules captured chromatin accessibility. Many of the more than 7000 differentially accessible DNA regions identified were in distal regions. Motif analyses revealed a lack of direct involvement of estrogen receptors or the androgen receptor (absence of canonical hormone response elements), suggesting an indirect regulatory role of sex hormones. Instead, analyses identified several transcription factors (TFs) ( Tead1 , Nfia/b , and Pou3f3 ) whose interplay with proximal tubule-specific TFs ( e.g. , Hnf1b , Hnf4a ) may contribute to sex differences. Finally, the whole-kidney proteome was correlated with the transcriptome, and many sex-biased proteins ( e.g. , Cyp2e1, Acsm2/3) were identified. CONCLUSIONS Sex-dependent cis-regulatory elements interact with TFs in ways that lead to sex-biased gene expression in proximal tubule cells. These data are provided as a user-friendly web page at https://esbl.nhlbi.nih.gov/MRECA/PT/ .
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Affiliation(s)
- Lihe Chen
- Epithelial Systems Biology Laboratory, Systems Biology Center, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland
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15
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Patil NP, Gómez-Hernández A, Zhang F, Cancel L, Feng X, Yan L, Xia K, Takematsu E, Yang EY, Le V, Fisher ME, Gonzalez-Rodriguez A, Garcia-Monzon C, Tunnell J, Tarbell J, Linhardt RJ, Baker AB. Rhamnan sulfate reduces atherosclerotic plaque formation and vascular inflammation. Biomaterials 2022; 291:121865. [DOI: 10.1016/j.biomaterials.2022.121865] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 09/09/2022] [Accepted: 10/17/2022] [Indexed: 11/28/2022]
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16
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Kamiya A, Ida K. Liver Injury and Cell Survival in Non-Alcoholic Steatohepatitis Regulated by Sex-Based Difference through B Cell Lymphoma 6. Cells 2022; 11:cells11233751. [PMID: 36497010 PMCID: PMC9737870 DOI: 10.3390/cells11233751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/14/2022] [Accepted: 11/20/2022] [Indexed: 11/25/2022] Open
Abstract
The liver is a crucial organ for maintaining homeostasis in living organisms and is the center of various metabolic functions. Therefore, abnormal metabolic activity, as in metabolic syndrome, leads to pathological conditions, such as abnormal accumulation of lipids in the liver. Inflammation and cell death are induced by several stresses in the fatty liver, namely steatohepatitis. In recent years, an increase in non-alcoholic steatohepatitis (NASH), which is not dependent on excessive alcohol intake, has become an issue as a major cause of liver cirrhosis and liver cancer. There are several recent findings on functional sex-based differences, NASH, and cell stress and death in the liver. In particular, NASH-induced liver injury and tumorigeneses were suppressed by B cell lymphoma 6, the transcriptional factor regulating sex-based liver functional gene expression. In this review, we discuss cell response to stress and lipotoxicity in NASH and its regulatory mechanisms.
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Affiliation(s)
- Akihide Kamiya
- Correspondence: ; Tel.: +81-463-93-1121 (ext. 2783); Fax: +81-463-95-3522
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17
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Abstract
Growth hormone orchestrates a complex, sex-dependent balancing act.
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Affiliation(s)
- David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
| | - Rhonda D Kineman
- Department of Medicine, Section of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Chicago, IL, USA
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18
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Rao S. Sex differences in HIV-1 persistence and the implications for a cure. Front Glob Womens Health 2022; 3:942345. [PMID: 36212905 PMCID: PMC9538461 DOI: 10.3389/fgwh.2022.942345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 09/05/2022] [Indexed: 11/13/2022] Open
Abstract
Of the 38 million people currently living with Human Immunodeficiency Virus type-1 (HIV-1), women, especially adolescents and young women, are disproportionally affected by the HIV-1 pandemic. Acquired immunodeficiency syndrome (AIDS) - related illnesses are the leading cause of death in women of reproductive age worldwide. Although combination antiretroviral therapy (cART) can suppress viral replication, cART is not curative due to the presence of a long-lived viral reservoir that persists despite treatment. Biological sex influences the characteristics of the viral reservoir as well as the immune responses to infection, factors that can have a significant impact on the design and quantification of HIV-1 curative interventions in which women are grossly underrepresented. This mini-review will provide an update on the current understanding of the impact of biological sex on the viral reservoir and will discuss the implications of these differences in the context of the development of potential HIV-1 curative strategies, with a focus on the shock and kill approach to an HIV-1 cure. This mini-review will also highlight the current gaps in the knowledge of sex-based differences in HIV-1 persistence and will speculate on approaches to address them to promote the development of more scalable, effective curative approaches for people living with HIV-1.
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19
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Goldfarb CN, Karri K, Pyatkov M, Waxman DJ. Interplay Between GH-regulated, Sex-biased Liver Transcriptome and Hepatic Zonation Revealed by Single-Nucleus RNA Sequencing. Endocrinology 2022; 163:6580481. [PMID: 35512247 PMCID: PMC9154260 DOI: 10.1210/endocr/bqac059] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Indexed: 11/19/2022]
Abstract
The zonation of liver metabolic processes is well-characterized; however, little is known about the cell type-specificity and zonation of sexually dimorphic gene expression or its growth hormone (GH)-dependent transcriptional regulators. We address these issues using single-nucleus RNA-sequencing of 32 000 nuclei representing 9 major liver cell types. Nuclei were extracted from livers from adult male and female mice; from males infused with GH continuously, mimicking the female plasma GH pattern; and from mice exposed to TCPOBOP, a xenobiotic agonist ligand of the nuclear receptor CAR that perturbs sex-biased gene expression. Analysis of these rich transcriptomic datasets revealed the following: 1) expression of sex-biased genes and their GH-dependent transcriptional regulators is primarily restricted to hepatocytes and is not a feature of liver nonparenchymal cells; 2) many sex-biased transcripts show sex-dependent zonation within the liver lobule; 3) gene expression is substantially feminized both in periportal and pericentral hepatocytes when male mice are infused with GH continuously; 4) sequencing nuclei increases the sensitivity for detecting thousands of nuclear-enriched long-noncoding RNAs (lncRNAs) and enables determination of their liver cell type-specificity, sex-bias and hepatocyte zonation profiles; 5) the periportal to pericentral hepatocyte cell ratio is significantly higher in male than female liver; and 6) TCPOBOP exposure disrupts both sex-specific gene expression and hepatocyte zonation within the liver lobule. These findings highlight the complex interconnections between hepatic sexual dimorphism and zonation at the single-cell level and reveal how endogenous hormones and foreign chemical exposure can alter these interactions across the liver lobule with large effects both on protein-coding genes and lncRNAs.
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Affiliation(s)
- Christine N Goldfarb
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Biomedical Engineering, Boston University, Boston, Massachusetts 02215, USA
| | - Kritika Karri
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
- Bioinformatics Program Boston University, Boston, Massachusetts 02215, USA
| | - Maxim Pyatkov
- Department of Biology, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Correspondence: David J. Waxman, PhD, Department of Biology, Boston University, 5 Cummington Mall, Boston, MA 02215, USA.
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20
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Chlamydas S, Markouli M, Strepkos D, Piperi C. Epigenetic mechanisms regulate sex-specific bias in disease manifestations. J Mol Med (Berl) 2022; 100:1111-1123. [PMID: 35764820 PMCID: PMC9244100 DOI: 10.1007/s00109-022-02227-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 06/02/2022] [Accepted: 06/20/2022] [Indexed: 12/15/2022]
Abstract
Abstract Sex presents a vital determinant of a person’s physiology, anatomy, and development. Recent clinical studies indicate that sex is also involved in the differential manifestation of various diseases, affecting both clinical outcome as well as response to therapy. Genetic and epigenetic changes are implicated in sex bias and regulate disease onset, including the inactivation of the X chromosome as well as sex chromosome aneuploidy. The differential expression of X-linked genes, along with the presence of sex-specific hormones, exhibits a significant impact on immune system function. Several studies have revealed differences between the two sexes in response to infections, including respiratory diseases and COVID-19 infection, autoimmune disorders, liver fibrosis, neuropsychiatric diseases, and cancer susceptibility, which can be explained by sex-biased immune responses. In the present review, we explore the input of genetic and epigenetic interplay in the sex bias underlying disease manifestation and discuss their effects along with sex hormones on disease development and progression, aiming to reveal potential new therapeutic targets. Key messages Sex is involved in the differential manifestation of various diseases. Epigenetic modifications influence X-linked gene expression, affecting immune response to infections, including COVID-19. Epigenetic mechanisms are responsible for the sex bias observed in several respiratory and autoimmune disorders, liver fibrosis, neuropsychiatric diseases, and cancer.
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Affiliation(s)
- Sarantis Chlamydas
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece.,Olink Proteomics, Uppsala, Sweden
| | - Mariam Markouli
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece
| | - Dimitrios Strepkos
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece
| | - Christina Piperi
- Department of Biological Chemistry, Medical School, National and Kapodistrian University of Athens, 75 M. Asias Street Bldg 16, 11527, Athens, Greece.
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21
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Grant OA, Wang Y, Kumari M, Zabet NR, Schalkwyk L. Characterising sex differences of autosomal DNA methylation in whole blood using the Illumina EPIC array. Clin Epigenetics 2022; 14:62. [PMID: 35568878 PMCID: PMC9107695 DOI: 10.1186/s13148-022-01279-7] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Accepted: 04/18/2022] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Sex differences are known to play a role in disease aetiology, progression and outcome. Previous studies have revealed autosomal epigenetic differences between males and females in some tissues, including differences in DNA methylation patterns. Here, we report for the first time an analysis of autosomal sex differences in DNAme using the Illumina EPIC array in human whole blood by performing a discovery (n = 1171) and validation (n = 2471) analysis. RESULTS We identified and validated 396 sex-associated differentially methylated CpG sites (saDMPs) with the majority found to be female-biased CpGs (74%). These saDMP's are enriched in CpG islands and CpG shores and located preferentially at 5'UTRs, 3'UTRs and enhancers. Additionally, we identified 266 significant sex-associated differentially methylated regions overlapping genes, which have previously been shown to exhibit epigenetic sex differences, and novel genes. Transcription factor binding site enrichment revealed enrichment of transcription factors related to critical developmental processes and sex determination such as SRY and ESR1. CONCLUSION Our study reports a reliable catalogue of sex-associated CpG sites and elucidates several characteristics of these sites using large-scale discovery and validation data sets. This resource will benefit future studies aiming to investigate sex specific epigenetic signatures and further our understanding of the role of DNA methylation in sex differences in human whole blood.
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Affiliation(s)
- Olivia A Grant
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- Institute of Social and Economic Research, University of Essex, Colchester, CO4 3SQ, UK
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK
| | - Yucheng Wang
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK
- School of Computer Science and Electronic Engineering, University of Essex, Colchester, CO4 3SQ, UK
| | - Meena Kumari
- Institute of Social and Economic Research, University of Essex, Colchester, CO4 3SQ, UK
| | - Nicolae Radu Zabet
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
- Blizard Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London, E1 2AT, UK.
| | - Leonard Schalkwyk
- School of Life Sciences, University of Essex, Colchester, CO4 3SQ, UK.
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22
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Blencowe M, Chen X, Zhao Y, Itoh Y, McQuillen CN, Han Y, Shou BL, McClusky R, Reue K, Arnold AP, Yang X. Relative contributions of sex hormones, sex chromosomes, and gonads to sex differences in tissue gene regulation. Genome Res 2022; 32:807-824. [PMID: 35396276 PMCID: PMC9104702 DOI: 10.1101/gr.275965.121] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 03/29/2022] [Indexed: 11/25/2022]
Abstract
Sex differences in physiology and disease in mammals result from the effects of three classes of factors that are inherently unequal in males and females: reversible (activational) effects of gonadal hormones, permanent (organizational) effects of gonadal hormones, and cell-autonomous effects of sex chromosomes, as well as genes driven by these classes of factors. Often, these factors act together to cause sex differences in specific phenotypes, but the relative contribution of each and the interactions among them remain unclear. Here, we used the four core genotypes (FCG) mouse model with or without hormone replacement to distinguish the effects of each class of sex-biasing factors on transcriptome regulation in liver and adipose tissues. We found that the activational hormone levels have the strongest influence on gene expression, followed by the organizational gonadal sex effect, and last, sex chromosomal effect, along with interactions among the three factors. Tissue specificity was prominent, with a major impact of estradiol on adipose tissue gene regulation and of testosterone on the liver transcriptome. The networks affected by the three sex-biasing factors include development, immunity and metabolism, and tissue-specific regulators were identified for these networks. Furthermore, the genes affected by individual sex-biasing factors and interactions among factors are associated with human disease traits such as coronary artery disease, diabetes, and inflammatory bowel disease. Our study offers a tissue-specific account of the individual and interactive contributions of major sex-biasing factors to gene regulation that have broad impact on systemic metabolic, endocrine, and immune functions.
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Affiliation(s)
- Montgomery Blencowe
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, California 90095, USA
| | - Xuqi Chen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095, USA
| | - Yutian Zhao
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, California 90095, USA
| | - Yuichiro Itoh
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095, USA
- Department of Neurology, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Caden N McQuillen
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
| | - Yanjie Han
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
| | - Benjamin L Shou
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
| | - Rebecca McClusky
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095, USA
| | - Karen Reue
- Department of Human Genetics and Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
| | - Arthur P Arnold
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, California 90095, USA
- Laboratory of Neuroendocrinology of the Brain Research Institute, University of California, Los Angeles, California 90095, USA
| | - Xia Yang
- Department of Integrative Biology and Physiology, University of California, Los Angeles, California 90095, USA
- Interdepartmental Program of Molecular, Cellular and Integrative Physiology, University of California, Los Angeles, California 90095, USA
- Department of Human Genetics and Molecular Biology Institute, David Geffen School of Medicine, University of California, Los Angeles, California 90095, USA
- Institute for Quantitative and Computational Biosciences, University of California, Los Angeles, California 90095, USA
- Molecular Biology Institute, University of California, Los Angeles, California 90095, USA
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23
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Lau-Corona D, Ma H, Vergato C, Sarmento-Cabral A, del Rio-Moreno M, Kineman RD, Waxman DJ. Constitutively Active STAT5b Feminizes Mouse Liver Gene Expression. Endocrinology 2022; 163:bqac046. [PMID: 35396838 PMCID: PMC9070516 DOI: 10.1210/endocr/bqac046] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Indexed: 11/19/2022]
Abstract
STAT5 is an essential transcriptional regulator of the sex-biased actions of GH in the liver. Delivery of constitutively active STAT5 (STAT5CA) to male mouse liver using an engineered adeno-associated virus with high tropism for the liver is shown to induce widespread feminization of the liver, with extensive induction of female-biased genes and repression of male-biased genes, largely mimicking results obtained when male mice are given GH as a continuous infusion. Many of the STAT5CA-responding genes were associated with nearby (< 50 kb) sites of STAT5 binding to liver chromatin, supporting the proposed direct role of persistently active STAT5 in continuous GH-induced liver feminization. The feminizing effects of STAT5CA were dose-dependent; moreover, at higher levels, STAT5CA overexpression resulted in some histopathology, including hepatocyte hyperplasia, and increased karyomegaly and multinuclear hepatocytes. These findings establish that the persistent activation of STAT5 by GH that characterizes female liver is by itself sufficient to account for the sex-dependent expression of a majority of hepatic sex-biased genes. Moreover, histological changes seen when STAT5CA is overexpressed highlight the importance of carefully evaluating such effects before considering STAT5 derivatives for therapeutic use in treating liver disease.
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Affiliation(s)
- Dana Lau-Corona
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Hong Ma
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Cameron Vergato
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, USA
| | - Andre Sarmento-Cabral
- Department of Medicine, Section of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago and Research and Development Division, Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Mercedes del Rio-Moreno
- Department of Medicine, Section of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago and Research and Development Division, Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - Rhonda D Kineman
- Department of Medicine, Section of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago and Research and Development Division, Jesse Brown VA Medical Center, Chicago, IL 60612, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA 02215, USA
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24
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Sandovici I, Fernandez-Twinn DS, Hufnagel A, Constância M, Ozanne SE. Sex differences in the intergenerational inheritance of metabolic traits. Nat Metab 2022; 4:507-523. [PMID: 35637347 DOI: 10.1038/s42255-022-00570-4] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Accepted: 04/05/2022] [Indexed: 02/02/2023]
Abstract
Strong evidence suggests that early-life exposures to suboptimal environmental factors, including those in utero, influence our long-term metabolic health. This has been termed developmental programming. Mounting evidence suggests that the growth and metabolism of male and female fetuses differ. Therefore, sexual dimorphism in response to pre-conception or early-life exposures could contribute to known sex differences in susceptibility to poor metabolic health in adulthood. However, until recently, many studies, especially those in animal models, focused on a single sex, or, often in the case of studies performed during intrauterine development, did not report the sex of the animal at all. In this review, we (a) summarize the evidence that male and females respond differently to a suboptimal pre-conceptional or in utero environment, (b) explore the potential biological mechanisms that underlie these differences and (c) review the consequences of these differences for long-term metabolic health, including that of subsequent generations.
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Affiliation(s)
- Ionel Sandovici
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK
| | - Denise S Fernandez-Twinn
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Antonia Hufnagel
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Miguel Constância
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
- Department of Obstetrics and Gynaecology and National Institute for Health Research Cambridge Biomedical Research Centre, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
| | - Susan E Ozanne
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge, UK.
- Centre for Trophoblast Research, Department of Physiology, Development and Neuroscience, University of Cambridge, Cambridge, UK.
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25
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Gueno J, Borg M, Bourdareau S, Cossard G, Godfroy O, Lipinska A, Tirichine L, Cock J, Coelho S. Chromatin landscape associated with sexual differentiation in a UV sex determination system. Nucleic Acids Res 2022; 50:3307-3322. [PMID: 35253891 PMCID: PMC8989524 DOI: 10.1093/nar/gkac145] [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: 05/06/2021] [Revised: 02/15/2022] [Accepted: 03/04/2022] [Indexed: 12/12/2022] Open
Abstract
In many eukaryotes, such as dioicous mosses and many algae, sex is determined by UV sex chromosomes and is expressed during the haploid phase of the life cycle. In these species, the male and female developmental programs are initiated by the presence of the U- or V-specific regions of the sex chromosomes but, as in XY and ZW systems, sexual differentiation is largely driven by autosomal sex-biased gene expression. The mechanisms underlying the regulation of sex-biased expression of genes during sexual differentiation remain elusive. Here, we investigated the extent and nature of epigenomic changes associated with UV sexual differentiation in the brown alga Ectocarpus, a model UV system. Six histone modifications were quantified in near-isogenic lines, leading to the identification of 16 chromatin signatures across the genome. Chromatin signatures correlated with levels of gene expression and histone PTMs changes in males versus females occurred preferentially at genes involved in sex-specific pathways. Despite the absence of chromosome scale dosage compensation and the fact that UV sex chromosomes recombine across most of their length, the chromatin landscape of these chromosomes was remarkably different to that of autosomes. Hotspots of evolutionary young genes in the pseudoautosomal regions appear to drive the exceptional chromatin features of UV sex chromosomes.
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Affiliation(s)
- Josselin Gueno
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Michael Borg
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
| | - Simon Bourdareau
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Guillaume Cossard
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Olivier Godfroy
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Agnieszka Lipinska
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
| | - Leila Tirichine
- Nantes Universite, CNRS, US2B, UMR 6286, F-44000, Nantes, France
| | - J Mark Cock
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Univ Paris 06, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tübingen72076, Tübingen, Germany
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26
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Le Corre L, Brulport A, Vaiman D, Chagnon MC. Epoxiconazole alters the histology and transcriptome of mouse liver in a transgenerational pattern. Chem Biol Interact 2022; 360:109952. [DOI: 10.1016/j.cbi.2022.109952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Revised: 04/08/2022] [Accepted: 04/12/2022] [Indexed: 11/30/2022]
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27
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Penn DJ, Zala SM, Luzynski KC. Regulation of Sexually Dimorphic Expression of Major Urinary Proteins. Front Physiol 2022; 13:822073. [PMID: 35431992 PMCID: PMC9008510 DOI: 10.3389/fphys.2022.822073] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 02/21/2022] [Indexed: 11/15/2022] Open
Abstract
Male house mice excrete large amounts of protein in their urinary scent marks, mainly composed of Major Urinary Proteins (MUPs), and these lipocalins function as pheromones and pheromone carriers. Here, we review studies on sexually dimorphic MUP expression in house mice, including the proximate mechanisms controlling MUP gene expression and their adaptive functions. Males excrete 2 to 8 times more urinary protein than females, though there is enormous variation in gene expression across loci in both sexes. MUP expression is dynamically regulated depending upon a variety of factors. Males regulate MUP expression according to social status, whereas females do not, and males regulate expression depending upon health and condition. Male-biased MUP expression is regulated by pituitary secretion of growth hormone (GH), which binds receptors in the liver, activating the JAK2-STAT5 signaling pathway, chromatin accessibility, and MUP gene transcription. Pulsatile male GH secretion is feminized by several factors, including caloric restriction, microbiota depletion, and aging, which helps explain condition-dependent MUP expression. If MUP production has sex-specific fitness optima, then this should generate sexual antagonism over allelic expression (intra-locus sexual conflict) selectively favoring sexually dimorphic expression. MUPs influence the sexual attractiveness of male urinary odor and increased urinary protein excretion is correlated with the reproductive success of males but not females. This finding could explain the selective maintenance of sexually dimorphic MUP expression. Producing MUPs entails energetic costs, but increased excretion may reduce the net energetic costs and predation risks from male scent marking as well as prolong the release of chemical signals. MUPs may also provide physiological benefits, including regulating metabolic rate and toxin removal, which may have sex-specific effects on survival. A phylogenetic analysis on the origins of male-biased MUP gene expression in Mus musculus suggests that this sexual dimorphism evolved by increasing male MUP expression rather than reducing female expression.
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28
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Sex differences in the genetic regulation of the blood transcriptome response to glucocorticoid receptor activation. Transl Psychiatry 2021; 11:632. [PMID: 34903727 PMCID: PMC8669026 DOI: 10.1038/s41398-021-01756-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 11/25/2021] [Indexed: 12/13/2022] Open
Abstract
Substantial sex differences have been reported in the physiological response to stress at multiple levels, including the release of the stress hormone, cortisol. Here, we explore the genomic variants in 93 females and 196 males regulating the initial transcriptional response to cortisol via glucocorticoid receptor (GR) activation. Gene expression levels in peripheral blood were obtained before and after GR-stimulation with the selective GR agonist dexamethasone to identify differential expression following GR-activation. Sex stratified analyses revealed that while the transcripts responsive to GR-stimulation were mostly overlapping between males and females, the quantitative trait loci (eQTLs) regulation differential transcription to GR-stimulation was distinct. Sex-stratified eQTL SNPs (eSNPs) were located in different functional genomic elements and sex-stratified transcripts were enriched within postmortem brain transcriptional profiles associated with Major Depressive Disorder (MDD) specifically in males and females in the cingulate cortex. Female eSNPs were enriched among SNPs linked to MDD in genome-wide association studies. Finally, transcriptional sensitive genetic profile scores derived from sex-stratified eSNPS regulating differential transcription to GR-stimulation were predictive of depression status and depressive symptoms in a sex-concordant manner in a child and adolescent cohort (n = 584). These results suggest the potential of eQTLs regulating differential transcription to GR-stimulation as biomarkers of sex-specific biological risk for stress-related psychiatric disorders.
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29
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Matthews BJ, Melia T, Waxman DJ. Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model. PLoS Genet 2021; 17:e1009588. [PMID: 34752452 PMCID: PMC8664386 DOI: 10.1371/journal.pgen.1009588] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 12/10/2021] [Accepted: 10/27/2021] [Indexed: 12/13/2022] Open
Abstract
Sex differences in gene expression are widespread in the liver, where many autosomal factors act in tandem with growth hormone signaling to regulate individual variability of sex differences in liver metabolism and disease. Here, we compare hepatic transcriptomic and epigenetic profiles of mouse strains C57BL/6J and CAST/EiJ, representing two subspecies separated by 0.5-1 million years of evolution, to elucidate the actions of genetic factors regulating liver sex differences. We identify 144 protein coding genes and 78 lncRNAs showing strain-conserved sex bias; many have gene ontologies relevant to liver function, are more highly liver-specific and show greater sex bias, and are more proximally regulated than genes whose sex bias is strain-dependent. The strain-conserved genes include key growth hormone-dependent transcriptional regulators of liver sex bias; however, three other transcription factors, Trim24, Tox, and Zfp809, lose their sex-biased expression in CAST/EiJ mouse liver. To elucidate the observed strain specificities in expression, we characterized the strain-dependence of sex-biased chromatin opening and enhancer marks at cis regulatory elements (CREs) within expression quantitative trait loci (eQTL) regulating liver sex-biased genes. Strikingly, 208 of 286 eQTLs with strain-specific, sex-differential effects on expression were associated with a complete gain, loss, or reversal of the sex differences in expression between strains. Moreover, 166 of the 286 eQTLs were linked to the strain-dependent gain or loss of localized sex-biased CREs. Remarkably, a subset of these CREs apparently lacked strain-specific genetic variants yet showed coordinated, strain-dependent sex-biased epigenetic regulation. Thus, we directly link hundreds of strain-specific genetic variants to the high variability in CRE activity and expression of sex-biased genes and uncover underlying genetically-determined epigenetic states controlling liver sex bias in genetically diverse mouse populations.
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Affiliation(s)
- Bryan J. Matthews
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
| | - Tisha Melia
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David J. Waxman
- Department of Biology, Boston University, Boston, Massachusetts, United States of America
- Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
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30
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Della Torre S. Beyond the X Factor: Relevance of Sex Hormones in NAFLD Pathophysiology. Cells 2021; 10:2502. [PMID: 34572151 PMCID: PMC8470830 DOI: 10.3390/cells10092502] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 09/12/2021] [Accepted: 09/14/2021] [Indexed: 12/12/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a major health issue worldwide, being frequently associated with obesity, unbalanced dietary regimens, and reduced physical activity. Despite their greater adiposity and reduced physical activity, women show a lower risk of developing NAFLD in comparison to men, likely a consequence of a sex-specific regulation of liver metabolism. In the liver, sex differences in the uptake, synthesis, oxidation, deposition, and mobilization of lipids, as well as in the regulation of inflammation, are associated with differences in NAFLD prevalence and progression between men and women. Given the major role of sex hormones in driving hepatic sexual dimorphism, this review will focus on the role of sex hormones and their signaling in the regulation of hepatic metabolism and in the molecular mechanisms triggering NAFLD development and progression.
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Affiliation(s)
- Sara Della Torre
- Department of Pharmaceutical Sciences, University of Milan, Via Balzaretti 9, 20133 Milan, Italy
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31
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AlOgayil N, Bauermeister K, Galvez JH, Venkatesh VS, Zhuang QKW, Chang ML, Davey RA, Zajac JD, Ida K, Kamiya A, Taketo T, Bourque G, Naumova AK. Distinct roles of androgen receptor, estrogen receptor alpha, and BCL6 in the establishment of sex-biased DNA methylation in mouse liver. Sci Rep 2021; 11:13766. [PMID: 34215813 PMCID: PMC8253761 DOI: 10.1038/s41598-021-93216-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Sexual dimorphism in gene regulation, including DNA methylation, is the main driver of sexual dimorphism in phenotypes. However, the questions of how and when sex shapes DNA methylation remain unresolved. Recently, using mice with different combinations of genetic and phenotypic sex, we identified sex-associated differentially methylated regions (sDMRs) that depended on the sex phenotype. Focusing on a panel of validated sex-phenotype dependent male- and female-biased sDMRs, we tested the developmental dynamics of sex bias in liver methylation and the impacts of mutations in the androgen receptor, estrogen receptor alpha, or the transcriptional repressor Bcl6 gene. True hermaphrodites that carry both unilateral ovaries and contralateral testes were also tested. Our data show that sex bias in methylation either coincides with or follows sex bias in the expression of sDMR-proximal genes, suggesting that sex bias in gene expression may be required for demethylation at certain sDMRs. Global ablation of AR, ESR1, or a liver-specific loss of BCL6, all alter sDMR methylation, whereas presence of both an ovary and a testis delays the establishment of male-type methylation levels in hermaphrodites. Moreover, the Bcl6-LKO shows dissociation between expression and methylation, suggesting a distinct role of BCL6 in demethylation of intragenic sDMRs.
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Affiliation(s)
- Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | | | | | - Varun S Venkatesh
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia
| | | | - Matthew L Chang
- Department of Biochemistry, McGill University, Montréal, QC, Canada
| | - Rachel A Davey
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia
| | - Jeffrey D Zajac
- Department of Medicine, Austin Health, The University of Melbourne, Heidelberg, VIC, 3084, Australia
| | - Kinuyo Ida
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Akihide Kamiya
- Department of Molecular Life Sciences, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa, 259-1193, Japan
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 1J3, Canada.,Department of Surgery, McGill University, Montreal, QC, Canada.,Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,Canadian Centre for Computational Genomics, Montréal, QC, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montréal, QC, Canada. .,The Research Institute of the McGill University Health Centre, Montreal, QC, H4A 1J3, Canada. .,Department of Obstetrics and Gynecology, McGill University, Montreal, QC, Canada.
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32
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Sari G, van Oord GW, van de Garde MDB, Voermans JJC, Boonstra A, Vanwolleghem T. Sexual Dimorphism in Hepatocyte Xenograft Models. Cell Transplant 2021; 30:9636897211006132. [PMID: 33938243 PMCID: PMC8114754 DOI: 10.1177/09636897211006132] [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: 12/19/2022] Open
Abstract
Humanized liver mouse models are crucial tools in liver research, specifically in the fields of liver cell biology, viral hepatitis and drug metabolism. The livers of these humanized mouse models are repopulated by 3-dimensional islands of fully functional primary human hepatocytes (PHH), which are notoriously difficult to maintain in vitro. As low efficiency and high cost hamper widespread use, optimization is of great importance. In the present study, we analyzed experimental factors associated with Hepatitis E virus (HEV) infection and PHH engraftment in 2 xenograft systems on a Nod-SCID-IL2Ry-/- background: the alb-urokinase plasminogen activator mouse model (uPA-NOG, n=399); and the alb-HSV thymidine kinase model (TK-NOG, n = 198). In a first analysis, HEV fecal shedding in liver humanized uPA-NOG and TK-NOG mice with comparable human albumin levels was found to be similar irrespective of the mouse genetic background. In a second analysis, sex, mouse age at transplantation and hepatocyte donor were the most determinant factors for xenograft success in both models. The sexual imbalance for xenograft success was related to higher baseline ALT levels and lower thresholds for ganciclovir induced liver morbidity and mortality in males. These data call for sexual standardization of human hepatocyte xenograft models, but also provide a platform for further studies on mechanisms behind sexual dimorphism in liver diseases.
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Affiliation(s)
- Gulce Sari
- Department of Gastroenterology and Hepatology, 6993Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Gertine W van Oord
- Department of Gastroenterology and Hepatology, 6993Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Martijn D B van de Garde
- Department of Gastroenterology and Hepatology, 6993Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Jolanda J C Voermans
- Department of Viroscience, 6993Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Andre Boonstra
- Department of Gastroenterology and Hepatology, 6993Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Thomas Vanwolleghem
- Department of Gastroenterology and Hepatology, 6993Erasmus University Medical Center, Rotterdam, The Netherlands.,Laboratory of Experimental Medicine and Pediatrics, Faculty of Medicine and Health Sciences, University of Antwerp and Netherlands.,Department of Gastroenterology and Hepatology, Antwerp University Hospital, Antwerp, Belgium, Netherlands
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33
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Le Magueresse-Battistoni B. Endocrine disrupting chemicals and metabolic disorders in the liver: What if we also looked at the female side? CHEMOSPHERE 2021; 268:129212. [PMID: 33359838 DOI: 10.1016/j.chemosphere.2020.129212] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Revised: 12/01/2020] [Accepted: 12/02/2020] [Indexed: 05/07/2023]
Abstract
Endocrine disrupting chemicals (EDCs) are linked to the worldwide epidemic incidence of metabolic disorders and fatty liver diseases, which affects quality of life and represents a high economic cost to society. Energy homeostasis exhibits strong sexual dimorphic traits, and metabolic organs respond to EDCs depending on sex, such as the liver, which orchestrates both drug elimination and glucose and lipid metabolism. In addition, fatty liver diseases show a strong sexual bias, which in part could also originate from sex differences observed in gut microbiota. The aim of this review is to highlight significant differences in endocrine and metabolic aspects of the liver, between males and females throughout development and into adulthood. It is also to illustrate how the male and female liver differently cope with exposure to various EDCs such as bisphenols, phthalates and persistent organic chemicals in order to draw attention to the need to include both sexes in experimental studies. Interesting data come from analyses of the composition and diversity of the gut microbiota in males exposed to the mentioned EDCs showing significant correlations with hepatic lipid accumulation and metabolic disorders but information on females is lacking or incomplete. As industrialization increases, the list of anthropogenic chemicals to which humans will be exposed will also likely increase. In addition to strengthening existing regulations, encouraging populations to protect themselves and promoting the substitution of harmful chemicals with safe products, innovative strategies based on sex differences in the gut microbiota and in the gut-liver axis could be optimistic outlook.
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34
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Goldfarb CN, Waxman DJ. Global analysis of expression, maturation and subcellular localization of mouse liver transcriptome identifies novel sex-biased and TCPOBOP-responsive long non-coding RNAs. BMC Genomics 2021; 22:212. [PMID: 33761883 PMCID: PMC7992343 DOI: 10.1186/s12864-021-07478-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 02/24/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND While nuclear transcription and RNA processing and localization are well established for protein coding genes (PCGs), these processes are poorly understood for long non-coding (lnc)RNAs. Here, we characterize global patterns of transcript expression, maturation and localization for mouse liver RNA, including more than 15,000 lncRNAs. PolyA-selected liver RNA was isolated and sequenced from four subcellular fractions (chromatin, nucleoplasm, total nucleus, and cytoplasm), and from the chromatin-bound fraction without polyA selection. RESULTS Transcript processing, determined from normalized intronic to exonic sequence read density ratios, progressively increased for PCG transcripts in going from the chromatin-bound fraction to the nucleoplasm and then on to the cytoplasm. Transcript maturation was similar for lncRNAs in the chromatin fraction, but was significantly lower in the nucleoplasm and cytoplasm. LncRNA transcripts were 11-fold more likely to be significantly enriched in the nucleus than cytoplasm, and 100-fold more likely to be significantly chromatin-bound than nucleoplasmic. Sequencing chromatin-bound RNA greatly increased the sensitivity for detecting lowly expressed lncRNAs and enabled us to discover and localize hundreds of novel regulated liver lncRNAs, including lncRNAs showing sex-biased expression or responsiveness to TCPOBOP a xenobiotic agonist ligand of constitutive androstane receptor (Nr1i3). CONCLUSIONS Integration of our findings with prior studies and lncRNA annotations identified candidate regulatory lncRNAs for a variety of hepatic functions based on gene co-localization within topologically associating domains or transcription divergent or antisense to PCGs associated with pathways linked to hepatic physiology and disease.
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Affiliation(s)
- Christine N Goldfarb
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
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35
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STAT5 Regulation of Sex-Dependent Hepatic CpG Methylation at Distal Regulatory Elements Mapping to Sex-Biased Genes. Mol Cell Biol 2021; 41:MCB.00166-20. [PMID: 33199496 DOI: 10.1128/mcb.00166-20] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 11/05/2020] [Indexed: 12/19/2022] Open
Abstract
Growth hormone-activated STAT5b is an essential regulator of sex-differential gene expression in mouse liver; however, its impact on hepatic gene expression and epigenetic responses is poorly understood. Here, we found a substantial, albeit incomplete loss of liver sex bias in hepatocyte-specific STAT5a/STAT5b (collectively, STAT5)-deficient mouse liver. In male liver, many male-biased genes were downregulated in direct association with the loss of STAT5 binding; many female-biased genes, which show low STAT5 binding, were derepressed, indicating an indirect mechanism for repression by STAT5. Extensive changes in CpG methylation were seen in STAT5-deficient liver, where sex differences were abolished at 88% of ∼1,500 sex-differentially methylated regions, largely due to increased DNA methylation upon STAT5 loss. STAT5-dependent CpG hypomethylation was rarely found at proximal promoters of STAT5-dependent genes. Rather, STAT5 primarily regulated the methylation of distal enhancers, where STAT5 deficiency induced widespread hypermethylation at genomic regions enriched for accessible chromatin, enhancer histone marks (histone H3 lysine 4 monomethylation [H3K4me1] and histone H3 lysine 27 acetylation [H3K27ac]), STAT5 binding, and DNA motifs for STAT5 and other transcription factors implicated in liver sex differences. Thus, the sex-dependent binding of STAT5 to liver chromatin is closely linked to the sex-dependent demethylation of distal regulatory elements linked to STAT5-dependent genes important for liver sex bias.
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Melia T, Waxman DJ. Genetic factors contributing to extensive variability of sex-specific hepatic gene expression in Diversity Outbred mice. PLoS One 2020; 15:e0242665. [PMID: 33264334 PMCID: PMC7710091 DOI: 10.1371/journal.pone.0242665] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2020] [Accepted: 11/09/2020] [Indexed: 12/12/2022] Open
Abstract
Sex-specific transcription characterizes hundreds of genes in mouse liver, many implicated in sex-differential drug and lipid metabolism and disease susceptibility. While the regulation of liver sex differences by growth hormone-activated STAT5 is well established, little is known about autosomal genetic factors regulating the sex-specific liver transcriptome. Here we show, using genotyping and expression data from a large population of Diversity Outbred mice, that genetic factors work in tandem with growth hormone to control the individual variability of hundreds of sex-biased genes, including many long non-coding RNA genes. Significant associations between single nucleotide polymorphisms and sex-specific gene expression were identified as expression quantitative trait loci (eQTLs), many of which showed strong sex-dependent associations. Remarkably, autosomal genetic modifiers of sex-specific genes were found to account for more than 200 instances of gain or loss of sex-specificity across eight Diversity Outbred mouse founder strains. Sex-biased STAT5 binding sites and open chromatin regions with strain-specific variants were significantly enriched at eQTL regions regulating correspondingly sex-specific genes, supporting the proposed functional regulatory nature of the eQTL regions identified. Binding of the male-biased, growth hormone-regulated repressor BCL6 was most highly enriched at trans-eQTL regions controlling female-specific genes. Co-regulated gene clusters defined by overlapping eQTLs included sets of highly correlated genes from different chromosomes, further supporting trans-eQTL action. These findings elucidate how an unexpectedly large number of autosomal factors work in tandem with growth hormone signaling pathways to regulate the individual variability associated with sex differences in liver metabolism and disease.
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Affiliation(s)
- Tisha Melia
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - David J. Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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37
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Lopes-Ramos CM, Quackenbush J, DeMeo DL. Genome-Wide Sex and Gender Differences in Cancer. Front Oncol 2020; 10:597788. [PMID: 33330090 PMCID: PMC7719817 DOI: 10.3389/fonc.2020.597788] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2020] [Accepted: 10/19/2020] [Indexed: 12/12/2022] Open
Abstract
Despite their known importance in clinical medicine, differences based on sex and gender are among the least studied factors affecting cancer susceptibility, progression, survival, and therapeutic response. In particular, the molecular mechanisms driving sex differences are poorly understood and so most approaches to precision medicine use mutational or other genomic data to assign therapy without considering how the sex of the individual might influence therapeutic efficacy. The mandate by the National Institutes of Health that research studies include sex as a biological variable has begun to expand our understanding on its importance. Sex differences in cancer may arise due to a combination of environmental, genetic, and epigenetic factors, as well as differences in gene regulation, and expression. Extensive sex differences occur genome-wide, and ultimately influence cancer biology and outcomes. In this review, we summarize the current state of knowledge about sex-specific genetic and genome-wide influences in cancer, describe how differences in response to environmental exposures and genetic and epigenetic alterations alter the trajectory of the disease, and provide insights into the importance of integrative analyses in understanding the interplay of sex and genomics in cancer. In particular, we will explore some of the emerging analytical approaches, such as the use of network methods, that are providing a deeper understanding of the drivers of differences based on sex and gender. Better understanding these complex factors and their interactions will improve cancer prevention, treatment, and outcomes for all individuals.
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Affiliation(s)
- Camila M Lopes-Ramos
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States
| | - John Quackenbush
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, United States.,Department of Data Science, Dana-Farber Cancer Institute, Boston, MA, United States.,Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States.,Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, United States
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Svoboda LK, Neier K, Wang K, Cavalcante RG, Rygiel CA, Tsai Z, Jones TR, Liu S, Goodrich JM, Lalancette C, Colacino JA, Sartor MA, Dolinoy DC. Tissue and sex-specific programming of DNA methylation by perinatal lead exposure: implications for environmental epigenetics studies. Epigenetics 2020; 16:1102-1122. [PMID: 33164632 DOI: 10.1080/15592294.2020.1841872] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Early developmental environment can influence long-term health through reprogramming of the epigenome. Human environmental epigenetics studies rely on surrogate tissues, such as blood, to assess the effects of environment on disease-relevant but inaccessible target tissues. However, the extent to which environment-induced epigenetic changes are conserved between these tissues is unclear. A better understanding of this conservation is imperative for effective design and interpretation of human environmental epigenetics studies. The Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription (TaRGET II) consortium was established by the National Institute of Environmental Health Sciences to address the utility of surrogate tissues as proxies for toxicant-induced epigenetic changes in target tissues. We and others have recently reported that perinatal exposure to lead (Pb) is associated with adverse metabolic outcomes. Here, we investigated the sex-specific effects of perinatal exposure to a human environmentally relevant level of Pb on DNA methylation in paired liver and blood samples from adult mice using enhanced reduced-representation bisulphite sequencing. Although Pb exposure ceased at 3 weeks of age, we observed thousands of sex-specific differentially methylated cytosines in the blood and liver of Pb-exposed animals at 5 months of age, including 44 genomically imprinted loci. We observed significant tissue overlap in the genes mapping to differentially methylated cytosines. A small but significant subset of Pb-altered genes exhibit basal sex differences in gene expression in the mouse liver. Collectively, these data identify potential molecular targets for Pb-induced metabolic diseases, and inform the design of more robust human environmental epigenomics studies.
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Affiliation(s)
- Laurie K Svoboda
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kari Neier
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Kai Wang
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | | | - Christine A Rygiel
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Zing Tsai
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Tamara R Jones
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Siyu Liu
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA
| | - Jaclyn M Goodrich
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Claudia Lalancette
- Epigenomics Core, University of Michigan, Medical School, Ann Arbor, MI, USA
| | - Justin A Colacino
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
| | - Maureen A Sartor
- Department of Computational Medicine and Bioinformatics, University of Michigan Medical School Palmer Commons, Ann Arbor, MI, USA.,Department of Biostatistics, University of Michigan, School of Public Health, Ann Arbor, MI, USA
| | - Dana C Dolinoy
- Environmental Health Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA.,Nutritional Sciences, University of Michigan School of Public Health, Ann Arbor, MI, USA
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Nail AN, Spear BT, Peterson ML. Highly homologous mouse Cyp2a4 and Cyp2a5 genes are differentially expressed in the liver and both express long non-coding antisense RNAs. Gene 2020; 767:145162. [PMID: 32987105 DOI: 10.1016/j.gene.2020.145162] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Revised: 09/04/2020] [Accepted: 09/17/2020] [Indexed: 11/16/2022]
Abstract
The mammalian Cytochrome P450 (Cyp) gene superfamily encodes enzymes involved in numerous metabolic pathways and are frequently expressed in the liver. Despite the remarkably high sequence similarity of Cyp2a4 and Cyp2a5 genes and their surrounding genomic regions, they exhibit differences in expression in the adult mouse liver. For example, Cyp2a4 is highly female-biased whereas Cyp2a5 is only moderately female-biased and Cyp2a4, but not Cyp2a5, is activated in liver cancer. We hypothesized that the limited sequence differences may help us identify the basis for this differential expression. An antisense expressed sequence tag had been uniquely annotated to the Cyp2a4 gene which led us to investigate this transcript as a possible regulator of this gene. We characterized the full-length antisense transcript and also discovered a similar transcript in the Cyp2a5 gene. These transcripts are nuclear long noncoding RNAs that are expressed similarly to their sense mRNA counterparts. This includes the sex-biased and liver tumor differences seen between the Cyp2a4 and Cyp2a5 genes, but we also find that these two genes and their antisense transcripts are expressed within different zones of the liver structure. Interestingly, while the differences in sex-biased expression of the mRNAs are established 1-2 months after birth, the antisense transcripts exhibit these expression differences earlier, at 3-4 weeks after birth. By analyzing published genomic data, we have identified candidate transcription factor binding sites that could account for differences in Cyp2a4/Cyp2a5 expression. Taken together, these studies characterize the first antisense RNAs within the Cyp supergene family and identify potential transcriptional and post-transcriptional mechanisms governing different Cyp2a4 and Cyp2a5 expression patterns in mouse liver.
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Affiliation(s)
- Alexandra N Nail
- Department of Microbiology, Immunology and Molecular Genetics, USA
| | - Brett T Spear
- Department of Microbiology, Immunology and Molecular Genetics, USA; Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA
| | - Martha L Peterson
- Department of Microbiology, Immunology and Molecular Genetics, USA; Markey Cancer Center, University of Kentucky College of Medicine, Lexington, KY 40536, USA.
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Della Torre S. Non-alcoholic Fatty Liver Disease as a Canonical Example of Metabolic Inflammatory-Based Liver Disease Showing a Sex-Specific Prevalence: Relevance of Estrogen Signaling. Front Endocrinol (Lausanne) 2020; 11:572490. [PMID: 33071979 PMCID: PMC7531579 DOI: 10.3389/fendo.2020.572490] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 08/20/2020] [Indexed: 12/11/2022] Open
Abstract
There is extensive evidence supporting the interplay between metabolism and immune response, that have evolved in close relationship, sharing regulatory molecules and signaling systems, to support biological functions. Nowadays, the disruption of this interaction in the context of obesity and overnutrition underlies the increasing incidence of many inflammatory-based metabolic diseases, even in a sex-specific fashion. During evolution, the interplay between metabolism and reproduction has reached a degree of complexity particularly high in female mammals, likely to ensure reproduction only under favorable conditions. Several factors may account for differences in the incidence and progression of inflammatory-based metabolic diseases between females and males, thus contributing to age-related disease development and difference in life expectancy between the two sexes. Among these factors, estrogens, acting mainly through Estrogen Receptors (ERs), have been reported to regulate several metabolic pathways and inflammatory processes particularly in the liver, the metabolic organ showing the highest degree of sexual dimorphism. This review aims to investigate on the interaction between metabolism and inflammation in the liver, focusing on the relevance of estrogen signaling in counteracting the development and progression of non-alcoholic fatty liver disease (NAFLD), a canonical example of metabolic inflammatory-based liver disease showing a sex-specific prevalence. Understanding the role of estrogens/ERs in the regulation of hepatic metabolism and inflammation may provide the basis for the development of sex-specific therapeutic strategies for the management of such an inflammatory-based metabolic disease and its cardio-metabolic consequences.
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Affiliation(s)
- Sara Della Torre
- Department of Pharmaceutical Sciences, University of Milan, Milan, Italy
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Sexually dimorphic effects of forkhead box a2 (FOXA2) and uterine glands on decidualization and fetoplacental development. Proc Natl Acad Sci U S A 2020; 117:23952-23959. [PMID: 32900950 DOI: 10.1073/pnas.2014272117] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Glands of the uterus are essential for pregnancy establishment. Forkhead box A2 (FOXA2) is expressed specifically in the glands of the uterus and a critical regulator of glandular epithelium (GE) differentiation, development, and function. Mice with a conditional deletion of FOXA2 in the adult uterus, created using the lactotransferrin iCre (Ltf-iCre) model, have a morphologically normal uterus with glands, but lack FOXA2-dependent GE-expressed genes, such as leukemia inhibitory factor (LIF). Adult FOXA2 conditional knockout (cKO; Ltf iCre/+ Foxa2 f/f ) mice are infertile due to defective embryo implantation arising from a lack of LIF, a critical implantation factor of uterine gland origin. However, intraperitoneal injections of LIF can initiate embryo implantation in the uterus of adult FOXA2 cKO mice with pregnancies maintained to term. Here, we tested the hypothesis that FOXA2-regulated genes in the uterine glands impact development of the decidua, placenta, and fetus. On gestational day 8.5, the antimesometrial and mesometrial decidua transcriptome was noticeably altered in LIF-replaced FOXA2 cKO mice. Viable fetuses were reduced in FOXA2 cKO mice on gestational days 12.5 and 17.5. Sex-dependent differences in fetal weight, placenta histoarchitecture, and the placenta and metrial gland transcriptome were observed between control and FOXA2 cKO mice. The transcriptome of the placenta with a female fetus was considerably more altered than the placenta with a male fetus in FOXA2 cKO dams. These studies reveal previously unrecognized sexually dimorphic effects of FOXA2 and uterine glands on fetoplacental development with potential impacts on offspring health into adulthood.
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Matthews BJ, Waxman DJ. Impact of 3D genome organization, guided by cohesin and CTCF looping, on sex-biased chromatin interactions and gene expression in mouse liver. Epigenetics Chromatin 2020; 13:30. [PMID: 32680543 PMCID: PMC7368777 DOI: 10.1186/s13072-020-00350-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2020] [Accepted: 07/03/2020] [Indexed: 12/13/2022] Open
Abstract
Several thousand sex-differential distal enhancers have been identified in mouse liver; however, their links to sex-biased genes and the impact of any sex-differences in nuclear organization and chromatin interactions are unknown. To address these issues, we first characterized 1847 mouse liver genomic regions showing significant sex differential occupancy by cohesin and CTCF, two key 3D nuclear organizing factors. These sex-differential binding sites were primarily distal to sex-biased genes but rarely generated sex-differential TAD (topologically associating domain) or intra-TAD loop anchors, and were sometimes found in TADs without sex-biased genes. A substantial subset of sex-biased cohesin-non-CTCF binding sites, but not sex-biased cohesin-and-CTCF binding sites, overlapped sex-biased enhancers. Cohesin depletion reduced the expression of male-biased genes with distal, but not proximal, sex-biased enhancers by >10-fold, implicating cohesin in long-range enhancer interactions regulating sex-biased genes. Using circularized chromosome conformation capture-based sequencing (4C-seq), we showed that sex differences in distal sex-biased enhancer-promoter interactions are common. Intra-TAD loops with sex-independent cohesin-and-CTCF anchors conferred sex specificity to chromatin interactions indirectly, by insulating sex-biased enhancer-promoter contacts and by bringing sex-biased genes into closer proximity to sex-biased enhancers. Furthermore, sex-differential chromatin interactions involving sex-biased gene promoters, enhancers, and lncRNAs were associated with sex-biased binding of cohesin and/or CTCF. These studies elucidate how 3D genome organization impacts sex-biased gene expression in a non-reproductive tissue through both direct and indirect effects of cohesin and CTCF looping on distal enhancer interactions with sex-differentially expressed genes.
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Affiliation(s)
- Bryan J Matthews
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, 5 Cummington Mall, Boston, MA, 02215, USA.
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Lopes-Ramos CM, Chen CY, Kuijjer ML, Paulson JN, Sonawane AR, Fagny M, Platig J, Glass K, Quackenbush J, DeMeo DL. Sex Differences in Gene Expression and Regulatory Networks across 29 Human Tissues. Cell Rep 2020; 31:107795. [PMID: 32579922 PMCID: PMC7898458 DOI: 10.1016/j.celrep.2020.107795] [Citation(s) in RCA: 172] [Impact Index Per Article: 43.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Revised: 04/01/2020] [Accepted: 05/29/2020] [Indexed: 11/25/2022] Open
Abstract
Sex differences manifest in many diseases and may drive sex-specific therapeutic responses. To understand the molecular basis of sex differences, we evaluated sex-biased gene regulation by constructing sample-specific gene regulatory networks in 29 human healthy tissues using 8,279 whole-genome expression profiles from the Genotype-Tissue Expression (GTEx) project. We find sex-biased regulatory network structures in each tissue. Even though most transcription factors (TFs) are not differentially expressed between males and females, many have sex-biased regulatory targeting patterns. In each tissue, genes that are differentially targeted by TFs between the sexes are enriched for tissue-related functions and diseases. In brain tissue, for example, genes associated with Parkinson's disease and Alzheimer's disease are targeted by different sets of TFs in each sex. Our systems-based analysis identifies a repertoire of TFs that play important roles in sex-specific architecture of gene regulatory networks, and it underlines sex-specific regulatory processes in both health and disease.
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Affiliation(s)
| | - Cho-Yi Chen
- Institute of Biomedical Informatics, National Yang-Ming University, Taipei, Taiwan
| | - Marieke L Kuijjer
- Centre for Molecular Medicine Norway (NCMM), Nordic EMBL Partnership, University of Oslo, Oslo, Norway
| | - Joseph N Paulson
- Department of Biostatistics, Product Development, Genentech Inc., San Francisco, CA, USA
| | - Abhijeet R Sonawane
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Maud Fagny
- Genetique Quantitative et Evolution-Le Moulon, Universite Paris-Saclay, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique, AgroParisTech, Gif-sur-Yvette, France
| | - John Platig
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Kimberly Glass
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - John Quackenbush
- Department of Biostatistics, Harvard School of Public Health, Boston, MA, USA; Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA.
| | - Dawn L DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA; Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA.
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Moore SR, Humphreys KL, Colich NL, Davis EG, Lin DTS, MacIsaac JL, Kobor MS, Gotlib IH. Distinctions between sex and time in patterns of DNA methylation across puberty. BMC Genomics 2020; 21:389. [PMID: 32493224 PMCID: PMC7268482 DOI: 10.1186/s12864-020-06789-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 05/20/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND There are significant sex differences in human physiology and disease; the genomic sources of these differences, however, are not well understood. During puberty, a drastic neuroendocrine shift signals physical changes resulting in robust sex differences in human physiology. Here, we explore how shifting patterns of DNA methylation may inform these pathways of biological plasticity during the pubertal transition. In this study we analyzed DNA methylation (DNAm) in saliva at two time points across the pubertal transition within the same individuals. Our purpose was to compare two domains of DNAm patterns that may inform processes of sexual differentiation 1) sex related sites, which demonstrated differences between males from females and 2) time related sites in which DNAm shifted significantly between timepoints. We further explored the correlated network structure sex and time related DNAm networks and linked these patterns to pubertal stage, assays of salivary testosterone, a reliable diagnostic of free, unbound hormone that is available to act on target tissues, and overlap with androgen response elements. RESULTS Sites that differed by biological sex were largely independent of sites that underwent change across puberty. Time-related DNAm sites, but not sex-related sites, formed correlated networks that were associated with pubertal stage. Both time and sex DNAm networks reflected salivary testosterone levels that were enriched for androgen response elements, with sex-related DNAm networks being informative of testosterone levels above and beyond biological sex later in the pubertal transition. CONCLUSIONS These results inform our understanding of the distinction between sex- and time-related differences in DNAm during the critical period of puberty and highlight a novel linkage between correlated patterns of sex-related DNAm and levels of salivary testosterone.
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Affiliation(s)
- Sarah Rose Moore
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada.
| | - Kathryn Leigh Humphreys
- Department of Psychology and Human Development, Vanderbilt University, 230 Appleton Pl, Nashville, TN, 37203, USA
| | - Natalie Lisanne Colich
- Department of Psychology, University of Washington Seattle, Guthrie Hall (GTH), 119A 98195-1525, Seattle, WA, 98105, USA
| | - Elena Goetz Davis
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA
| | - David Tse Shen Lin
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Julia Lynn MacIsaac
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Michael Steffen Kobor
- Department of Medical Genetics, University of British Columbia
- BC Children's Hospital Research Institute, 938 W 28th Ave, Vancouver, BC, V5Z 4H4, Canada
| | - Ian Henry Gotlib
- Department of Psychology, Stanford University, 450 Jane Stanford Way, Stanford, CA, 94305, USA
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Lau-Corona D, Bae WK, Hennighausen L, Waxman DJ. Sex-biased genetic programs in liver metabolism and liver fibrosis are controlled by EZH1 and EZH2. PLoS Genet 2020; 16:e1008796. [PMID: 32428001 PMCID: PMC7263639 DOI: 10.1371/journal.pgen.1008796] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 06/01/2020] [Accepted: 04/24/2020] [Indexed: 12/15/2022] Open
Abstract
Sex differences in the incidence and progression of many liver diseases, including liver fibrosis and hepatocellular carcinoma, are associated with sex-biased hepatic expression of hundreds of genes. This sexual dimorphism is largely determined by the sex-specific pattern of pituitary growth hormone secretion, which controls a transcriptional regulatory network operative in the context of sex-biased and growth hormone-regulated chromatin states. Histone H3K27-trimethylation yields a major sex-biased repressive chromatin mark deposited at many strongly female-biased genes in male mouse liver, but not at male-biased genes in female liver, and is catalyzed by polycomb repressive complex-2 through its homologous catalytic subunits, Ezh1 and Ezh2. Here, we used Ezh1-knockout mice with a hepatocyte-specific knockout of Ezh2 to investigate the sex bias of liver H3K27-trimethylation and its functional role in regulating sex-differences in the liver. Combined hepatic Ezh1/Ezh2 deficiency led to a significant loss of sex-biased gene expression, particularly in male liver, where many female-biased genes were increased in expression while male-biased genes showed decreased expression. The associated loss of H3K27me3 marks, and increases in the active enhancer marks H3K27ac and H3K4me1, were also more pronounced in male liver. Further, Ezh1/Ezh2 deficiency in male liver, and to a lesser extent in female liver, led to up regulation of many genes linked to liver fibrosis and liver cancer, which may contribute to the observed liver pathologies and the increased sensitivity of these mice to hepatotoxin exposure. Thus, Ezh1/Ezh2-catalyzed H3K27-trimethyation regulates sex-dependent genetic programs in liver metabolism and liver fibrosis through its sex-dependent effects on the epigenome, and may thereby determine the sex-bias in liver disease susceptibility. Sex-differences in the expression of genes in liver have a direct impact on liver diseases whose incidence and severity is sex-biased, and is controlled by hormones that regulate chemical alterations to histone proteins used to package chromosomal DNA. However, a direct demonstration of the functional importance of such sex differences in histone protein modifications has been elusive. Here, we address this question using a mouse model deficient in two enzymes, Ezh1/Ezh2, which generate the histone repressive mark H3K27me3. Remarkably, although H3K27me3 marks are formed by Ezh1/Ezh2 throughout the genome, loss of liver Ezh1/Ezh2 preferentially disrupts the control of sex-biased genes, with expression increasing in male mouse liver for many female-biased genes and decreasing for many male-biased genes. Sex-biased H3K27me3 repressive marks were abolished, and there was a gain of active histone marks at gene enhancers. We also found increased expression of many genes associated with liver fibrosis and hepatocellular carcinoma, which may help explain the increased sensitivity of Ezh1/Ezh2-deficient livers to hepatotoxic chemicals whose exposure may lead to sex differences in liver disease incidence and susceptibility. Thus, our findings highlight the potential role of sex differences in histone modifications catalyzed by Ezh1/Ezh2 in widespread sex differences in liver diseases.
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Affiliation(s)
- Dana Lau-Corona
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
| | - Woo Kyun Bae
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
- Department of Internal Medicine, Chonnam National University Medical School, Gwangju, Korea
| | - Lothar Hennighausen
- Laboratory of Genetics and Physiology, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, Maryland, United States of America
| | - David J. Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts, United States of America
- * E-mail:
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Abstract
Growth hormone (GH) plays a pivotal role in many physiological processes in humans, and in other mammalian and non-mammalian vertebrate species, through actions on somatic growth, tissue development and repair, and intermediary metabolism. This review will focus on mechanisms of GH actions on gene expression, primarily from the perspective of the genes that encode proteins stimulated by GH to regulate somatic growth, especially insulin-like growth factor 1 (IGF-I), but also others that are induced or repressed by GH. Topics to be discussed will include a brief overview of GH-mediated signal transduction pathways and how these cascades alter the functions of responsive transcription factors, with a specific focus on STAT5B, a key member of the signal transducers and activators of transcription family, characterization of essential GH-regulated genes, and elucidation of mechanisms of their regulation from biochemical, genetic, and genomic perspectives.
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Affiliation(s)
- Peter Rotwein
- Department of Molecular and Translational Medicine, Paul L. Foster School of Medicine, Texas Tech Health University Health Sciences Center, El Paso, TX, 79905, USA.
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47
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Kroon J, Pereira AM, Meijer OC. Glucocorticoid Sexual Dimorphism in Metabolism: Dissecting the Role of Sex Hormones. Trends Endocrinol Metab 2020; 31:357-367. [PMID: 32037025 DOI: 10.1016/j.tem.2020.01.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/11/2019] [Revised: 12/20/2019] [Accepted: 01/13/2020] [Indexed: 12/15/2022]
Abstract
Glucocorticoids are steroid hormones that are of pivotal importance in human physiology. Glucocorticoid signaling is complex in nature and dependent on many interacting factors. As glucocorticoids exhibit sexually dimorphic effects on several key processes including in metabolism, crosstalk with the sex steroid hormones (androgens and estrogens) is relevant. In this review, we highlight the state-of-the-art knowledge on glucocorticoid sexual dimorphism and sex hormone crosstalk. We include current insight in the molecular mechanisms that underlie nuclear steroid receptor crosstalk, and sex hormone effects on glucocorticoid metabolism. Finally, we show how these findings translate to humans exposed to excess glucocorticoid signaling, and we propose future avenues in the emerging field of steroid hormone crosstalk.
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Affiliation(s)
- Jan Kroon
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands.
| | - Alberto M Pereira
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
| | - Onno C Meijer
- Department of Medicine, Division of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands; Einthoven Laboratory for Experimental Vascular Medicine, Leiden University Medical Center, Leiden, The Netherlands
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48
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Gao B, Xie W, Wu X, Wang L, Guo J. Functionally analyzing the important roles of hepatocyte nuclear factor 3 (FoxA) in tumorigenesis. Biochim Biophys Acta Rev Cancer 2020; 1873:188365. [PMID: 32325165 DOI: 10.1016/j.bbcan.2020.188365] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/14/2020] [Accepted: 04/14/2020] [Indexed: 12/19/2022]
Abstract
Transcriptional factors (TFs) play a central role in governing gene expression under physiological conditions including the processes of embryonic development, metabolic homeostasis and response to extracellular stimuli. Conceivably, the aberrant dysregulations of TFs would dominantly result in various human disorders including tumorigenesis, diabetes and neurodegenerative diseases. Serving as the most evolutionarily reserved TFs, Fox family TFs have been explored to exert distinct biological functions in neoplastic development, by manipulating diverse gene expression. Recently, among the Fox family members, the pilot roles of FoxAs attract more attention due to their functions as both pioneer factor and transcriptional factor in human tumorigenesis, particularly in the sex-dimorphism tumors. Therefore, the pathological roles of FoxAs in tumorigenesis have been well-explored in modulating inflammation, immune response and metabolic homeostasis. In this review, we comprehensively summarize the impressive progression of FoxA functional annotation, clinical relevance, upstream regulators and downstream effectors, as well as valuable animal models, and highlight the potential strategies to target FoxAs for cancer therapies.
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Affiliation(s)
- Bing Gao
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Wei Xie
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Xueji Wu
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Lei Wang
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China
| | - Jianping Guo
- Institute of Precision Medicine, the First Affiliated Hospital, Sun Yat-sen University, Guangzhou, Guangdong 510275, China.
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49
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Sex differences in adult mood and in stress-induced transcriptional coherence across mesocorticolimbic circuitry. Transl Psychiatry 2020; 10:59. [PMID: 32066699 PMCID: PMC7026087 DOI: 10.1038/s41398-020-0742-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Revised: 12/26/2019] [Accepted: 01/08/2020] [Indexed: 12/22/2022] Open
Abstract
Women are approximately two times as likely to be diagnosed with major depressive disorder (MDD) compared to men. While sex differences in MDD might be driven by circulating gonadal hormones, we hypothesized that developmental hormone exposure and/or genetic sex might play a role. Mice were gonadectomized in adulthood to isolate the role of developmental hormones. We examined the effects of developmental gonadal and genetic sex on anhedonia-/depressive-like behaviors under non-stress and chronic stress conditions and performed RNA-sequencing in three mood-relevant brain regions. We used an integrative network approach to identify transcriptional modules and stress-specific hub genes regulating stress susceptibility, with a focus on whether these differed by sex. After identifying sex differences in anhedonia-/depressive-like behaviors (female > male), we show that both developmental hormone exposure (gonadal female > gonadal male) and genetic sex (XX > XY) contribute to the sex difference. The top biological pathways represented by differentially expressed genes were related to immune function; we identify which differentially expressed genes are driven by developmental gonadal or genetic sex. There was very little overlap in genes affected by chronic stress in males and females. We also identified highly co-expressed gene modules affected by stress, some of which were affected in opposite directions in males and females. Since all mice had equivalent hormone exposure in adulthood, these results suggest that sex differences in gonadal hormone exposure during sensitive developmental periods program adult sex differences in mood, and that these sex differences are independent of adult circulating gonadal hormones.
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50
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Touloupi K, Küblbeck J, Magklara A, Molnár F, Reinisalo M, Konstandi M, Honkakoski P, Pappas P. The Basis for Strain-Dependent Rat Aldehyde Dehydrogenase 1A7 ( ALDH1A7) Gene Expression. Mol Pharmacol 2019; 96:655-663. [PMID: 31575620 DOI: 10.1124/mol.119.117424] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 09/06/2019] [Indexed: 11/22/2022] Open
Abstract
Aldehyde hydrogenases (ALDHs) belong to a large gene family involved in oxidation of both endogenous and exogenous compounds in mammalian tissues. Among ALDHs, the rat ALDH1A7 gene displays a curious strain dependence in phenobarbital (PB)-induced hepatic expression: the responsive RR strains exhibit induction of both ALDH1A7 and CYP2B mRNAs and activities, whereas the nonresponsive rr strains show induction of CYP2B only. Here, we investigated the responsiveness of ALDH1A1, ALDH1A7, CYP2B1, and CYP3A23 genes to prototypical P450 inducers, expression of nuclear receptors CAR and pregnane X receptor, and structure of the ALDH1A7 promoter in both rat strains. ALDH1A7 mRNA, associated protein and activity were strongly induced by PB and modestly induced by pregnenolone 16α-carbonitrile in the RR strain but negligibly in the rr strain, whereas induction of ALDH1A1 and P450 mRNAs was similar between the strains. Reporter gene and chromatin immunoprecipitation assays indicated that the loss of ALDH1A7 inducibility in the rr strain is profoundly linked with a 16-base pair deletion in the proximal promoter and inability of the upstream DNA sequences to recruit constitutive androstane receptor-retinoid X receptor heterodimers. SIGNIFICANCE STATEMENT: Genetic variation in rat ALDH1A7 promoter sequences underlie the large strain-dependent differences in expression and inducibility by phenobarbital of the aldehyde dehydrogenase activity. This finding has implications for the design and interpretation of pharmacological and toxicological studies on the effects and disposition of aldehydes.
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Affiliation(s)
- Katerina Touloupi
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Jenni Küblbeck
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Angeliki Magklara
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Ferdinand Molnár
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Mika Reinisalo
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Maria Konstandi
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Paavo Honkakoski
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
| | - Periklis Pappas
- Departments of Pharmacology (K.T., M.K., P.P.) and Clinical Chemistry (A.M.), Faculty of Medicine, School of Health Sciences, University of Ioannina, and Department of Biomedical Research, Institute of Molecular Biology and Biotechnology, Foundation of Research and Technology (A.M.), Ioannina, Greece; School of Pharmacy, Faculty of Health Sciences, University of Eastern Finland, Kuopio, Finland (J.K., F.M., M.R., P.H.);Department of Biology, School of Science and Technology, Nazarbayev University, Nur-Sultan City, Kazakhstan (F.M.); Division of Pharmacotherapy and Experimental Therapeutics, UNC Eshelman School of Pharmacy, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina (P.H.)
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