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Chakraborty S, Anand S, Bhandari RK. Medaka liver developed Human NAFLD-NASH transcriptional signatures in response to ancestral bisphenol A exposure. RESEARCH SQUARE 2024:rs.3.rs-4585175. [PMID: 39070641 PMCID: PMC11275980 DOI: 10.21203/rs.3.rs-4585175/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: 07/30/2024]
Abstract
The progression of fatty liver disease to non-alcoholic steatohepatitis (NASH) is a leading cause of death in humans. Lifestyles and environmental chemical exposures can increase the susceptibility of humans to NASH. In humans, the presence of bisphenol A (BPA) in urine is associated with fatty liver disease, but whether ancestral BPA exposure leads to the activation of human NAFLD-NASH-associated genes in the unexposed descendants is unclear. In this study, using medaka fish as an animal model for human NAFLD, we investigated the transcriptional signatures of human NAFLD-NASH and their associated roles in the pathogenesis of the liver of fish that were not directly exposed, but their ancestors were exposed to BPA during embryonic and perinatal development three generations prior. Comparison of bulk RNA-Seq data of the liver in BPA lineage male and female medaka with publicly available human NAFLD-NASH patient data revealed transgenerational alterations in the transcriptional signature of human NAFLD-NASH in medaka liver. Twenty percent of differentially expressed genes (DEGs) were upregulated in both human NAFLD patients and medaka. Specifically in females, among the total shared DEGs in the liver of BPA lineage fish and NAFLD patient groups, 27.69% were downregulated, and 20% were upregulated. Of all DEGs, 52.31% of DEGs were found in ancestral BPA-lineage females, suggesting that NAFLD in females shared the majority of human NAFLD gene networks. Pathway analysis revealed beta-oxidation, lipoprotein metabolism, and HDL/LDL-mediated transport processes linked to downregulated DEGs in BPA lineage males and females. In contrast, the expression of genes encoding lipogenesis-related proteins was significantly elevated in the liver of BPA lineage females only. BPA lineage females exhibiting activation of myc, atf4, xbp1, stat4, and cancerous pathways, as well as inactivation of igf1, suggest their possible association with an advanced NAFLD phenotype. The present results suggest that gene networks involved in the progression of human NAFLD and the transgenerational NAFLD in medaka are conserved and that medaka can be an excellent animal model to understand the development and progression of liver disease and environmental influences in the liver.
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2
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Chakraborty S, Anand S, Bhandari RK. Sex-specific expression of the human NAFLD-NASH transcriptional signatures in the liver of medaka with a history of ancestral bisphenol A exposure. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.19.594843. [PMID: 38826193 PMCID: PMC11142124 DOI: 10.1101/2024.05.19.594843] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2024]
Abstract
The progression of fatty liver disease to non-alcoholic steatohepatitis (NASH) is a leading cause of death in humans. Lifestyles and environmental chemical exposures can increase the susceptibility of humans to NASH. In humans, the presence of bisphenol A (BPA) in urine is associated with fatty liver disease, but whether ancestral BPA exposure leads to the activation of human NAFLD-NASH-associated genes in the unexposed descendants is unclear. In this study, using medaka fish as an animal model for human NAFLD, we investigated the transcriptional signatures of human NAFLD-NASH and their associated roles in the pathogenesis of the liver of fish who were not directly exposed but their ancestors were exposed to BPA during embryonic and perinatal development three generations prior. Comparison of bulk RNA-Seq data of the liver in BPA lineage male and female medaka with publicly available human NAFLD-NASH patient data revealed transgenerational alterations in the transcriptional signature of human NAFLD-NASH in medaka liver. Twenty percent of differentially expressed genes (DEGs) were upregulated in both human NAFLD patients and medaka. Specifically in females, among the total shared DEGs in the liver of BPA lineage fish and NAFLD patient groups, 27.69% DEGs were downregulated and 20% DEGs were upregulated. Off all DEGs, 52.31% DEGs were found in ancestral BPA-lineage females, suggesting that NAFLD in females shared majority of human NAFLD gene networks. Pathway analysis revealed beta-oxidation, lipoprotein metabolism, and HDL/LDL-mediated transport processes linked to downregulated DEGs in BPA lineage males and females. In contrast, the expression of genes encoding lipogenesis-related proteins was significantly elevated in the liver of BPA lineage females only. BPA lineage females exhibiting activation of myc, atf4, xbp1, stat4, and cancerous pathways, as well as inactivation of igf1, suggest their possible association with an advanced NAFLD phenotype. The present results suggest that gene networks involved in the progression of human NAFLD and the transgenerational NAFLD in medaka are conserved and that medaka can be an excellent animal model to understand the development and progression of liver disease and environmental influences in the liver.
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Affiliation(s)
- Sourav Chakraborty
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, U.S.A
| | - Santosh Anand
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, U.S.A
| | - Ramji Kumar Bhandari
- Division of Biological Sciences, University of Missouri, Columbia, MO 65211, U.S.A
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3
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Bauer R, Meyer SP, Raue R, Palmer MA, Guerrero Ruiz VM, Cardamone G, Rösser S, Heffels M, Roesmann F, Wilhelm A, Lütjohann D, Zarnack K, Fuhrmann DC, Widera M, Schmid T, Brüne B. Hypoxia-altered cholesterol homeostasis enhances the expression of interferon-stimulated genes upon SARS-CoV-2 infections in monocytes. Front Immunol 2023; 14:1121864. [PMID: 37377965 PMCID: PMC10291055 DOI: 10.3389/fimmu.2023.1121864] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Hypoxia contributes to numerous pathophysiological conditions including inflammation-associated diseases. We characterized the impact of hypoxia on the immunometabolic cross-talk between cholesterol and interferon (IFN) responses. Specifically, hypoxia reduced cholesterol biosynthesis flux and provoked a compensatory activation of sterol regulatory element-binding protein 2 (SREBP2) in monocytes. Concomitantly, a broad range of interferon-stimulated genes (ISGs) increased under hypoxia in the absence of an inflammatory stimulus. While changes in cholesterol biosynthesis intermediates and SREBP2 activity did not contribute to hypoxic ISG induction, intracellular cholesterol distribution appeared critical to enhance hypoxic expression of chemokine ISGs. Importantly, hypoxia further boosted chemokine ISG expression in monocytes upon infection with severe acute respiratory syndrome coronavirus type 2 (SARS-CoV-2). Mechanistically, hypoxia sensitized toll-like receptor 4 (TLR4) signaling to activation by SARS-CoV-2 spike protein, which emerged as a major signaling hub to enhance chemokine ISG induction following SARS-CoV-2 infection of hypoxic monocytes. These data depict a hypoxia-regulated immunometabolic mechanism with implications for the development of systemic inflammatory responses in severe cases of coronavirus disease-2019 (COVID-19).
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Affiliation(s)
- Rebekka Bauer
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Sofie Patrizia Meyer
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Rebecca Raue
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Megan A. Palmer
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | | | - Giulia Cardamone
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Silvia Rösser
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Milou Heffels
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
| | - Fabian Roesmann
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Alexander Wilhelm
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Dieter Lütjohann
- Institute of Clinical Chemistry and Clinical Pharmacology, University of Bonn, Bonn, Germany
| | - Kathi Zarnack
- Buchmann Institute for Molecular Life Sciences (BMLS), Faculty of Biological Sciences, Goethe University Frankfurt, Frankfurt, Germany
| | - Dominik Christian Fuhrmann
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
| | - Marek Widera
- Institute of Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
| | - Tobias Schmid
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
| | - Bernhard Brüne
- Institute of Biochemistry I, Faculty of Medicine, Goethe University Frankfurt, Frankfurt, Germany
- German Cancer Consortium (DKTK), Partner Site Frankfurt, Frankfurt, Germany
- Frankfurt Cancer Institute, Goethe University Frankfurt, Frankfurt, Germany
- Fraunhofer Institute for Translational Medicine and Pharmacology ITMP, Frankfurt, Germany
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4
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Coates HW, Capell-Hattam IM, Olzomer EM, Du X, Farrell R, Yang H, Byrne FL, Brown AJ. Hypoxia truncates and constitutively activates the key cholesterol synthesis enzyme squalene monooxygenase. eLife 2023; 12:82843. [PMID: 36655986 PMCID: PMC9851614 DOI: 10.7554/elife.82843] [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] [Received: 08/19/2022] [Accepted: 12/13/2022] [Indexed: 01/20/2023] Open
Abstract
Cholesterol synthesis is both energy- and oxygen-intensive, yet relatively little is known of the regulatory effects of hypoxia on pathway enzymes. We previously showed that the rate-limiting and first oxygen-dependent enzyme of the committed cholesterol synthesis pathway, squalene monooxygenase (SM), can undergo partial proteasomal degradation that renders it constitutively active. Here, we show hypoxia is a physiological trigger for this truncation, which occurs through a two-part mechanism: (1) increased targeting of SM to the proteasome via stabilization of the E3 ubiquitin ligase MARCHF6 and (2) accumulation of the SM substrate, squalene, which impedes the complete degradation of SM and liberates its truncated form. This preserves SM activity and downstream pathway flux during hypoxia. These results uncover a feedforward mechanism that allows SM to accommodate fluctuating substrate levels and may contribute to its widely reported oncogenic properties.
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Affiliation(s)
- Hudson W Coates
- School of Biotechnology and Biomolecular Sciences, UNSW SydneySydneyAustralia
| | | | - Ellen M Olzomer
- School of Biotechnology and Biomolecular Sciences, UNSW SydneySydneyAustralia
| | - Ximing Du
- School of Biotechnology and Biomolecular Sciences, UNSW SydneySydneyAustralia
| | - Rhonda Farrell
- Prince of Wales Private HospitalRandwickAustralia
- Chris O’Brien LifehouseCamperdownAustralia
| | - Hongyuan Yang
- School of Biotechnology and Biomolecular Sciences, UNSW SydneySydneyAustralia
| | - Frances L Byrne
- School of Biotechnology and Biomolecular Sciences, UNSW SydneySydneyAustralia
| | - Andrew J Brown
- School of Biotechnology and Biomolecular Sciences, UNSW SydneySydneyAustralia
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5
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Chua NK, Coates HW, Brown AJ. Squalene monooxygenase: a journey to the heart of cholesterol synthesis. Prog Lipid Res 2020; 79:101033. [DOI: 10.1016/j.plipres.2020.101033] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 04/21/2020] [Accepted: 04/24/2020] [Indexed: 02/07/2023]
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6
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Zuniga-Hertz JP, Patel HH. The Evolution of Cholesterol-Rich Membrane in Oxygen Adaption: The Respiratory System as a Model. Front Physiol 2019; 10:1340. [PMID: 31736773 PMCID: PMC6828933 DOI: 10.3389/fphys.2019.01340] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/08/2019] [Indexed: 12/14/2022] Open
Abstract
The increase in atmospheric oxygen levels imposed significant environmental pressure on primitive organisms concerning intracellular oxygen concentration management. Evidence suggests the rise of cholesterol, a key molecule for cellular membrane organization, as a cellular strategy to restrain free oxygen diffusion under the new environmental conditions. During evolution and the increase in organismal complexity, cholesterol played a pivotal role in the establishment of novel and more complex functions associated with lipid membranes. Of these, caveolae, cholesterol-rich membrane domains, are signaling hubs that regulate important in situ functions. Evolution resulted in complex respiratory systems and molecular response mechanisms that ensure responses to critical events such as hypoxia facilitated oxygen diffusion and transport in complex organisms. Caveolae have been structurally and functionally associated with respiratory systems and oxygen diffusion control through their relationship with molecular response systems like hypoxia-inducible factors (HIF), and particularly as a membrane-localized oxygen sensor, controlling oxygen diffusion balanced with cellular physiological requirements. This review will focus on membrane adaptations that contribute to regulating oxygen in living systems.
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Affiliation(s)
- Juan Pablo Zuniga-Hertz
- Department of Anesthesiology, VA San Diego Healthcare System, University of California, San Diego, San Diego, CA, United States
| | - Hemal H Patel
- Department of Anesthesiology, VA San Diego Healthcare System, University of California, San Diego, San Diego, CA, United States
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7
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Reijnders D, Olson KN, Liu CC, Beckers KF, Ghosh S, Redman LM, Sones JL. Dyslipidemia and the role of adipose tissue in early pregnancy in the BPH/5 mouse model for preeclampsia. Am J Physiol Regul Integr Comp Physiol 2019; 317:R49-R58. [PMID: 30995083 DOI: 10.1152/ajpregu.00334.2018] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The hypertensive pregnancy disorder preeclampsia (PE) is a leading cause of fetal and maternal morbidity/mortality. Obesity increases the risk to develop PE, presumably via the release of inflammatory mediators from the adipose tissue, but the exact etiology remains largely unknown. Using obese PE-like blood pressure high subline 5 (BPH/5) and lean gestational age-matched C57Bl6 mice, we aimed to obtain insight into differential reproductive white adipose tissue (rWAT) gene expression, circulating lipids and inflammation at the maternal-fetal interface during early pregnancy. In addition, we investigated the effect of 7 days 25% calorie restriction (CR) in early pregnancy on gene expression in rWAT and implantation sites. Compared with C57Bl6, female BPH/5 are dyslipidemic before pregnancy and show an amplification of rWAT mass, circulating cholesterol, free fatty acids, and triacylglycerol levels throughout pregnancy. RNA sequencing showed that pregnant BPH/5 mice have elevated gene enrichment in pathways related to inflammation and cholesterol biosynthesis at embryonic day (e) 7.5. Expression of cholesterol-related HMGCS1, MVD, Cyp51a1, and DHCR was validated by quantitative reverse-transcription-polymerase chain reaction. CR during the first 7 days of pregnancy restored the relative mRNA expression of these genes to a level comparable to C57Bl6 pregnant females and reduced the expression of circulating leptin and proinflammatory prostaglandin synthase 2 in both rWAT and implantation sites in BPH/5 mice at e7.5. Our data suggest a possible role for rWAT in the dyslipidemic state and inflammatory uterine milieu that might underlie the pathogenesis of PE. Future studies should further address the physiological functioning of the adipose tissue in relation to PE-related pregnancy outcomes.
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Affiliation(s)
- Dorien Reijnders
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University , Baton Rouge, Louisiana.,Reproductive Endocrinology & Women's Health Lab, Pennington Biomedical Research Center , Baton Rouge, Louisiana
| | - Kelsey N Olson
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University , Baton Rouge, Louisiana.,Reproductive Endocrinology & Women's Health Lab, Pennington Biomedical Research Center , Baton Rouge, Louisiana
| | - Chin-Chi Liu
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University , Baton Rouge, Louisiana
| | - Kalie F Beckers
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University , Baton Rouge, Louisiana
| | - Sujoy Ghosh
- Center for Computational Biology, Duke-National University of Singapore Medical School, Singapore.,Nutrient Sensing and Adipocyte Signaling Laboratory, Pennington Biomedical Research Center , Baton Rouge, Louisiana
| | - Leanne M Redman
- Reproductive Endocrinology & Women's Health Lab, Pennington Biomedical Research Center , Baton Rouge, Louisiana
| | - Jenny L Sones
- Veterinary Clinical Sciences, School of Veterinary Medicine, Louisiana State University , Baton Rouge, Louisiana
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8
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Liu J, Gao W, Pu L, Wei J, Xin Z, Wang Y, Shi T, Guo C. Modulation of hepatic gene expression profiles by vitamin B 1, vitamin B 2, and niacin supplementation in mice exposed to acute hypoxia. Appl Physiol Nutr Metab 2018; 43:844-853. [PMID: 29566343 DOI: 10.1139/apnm-2017-0468] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study was aimed to observe the effects of vitamin B1, vitamin B2, and niacin supplementation on hepatic gene expression profiles in mice exposed to acute hypoxia. Thirty mice were randomly divided into normal, acute hypoxia, and acute hypoxia plus vitamin B1, vitamin B2, and niacin supplementation groups and fed corresponding diets for 2 weeks and then exposed to a simulated altitude of 6000 m for 8 h. Hepatic gene expression profiles were analyzed using a microarray technique. Several biochemical markers were also assayed. The results showed that a total of 2476 genes were expressed differentially after acute hypoxia exposure (1508 upregulated genes and 968 downregulated genes). Compared with the acute hypoxia group, there were 1382 genes differentially expressed (626 upregulated genes and 756 downregulated genes) in the acute hypoxia plus vitamin B1, vitamin B2, and niacin supplementation group. Pathway analysis indicated that carbohydrate, lipid, and amino acid metabolism, as well as electron transfer chain, were improved to some extent after vitamin B1, vitamin B2, and niacin supplementation. Supportive results were obtained from biochemical assays. Our findings suggest that the supplementation of vitamin B1, vitamin B2, and niacin is beneficial in improving nutritional metabolism partly via gene expression under acute hypoxia condition.
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Affiliation(s)
- Jin Liu
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Weina Gao
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Lingling Pu
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Jingyu Wei
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Zhonghao Xin
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Yawen Wang
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Tala Shi
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
| | - Changjiang Guo
- Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China.,Department of Nutrition, Tianjin Institute of Health and Environmental Medicine, Tianjin, 300050, China
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9
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Gan Z, Powell FL, Zambon AC, Buchholz KS, Fu Z, Ocorr K, Bodmer R, Moya EA, Stowe JC, Haddad GG, McCulloch AD. Transcriptomic analysis identifies a role of PI3K-Akt signalling in the responses of skeletal muscle to acute hypoxia in vivo. J Physiol 2017; 595:5797-5813. [PMID: 28688178 PMCID: PMC5577531 DOI: 10.1113/jp274556] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 06/19/2017] [Indexed: 01/13/2023] Open
Abstract
KEY POINTS Changes in gene expression that occur within hours of exposure to hypoxia in in vivo skeletal muscles remain unexplored. Two hours of hypoxia caused significant down-regulation of extracellular matrix genes followed by a shift at 6 h to altered expression of genes associated with the nuclear lumen while respiratory and blood gases were stabilized. Enrichment analysis of mRNAs classified by stability rates suggests an attenuation of post-transcriptional regulation within hours of hypoxic exposure, where PI3K-Akt signalling was suggested to have a nodal role by pathway analysis. Experimental measurements and bioinformatic analyses suggested that the dephosphorylation of Akt after 2 h of hypoxic exposure might deactivate RNA-binding protein BRF1, hence resulting in the selective degradation of mRNAs. ABSTRACT The effects of acute hypoxia have been widely studied, but there are few studies of transcriptional responses to hours of hypoxia in vivo, especially in hypoxia-tolerant tissues like skeletal muscles. We used RNA-seq to analyse gene expression in plantaris muscles while monitoring respiration, arterial blood gases, and blood glucose in mice exposed to 8% O2 for 2 or 6 h. Rapid decreases in blood gases and a slower reduction in blood glucose suggest stress, which was accompanied by widespread changes in gene expression. Early down-regulation of genes associated with the extracellular matrix was followed by a shift to genes associated with the nuclear lumen. Most of the early down-regulated genes had mRNA half-lives longer than 2 h, suggesting a role for post-transcriptional regulation. These transcriptional changes were enriched in signalling pathways in which the PI3K-Akt signalling pathway was identified as a hub. Our analyses indicated that gene targets of PI3K-Akt but not HIF were enriched in early transcriptional responses to hypoxia. Among the PI3K-Akt targets, 75% could be explained by a deactivation of adenylate-uridylate-rich element (ARE)-binding protein BRF1, a target of PI3K-Akt. Consistent decreases in the phosphorylation of Akt and BRF1 were experimentally confirmed following 2 h of hypoxia. These results suggest that the PI3K-Akt signalling pathway might play a role in responses induced by acute hypoxia in skeletal muscles, partially through the dephosphorylation of ARE-binding protein BRF1.
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Affiliation(s)
- Zhuohui Gan
- School of Basic Medical SciencesWenzhou Medical UniversityWenzhou325035ZhejiangChina
- Department of BioengineeringUniversity of California San DiegoLa JollaCA92093USA
| | - Frank L. Powell
- Department of MedicineUniversity of California San DiegoLa JollaCA92093USA
| | - Alexander C. Zambon
- Department of Biopharmaceutical SciencesKeck Graduate InstituteClaremontCA91711USA
| | - Kyle S. Buchholz
- Department of BioengineeringUniversity of California San DiegoLa JollaCA92093USA
| | - Zhenxing Fu
- Department of MedicineUniversity of California San DiegoLa JollaCA92093USA
| | - Karen Ocorr
- Development, Aging and Regeneration ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaCA92037USA
| | - Rolf Bodmer
- Development, Aging and Regeneration ProgramSanford Burnham Prebys Medical Discovery InstituteLa JollaCA92037USA
| | - Esteban A. Moya
- Department of MedicineUniversity of California San DiegoLa JollaCA92093USA
| | - Jennifer C. Stowe
- Department of BioengineeringUniversity of California San DiegoLa JollaCA92093USA
| | - Gabriel G. Haddad
- Department of PediatricsUniversity of California San DiegoLa JollaCA92093USA
- Department of NeurosciencesUniversity of California San DiegoLa JollaCA92093USA
- Rady Children's Hospital San Diego3020 Children's WaySan DiegoCA92123USA
| | - Andrew D. McCulloch
- Department of BioengineeringUniversity of California San DiegoLa JollaCA92093USA
- Department of MedicineUniversity of California San DiegoLa JollaCA92093USA
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10
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Hwang S, Nguyen AD, Jo Y, Engelking LJ, Brugarolas J, DeBose-Boyd RA. Hypoxia-inducible factor 1α activates insulin-induced gene 2 (Insig-2) transcription for degradation of 3-hydroxy-3-methylglutaryl (HMG)-CoA reductase in the liver. J Biol Chem 2017; 292:9382-9393. [PMID: 28416613 DOI: 10.1074/jbc.m117.788562] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Revised: 04/14/2017] [Indexed: 12/15/2022] Open
Abstract
Cholesterol synthesis is a highly oxygen-consuming process. As such, oxygen deprivation (hypoxia) limits cholesterol synthesis through incompletely understood mechanisms mediated by the oxygen-sensitive transcription factor hypoxia-inducible factor 1α (HIF-1α). We show here that HIF-1α links pathways for oxygen sensing and feedback control of cholesterol synthesis in human fibroblasts by directly activating transcription of the INSIG-2 gene. Insig-2 is one of two endoplasmic reticulum membrane proteins that inhibit cholesterol synthesis by mediating sterol-induced ubiquitination and subsequent endoplasmic reticulum-associated degradation of the rate-limiting enzyme in the pathway, HMG-CoA reductase (HMGCR). Consistent with the results in cultured cells, hepatic levels of Insig-2 mRNA were enhanced in mouse models of hypoxia. Moreover, pharmacologic stabilization of HIF-1α in the liver stimulated HMGCR degradation via a reaction that requires the protein's prior ubiquitination and the presence of the Insig-2 protein. In summary, our results show that HIF-1α activates INSIG-2 transcription, leading to accumulation of Insig-2 protein, which binds to HMGCR and triggers its accelerated ubiquitination and degradation. These results indicate that HIF-mediated induction of Insig-2 and degradation of HMGCR are physiologically relevant events that guard against wasteful oxygen consumption and inappropriate cell growth during hypoxia.
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Affiliation(s)
| | | | - Youngah Jo
- From the Department of Molecular Genetics and
| | | | - James Brugarolas
- Simmons Comprehensive Cancer Center, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9046
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11
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Li F, Liu W. Genome-wide identification, classification, and functional analysis of the basic helix-loop-helix transcription factors in the cattle, Bos Taurus. Mamm Genome 2017; 28:176-197. [PMID: 28299435 DOI: 10.1007/s00335-017-9683-x] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2016] [Accepted: 03/04/2017] [Indexed: 10/20/2022]
Abstract
The basic helix-loop-helix (bHLH) transcription factors (TFs) form a huge superfamily and play crucial roles in many essential developmental, genetic, and physiological-biochemical processes of eukaryotes. In total, 109 putative bHLH TFs were identified and categorized successfully in the genomic databases of cattle, Bos Taurus, after removing redundant sequences and merging genetic isoforms. Through phylogenetic analyses, 105 proteins among these bHLH TFs were classified into 44 families with 46, 25, 14, 3, 13, and 4 members in the high-order groups A, B, C, D, E, and F, respectively. The remaining 4 bHLH proteins were sorted out as 'orphans.' Next, these 109 putative bHLH proteins identified were further characterized as significantly enriched in 524 significant Gene Ontology (GO) annotations (corrected P value ≤ 0.05) and 21 significantly enriched pathways (corrected P value ≤ 0.05) that had been mapped by the web server KOBAS 2.0. Furthermore, 95 bHLH proteins were further screened and analyzed together with two uncharacterized proteins in the STRING online database to reconstruct the protein-protein interaction network of cattle bHLH TFs. Ultimately, 89 bHLH proteins were fully mapped in a network with 67 biological process, 13 molecular functions, 5 KEGG pathways, 12 PFAM protein domains, and 25 INTERPRO classified protein domains and features. These results provide much useful information and a good reference for further functional investigations and updated researches on cattle bHLH TFs.
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Affiliation(s)
- Fengmei Li
- Faculty of Biological and Food Engineering, Fuyang Normal University, Qing He West Road No. 100, Fuyang, 236037, People's Republic of China
| | - Wuyi Liu
- Faculty of Biological and Food Engineering, Fuyang Normal University, Qing He West Road No. 100, Fuyang, 236037, People's Republic of China. .,Medical Faculty, Zhejiang University, Hangzhou, 310003, People's Republic of China.
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12
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Duivenvoorde LPM, van Schothorst EM, Swarts HJM, Keijer J. Assessment of Metabolic Flexibility of Old and Adult Mice Using Three Noninvasive, Indirect Calorimetry-Based Treatments. J Gerontol A Biol Sci Med Sci 2014; 70:282-93. [DOI: 10.1093/gerona/glu027] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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13
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Laursen KB, Wong PM, Gudas LJ. Epigenetic regulation by RARα maintains ligand-independent transcriptional activity. Nucleic Acids Res 2011; 40:102-15. [PMID: 21911359 PMCID: PMC3245912 DOI: 10.1093/nar/gkr637] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Retinoic acid receptors (RARs) α, β and γ are key regulators of embryonic development. Hematopoietic differentiation is regulated by RARα, and several types of leukemia show aberrant RARα activity. Through microarray expression analysis, we identified transcripts differentially expressed between F9 wild-type (Wt) and RARα knockout cells cultured in the absence or presence of the RAR-specific ligand all trans retinoic acid (RA). We validated the decreased Mest, Tex13, Gab1, Bcl11a, Tcfap2a and HMGcs1 transcript levels, and increased Slc38a4, Stmn2, RpL39l, Ref2L, Mobp and Rlf1 transcript levels in the RARa knockout cells. The decreased Mest and Tex13 transcript levels were associated with increased promoter CpG-island methylation and increased repressive histone modifications (H3K9me3) in RARα knockout cells. Increased Slc38a4 and Stmn2 transcript levels were associated with decreased promoter CpG-island methylation and increased permissive histone modifications (H3K9/K14ac, H3K4me3) in RARα knockout cells. We demonstrated specific association of RARα and RXRα with the Mest promoter. Importantly, stable expression of a dominant negative, oncogenic PML–RARα fusion protein in F9 Wt cells recapitulated the decreased Mest transcript levels observed in RARα knockout cells. We propose that RARα plays an important role in cellular memory and imprinting by regulating the CpG methylation status of specific promoter regions.
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Affiliation(s)
- Kristian B Laursen
- Pharmacology Department of Weill Cornell Medical College of Cornell University, NY 10065, USA
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Hypoxia Stimulates Low-Density Lipoprotein Receptor–Related Protein-1 Expression Through Hypoxia-Inducible Factor-1α in Human Vascular Smooth Muscle Cells. Arterioscler Thromb Vasc Biol 2011; 31:1411-20. [DOI: 10.1161/atvbaha.111.225490] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Objective—
Hypoxia is considered a key factor in the progression of atherosclerotic lesions. Low-density lipoprotein receptor–related protein (LRP1) plays a pivotal role in the vasculature. The aim of this study was to investigate the effect of hypoxia on LRP1 expression and function in vascular smooth muscle cells (VSMC) and the role of hypoxia-inducible factor-α (HIF-1α).
Methods and Results—
Real-time polymerase chain reaction and Western blot analysis demonstrated that hypoxia (1% O
2
) time-dependently induced LRP1 mRNA (maximum levels at 1 to 2 hours) and protein expression (maximum levels at 12 to 24 hours). The delayed hypoxic upregulation of LRP1 protein versus mRNA may be explained by the long half-life of LRP1 protein. Luciferase assays demonstrated that hypoxia and HIF-1α overaccumulation induced LRP1 promoter activity and that 2 consensus hypoxia response element sites located at −1072/−1069 and −695/−692 participate in the induction. Chromatin immunoprecipitation showed the in vivo binding of HIF-1α to LRP1 promoter in hypoxic VSMC. Hypoxia effects on LRP1 protein expression were functionally translated into an increased cholesteryl ester (CE) accumulation from aggregated low-density lipoprotein (agLDL) uptake. The blockade of HIF-1α expression inhibited the upregulatory effect of hypoxia on LRP1 expression and agLDL-derived intracellular CE overaccumulation, suggesting that both LRP1 overexpression and CE overaccumulation in hypoxic vascular cells are dependent on HIF-1α. Immunohistochemical analysis showed the colocalization of LRP1 and HIF-1α in vascular cells of human advanced atherosclerotic plaques.
Conclusion—
Hypoxia upregulates LRP1 expression and agLDL-derived intracellular CE accumulation in human VSMC through HIF-1α induction.
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Upregulation of transcription factor NRF2-mediated oxidative stress response pathway in rat brain under short-term chronic hypobaric hypoxia. Funct Integr Genomics 2010; 11:119-37. [PMID: 20922447 DOI: 10.1007/s10142-010-0195-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2010] [Revised: 08/06/2010] [Accepted: 09/13/2010] [Indexed: 02/03/2023]
Abstract
Exposure to high altitude (and thus hypobaric hypoxia) induces electrophysiological, metabolic, and morphological modifications in the brain leading to several neurological clinical syndromes. Despite the known fact that hypoxia episodes in brain are a common factor for many neuropathologies, limited information is available on the underlying cellular and molecular mechanisms. In this study, we investigated the temporal effect of short-term (0-12 h) chronic hypobaric hypoxia on global gene expression of rat brain followed by detailed canonical pathway analysis and regulatory network identification. Our analysis revealed significant alteration of 33, 17, 53, 81, and 296 genes (p < 0.05, <1.5-fold) after 0.5, 1, 3, 6, and 12 h of hypoxia, respectively. Biological processes like regulation, metabolic, and transport pathways are temporally activated along with anti- and proinflammatory signaling networks like PI3K/AKT, NF-κB, ERK/MAPK, IL-6 and IL-8 signaling. Irrespective of exposure durations, nuclear factor (erythroid-derived 2)-like 2 (NRF2)-mediated oxidative stress response pathway and genes were detected at all time points suggesting activation of NRF2-ARE antioxidant defense system. The results were further validated by assessing the expression levels of selected genes in temporal as well as brain regions with quantitative RT-PCR and western blot. In conclusion, our whole brain approach with temporal monitoring of gene expression patterns during hypobaric hypoxia has resulted in (1) deciphering sequence of pathways and signaling networks activated during onset of hypoxia, and (2) elucidation of NRF2-orchestrated antioxidant response as a major intrinsic defense mechanism. The results of this study will aid in better understanding and management of hypoxia-induced brain pathologies.
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16
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Baze MM, Schlauch K, Hayes JP. Gene expression of the liver in response to chronic hypoxia. Physiol Genomics 2010; 41:275-88. [PMID: 20103700 DOI: 10.1152/physiolgenomics.00075.2009] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Hypoxia is an important ecological, evolutionary, and biomedical stressor. While physiological acclimatization of mammals to hypoxia is well studied, the variation in gene expression that underlies acclimatization is not well studied. We acclimatized inbred mice for 32 days to hypoxic conditions that simulated altitudes of 1400, 3000, and 4500 m. We used oligonucleotide microarrays to measure changes in steady-state abundance of mRNA in the livers of these mice. Mice exposed to more severe hypoxia (simulated altitude of 4500 m) were smaller in mass and had higher hematocrit than mice exposed to less severe hypoxia. ANOVA and false discovery rate tests indicated that 580 genes were significantly differentially expressed in response to chronic hypoxia. Few of these 580 genes have previously been reported to respond to hypoxia. In contrast, many of these 580 genes belonged to same functional groups typically respond to acute hypoxia. That is, both chronic and acute hypoxia elicit changes in transcript abundance for genes involved in angiogenesis, glycolysis, lipid metabolism, carbohydrate metabolism, and protein amino acid phosphorylation, but the particular genes affected by the two types of hypoxia were mostly different. Numerous genes affecting the immune system were differentially expressed in response to chronic hypoxia, which supports recently proposed hypotheses that link immune function and hypoxia. Furthermore, our results discovered novel elevated mRNA abundance of genes involved in hematopoiesis and oxygen transport not reported previously, but consistent with extreme hematocrits found in hypoxic mice.
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Affiliation(s)
- Monica M Baze
- Program in Ecology, Evolution and Conservation Biology and Department of Biology, and
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17
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Serkova NJ, Reisdorph NA, Tissot van Patot MC. Metabolic Markers of Hypoxia: Systems Biology Application in Biomedicine. Toxicol Mech Methods 2008; 18:81-95. [DOI: 10.1080/15376510701795769] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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18
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Karar J, Dolt KS, Qadar Pasha M. Endoplasmic reticulum stress response in murine kidney exposed to acute hypobaric hypoxia. FEBS Lett 2008; 582:2521-6. [DOI: 10.1016/j.febslet.2008.06.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2008] [Accepted: 06/13/2008] [Indexed: 11/16/2022]
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Rome S, Lecomte V, Meugnier E, Rieusset J, Debard C, Euthine V, Vidal H, Lefai E. Microarray analyses of SREBP-1a and SREBP-1c target genes identify new regulatory pathways in muscle. Physiol Genomics 2008; 34:327-37. [PMID: 18559965 DOI: 10.1152/physiolgenomics.90211.2008] [Citation(s) in RCA: 58] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
In this study we have identified the target genes of sterol regulatory element binding protein (SREBP)-1a and SREBP-1c in primary cultures of human skeletal muscle cells, using adenoviral vectors expressing the mature nuclear form of human SREBP-1a or SREBP-1c combined with oligonucleotide microarrays. Overexpression of SREBP-1a led to significant changes in the expression of 1,315 genes (655 upregulated and 660 downregulated), whereas overexpression of SREBP-1c modified the mRNA level of 514 genes (310 upregulated and 204 downregulated). Gene ontology analysis indicated that in human muscle cells SREBP-1a and -1c are involved in the regulation of a large number of genes that are at the crossroads of different functional pathways, several of which are not directly connected with cholesterol and lipid metabolism. Six hundred fifty-two of all genes identified to be differentially regulated on SREBP overexpression had a sterol regulatory element (SRE) motif in their promoter sequences. Among these, 429 were specifically regulated by SREBP-1a, 69 by SREBP-1c, and 154 by both 1a and 1c. Because both isoforms recognize the same binding motif, we determined whether some of these functional differences could depend on the environment of the SRE motifs in the promoters. Results from promoter analysis showed that different combinations of transcription factor binding sites around the SRE binding motifs may determine regulatory networks of transcription that could explain the superposition of lipid and cholesterol metabolism with various other pathways involved in adaptive responses to stress like hypoxia and heat shock, or involvement in the immune response.
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Affiliation(s)
- Sophie Rome
- INSERM U870, INRA UMR1235, Régulations Métaboliques, Nutrition, et Diabètes, Université Lyon 1, Faculté de Médecine Lyon-Sud, Oullins, INSA-Lyon, RMND, Villeurbanne, Lyon, France.
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Rupert JL. Genomics and Environmental Hypoxia: What (and How) We Can Learn from the Transcriptome. High Alt Med Biol 2008; 9:115-22. [DOI: 10.1089/ham.2007.1070] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Affiliation(s)
- Jim L. Rupert
- School of Human Kinetics, University of British Columbia, Vancouver, B.C., Canada
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Nguyen AD, McDonald JG, Bruick RK, DeBose-Boyd RA. Hypoxia Stimulates Degradation of 3-Hydroxy-3-methylglutaryl-coenzyme A Reductase through Accumulation of Lanosterol and Hypoxia-Inducible Factor-mediated Induction of Insigs. J Biol Chem 2007; 282:27436-27446. [PMID: 17635920 DOI: 10.1074/jbc.m704976200] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Endoplasmic reticulum-associated degradation of the enzyme 3-hydroxy-3-methylglutaryl-CoA reductase represents one mechanism by which cholesterol synthesis is controlled in mammalian cells. The key reaction in this degradation is binding of reductase to Insig proteins in the endoplasmic reticulum, which is stimulated by the cholesterol precursor lanosterol. Conversion of lanosterol to cholesterol requires removal of three methyl groups, which consumes nine molecules of dioxygen. Here, we report that oxygen deprivation (hypoxia) slows demethylation of lanosterol and its metabolite 24,25-dihydrolanosterol, causing both sterols to accumulate in cells. In addition, hypoxia increases the amount of Insig-1 and Insig-2 in a response mediated by hypoxia-inducible factor (HIF)-1alpha. Accumulation of lanosterol together with increased Insigs accelerates degradation of reductase, which ultimately slows a rate-determining step in cholesterol synthesis. These results define a novel oxygen-sensing mechanism mediated by the combined actions of methylated intermediates in cholesterol synthesis and the hypoxia-activated transcription factor HIF-1alpha.
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Affiliation(s)
- Andrew D Nguyen
- Departments of Molecular Genetics and University of Texas Southwestern Medical Center, Dallas, Texas 75390-9046
| | - Jeffrey G McDonald
- Departments of Molecular Genetics and University of Texas Southwestern Medical Center, Dallas, Texas 75390-9046
| | - Richard K Bruick
- Departments of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-9046
| | - Russell A DeBose-Boyd
- Departments of Molecular Genetics and University of Texas Southwestern Medical Center, Dallas, Texas 75390-9046.
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Karar J, Dolt KS, Mishra MK, Arif E, Javed S, Pasha MAQ. Expression and functional activity of pro-oxidants and antioxidants in murine heart exposed to acute hypobaric hypoxia. FEBS Lett 2007; 581:4577-82. [PMID: 17825300 DOI: 10.1016/j.febslet.2007.08.044] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 08/08/2007] [Accepted: 08/20/2007] [Indexed: 11/28/2022]
Abstract
Under hypobaric hypoxia, antioxidant defenses of the heart are stressed by the enhanced production of ROS. Mammalian heart acclimatizes to hypoxia through altered gene expression, which we studied in murine heart exposed to 10h of acute hypobaric hypoxia (AHH), equivalent to 15000ft, using cDNA arrays. Functional classification of genes with a > or =2-fold change revealed a number of pro-oxidants like Cyba, Xdh, Txnip, Ppp1r15b and antioxidants like Cat, Gpx1, Mt1, Mgst1. Interestingly, the protein level of Cyba, a subunit of NADPH oxidase, was markedly decreased in AHH exposed heart, suggesting the involvement of some stress response pathways. The AHH exposure also caused a significant reduction (50%) in the level of GSH (P<0.05). The present study provides a retrospective insight on the cellular antioxidant defense mechanisms under AHH.
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Affiliation(s)
- Jayashree Karar
- Institute of Genomics and Integrative Biology, Mall Road, Delhi 110 007, India
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