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Poudel SB, Ruff RR, He Z, Dixit M, Yildirim G, Jayarathne H, Manchanayake DH, Basta-Pljakic J, Duran-Ortiz S, Schaffler MB, Kopchick JJ, Sadagurski M, Yakar S. The impact of inactivation of the GH/IGF axis during aging on healthspan. GeroScience 2024:10.1007/s11357-024-01426-3. [PMID: 39535693 DOI: 10.1007/s11357-024-01426-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2024] [Accepted: 11/03/2024] [Indexed: 11/16/2024] Open
Abstract
Several mouse lines with congenital growth hormone (GH)/insulin-like growth factor-1 (IGF-1) axis disruption have shown improved health and extended lifespan. The current study investigated how inactivating this axis, specifically during aging, impacts the healthspan. We used a tamoxifen-inducible global GH receptor (GHR) knockout mouse model starting at 12 months and followed the mice until 24 months of age (iGHRKO12-24 mice). We found sex- and tissue-specific effects, with some being pro-aging and others anti-aging. Measuring an array of cytokines in serum revealed that inactivation of the GH/IGF-1 axis at 12 months did not affect systemic inflammation during aging. On the other hand, hypothalamic inflammation was significantly reduced in iGHRKO12-24 mice, evidenced by GFAP+ (glial fibrillary acidic protein, a marker of astrocytes) and Iba-1+ (a marker for microglia). Liver RNAseq analysis indicated feminization of the male transcriptome, with significant changes in the expression of monooxygenase, sulfotransferase, and solute-carrier-transporter gene clusters. Finally, we found impaired bone morphology, more pronounced in male iGHRKO12-24 mice and correlated with GH/IGF-1 inactivation onset age. We conclude that inhibiting the GH/IGF-1 axis during aging only partially preserves the beneficial healthspan effects observed with congenital GH deficiency.
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Affiliation(s)
- Sher Bahadur Poudel
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24Th Street, New York, NY, 10010-4086, USA
| | - Ryan R Ruff
- David B. Kriser Dental Center, Department of Epidemiology and Health Promotion, New York University College of Dentistry, New York, NY, 10010-4086, USA
| | - Zhiming He
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24Th Street, New York, NY, 10010-4086, USA
| | - Manisha Dixit
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24Th Street, New York, NY, 10010-4086, USA
| | - Godze Yildirim
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24Th Street, New York, NY, 10010-4086, USA
| | - Hashan Jayarathne
- Department of Biological Sciences, iBio (Integrative Biosciences Center), Integrative Biosciences Center, and Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Dulmalika Herath Manchanayake
- Department of Biological Sciences, iBio (Integrative Biosciences Center), Integrative Biosciences Center, and Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Jelena Basta-Pljakic
- Department of Biomedical Engineering, City College of New York, New York, NY, 10031, USA
| | - Silvana Duran-Ortiz
- Edison Biotechnology Institute and Department of Biomedical Sciences, Ohio University, Athens, OH, USA
| | - Mitchell B Schaffler
- Department of Biomedical Engineering, City College of New York, New York, NY, 10031, USA
| | - John J Kopchick
- Edison Biotechnology Institute and Department of Biomedical Sciences, Ohio University, Athens, OH, USA
| | - Marianna Sadagurski
- Department of Biological Sciences, iBio (Integrative Biosciences Center), Integrative Biosciences Center, and Institute of Environmental Health Sciences, Wayne State University, Detroit, MI, 48202, USA
| | - Shoshana Yakar
- David B. Kriser Dental Center, Department of Molecular Pathobiology, New York University College of Dentistry, 345 East 24Th Street, New York, NY, 10010-4086, USA.
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2
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Meda C, Benedusi V, Cherubini A, Valenti L, Maggi A, Della Torre S. Hepatic estrogen receptor alpha drives masculinization in post-menopausal women with metabolic dysfunction-associated steatotic liver disease. JHEP Rep 2024; 6:101143. [PMID: 39308985 PMCID: PMC11414671 DOI: 10.1016/j.jhepr.2024.101143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/05/2024] [Revised: 05/24/2024] [Accepted: 06/07/2024] [Indexed: 09/25/2024] Open
Abstract
Background & Aims The loss of ovarian functions defining menopause leads to profound metabolic changes and heightens the risk of developing metabolic dysfunction-associated steatotic liver disease (MASLD). Although estrogens primarily act on the female liver through estrogen receptor alpha (ERα), the specific contribution of impaired ERα signaling in triggering MASLD after menopause remains unclear. Methods To address this gap in knowledge, we compared the liver transcriptomes of sham-operated (SHAM) and ovariectomized (OVX) control and liver ERα knockout (LERKO) female mice by performing RNA-Seq analysis. Results OVX led to 1426 differentially expressed genes (DEGs) in the liver of control mice compared to 245 DEGs in LERKO mice. Gene ontology analysis revealed a distinct ovariectomy-induced modulation of the liver transcriptome in LERKO compared with controls, indicating that hepatic ERα is functional and necessary for the complete reprogramming of liver metabolism in response to estrogen depletion. Additionally, we observed an ovariectomy-dependent induction of male-biased genes, especially in the liver of control females, pointing to hepatic ERα involvement in the masculinization of the liver after estrogen loss. To investigate the translational relevance of such findings, we assessed liver samples from a cohort of 60 severely obese individuals (51 women; 9 men). Notably, a shift of the liver transcriptome toward a male-like profile was also observed only in obese women with MASLD (n = 43), especially in women ≥51 years old (15/15), suggesting that masculinization of the female liver contributes to MASLD development in obese women. Conclusions These results highlight the role of hepatic ERα in driving masculinization of the liver transcriptome following menopause, pointing to this receptor as a potential pharmacological target for preventing MASLD in post-menopausal women. Impact and implications Despite the increased risk of developing MASLD after menopause, the specific contribution of impaired hepatic estrogen signaling in driving MASLD in females has not been a major research focus, and, thus, has limited the development of tailored strategies that address the specific mechanisms underlying MASLD in post-menopausal women. This study reveals the functional role of hepatic ERα in mediating liver metabolic changes in response to estrogens loss, leading to a shift in the liver transcriptome towards a male-like profile. In women with obesity, this shift is associated with the development of MASLD. These findings underscore the potential of targeting hepatic ERα as a promising approach for developing effective, sex-specific treatments to preserve liver health and prevent or limit the development and progression of MASLD in post-menopausal women.
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Affiliation(s)
- Clara Meda
- Department of Health Sciences, Università degli Studi di Milano, Milan, Italy
| | - Valeria Benedusi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy
| | - Alessandro Cherubini
- Precision Medicine–Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
| | - Luca Valenti
- Precision Medicine–Biological Resource Center and Department of Transfusion Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, Milan, Italy
- Department of Pathophysiology and Transplantation, Università degli Studi di Milano, Milan, Italy
| | - Adriana Maggi
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy
| | - Sara Della Torre
- Department of Pharmaceutical Sciences, Università degli Studi di Milano, Milan, Italy
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3
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Kineman RD, Del Rio-Moreno M, Waxman DJ. Liver-specific actions of GH and IGF1 that protect against MASLD. Nat Rev Endocrinol 2024:10.1038/s41574-024-01037-0. [PMID: 39322791 DOI: 10.1038/s41574-024-01037-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 08/29/2024] [Indexed: 09/27/2024]
Abstract
Metabolic dysfunction-associated steatotic liver disease (MASLD; also known as nonalcoholic fatty liver disease) is a chronic condition associated with metabolic syndrome, a group of conditions that includes obesity, insulin resistance, hyperlipidaemia and cardiovascular disease. Primary growth hormone (GH) deficiency is associated with MASLD, and the decline in circulating levels of GH with weight gain might contribute to the development of MASLD. Raising endogenous GH secretion or administering GH replacement therapy in the context of MASLD enhances insulin-like growth factor 1 (IGF1) production and reduces steatosis and the severity of liver injury. GH and IGF1 indirectly control MASLD progression by regulating systemic metabolic function. Evidence supports the proposal that GH and IGF1 also have a direct role in regulating liver metabolism and health. This Review focuses on how GH acts on the hepatocyte in a sex-dependent manner to limit lipid accumulation, reduce stress, and promote survival and regeneration. In addition, we discuss how GH and IGF1 might regulate non-parenchymal cells of the liver to control inflammation and fibrosis, which have a major effect on hepatocyte survival and regeneration. Development of a better understanding of how GH and IGF1 coordinate the functions of specific, individual liver cell types might provide insight into the aetiology of MASLD initiation and progression and suggest novel approaches for the treatment of MASLD.
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Affiliation(s)
- 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, Research and Development Division, Chicago, IL, USA.
| | - Mercedes Del Rio-Moreno
- Department of Medicine, Section of Endocrinology, Diabetes, and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Research and Development Division, Chicago, IL, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, MA, USA
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4
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Sonkar R, Ma H, Waxman DJ. Steatotic liver disease induced by TCPOBOP-activated hepatic constitutive androstane receptor: primary and secondary gene responses with links to disease progression. Toxicol Sci 2024; 200:324-345. [PMID: 38710495 DOI: 10.1093/toxsci/kfae057] [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: 05/08/2024] Open
Abstract
Constitutive androstane receptor (CAR, Nr1i3), a liver nuclear receptor and xenobiotic sensor, induces drug, steroid, and lipid metabolizing enzymes, stimulates liver hypertrophy and hyperplasia, and ultimately, hepatocellular carcinogenesis. The mechanisms linking early CAR responses to later disease development are poorly understood. Here we show that exposure of CD-1 mice to TCPOBOP (1,4-bis[2-(3,5-dichloropyridyloxy)]benzene), a halogenated xenochemical and selective CAR agonist ligand, induces pericentral steatosis marked by hepatic accumulation of cholesterol and neutral lipid, and elevated circulating alanine aminotransferase, indicating hepatocyte damage. TCPOBOP-induced steatosis was weaker in the pericentral region but stronger in the periportal region in females compared with males. Early (1 day) TCPOBOP transcriptional responses were enriched for CAR-bound primary response genes, and for lipogenesis and xenobiotic metabolism and oxidative stress protection pathways; late (2 weeks) TCPOBOP responses included many CAR binding-independent secondary response genes, with enrichment for macrophage activation, immune response, and cytokine and reactive oxygen species production. Late upstream regulators specific to TCPOBOP-exposed male liver were linked to proinflammatory responses and hepatocellular carcinoma progression. TCPOBOP administered weekly to male mice using a high corn oil vehicle induced carbohydrate-responsive transcription factor (MLXIPL)-regulated target genes, dysregulated mitochondrial respiratory and translation regulatory pathways, and induced more advanced liver pathology. Overall, TCPOBOP exposure recapitulates histological and gene expression changes characteristic of emerging steatotic liver disease, including secondary gene responses in liver nonparenchymal cells indicative of transition to a more advanced disease state. Upstream regulators of both the early and late TCPOBOP response genes include novel biomarkers for foreign chemical-induced metabolic dysfunction-associated steatotic liver disease.
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Affiliation(s)
- Ravi Sonkar
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - Hong Ma
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
| | - David J Waxman
- Department of Biology and Bioinformatics Program, Boston University, Boston, Massachusetts 02215, USA
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Ye J, Zeng J, Zheng H, Zhang C, Zhang H, Zheng H. Genome-wide identification of STATs and analysis of their role in sex determination in Pacific oysters (Crassostrea gigas). Comp Biochem Physiol B Biochem Mol Biol 2024; 270:110933. [PMID: 38110171 DOI: 10.1016/j.cbpb.2023.110933] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2023] [Revised: 12/15/2023] [Accepted: 12/15/2023] [Indexed: 12/20/2023]
Abstract
STAT (signal transducer and activator of the transcription) proteins, are a group of highly conserved transcription factors and fundamental components of the JAK-STAT signaling pathway. They play crucial roles in a variety of biological processes, such as immunity, proliferation, differentiation, and growth. However, little information is known regarding their role in gonad development and sex determination in mollusks. In this study, we identified 3 STAT genes in Pacific Oyster Crassostrea gigas. Phylogenetic analysis showed that STATs from mollusks were highly conserved, and most of them had four identical motif regions, except for the STAT1 and STAT3 predicted sequences from Crassostrea hongkongensis. Tissue expression analysis indicated CgSTAT1 had a high expression level in most tissues, while CgSTAT3 had a low expression level in most tissues. Expression analysis of early developmental stages showed CgSTAT1 had a higher expression level from egg to D shaped larva and a lower expression level in subsequent stages. In contrast CgSTAT1, CgSTAT2 had a reverse expression pattern. Expression analysis of different developmental stages of diploid gonads indicated that CgSTAT1 had a higher expression level at the S1 and S3 stages relative to the S2 stage in females, while in males the S3 stage had a higher expression than than the S2 stage. The expression level of CgSTAT1 between diploids and triploids in females differed significantly, but there were no significant differences in males. Expression of CgSTAT2 differed significantly between diploid and triploid males. These data suggest an important role for STATs in sex differentiation in diploid and triploid oysters. Our study is the first to explore the role of STATs in sex differentiation and gonadal development in oysters, and will help us better understand the molecular mechanisms of sex differentiation in shellfish.
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Affiliation(s)
- Jianming Ye
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Junxi Zeng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Haiqian Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Chuanxu Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China
| | - Hongkuan Zhang
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China.
| | - Huaiping Zheng
- Key Laboratory of Marine Biotechnology of Guangdong Province, Marine Sciences Institute, Shantou University, Shantou 515063, China; Research Center of Engineering Technology for Subtropical Mariculture of Guangdong Province, Shantou 515063, China.
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Brie B, Sarmento-Cabral A, Pascual F, Cordoba-Chacon J, Kineman RD, Becu-Villalobos D. Modifications of the GH Axis Reveal Unique Sexually Dimorphic Liver Signatures for Lcn13, Asns, Hamp2, Hao2, and Pgc1a. J Endocr Soc 2024; 8:bvae015. [PMID: 38370444 PMCID: PMC10872697 DOI: 10.1210/jendso/bvae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/23/2023] [Indexed: 02/20/2024] Open
Abstract
Growth hormone (GH) modifies liver gene transcription in a sexually dimorphic manner to meet liver metabolic demands related to sex; thus, GH dysregulation leads to sex-biased hepatic disease. We dissected the steps of the GH regulatory cascade modifying GH-dependent genes involved in metabolism, focusing on the male-predominant genes Lcn13, Asns, and Cyp7b1, and the female-predominant genes Hao2, Pgc1a, Hamp2, Cyp2a4, and Cyp2b9. We explored mRNA expression in 2 settings: (i) intact liver GH receptor (GHR) but altered GH and insulin-like growth factor 1 (IGF1) levels (NeuroDrd2KO, HiGH, aHepIGF1kd, and STAT5bCA mouse lines); and (ii) liver loss of GHR, with or without STAT5b reconstitution (aHepGHRkd, and aHepGHRkd + STAT5bCA). Lcn13 was downregulated in males in most models, while Asns and Cyp7b1 were decreased in males by low GH levels or action, or constant GH levels, but unexpectedly upregulated in both sexes by the loss of liver Igf1 or constitutive Stat5b expression. Hao, Cyp2a4, and Cyp2b9 were generally decreased in female mice with low GH levels or action (NeuroDrd2KO and/or aHepGHRkd mice) and increased in HiGH females, while in contrast, Pgc1a was increased in female NeuroDrd2KO but decreased in STAT5bCA and aHepIGF1kd females. Bioinformatic analysis of RNAseq from aHepGHRkd livers stressed the greater impact of GHR loss on wide gene expression in males and highlighted that GH modifies almost completely different gene signatures in each sex. Concordantly, we show that altering different steps of the GH cascade in the liver modified liver expression of Lcn13, Asns, Cyp7b1, Hao2, Hamp2, Pgc1a, Cyp2a4, and Cyp2b9 in a sex- and gene-specific manner.
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Affiliation(s)
- Belen Brie
- Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Andre Sarmento-Cabral
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Florencia Pascual
- Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
| | - Jose Cordoba-Chacon
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL 60612, USA
| | - Rhonda Denise Kineman
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL 60612, USA
- Research and Development Division, Jesse Brown Veterans Affairs Medical Center, Chicago, IL 60612, USA
| | - Damasia Becu-Villalobos
- Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1428 Ciudad de Buenos Aires, Argentina
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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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8
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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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Budkina A, Medvedeva YA, Stupnikov A. Assessing the Differential Methylation Analysis Quality for Microarray and NGS Platforms. Int J Mol Sci 2023; 24:ijms24108591. [PMID: 37239934 DOI: 10.3390/ijms24108591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 04/28/2023] [Accepted: 05/07/2023] [Indexed: 05/28/2023] Open
Abstract
Differential methylation (DM) is actively recruited in different types of fundamental and translational studies. Currently, microarray- and NGS-based approaches for methylation analysis are the most widely used with multiple statistical models designed to extract differential methylation signatures. The benchmarking of DM models is challenging due to the absence of gold standard data. In this study, we analyze an extensive number of publicly available NGS and microarray datasets with divergent and widely utilized statistical models and apply the recently suggested and validated rank-statistic-based approach Hobotnica to evaluate the quality of their results. Overall, microarray-based methods demonstrate more robust and convergent results, while NGS-based models are highly dissimilar. Tests on the simulated NGS data tend to overestimate the quality of the DM methods and therefore are recommended for use with caution. Evaluation of the top 10 DMC and top 100 DMC in addition to the not-subset signature also shows more stable results for microarray data. Summing up, given the observed heterogeneity in NGS methylation data, the evaluation of newly generated methylation signatures is a crucial step in DM analysis. The Hobotnica metric is coordinated with previously developed quality metrics and provides a robust, sensitive, and informative estimation of methods' performance and DM signatures' quality in the absence of gold standard data solving a long-existing problem in DM analysis.
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Affiliation(s)
- Anna Budkina
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
| | - Yulia A Medvedeva
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», 119071 Moscow, Russia
| | - Alexey Stupnikov
- Department of Biomedical Physics, Moscow Institute of Physics and Technology, 141701 Dolgoprudny, Russia
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Everton E, Del Rio-Moreno M, Villacorta-Martin C, Singh Bawa P, Lindstrom-Vautrin J, Muramatsu H, Rizvi F, Smith AR, Tam Y, Pardi N, Kineman R, Waxman DJ, Gouon-Evans V. Growth Hormone Accelerates Recovery From Acetaminophen-Induced Murine Liver Injury. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.17.537197. [PMID: 37131727 PMCID: PMC10153200 DOI: 10.1101/2023.04.17.537197] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Background and Aims Acetaminophen (APAP) overdose is the leading cause of acute liver failure, with one available treatment, N-acetyl cysteine (NAC). Yet, NAC effectiveness diminishes about ten hours after APAP overdose, urging for therapeutic alternatives. This study addresses this need by deciphering a mechanism of sexual dimorphism in APAP-induced liver injury, and leveraging it to accelerate liver recovery via growth hormone (GH) treatment. GH secretory patterns, pulsatile in males and near-continuous in females, determine the sex bias in many liver metabolic functions. Here, we aim to establish GH as a novel therapy to treat APAP hepatotoxicity. Approach and Results Our results demonstrate sex-dependent APAP toxicity, with females showing reduced liver cell death and faster recovery than males. Single-cell RNA sequencing analyses reveal that female hepatocytes have significantly greater levels of GH receptor expression and GH pathway activation compared to males. In harnessing this female-specific advantage, we demonstrate that a single injection of recombinant human GH protein accelerates liver recovery, promotes survival in males following sub-lethal dose of APAP, and is superior to standard-of-care NAC. Alternatively, slow-release delivery of human GH via the safe nonintegrative lipid nanoparticle-encapsulated nucleoside-modified mRNA (mRNA-LNP), a technology validated by widely used COVID-19 vaccines, rescues males from APAP-induced death that otherwise occurred in control mRNA-LNP-treated mice. Conclusions Our study demonstrates a sexually dimorphic liver repair advantage in females following APAP overdose, leveraged by establishing GH as an alternative treatment, delivered either as recombinant protein or mRNA-LNP, to potentially prevent liver failure and liver transplant in APAP-overdosed patients.
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11
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Batdorj E, AlOgayil N, Zhuang QKW, Galvez JH, Bauermeister K, Nagata K, Kimura T, Ward MA, Taketo T, Bourque G, Naumova AK. Genetic variation in the Y chromosome and sex-biased DNA methylation in somatic cells in the mouse. Mamm Genome 2023; 34:44-55. [PMID: 36454369 PMCID: PMC9947081 DOI: 10.1007/s00335-022-09970-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 11/22/2022] [Indexed: 12/05/2022]
Abstract
Several lines of evidence suggest that the presence of the Y chromosome influences DNA methylation of autosomal loci. To better understand the impact of the Y chromosome on autosomal DNA methylation patterns and its contribution to sex bias in methylation, we identified Y chromosome dependent differentially methylated regions (yDMRs) using whole-genome bisulfite sequencing methylation data from livers of mice with different combinations of sex-chromosome complement and gonadal sex. Nearly 90% of the autosomal yDMRs mapped to transposable elements (TEs) and most of them had lower methylation in XY compared to XX or XO mice. Follow-up analyses of four reporter autosomal yDMRs showed that Y-dependent methylation levels were consistent across most somatic tissues but varied in strains with different origins of the Y chromosome, suggesting that genetic variation in the Y chromosome influenced methylation levels of autosomal regions. Mice lacking the q-arm of the Y chromosome (B6.NPYq-2) as well as mice with a loss-of-function mutation in Kdm5d showed no differences in methylation levels compared to wild type mice. In conclusion, the Y-linked modifier of TE methylation is likely to reside on the short arm of Y chromosome and further studies are required to identify this gene.
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Affiliation(s)
- Enkhjin Batdorj
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Najla AlOgayil
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Qinwei Kim-Wee Zhuang
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Jose Hector Galvez
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Klara Bauermeister
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
| | - Kei Nagata
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Tohru Kimura
- Laboratory of Stem Cell Biology, Department of Biosciences, Kitasato University School of Science, 1-15-1 Kitasato, Minami-Ku, Sagamihara, Kanagawa, 252-0373, Japan
| | - Monika A Ward
- Institute for Biogenesis Research, John A. Burns School of Medicine, University of Hawaii, 1960 East-West Road, HonoluluHonolulu, HIHI, 96822, USA
| | - Teruko Taketo
- The Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada
- Department of Surgery, McGill University, Montréal, QC, H4A 3J1, Canada
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC, H4A 3J1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada
- Canadian Centre for Computational Genomics, Montréal, QC, H3A 0G1, Canada
| | - Anna K Naumova
- Department of Human Genetics, McGill University, Montréal, QC, H3A 1C7, Canada.
- The Research Institute of the McGill University Health Centre, Montréal, QC, H4A 3J1, Canada.
- Department of Obstetrics and Gynecology, McGill University, Montréal, QC, H4A 3J1, Canada.
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12
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Yao D, Guo D, Zhang Y, Chen Z, Gao X, Xing G, Yang X, Wang X, Di S, Cai J, Niu B. Identification of mutations in porcine STAT5A that contributes to the transcription of CISH. Front Vet Sci 2023; 9:1090833. [PMID: 36733428 PMCID: PMC9887310 DOI: 10.3389/fvets.2022.1090833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2022] [Accepted: 12/28/2022] [Indexed: 01/18/2023] Open
Abstract
Identification of causative genes or genetic variants associated with phenotype traits benefits the genetic improvement of animals. CISH plays a role in immunity and growth, however, the upstream transcriptional factors of porcine CISH and the genetic variations in these factors remain unclear. In this study, we firstly identified the minimal core promoter of porcine CISH and confirmed the existence of STATx binding sites. Overexpression and RT-qPCR demonstrated STAT5A increased CISH transcriptional activity (P < 0.01) and mRNA expression (P < 0.01), while GATA1 inhibited CISH transcriptional activity (P < 0.01) and the following mRNA expression (P < 0.05 or P < 0.01). Then, the putative functional genetic variations of porcine STAT5A were screened and a PCR-SSCP was established for genotype g.508A>C and g.566C>T. Population genetic analysis showed the A allele frequency of g.508A>C and C allele frequency of g.566C>T was 0.61 and 0.94 in Min pigs, respectively, while these two alleles were fixed in the Landrace population. Statistical analysis showed that Min piglets with CC genotype at g.566C>T or Hap1: AC had higher 28-day body weight, 35-day body weight, and ADG than TC or Hap3: CT animals (P < 0.05, P < 0.05). Further luciferase activity assay demonstrated that the activity of g.508A>C in the C allele was lower than the A allele (P < 0.05). Collectively, the present study demonstrated that STAT5A positively regulated porcine CISH transcription, and SNP g.566C>T in the STAT5A was associated with the Min piglet growth trait.
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Affiliation(s)
- Diwen Yao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Dongchun Guo
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Harbin, China
| | - Yingkun Zhang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Zhihua Chen
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiaowen Gao
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Guiling Xing
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xiuqin Yang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Xibiao Wang
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | - Shengwei Di
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China
| | | | - Buyue Niu
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, China,*Correspondence: Buyue Niu ✉
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13
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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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14
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Dichtel LE, Cordoba-Chacon J, Kineman RD. Growth Hormone and Insulin-Like Growth Factor 1 Regulation of Nonalcoholic Fatty Liver Disease. J Clin Endocrinol Metab 2022; 107:1812-1824. [PMID: 35172328 PMCID: PMC9202731 DOI: 10.1210/clinem/dgac088] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Indexed: 11/19/2022]
Abstract
Patients with obesity have a high prevalence of nonalcoholic fatty liver disease (NAFLD), representing a spectrum of simple steatosis to nonalcoholic steatohepatitis (NASH), without and with fibrosis. Understanding the etiology of NAFLD is clinically relevant since NAFLD is an independent risk factor for diabetes and cardiovascular disease. In addition, NASH predisposes patients to the development of cirrhosis and hepatocellular carcinoma, and NASH cirrhosis represents the fastest growing indication for liver transplantation in the United States. It is appreciated that multiple factors are involved in the development and progression of NAFLD. Growth hormone (GH) and insulin-like growth factor 1 (IGF1) regulate metabolic, immune, and hepatic stellate cell function, and alterations in the production and function of GH is associated with obesity and NAFLD/NASH. Therefore, this review will focus on the potential role of GH and IGF1 in the regulation of hepatic steatosis, inflammation, and fibrosis.
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Affiliation(s)
- Laura E Dichtel
- Neuroendocrine Unit, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Jose Cordoba-Chacon
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
| | - Rhonda D Kineman
- Department of Medicine, Division of Endocrinology, Diabetes and Metabolism, University of Illinois at Chicago, Chicago, IL, USA
- Jesse Brown VA Medical Center, Research and Development Division, Chicago, IL, USA
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15
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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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16
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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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17
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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: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [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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Affiliation(s)
- Dustin J. Penn
- Department of Interdisciplinary Life Sciences, Konrad Lorenz Institute of Ethology, University of Veterinary Medicine Vienna, Vienna, Austria
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18
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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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19
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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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20
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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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