1
|
Rastinejad F. The protein architecture and allosteric landscape of HNF4α. Front Endocrinol (Lausanne) 2023; 14:1219092. [PMID: 37732120 PMCID: PMC10507258 DOI: 10.3389/fendo.2023.1219092] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Accepted: 08/01/2023] [Indexed: 09/22/2023] Open
Abstract
Hepatocyte nuclear factor 4 alpha (HNF4α) is a multi-faceted nuclear receptor responsible for governing the development and proper functioning of liver and pancreatic islet cells. Its transcriptional functions encompass the regulation of vital metabolic processes including cholesterol and fatty acid metabolism, and glucose sensing and control. Various genetic mutations and alterations in HNF4α are associated with diabetes, metabolic disorders, and cancers. From a structural perspective, HNF4α is one of the most comprehensively understood nuclear receptors due to its crystallographically observed architecture revealing interconnected DNA binding domains (DBDs) and ligand binding domains (LBDs). This review discusses key properties of HNF4α, including its mode of homodimerization, its binding to fatty acid ligands, the importance of post-translational modifications, and the mechanistic basis for allosteric functions. The surfaces linking HNF4α's DBDs and LBDs create a convergence zone that allows signals originating from any one domain to influence distant domains. The HNF4α-DNA complex serves as a prime illustration of how nuclear receptors utilize individual domains for specific functions, while also integrating these domains to create cohesive higher-order architectures that allow signal responsive functions.
Collapse
Affiliation(s)
- Fraydoon Rastinejad
- Nuffield Department of Medicine, Target Discovery Institute (NDMRB), University of Oxford, Oxford, United Kingdom
| |
Collapse
|
2
|
Radi SH, Vemuri K, Martinez-Lomeli J, Sladek FM. HNF4α isoforms: the fraternal twin master regulators of liver function. Front Endocrinol (Lausanne) 2023; 14:1226173. [PMID: 37600688 PMCID: PMC10438950 DOI: 10.3389/fendo.2023.1226173] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/20/2023] [Accepted: 07/18/2023] [Indexed: 08/22/2023] Open
Abstract
In the more than 30 years since the purification and cloning of Hepatocyte Nuclear Factor 4 (HNF4α), considerable insight into its role in liver function has been gleaned from its target genes and mouse experiments. HNF4α plays a key role in lipid and glucose metabolism and intersects with not just diabetes and circadian rhythms but also with liver cancer, although much remains to be elucidated about those interactions. Similarly, while we are beginning to elucidate the role of the isoforms expressed from its two promoters, we know little about the alternatively spliced variants in other portions of the protein and their impact on the 1000-plus HNF4α target genes. This review will address how HNF4α came to be called the master regulator of liver-specific gene expression with a focus on its role in basic metabolism, the contributions of the various isoforms and the intriguing intersection with the circadian clock.
Collapse
Affiliation(s)
- Sarah H. Radi
- Department of Biochemistry, University of California, Riverside, Riverside, CA, United States
| | - Kiranmayi Vemuri
- Department of Genetics, Human Genetics Institute of New Jersey, Rutgers, The State University of New Jersey, Piscataway, NJ, United States
- Cancer Institute of New Jersey, Rutgers, The State University of New Jersey, New Brunswick, NJ, United States
| | - Jose Martinez-Lomeli
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| | - Frances M. Sladek
- Department of Molecular, Cell and Systems Biology, University of California, Riverside, Riverside, CA, United States
| |
Collapse
|
3
|
Beinsteiner B, Billas IML, Moras D. Structural insights into the HNF4 biology. Front Endocrinol (Lausanne) 2023; 14:1197063. [PMID: 37404310 PMCID: PMC10315846 DOI: 10.3389/fendo.2023.1197063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 06/01/2023] [Indexed: 07/06/2023] Open
Abstract
Hepatocyte Nuclear Factor 4 (HNF4) is a transcription factor (TF) belonging to the nuclear receptor (NR) family that is expressed in liver, kidney, intestine and pancreas. It is a master regulator of liver-specific gene expression, in particular those genes involved in lipid transport and glucose metabolism and is crucial for the cellular differentiation during development. Dysregulation of HNF4 is linked to human diseases, such as type I diabetes (MODY1) and hemophilia. Here, we review the structures of the isolated HNF4 DNA binding domain (DBD) and ligand binding domain (LBD) and that of the multidomain receptor and compare them with the structures of other NRs. We will further discuss the biology of the HNF4α receptors from a structural perspective, in particular the effect of pathological mutations and of functionally critical post-translational modifications on the structure-function of the receptor.
Collapse
Affiliation(s)
- Brice Beinsteiner
- Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre for Integrative Biology (CBI), Illkirch, France
- Université de Strasbourg (Unistra), Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Isabelle M. L. Billas
- Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre for Integrative Biology (CBI), Illkirch, France
- Université de Strasbourg (Unistra), Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| | - Dino Moras
- Laboratory IGBMC (Institute of Genetics and of Molecular and Cellular Biology), Centre for Integrative Biology (CBI), Illkirch, France
- Université de Strasbourg (Unistra), Strasbourg, France
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1258, Illkirch, France
- Centre National de la Recherche Scientifique (CNRS) UMR 7104, Illkirch, France
| |
Collapse
|
4
|
Emerging Role of SMILE in Liver Metabolism. Int J Mol Sci 2023; 24:ijms24032907. [PMID: 36769229 PMCID: PMC9917820 DOI: 10.3390/ijms24032907] [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: 11/29/2022] [Revised: 01/29/2023] [Accepted: 01/31/2023] [Indexed: 02/05/2023] Open
Abstract
Small heterodimer partner-interacting leucine zipper (SMILE) is a member of the CREB/ATF family of basic leucine zipper (bZIP) transcription factors. SMILE has two isoforms, a small and long isoform, resulting from alternative usage of the initiation codon. Interestingly, although SMILE can homodimerize similar to other bZIP proteins, it cannot bind to DNA. As a result, SMILE acts as a co-repressor in nuclear receptor signaling and other transcription factors through its DNA binding inhibition, coactivator competition, and direct repression, thereby regulating the expression of target genes. Therefore, the knockdown of SMILE increases the transactivation of transcription factors. Recent findings suggest that SMILE is an important regulator of metabolic signals and pathways by causing changes in glucose, lipid, and iron metabolism in the liver. The regulation of SMILE plays an important role in pathological conditions such as hepatitis, diabetes, fatty liver disease, and controlling the energy metabolism in the liver. This review focuses on the role of SMILE and its repressive actions on the transcriptional activity of nuclear receptors and bZIP transcription factors and its effects on liver metabolism. Understanding the importance of SMILE in liver metabolism and signaling pathways paves the way to utilize SMILE as a target in treating liver diseases.
Collapse
|
5
|
Sadasivam N, Radhakrishnan K, Choi HS, Kim DK. Emerging Role of SMILE in Liver Metabolism. Int J Mol Sci 2023; 24:2907. [DOI: https:/doi.org/10.3390/ijms24032907 academic] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/18/2023] Open
Abstract
Small heterodimer partner-interacting leucine zipper (SMILE) is a member of the CREB/ATF family of basic leucine zipper (bZIP) transcription factors. SMILE has two isoforms, a small and long isoform, resulting from alternative usage of the initiation codon. Interestingly, although SMILE can homodimerize similar to other bZIP proteins, it cannot bind to DNA. As a result, SMILE acts as a co-repressor in nuclear receptor signaling and other transcription factors through its DNA binding inhibition, coactivator competition, and direct repression, thereby regulating the expression of target genes. Therefore, the knockdown of SMILE increases the transactivation of transcription factors. Recent findings suggest that SMILE is an important regulator of metabolic signals and pathways by causing changes in glucose, lipid, and iron metabolism in the liver. The regulation of SMILE plays an important role in pathological conditions such as hepatitis, diabetes, fatty liver disease, and controlling the energy metabolism in the liver. This review focuses on the role of SMILE and its repressive actions on the transcriptional activity of nuclear receptors and bZIP transcription factors and its effects on liver metabolism. Understanding the importance of SMILE in liver metabolism and signaling pathways paves the way to utilize SMILE as a target in treating liver diseases.
Collapse
Affiliation(s)
- Nanthini Sadasivam
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Kamalakannan Radhakrishnan
- Clinical Vaccine R&D Centre, Department of Microbiology, Combinatorial Tumour Immunotheraphy MRC, Medical School, Chonnam National University, Gwangju 58128, Republic of Korea
| | - Hueng-Sik Choi
- School of Biological Sciences and Technology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Don-Kyu Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| |
Collapse
|
6
|
A potent HNF4α agonist reveals that HNF4α controls genes important in inflammatory bowel disease and Paneth cells. PLoS One 2022; 17:e0266066. [PMID: 35385524 PMCID: PMC8985954 DOI: 10.1371/journal.pone.0266066] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 03/11/2022] [Indexed: 11/19/2022] Open
Abstract
HNF4α has been implicated in IBD through a number of genome-wide association studies. Recently, we developed potent HNF4α agonists, including N-trans caffeoyltyramine (NCT). NCT was identified by structural similarity to previously the previously identified but weak HNF4α agonists alverine and benfluorex. Here, we administered NCT to mice fed a high fat diet, with the goal of studying the role of HNF4α in obesity-related diseases. Intestines from NCT-treated mice were examined by RNA-seq to determine the role of HNF4α in that organ. Surprisingly, the major classes of genes altered by HNF4α were involved in IBD and Paneth cell biology. Multiple genes downregulated in IBD were induced by NCT. Paneth cells identified by lysozyme expression were reduced in high fat fed mice. NCT reversed the effect of high fat diet on Paneth cells, with multiple markers being induced, including a number of defensins, which are critical for Paneth cell function and intestinal barrier integrity. NCT upregulated genes that play important role in IBD and that are downregulated in that disease. It reversed the loss of Paneth cell markers that occurred in high fat diet fed mice. These data suggest that HNF4α could be a therapeutic target for IBD and that the agonists that we have identified could be candidate therapeutics.
Collapse
|
7
|
Wang Z, Zhang Y, Zhang J, Deng Q, Liang H. Controversial roles of hepatocyte nuclear receptor 4 α on tumorigenesis. Oncol Lett 2021; 21:356. [PMID: 33747213 PMCID: PMC7968000 DOI: 10.3892/ol.2021.12617] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Accepted: 02/09/2021] [Indexed: 02/06/2023] Open
Abstract
Hepatocyte nuclear receptor 4 α (HNF4α) is known to be a master transcription regulator of gene expression in multiple biological processes, particularly in liver development and liver function. To date, the function of HNF4α in human cancers has been widely investigated; however, the critical roles of HNF4α in tumorigenesis remain unclear. Numerous controversies exist, even in studies from different research groups but on the same type of cancer. In the present review, the critical roles of HNF4α in tumorigenesis will be summarized and discussed. Furthermore, HNF4α expression profile and alterations will be examined by pan-cancer analysis through bioinformatics, in order to provide a better understanding of the functional roles of this gene in human cancers.
Collapse
Affiliation(s)
- Zhu Wang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Ying Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Jianwen Zhang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Qiong Deng
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| | - Hui Liang
- Department of Urology, People's Hospital of Longhua, Southern Medical University, Shenzhen, Guangdong 518109, P.R. China
| |
Collapse
|
8
|
Marchesin V, Pérez-Martí A, Le Meur G, Pichler R, Grand K, Klootwijk ED, Kesselheim A, Kleta R, Lienkamp S, Simons M. Molecular Basis for Autosomal-Dominant Renal Fanconi Syndrome Caused by HNF4A. Cell Rep 2020; 29:4407-4421.e5. [PMID: 31875549 PMCID: PMC6941224 DOI: 10.1016/j.celrep.2019.11.066] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Revised: 10/08/2019] [Accepted: 11/15/2019] [Indexed: 12/26/2022] Open
Abstract
HNF4A is a nuclear hormone receptor that binds DNA as an obligate homodimer. While all known human heterozygous mutations are associated with the autosomal-dominant diabetes form MODY1, one particular mutation (p.R85W) in the DNA-binding domain (DBD) causes additional renal Fanconi syndrome (FRTS). Here, we find that expression of the conserved fly ortholog dHNF4 harboring the FRTS mutation in Drosophila nephrocytes caused nuclear depletion and cytosolic aggregation of a wild-type dHNF4 reporter protein. While the nuclear depletion led to mitochondrial defects and lipid droplet accumulation, the cytosolic aggregates triggered the expansion of the endoplasmic reticulum (ER), autophagy, and eventually cell death. The latter effects could be fully rescued by preventing nuclear export through interfering with serine phosphorylation in the DBD. Our data describe a genomic and a non-genomic mechanism for FRTS in HNF4A-associated MODY1 with important implications for the renal proximal tubule and the regulation of other nuclear hormone receptors. HNF4 controls lipid metabolism in Drosophila nephrocytes The kidney disease mutation R85W shows dominant-negative effects in nephrocytes Dephosphorylation at S87 prevents the dominant-negative effects R85W mutation causes mitochondrial dysfunction in reprogrammed renal epithelial cells
Collapse
Affiliation(s)
- Valentina Marchesin
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Albert Pérez-Martí
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Gwenn Le Meur
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France
| | - Roman Pichler
- Renal Division, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany
| | - Kelli Grand
- Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Enriko D Klootwijk
- Department of Renal Medicine, University College London, London NW3 2PF, UK
| | - Anne Kesselheim
- Department of Renal Medicine, University College London, London NW3 2PF, UK
| | - Robert Kleta
- Department of Renal Medicine, University College London, London NW3 2PF, UK
| | - Soeren Lienkamp
- Renal Division, University Medical Center Freiburg, Faculty of Medicine, University of Freiburg, 79098 Freiburg, Germany; Institute of Anatomy, University of Zurich, 8057 Zurich, Switzerland
| | - Matias Simons
- INSERM UMR1163, Laboratory of Epithelial Biology and Disease, Imagine Institute, Paris Descartes University, Sorbonne Paris Cité, Hôpital Necker-Enfants Malades, 75015 Paris, France.
| |
Collapse
|
9
|
Control of Cell Identity by the Nuclear Receptor HNF4 in Organ Pathophysiology. Cells 2020; 9:cells9102185. [PMID: 32998360 PMCID: PMC7600215 DOI: 10.3390/cells9102185] [Citation(s) in RCA: 36] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 09/25/2020] [Accepted: 09/26/2020] [Indexed: 12/14/2022] Open
Abstract
Hepatocyte Nuclear Factor 4 (HNF4) is a transcription factor (TF) belonging to the nuclear receptor family whose expression and activities are restricted to a limited number of organs including the liver and gastrointestinal tract. In this review, we present robust evidence pointing to HNF4 as a master regulator of cellular differentiation during development and a safekeeper of acquired cell identity in adult organs. Importantly, we discuss that transient loss of HNF4 may represent a protective mechanism upon acute organ injury, while prolonged impairment of HNF4 activities could contribute to organ dysfunction. In this context, we describe in detail mechanisms involved in the pathophysiological control of cell identity by HNF4, including how HNF4 works as part of cell-specific TF networks and how its expression/activities are disrupted in injured organs.
Collapse
|
10
|
Xia C, Tang W, Geng P, Zhu H, Zhou W, Huang H, Zhou P, Shi X. Baicalin down-regulating hepatitis B virus transcription depends on the liver-specific HNF4α-HNF1α axis. Toxicol Appl Pharmacol 2020; 403:115131. [PMID: 32687838 DOI: 10.1016/j.taap.2020.115131] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2020] [Revised: 06/06/2020] [Accepted: 07/02/2020] [Indexed: 02/07/2023]
Abstract
Baicalin (BA) inhibits hepatitis B virus (HBV) RNAs production and reduces levels of the related hepatocyte nuclear factors (HNFs), although the underlying mechanism is unclear. In this study, we investigated the specific pathway by which BA regulates HBV transcription through the HBV-related HNFs. Following transfection of HepG2 cells with pHBV1.2, we observed that BA inhibited the production of HBV RNAs and viral proteins in a time- and dose-dependent manner. These effects were consistent with the downregulation of HNF1α, which was abolished by HNF1α-shRNA. The shRNA of HNF4α, the upstream gene of HNF1α, also remarkedly reduced HNF1α expression and impaired the anti-HBV efficacy of BA, indicating that this function of BA depended on HNF4α/HNF1α axis. Furthermore, chromatin immunoprecipitation assay showed that BA significantly reduced HNF4α-HNF1α transactivation activity. The similar effects of BA were observed in entecavir (ETV)-resistant HBVrtM204V/rtLl80M transfected HepG2 cells. Thus, we proposed a mechanism for the anti-HBV activity of BA in an HNF4α-HNF1α-dependent manner, which impaired HNF4α and HNF1α transactivation, and effectively inhibited HBV transcription and viral replication.
Collapse
Affiliation(s)
- Chengjie Xia
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Wenyi Tang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Ping Geng
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Haiyan Zhu
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Wei Zhou
- Department of Chemistry, Fudan University, 220 Han Dan Road, Shanghai 200433, PR China
| | - Hai Huang
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Pei Zhou
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China
| | - Xunlong Shi
- Department of Biological Medicines & Shanghai Engineering Research Center of Immunotherapeutics, School of Pharmacy, Fudan University, Shanghai 201203, PR China.
| |
Collapse
|
11
|
Liu S, Yang R, Yin N, Faiola F. Effects of per- and poly-fluorinated alkyl substances on pancreatic and endocrine differentiation of human pluripotent stem cells. CHEMOSPHERE 2020; 254:126709. [PMID: 32348926 DOI: 10.1016/j.chemosphere.2020.126709] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 04/03/2020] [Accepted: 04/03/2020] [Indexed: 05/27/2023]
Abstract
Perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS) are typical per- and poly-fluorinated alkyl substances (PFASs) that epidemiological studies have already associated with diabetes. However, insufficient data on their toxicity have been reported to explain any mechanism of action, which could justify such an association. Meanwhile, short-chain PFASs designed to substitute PFOA and PFOS, have already raised increasing concerns for their biosafety. Here, we evaluated whether common PFASs affected pancreatic and endocrine cell development using a human pluripotent stem cell pancreatic induction model and human pancreatic progenitor cell (hPP) endocrine induction model. The short-chain PFASs, pentafluorobenzoic acid, perfluorohexanoic acid, perfluorobutanesulfonic acid, and perfluorohexanesulfonic acid, homologous to PFOA or PFOS, did not significantly disrupt hPP generation, unlike PFOA and PFOS, based on pancreatic and duodenal homeobox 1 (PDX1) expression. However, SRY box 9 (SOX9) expression was suppressed in PDX1+ hPPs. All six PFASs did not disrupt SOX9 expression or hPP proliferation. However, endocrine differentiation of hPPs was affected, as indicated by neurogenin-3 (NGN3) downregulation, owing to abnormal increases in SOX9 and hairy and enhancer of split-1 (HES1) expressions. Thus, hyperactivation of NOTCH signaling was repressed after hPPs committed to the endocrine lineage. In conclusion, our study demonstrates how powerful human pluripotent stem cell-based pancreatic differentiation models can be in developmental toxicity evaluations, compared to traditional toxicity assays, mostly based on live animals. Moreover, our findings suggest that PFASs may alter pancreatic development after the pancreatic domain emerges from the gut tube, and provide insights into their toxicity mechanisms.
Collapse
Affiliation(s)
- Shuyu Liu
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China; Wellcome Trust/CRUK Gurdon Institute, Department of Pathology, University of Cambridge, Cambridge CB2 1QN, UK
| | - Renjun Yang
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Nuoya Yin
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Francesco Faiola
- State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, 100085, China; College of Resources and Environment, University of Chinese Academy of Sciences, Beijing, 100049, China.
| |
Collapse
|
12
|
Singh P, Tung SP, Han EH, Lee IK, Chi YI. Dimerization defective MODY mutations of hepatocyte nuclear factor 4α. Mutat Res 2019; 814:1-6. [PMID: 30648609 DOI: 10.1016/j.mrfmmm.2019.01.002] [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] [Received: 09/04/2018] [Revised: 11/13/2018] [Accepted: 01/08/2019] [Indexed: 10/27/2022]
Abstract
HNF4α is a culprit gene product for a monogenic and dominantly-inherited form of diabetes, referred to as MODY1 (Maturity Onset Diabetes of the Young type 1). Reduced HNF4α activities have been linked to impaired insulin secretion and β-cell function. Numerous mutations have been identified from the patients and they have been instructive as to the individual residue's role in protein structure-function and dysfunction. As a member of the nuclear receptor (NR) superfamily, HNF4α is made of characteristic modular domains and it functions exclusively as a homodimer despite its sequence homology to RXR, a common heterodimer partner of non-steroidal NRs. Transcription factors commonly dimerize to enhance their molecular functions mainly by facilitating the recognition of double helix target DNAs that display an intrinsic pseudo-2-fold symmetry and the recruitment of the remainder of the main transcriptional machinery. HNF4α is no exception and its dimerization is maintained by the ligand binding domain (LBD) mainly through the leucine-zipper-like interactions at the stalk of two interacting helices. Although many MODY1 mutations have been previously characterized, including DNA binding disruptors, ligand binding disruptors, coactivator binding disruptors, and protein stability disruptors, protein dimerization disruptors have not been formally reported. In this report, we present a set of data for the two MODY1 mutations found right at the dimerization interface (L332 P and L328del mutations) which clearly exhibit the disruptive effects of directly affecting dimerization, protein stability, and transcriptional activities. These data reinforced the fact that MODY mutations are loss-of-function mutations and HNF4α dimerization is essential for its optimal function and normal physiology.
Collapse
Affiliation(s)
- Puja Singh
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, MN, United States
| | - Shu-Ping Tung
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, MN, United States
| | - Eun Hee Han
- Drug & Disease Target Group, Division of Life Science, Korea Basic Science Institute, Cheongju, Republic of Korea
| | - In-Kyu Lee
- Department of Internal Medicine, School of Medicine, Kyungpook National University, Kyungpook National University Hospital, Daegu, Republic of Korea
| | - Young-In Chi
- Section of Structural Biology, Hormel Institute, University of Minnesota, Austin, MN, United States.
| |
Collapse
|
13
|
Qu M, Duffy T, Hirota T, Kay SA. Nuclear receptor HNF4A transrepresses CLOCK:BMAL1 and modulates tissue-specific circadian networks. Proc Natl Acad Sci U S A 2018; 115:E12305-E12312. [PMID: 30530698 PMCID: PMC6310821 DOI: 10.1073/pnas.1816411115] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Either expression level or transcriptional activity of various nuclear receptors (NRs) have been demonstrated to be under circadian control. With a few exceptions, little is known about the roles of NRs as direct regulators of the circadian circuitry. Here we show that the nuclear receptor HNF4A strongly transrepresses the transcriptional activity of the CLOCK:BMAL1 heterodimer. We define a central role for HNF4A in maintaining cell-autonomous circadian oscillations in a tissue-specific manner in liver and colon cells. Not only transcript level but also genome-wide chromosome binding of HNF4A is rhythmically regulated in the mouse liver. ChIP-seq analyses revealed cooccupancy of HNF4A and CLOCK:BMAL1 at a wide array of metabolic genes involved in lipid, glucose, and amino acid homeostasis. Taken together, we establish that HNF4A defines a feedback loop in tissue-specific mammalian oscillators and demonstrate its recruitment in the circadian regulation of metabolic pathways.
Collapse
Affiliation(s)
- Meng Qu
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089
| | - Tomas Duffy
- Department of Molecular Medicine, The Scripps Research Institute, La Jolla, CA 92037
| | - Tsuyoshi Hirota
- Institute of Transformative Bio-Molecules, Nagoya University, 464-8602 Nagoya, Japan
| | - Steve A Kay
- Keck School of Medicine, University of Southern California, Los Angeles, CA 90089;
| |
Collapse
|
14
|
Reitzel AM, Macrander J, Mane-Padros D, Fang B, Sladek FM, Tarrant AM. Conservation of DNA and ligand binding properties of retinoid X receptor from the placozoan Trichoplax adhaerens to human. J Steroid Biochem Mol Biol 2018; 184:3-10. [PMID: 29510228 PMCID: PMC6120813 DOI: 10.1016/j.jsbmb.2018.02.010] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 02/19/2018] [Indexed: 12/13/2022]
Abstract
Nuclear receptors are a superfamily of transcription factors restricted to animals. These transcription factors regulate a wide variety of genes with diverse roles in cellular homeostasis, development, and physiology. The origin and specificity of ligand binding within lineages of nuclear receptors (e.g., subfamilies) continues to be a focus of investigation geared toward understanding how the functions of these proteins were shaped over evolutionary history. Among early-diverging animal lineages, the retinoid X receptor (RXR) is first detected in the placozoan, Trichoplax adhaerens. To gain insight into RXR evolution, we characterized ligand- and DNA-binding activity of the RXR from T. adhaerens (TaRXR). Like bilaterian RXRs, TaRXR specifically bound 9-cis-retinoic acid, which is consistent with a recently published result and supports a conclusion that the ancestral RXR bound ligand. DNA binding site specificity of TaRXR was determined through protein binding microarrays (PBMs) and compared with human RXRɑ. The binding sites for these two RXR proteins were broadly conserved (∼85% shared high-affinity sequences within a targeted array), suggesting evolutionary constraint for the regulation of downstream genes. We searched for predicted binding motifs of the T. adhaerens genome within 1000 bases of annotated genes to identify potential regulatory targets. We identified 648 unique protein coding regions with predicted TaRXR binding sites that had diverse predicted functions, with enriched processes related to intracellular signal transduction and protein transport. Together, our data support hypotheses that the original RXR protein in animals bound a ligand with structural similarity to 9-cis-retinoic acid; the DNA motif recognized by RXR has changed little in more than 1 billion years of evolution; and the suite of processes regulated by this transcription factor diversified early in animal evolution.
Collapse
Affiliation(s)
- Adam M Reitzel
- Department of Biological Sciences, University of North Carolina, Charlotte, Charlotte, NC 28223 USA
| | - Jason Macrander
- Department of Biological Sciences, University of North Carolina, Charlotte, Charlotte, NC 28223 USA
| | - Daniel Mane-Padros
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, CA 95251, USA
| | - Bin Fang
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, CA 95251, USA
| | - Frances M Sladek
- Department of Cell Biology and Neuroscience, University of California, Riverside, Riverside, CA 95251, USA
| | - Ann M Tarrant
- Biology Department, Woods Hole Oceanographic Institution, 45 Water Street, Mailstop 33, Woods Hole, MA 02543 USA.
| |
Collapse
|
15
|
Mutual amplification of HNF4α and IL-1R1 composes an inflammatory circuit in Helicobacter pylori associated gastric carcinogenesis. Oncotarget 2017; 7:11349-63. [PMID: 26870992 PMCID: PMC4905478 DOI: 10.18632/oncotarget.7239] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 01/23/2016] [Indexed: 01/18/2023] Open
Abstract
Helicobacter pylori (Hp) is an environmental inducer of gastritis and gastric cancer (GC). The immune response to Hp and the associated changes in somatic gene expression are key determinants governing the transition from gastritis to GC. We show that hepatocyte nuclear factor 4α (HNF4α) is upregulated by Hp infection via NF-κB signaling and that its protein and mRNA levels are elevated in GC. HNF4α in turn stimulates expression of interleukin-1 receptor 1(IL-1R1), which amplifies the inflammatory response evoked by its ligand IL-1β. IL-1β/IL-1R1 activates NF-κB signaling, thereby increasing HNF4α expression and forming a feedback loop that sustains activation of the NF-κB pathway and drives the inflammation towards GC. Examination of clinical samples revealed that HNF4α and IL-1R1 levels increase with increasing severity of Hp-induced gastritis and reach their highest levels in GC. Co-expression of HNF4α and IL-1R1 was a crucial indicator of malignant transformation from gastritis to GC, and was associated with a poorer prognosis in GC patients. Disruption of the HNF4α/IL-1R1/IL-1β/NF-κB circuit during Hp infection maybe an effective means of preventing the associated GC.
Collapse
|
16
|
The transcriptional activity of hepatocyte nuclear factor 4 alpha is inhibited via phosphorylation by ERK1/2. PLoS One 2017; 12:e0172020. [PMID: 28196117 PMCID: PMC5308853 DOI: 10.1371/journal.pone.0172020] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 01/30/2017] [Indexed: 12/13/2022] Open
Abstract
Hepatocyte nuclear factor 4 alpha (HNF4α) nuclear receptor is a master regulator of hepatocyte development, nutrient transport and metabolism. HNF4α is regulated both at the transcriptional and post-transcriptional levels by different mechanisms. Several kinases (PKA, PKC, AMPK) were shown to phosphorylate and decrease the activity of HNF4α. Activation of the ERK1/2 signalling pathway, inducing proliferation and survival, inhibits the expression of HNF4α. However, based on our previous results we hypothesized that HNF4α is also regulated at the post-transcriptional level by ERK1/2. Here we show that ERK1/2 is capable of directly phosphorylating HNF4α in vitro at several phosphorylation sites including residues previously shown to be targeted by other kinases, as well. Furthermore, we also demonstrate that phosphorylation of HNF4α leads to a reduced trans-activational capacity of the nuclear receptor in luciferase reporter gene assay. We confirm the functional relevance of these findings by demonstrating with ChIP-qPCR experiments that 30-minute activation of ERK1/2 leads to reduced chromatin binding of HNF4α. Accordingly, we have observed decreasing but not disappearing binding of HNF4α to the target genes. In addition, 24-hour activation of the pathway further decreased HNF4α chromatin binding to specific loci in ChIP-qPCR experiments, which confirms the previous reports on the decreased expression of the HNF4a gene due to ERK1/2 activation. Our data suggest that the ERK1/2 pathway plays an important role in the regulation of HNF4α-dependent hepatic gene expression.
Collapse
|
17
|
Diamanti K, Umer HM, Kruczyk M, Dąbrowski MJ, Cavalli M, Wadelius C, Komorowski J. Maps of context-dependent putative regulatory regions and genomic signal interactions. Nucleic Acids Res 2016; 44:9110-9120. [PMID: 27625394 PMCID: PMC5100580 DOI: 10.1093/nar/gkw800] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 08/31/2016] [Indexed: 12/24/2022] Open
Abstract
Gene transcription is regulated mainly by transcription factors (TFs). ENCODE and Roadmap Epigenomics provide global binding profiles of TFs, which can be used to identify regulatory regions. To this end we implemented a method to systematically construct cell-type and species-specific maps of regulatory regions and TF-TF interactions. We illustrated the approach by developing maps for five human cell-lines and two other species. We detected ∼144k putative regulatory regions among the human cell-lines, with the majority of them being ∼300 bp. We found ∼20k putative regulatory elements in the ENCODE heterochromatic domains suggesting a large regulatory potential in the regions presumed transcriptionally silent. Among the most significant TF interactions identified in the heterochromatic regions were CTCF and the cohesin complex, which is in agreement with previous reports. Finally, we investigated the enrichment of the obtained putative regulatory regions in the 3D chromatin domains. More than 90% of the regions were discovered in the 3D contacting domains. We found a significant enrichment of GWAS SNPs in the putative regulatory regions. These significant enrichments provide evidence that the regulatory regions play a crucial role in the genomic structural stability. Additionally, we generated maps of putative regulatory regions for prostate and colorectal cancer human cell-lines.
Collapse
Affiliation(s)
- Klev Diamanti
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden
| | - Husen M Umer
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden
| | - Marcin Kruczyk
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden
| | - Michał J Dąbrowski
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala SE-751-08, Sweden
| | - Marco Cavalli
- Institute of Computer Science, Polish Academy of Sciences, Warsaw 012-48, Poland
| | - Claes Wadelius
- Institute of Computer Science, Polish Academy of Sciences, Warsaw 012-48, Poland
| | - Jan Komorowski
- Department of Cell and Molecular Biology, Uppsala University, Uppsala SE-751-24, Sweden .,Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala SE-751-08, Sweden
| |
Collapse
|
18
|
Dong Y, Wang S, Chen J, Zhang Q, Liu Y, You C, Monroig Ó, Tocher DR, Li Y. Hepatocyte Nuclear Factor 4α (HNF4α) Is a Transcription Factor of Vertebrate Fatty Acyl Desaturase Gene as Identified in Marine Teleost Siganus canaliculatus. PLoS One 2016; 11:e0160361. [PMID: 27472219 PMCID: PMC4966944 DOI: 10.1371/journal.pone.0160361] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 07/18/2016] [Indexed: 11/18/2022] Open
Abstract
Rabbitfish Siganus canaliculatus was the first marine teleost demonstrated to have the capability of biosynthesizing long-chain polyunsaturated fatty acids (LC-PUFA) from C18 precursors, and to possess a Δ4 fatty acyl desaturase (Δ4 Fad) which was the first report in vertebrates, and is a good model for studying the regulatory mechanisms of LC-PUFA biosynthesis in teleosts. In order to understand regulatory mechanisms of transcription of Δ4 Fad, the gene promoter was cloned and characterized in the present study. An upstream sequence of 1859 bp from the initiation codon ATG was cloned as the promoter candidate. On the basis of bioinformatic analysis, several binding sites of transcription factors (TF) including GATA binding protein 2 (GATA-2), CCAAT enhancer binding protein (C/EBP), nuclear factor 1 (NF-1), nuclear factor Y (NF-Y), hepatocyte nuclear factor 4α (HNF4α) and sterol regulatory element (SRE), were identified in the promoter by site-directed mutation and functional assays. HNF4α and NF-1 were confirmed to interact with the core promoter of Δ4 Fad by gel shift assay and mass spectrometry. Moreover, over-expression of HNF4α increased promoter activity in HEK 293T cells and mRNA level of Δ4 Fad in rabbitfish primary hepatocytes, respectively. The results indicated that HNF4α is a TF of rabbitfish Δ4 Fad. To our knowledge, this is the first report on promoter structure of a Δ4 Fad, and also the first demonstration of HNF4α as a TF of vertebrate Fad gene involved in transcription regulation of LC-PUFA biosynthesis.
Collapse
Affiliation(s)
- Yewei Dong
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Shuqi Wang
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Junliang Chen
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Qinghao Zhang
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Yang Liu
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Cuihong You
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
| | - Óscar Monroig
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK94LA, Scotland, United Kingdom
| | - Douglas R. Tocher
- Institute of Aquaculture, School of Natural Sciences, University of Stirling, Stirling, FK94LA, Scotland, United Kingdom
| | - Yuanyou Li
- Marine Biology Institute & Guangdong Provincial Key Laboratory of Marine Biotechnology, Shantou University, Shantou, 515063, Guangdong, China
- * E-mail:
| |
Collapse
|
19
|
Patel SR, Skafar DF. Modulation of nuclear receptor activity by the F domain. Mol Cell Endocrinol 2015; 418 Pt 3:298-305. [PMID: 26184856 DOI: 10.1016/j.mce.2015.07.009] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/01/2015] [Revised: 07/09/2015] [Accepted: 07/09/2015] [Indexed: 10/23/2022]
Abstract
The F domain located at the C-terminus of proteins is one of the least conserved regions of the estrogen receptors alpha and beta, members of the nuclear hormone receptor superfamily. Indeed, many members of the superfamily lack the F domain. However, when present, removing the F domain entirely or mutating it alters transactivation, dimerization, and the responses to agonist and antagonist ligands. This review focuses on the functions of the F domain of the estrogen receptors, particularly in relation to other members of the superfamily.
Collapse
Affiliation(s)
- Shivali R Patel
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA
| | - Debra F Skafar
- Department of Physiology, Wayne State University School of Medicine, Detroit, MI, USA.
| |
Collapse
|
20
|
Early-onset type 2 diabetes mellitus is associated to HNF4A T130I polymorphism in families of central Spain. J Investig Med 2014; 62:968-74. [PMID: 25361053 DOI: 10.1097/jim.0000000000000114] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
PURPOSE Type 2 diabetes mellitus (type 2 DM) and maturity-onset diabetes of the young present some similar clinical and biochemical characteristics that make them difficult to differentiate. Currently, the polymorphism T130I (rs1800961) in the HNF4A (hepatocyte nuclear factor 4A) gene has been described as a risk factor to type 2 DM and shows an autosomal dominant inheritance pattern associated to β-cell function decrease. The aim of the present work was to characterize the phenotypic profile of the T130I carrier and noncarrier relatives included in 3 unrelated families. METHODS We studied GCK, HNF1A, and HNF4A genes by polymerase chain reaction and sequencing in 3 unrelated subjects from Valladolid, Spain, in which maturity-onset diabetes of the young was suspected. We collected genetic, clinical, and biochemical data from these subjects and their relatives in order to check the presence of the T130I polymorphism. RESULTS The heterozygous T130I mutation was the unique functional gene variation that could explain diabetes phenotype. We observed significant differences in glucose metabolism, lipid profile, and Homeostasis Model Assessment index when we compared T130I mutation carriers and noncarriers. Diabetes diagnosed in T130I mutation carriers was related to stressful situations in an earlier age and tightly associated with gestational diabetes. Fasting plasma glucose and HbA(1c) levels increased with age in all carriers (r = 0.69 and r = 0.66, P < 0.01), respectively. CONCLUSIONS Our study supports the T130I variant in HNF4A as a major susceptibility genotype associated with early-onset type 2 DM. Healthy carriers of this mutation require a stricter control in the population of central Spain.
Collapse
|
21
|
Systematic dissection of coding exons at single nucleotide resolution supports an additional role in cell-specific transcriptional regulation. PLoS Genet 2014; 10:e1004592. [PMID: 25340400 PMCID: PMC4207465 DOI: 10.1371/journal.pgen.1004592] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2014] [Accepted: 07/09/2014] [Indexed: 12/22/2022] Open
Abstract
In addition to their protein coding function, exons can also serve as transcriptional enhancers. Mutations in these exonic-enhancers (eExons) could alter both protein function and transcription. However, the functional consequence of eExon mutations is not well known. Here, using massively parallel reporter assays, we dissect the enhancer activity of three liver eExons (SORL1 exon 17, TRAF3IP2 exon 2, PPARG exon 6) at single nucleotide resolution in the mouse liver. We find that both synonymous and non-synonymous mutations have similar effects on enhancer activity and many of the deleterious mutation clusters overlap known liver-associated transcription factor binding sites. Carrying a similar massively parallel reporter assay in HeLa cells with these three eExons found differences in their mutation profiles compared to the liver, suggesting that enhancers could have distinct operating profiles in different tissues. Our results demonstrate that eExon mutations could lead to multiple phenotypes by disrupting both the protein sequence and enhancer activity and that enhancers can have distinct mutation profiles in different cell types. Exons that code for protein can also have additional functions, such as regulating gene transcription through enhancer activity. Here, we changed every nucleotide in three different exons that also function as enhancers, and examined their enhancer activity to test whether nucleotide changes in these exons can affect both the protein sequence and enhancer function. We found that mutations with a significant effect on enhancer function can reside both in regions that change the protein sequence (non-synonymous) and regions that do not change it (synonymous). When we conducted a similar analysis in a different cell type, we observed a difference in the nucleotide changes that cause a significant effect on enhancer activity, suggesting that the enhancer functional units can differ between tissues.
Collapse
|
22
|
Prestin K, Wolf S, Feldtmann R, Hussner J, Geissler I, Rimmbach C, Kroemer HK, Zimmermann U, Meyer zu Schwabedissen HE. Transcriptional regulation of urate transportosome member SLC2A9 by nuclear receptor HNF4α. Am J Physiol Renal Physiol 2014; 307:F1041-51. [PMID: 25209865 DOI: 10.1152/ajprenal.00640.2013] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Renal tubular handling of urate is realized by a network of uptake and efflux transporters, including members of drug transporter families such as solute carrier proteins and ATP-binding cassette transporters. Solute carrier family 2, member 9 (SLC2A9), is one key factor of this so called "urate transportosome." The aim of the present study was to understand the transcriptional regulation of SLC2A9 and to test whether identified factors might contribute to a coordinated transcriptional regulation of the transporters involved in urate handling. In silico analysis and cell-based reporter gene assays identified a hepatocyte nuclear factor (HNF)4α-binding site in the promoter of SLC2A9 isoform 1, whose activity was enhanced by transient HNF4α overexpression, whereas mutation of the binding site diminished activation. HNF4α overexpression induced endogenous SLC2A9 expression in vitro. The in vivo role of HNF4α in the modulation of renal SLC2A9 gene expression was supported by findings of quantitative real-time RT-PCR analyses and chromatin immunoprecipitation assays. Indeed, mRNA expression of SLC2A9 and HNF4α in human kidney samples was significantly correlated. We also showed that in renal clear cell carcinoma, downregulation of HNF4α mRNA and protein expression was associated with a significant decline in expression of the transporter. Taken together, our data suggest that nuclear receptor family member HNF4α contributes to the transcriptional regulation of SLC2A9 isoform 1. Since HNF4α has previously been assumed to be a modulator of several urate transporters, our findings support the notion that there could be a transcriptional network providing synchronized regulation of the functional network of the urate transportosome.
Collapse
Affiliation(s)
- Katharina Prestin
- University of Basel, Department of Pharmaceutical Sciences, Biopharmacy, Basel, Switzerland
| | - Stephanie Wolf
- University Medicine, Ernst Moritz Arndt University Greifswald, Center of Drug Absorption and Transport, Institute of Pharmacology, Greifswald, Germany
| | - Rico Feldtmann
- University Medicine, Ernst Moritz Arndt University Greifswald, Center of Drug Absorption and Transport, Institute of Pharmacology, Greifswald, Germany
| | - Janine Hussner
- University of Basel, Department of Pharmaceutical Sciences, Biopharmacy, Basel, Switzerland
| | - Ingrid Geissler
- University Medicine, Ernst Moritz Arndt University Greifswald, Center of Drug Absorption and Transport, Institute of Pharmacology, Greifswald, Germany
| | - Christian Rimmbach
- University Medicine, Ernst Moritz Arndt University Greifswald, Center of Drug Absorption and Transport, Institute of Pharmacology, Greifswald, Germany
| | - Heyo K Kroemer
- University of Goettingen, Medical Faculty, Goettingen, Germany; and
| | - Uwe Zimmermann
- University Medicine, Ernst Moritz Arndt University Greifswald, Department of Urology, Greifswald, Germany
| | | |
Collapse
|
23
|
Li R, Zhang R, Li Y, Zhu B, Chen W, Zhang Y, Chen G. A RARE of hepatic Gck promoter interacts with RARα, HNF4α and COUP-TFII that affect retinoic acid- and insulin-induced Gck expression. J Nutr Biochem 2014; 25:964-76. [PMID: 24973045 DOI: 10.1016/j.jnutbio.2014.04.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 04/13/2014] [Accepted: 04/22/2014] [Indexed: 02/07/2023]
Abstract
The expression of hepatic glucokinase gene (Gck) is regulated by hormonal and nutritional signals. How these signals integrate to regulate the hepatic Gck expression is unclear. We have shown that the hepatic Gck expression is affected by Vitamin A status and synergistically induced by insulin and retinoids in primary rat hepatocytes. We hypothesized that this is mediated by a retinoic acid responsive element (RARE) in the hepatic Gck promoter. Here, we identified the RARE in the hepatic Gck promoter using standard molecular biology techniques. The single nucleotide mutations affecting the promoter activation by retinoic acid (RA) were also determined for detail analysis of protein and DNA interactions. We have optimized experimental conditions for performing electrophoresis mobility shift assay and demonstrated the interactions of the retinoic acid receptor α (RARα), retinoid X receptor α (RXRα), hepatocyte nuclear factor 4α (HNF4α) and chicken ovalbumin upstream promoter-transcription factor II (COUP-TFII) in the rat nuclear extract with this RARE, suggesting their roles in the regulation of Gck expression. Chromatin immunoprecipitation assays demonstrated that recombinant adenovirus-mediated overexpression of RARα, HNF4α and COUP-TFII, but not RXRα, significantly increased their occupancy in the hepatic Gck promoter in primary rat hepatocytes. Overexpression of RARα, HNF4α and COUP-TFII, but not RXRα, also affected the RA- and insulin-mediated Gck expression in primary rat hepatocytes. In summary, this hepatic Gck promoter RARE interacts with RARα, HNF4α and COUP-TFII to integrate Vitamin A and insulin signals.
Collapse
Affiliation(s)
- Rui Li
- School of Public Health, Wuhan University, Wuhan, Hubei, 430071, P. R. China; Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Rui Zhang
- Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Yang Li
- Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Bing Zhu
- Central Laboratory, Guangzhou Children's Hospital, Guangzhou, Guangdong, P. R. China
| | - Wei Chen
- Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Yan Zhang
- Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA
| | - Guoxun Chen
- Department of Nutrition, University of Tennessee at Knoxville, Knoxville, TN 37996, USA.
| |
Collapse
|
24
|
Ogata M, Awaji T, Iwasaki N, Fujimaki R, Takizawa M, Maruyama K, Bell GI, Iwamoto Y, Uchigata Y. Localization of hepatocyte nuclear factor-4α in the nucleolus and nucleus is regulated by its C-terminus. J Diabetes Investig 2014; 3:449-56. [PMID: 24843605 PMCID: PMC4019245 DOI: 10.1111/j.2040-1124.2012.00210.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Aims/Introduction: Mutations in hepatocyte nuclear factor‐4α (HNF4α) lead to various diseases, among which C‐terminal deletions of HNF4α are exclusively responsible for maturity onset diabetes of the young 1 (MODY1). MODY is an autosomal dominant disease characterized by a primary defect in insulin response to glucose, suggesting that the C‐terminus of HNF4α is important for pancreatic β‐cell function. To clarify the role of the C‐terminus of HNF4α, changes in cellular localization and the binding ability to its regulator were examined, specifically in the region containing Q268, which deletion causes MODY1. Materials and Methods: Cellular localization of mutant HNF4α were examined in monkey kidney 7 (COS7), Chinese hamster ovary, rat insulinoma and mouse insulinoma cells, and their binding activity to other proteins were examined by fluorescence resonance energy transfer (FRET) in COS7 cells. Results: Although wild‐type HNF4α was localized in the nucleoplasm in transfected cultured cells, Q268X‐HNF4α was located predominantly in the nucleolus. Deletion analysis of the C‐terminus of HNF4α showed that the S337X‐HNF4α mutant, and other mutants with shorter amino acid sequences (S337‐K194), were mostly localized in the nucleolus. HNF4α mutants with amino acid sequences shorter than the W192X‐HNF4α mutant gradually spread to the nucleoplasm in accordance with their lengths. The A250X‐HNF4α mutant was capable of causing the accumulation of HNF4α or the small heterodimer partner (SHP), one of the HNF4α regulators, in the nucleolus. However, the R154X‐HNF4α mutant did not have binding ability to wild‐type HNF4α or SHP, and thus was seen in the nucleus. Conclusions: The C‐terminus sites might play a key role in facilitating the nucleolar and subnucleolar localization of HNF4α. (J Diabetes Invest, doi: 10.1111/j.2040‐1124.2012.00210.x, 2012)
Collapse
Affiliation(s)
- Makiko Ogata
- Department of Medicine III and Diabetes Center, Tokyo Women's Medical University School of Medicine, Tokyo
| | - Takeo Awaji
- Department of Pharmacology, Saitama Medical University School of Medicine, Saitama, Japan
| | - Naoko Iwasaki
- Department of Medicine III and Diabetes Center, Tokyo Women's Medical University School of Medicine, Tokyo
| | - Risa Fujimaki
- Department of Medicine III and Diabetes Center, Tokyo Women's Medical University School of Medicine, Tokyo
| | - Miho Takizawa
- Department of Medicine III and Diabetes Center, Tokyo Women's Medical University School of Medicine, Tokyo
| | - Kei Maruyama
- Department of Pharmacology, Saitama Medical University School of Medicine, Saitama, Japan
| | - Graeme I Bell
- Department of Medicine and Human Genetics, University of Chicago, Chicago, IL, USA
| | - Yasuhiko Iwamoto
- Department of Medicine III and Diabetes Center, Tokyo Women's Medical University School of Medicine, Tokyo
| | - Yasuko Uchigata
- Department of Medicine III and Diabetes Center, Tokyo Women's Medical University School of Medicine, Tokyo
| |
Collapse
|
25
|
Kiselyuk A, Lee SH, Farber-Katz S, Zhang M, Athavankar S, Cohen T, Pinkerton AB, Ye M, Bushway P, Richardson AD, Hostetler HA, Rodriguez-Lee M, Huang L, Spangler B, Smith L, Higginbotham J, Cashman J, Freeze H, Itkin-Ansari P, Dawson MI, Schroeder F, Cang Y, Mercola M, Levine F. HNF4α antagonists discovered by a high-throughput screen for modulators of the human insulin promoter. ACTA ACUST UNITED AC 2014; 19:806-18. [PMID: 22840769 DOI: 10.1016/j.chembiol.2012.05.014] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Revised: 05/10/2012] [Accepted: 05/17/2012] [Indexed: 12/30/2022]
Abstract
Hepatocyte nuclear factor (HNF)4α is a central regulator of gene expression in cell types that play a critical role in metabolic homeostasis, including hepatocytes, enterocytes, and pancreatic β cells. Although fatty acids were found to occupy the HNF4α ligand-binding pocket and were proposed to act as ligands, there is controversy about both the nature of HNF4α ligands as well as the physiological role of the binding. Here, we report the discovery of potent synthetic HNF4α antagonists through a high-throughput screen for effectors of the human insulin promoter. These molecules bound to HNF4α with high affinity and modulated the expression of known HNF4α target genes. Notably, they were found to be selectively cytotoxic to cancer cell lines in vitro and in vivo, although in vivo potency was limited by suboptimal pharmacokinetic properties. The discovery of bioactive modulators for HNF4α raises the possibility that diseases involving HNF4α, such as diabetes and cancer, might be amenable to pharmacologic intervention by modulation of HNF4α activity.
Collapse
Affiliation(s)
- Alice Kiselyuk
- Department of Bioengineering, University of California, San Diego, La Jolla, CA 92093, USA
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Nakamura MT, Yudell BE, Loor JJ. Regulation of energy metabolism by long-chain fatty acids. Prog Lipid Res 2013; 53:124-44. [PMID: 24362249 DOI: 10.1016/j.plipres.2013.12.001] [Citation(s) in RCA: 497] [Impact Index Per Article: 45.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/12/2022]
Abstract
In mammals, excess energy is stored primarily as triglycerides, which are mobilized when energy demands arise. This review mainly focuses on the role of long chain fatty acids (LCFAs) in regulating energy metabolism as ligands of peroxisome proliferator-activated receptors (PPARs). PPAR-alpha expressed primarily in liver is essential for metabolic adaptation to starvation by inducing genes for beta-oxidation and ketogenesis and by downregulating energy expenditure through fibroblast growth factor 21. PPAR-delta is highly expressed in skeletal muscle and induces genes for LCFA oxidation during fasting and endurance exercise. PPAR-delta also regulates glucose metabolism and mitochondrial biogenesis by inducing FOXO1 and PGC1-alpha. Genes targeted by PPAR-gamma in adipocytes suggest that PPAR-gamma senses incoming non-esterified LCFAs and induces the pathways to store LCFAs as triglycerides. Adiponectin, another important target of PPAR-gamma may act as a spacer between adipocytes to maintain their metabolic activity and insulin sensitivity. Another topic of this review is effects of skin LCFAs on energy metabolism. Specific LCFAs are required for the synthesis of skin lipids, which are essential for water barrier and thermal insulation functions of the skin. Disturbance of skin lipid metabolism often causes apparent resistance to developing obesity at the expense of normal skin function.
Collapse
Affiliation(s)
- Manabu T Nakamura
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 905 South Goodwin Avenue, Urbana, IL 61801, USA.
| | - Barbara E Yudell
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 905 South Goodwin Avenue, Urbana, IL 61801, USA
| | - Juan J Loor
- Division of Nutritional Sciences, University of Illinois at Urbana-Champaign, 905 South Goodwin Avenue, Urbana, IL 61801, USA
| |
Collapse
|
27
|
McIntosh AL, Petrescu AD, Hostetler HA, Kier AB, Schroeder F. Liver-type fatty acid binding protein interacts with hepatocyte nuclear factor 4α. FEBS Lett 2013; 587:3787-91. [PMID: 24140341 DOI: 10.1016/j.febslet.2013.09.043] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2013] [Accepted: 09/01/2013] [Indexed: 10/26/2022]
Abstract
Hepatocyte nuclear factor 4α (HNF4α) regulates liver type fatty acid binding protein (L-FABP) gene expression. Conversely as shown herein, L-FABP structurally and functionally also interacts with HNF4α. Fluorescence resonance energy transfer (FRET) between Cy3-HNF4α (donor) and Cy5-L-FABP (acceptor) as well as FRET microscopy detected L-FABP in close proximity (~80 Å) to HNF4α, binding with high affinity Kd ~250-300 nM. Circular dichroism (CD) determined that the HNF4α/L-FABP interaction altered protein secondary structure. Finally, L-FABP potentiated transactivation of HNF4α in COS7 cells. Taken together, these data suggest that L-FABP provides a signaling path to HNF4α activation in the nucleus.
Collapse
Affiliation(s)
- Avery L McIntosh
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX 77843-4466, United States
| | | | | | | | | |
Collapse
|
28
|
Colclough K, Bellanne-Chantelot C, Saint-Martin C, Flanagan SE, Ellard S. Mutations in the genes encoding the transcription factors hepatocyte nuclear factor 1 alpha and 4 alpha in maturity-onset diabetes of the young and hyperinsulinemic hypoglycemia. Hum Mutat 2013; 34:669-85. [PMID: 23348805 DOI: 10.1002/humu.22279] [Citation(s) in RCA: 141] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 01/08/2013] [Indexed: 12/16/2022]
Abstract
Maturity-onset diabetes of the young (MODY) is a monogenic disorder characterized by autosomal dominant inheritance of young-onset (typically <25 years), noninsulin-dependent diabetes due to defective insulin secretion. MODY is both clinically and genetically heterogeneous with mutations in at least 10 genes. Mutations in the HNF1A gene encoding hepatocyte nuclear factor-1 alpha are the most common cause of MODY in most adult populations studied. The number of different pathogenic HNF1A mutations totals 414 in 1,247 families. Mutations in the HNF4A gene encoding hepatocyte nuclear factor-4 alpha are a rarer cause of MODY with 103 different mutations reported in 173 families to date. Sensitivity to treatment with sulfonylurea tablets is a feature of both HNF1A and HNF4A mutations. The HNF4A MODY phenotype has been expanded by the reports of macrosomia in ∼50% of babies, and more rarely, neonatal hyperinsulinemic hypoglycemia. The identification of an HNF1A or HNF4A gene mutation has important implications for clinical management in diabetes and pregnancy, but MODY is significantly underdiagnosed. Current research is focused on identifying biomarkers and developing probability models to identify those patients most likely to have MODY, until next generation sequencing technology enables cost-effective gene analysis for all patients with young onset diabetes.
Collapse
Affiliation(s)
- Kevin Colclough
- Department of Molecular Genetics, Royal Devon & Exeter NHS Foundation Trust, Exeter, UK
| | | | | | | | | |
Collapse
|
29
|
Abstract
The cytosolic sulfotransferases (SULTs) are a multigene family of enzymes that catalyze the transfer of a sulfonate group from the physiologic sulfate donor, 3'-phosphoadenosine-5'-phosphosulfate, to a nucleophilic substrate to generate a polar product that is more amenable to elimination from the body. As catalysts of both xenobiotic and endogenous metabolism, the SULTs are major points of contact between the external and physiological environments, and modulation of SULT-catalyzed metabolism can not only affect xenobiotic disposition, but it can also alter endogenous metabolic processes. Therefore, it is not surprising that SULT expression is regulated by numerous members of the nuclear receptor (NR) superfamily that function as sensors of xenobiotics as well as endogenous molecules, such as fatty acids, bile acids, and oxysterols. These NRs include the peroxisome proliferator-activated receptors, pregnane X receptor, constitutive androstane receptor, vitamin D receptor, liver X receptors, farnesoid X receptor, retinoid-related orphan receptors, and estrogen-related receptors. This review summarizes current information about NR regulation of SULT expression. Because species differences in SULT subfamily composition and tissue-, sex-, development-, and inducer-dependent regulation are prominent, these differences will be emphasized throughout the review. In addition, because of the central role of the SULTs in cellular physiology, the effect of NR-mediated SULT regulation on physiological and pathophysiological processes will be discussed. Gaps in current knowledge that require further investigation are also highlighted.
Collapse
Affiliation(s)
- Melissa Runge-Morris
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan 48201, USA.
| | | | | |
Collapse
|
30
|
Epigenetic obstacles encountered by transcription factors: reprogramming against all odds. Curr Opin Genet Dev 2012; 22:409-15. [PMID: 22922161 DOI: 10.1016/j.gde.2012.08.002] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Revised: 07/24/2012] [Accepted: 08/02/2012] [Indexed: 12/24/2022]
Abstract
Reprogramming of a somatic nucleus to an induced pluripotent state can be achieved in vitro through ectopic expression of Oct4 (Pou5f1), Sox2, Klf4 and c-Myc. While the ability of these factors to regulate transcription in a pluripotent context has been studied extensively, their ability to interact with and remodel a somatic genome remains underexplored. Several recent studies have begun to provide mechanistic insights that will eventually lead to a more rational design and improved understanding of nuclear reprogramming.
Collapse
|
31
|
Zhou W, Hannoun Z, Jaffray E, Medine CN, Black JR, Greenhough S, Zhu L, Ross JA, Forbes S, Wilmut I, Iredale JP, Hay RT, Hay DC. SUMOylation of HNF4α regulates protein stability and hepatocyte function. J Cell Sci 2012; 125:3630-5. [PMID: 22505616 PMCID: PMC3445325 DOI: 10.1242/jcs.102889] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
The coordination of signalling pathways within the cell is vital for normal human development and post-natal tissue homeostasis. Gene expression and function is therefore tightly controlled at a number of levels. We investigated the role that post-translational modifications play during human hepatocyte differentiation. In particular, we examined the role of the small ubiquitin-like modifier (SUMO) proteins in this process. We used a human embryonic stem cell (hESC)-based model of hepatocyte differentiation to follow changes in protein SUMOylation. Moreover, to confirm the results derived from our cell-based system, we performed in vitro conjugation assays to characterise SUMO modification of a key liver-enriched transcription factor, HNF4α. Our analyses indicate that SUMOylation plays an important role during hepatocellular differentiation and this is mediated, in part, through regulation of the stability of HNF4α in a ubiquitin-dependent manner. Our study provides a better understanding of SUMOylation during human hepatocyte differentiation and maturation. Moreover, we believe the results will stimulate interest in the differentiation and phenotypic regulation of other somatic cell types.
Collapse
Affiliation(s)
- Wenli Zhou
- Medical Research Council Centre for Regenerative Medicine, University of Edinburgh, Edinburgh Bio Quarter, 5 Little France Drive, Edinburgh EH16 4UU, UK
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Abstract
Consumption of specific dietary fatty acids has been shown to influence risk and progression of several chronic diseases, such as cardiovascular disease, obesity, cancer, and arthritis. In recent years, insights into the mechanisms underlying the biological effects of fatty acids have improved considerably and have provided the foundation for the emerging concept of fatty acid sensing, which can be interpreted as the property of fatty acids to influence biological processes by serving as signaling molecules. An important mechanism of fatty acid sensing is via stimulation or inhibition of DNA transcription. Here, we focus on fatty acid sensing via regulation of gene transcription and address the role of peroxisome proliferator-activated receptors, sterol regulatory element binding protein 1, Toll-like receptor 4, G protein-coupled receptors, and other putative mediators.
Collapse
Affiliation(s)
- Anastasia Georgiadi
- Nutrition, Metabolism and Genomics Group, Wageningen University, Wageningen, the Netherlands
| | - Sander Kersten
- Nutrition, Metabolism and Genomics Group, Wageningen University, Wageningen, the Netherlands
| |
Collapse
|
33
|
Algamas-Dimantov A, Davidovsky D, Ben-Ari J, Kang JX, Peri I, Hertz R, Bar-Tana J, Schwartz B. Amelioration of diabesity-induced colorectal ontogenesis by omega-3 fatty acids in mice. J Lipid Res 2012; 53:1056-70. [PMID: 22357704 DOI: 10.1194/jlr.m021949] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Postnatal intestinal ontogenesis in an animal model of diabesity may recapitulate morphological and transduction features of diabesity-induced intestinal dysplasia and its amelioration by endogenous (n-3) polyunsaturated fatty acids (PUFA). Proliferation, differentiation, and transduction aspects of intestinal ontogenesis have been studied here in obese, insulin-resistant db/db mice, in fat-1 transgene coding for desaturation of (n-6) PUFA into (n-3) PUFA, in db/db crossed with fat-1 mice, and in control mice. Diabesity resulted in increased colonic proliferation and dedifferentiation of epithelial colonocytes and goblet cells, with increased colonic β-catenin and hepatocyte nuclear factor (HNF)-4α transcriptional activities accompanied by enrichment in HNF-4α-bound (n-6) PUFA. In contrast, in fat-1 mice, colonic proliferation was restrained, accompanied by differentiation of crypt stem cells into epithelial colonocytes and goblet cells and by decrease in colonic β-catenin and HNF-4α transcriptional activities, with concomitant enrichment in HNF-4α-bound (n-3) PUFA at the expense of (n-6) PUFA. Colonic proliferation and differentiation, the profile of β-catenin and HNF-4α-responsive genes, and the composition of HNF-4α-bound PUFA of db/db mice reverted to wild-type by introducing the fat-1 gene into the db/db context. Suppression of intestinal HNF-4α activity by (n-3) PUFA may ameliorate diabesity-induced intestinal ontogenesis and offer an effective preventive modality for colorectal cancer.
Collapse
Affiliation(s)
- Anna Algamas-Dimantov
- Institute of Biochemistry, Food Science, and Nutrition and Interdepartmental Equipment Facility, Hebrew University of Jerusalem, Jerusalem, Israel
| | | | | | | | | | | | | | | |
Collapse
|
34
|
Abstract
Nuclear receptors (NRs) are a family of highly conserved transcription factors that regulate transcription in response to small lipophilic compounds. They play a role in every aspect of development, physiology and disease in humans. They are also ubiquitous in and unique to the animal kingdom suggesting that they may have played an important role in their evolution. In contrast to the classical endocrine receptors that originally defined the family, recent studies suggest that the first NRs might have been sensors of their environment, binding ligands that were external to the host organism. The purpose of this review is to provide a broad perspective on NR ligands and address the issue of exactly what constitutes a NR ligand from historical, biological and evolutionary perspectives. This discussion will lay the foundation for subsequent reviews in this issue as well as pose new questions for future investigation.
Collapse
Affiliation(s)
- Frances M Sladek
- Department of Cell Biology and Neuroscience, University of California, 2115 Biological Sciences Building, Riverside, CA 92521, United States.
| |
Collapse
|
35
|
Daigo K, Kawamura T, Ohta Y, Ohashi R, Katayose S, Tanaka T, Aburatani H, Naito M, Kodama T, Ihara S, Hamakubo T. Proteomic analysis of native hepatocyte nuclear factor-4α (HNF4α) isoforms, phosphorylation status, and interactive cofactors. J Biol Chem 2011; 286:674-86. [PMID: 21047794 PMCID: PMC3013027 DOI: 10.1074/jbc.m110.154732] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023] Open
Abstract
Hepatocyte nuclear factor-4α (HNF4α, NR2A1) is a nuclear receptor that has a critical role in hepatocyte differentiation and the maintenance of homeostasis in the adult liver. However, a detailed understanding of native HNF4α in the steady-state remains to be elucidated. Here we report the native HNF4α isoform, phosphorylation status, and complexes in the steady-state, as shown by shotgun proteomics in HepG2 hepatocarcinoma cells. Shotgun proteomic analysis revealed the complexity of native HNF4α, including multiple phosphorylation sites and inter-isoform heterodimerization. The associating complexes identified by label-free semiquantitative proteomic analysis include the following: the DNA-dependent protein kinase catalytic subunit, histone acetyltransferase complexes, mRNA splicing complex, other nuclear receptor coactivator complexes, the chromatin remodeling complex, and the nucleosome remodeling and histone deacetylation complex. Among the associating proteins, GRB10 interacting GYF protein 2 (GIGYF2, PERQ2) is a new candidate cofactor in metabolic regulation. Moreover, an unexpected heterodimerization of HNF4α and hepatocyte nuclear factor-4γ was found. A biochemical and genomewide analysis of transcriptional regulation showed that this heterodimerization activates gene transcription. The genes thus transcribed include the cell death-inducing DEF45-like effector b (CIDEB) gene, which is an important regulator of lipid metabolism in the liver. This suggests that the analysis of the distinctive stoichiometric balance of native HNF4α and its cofactor complexes described here are important for an accurate understanding of transcriptional regulation.
Collapse
Affiliation(s)
- Kenji Daigo
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Takeshi Kawamura
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Yoshihiro Ohta
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Riuko Ohashi
- the Division of Cellular and Molecular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, and
| | - Satoshi Katayose
- the Tsukuba Research Laboratories, JSR Corporation, Ibaraki 305-0841, Japan
| | - Toshiya Tanaka
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Hiroyuki Aburatani
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Makoto Naito
- the Division of Cellular and Molecular Pathology, Niigata University Graduate School of Medical and Dental Sciences, Niigata 951-8510, and
| | - Tatsuhiko Kodama
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Sigeo Ihara
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
| | - Takao Hamakubo
- From the Research Center for Advanced Science and Technology, University of Tokyo, Tokyo 153-8904
- To whom correspondence should be addressed: Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro, Tokyo 153-8904, Japan. Tel./Fax: 81-3-5452-5231; E-mail:
| |
Collapse
|
36
|
Sugatani J, Sadamitsu S, Kurosawa M, Ikushiro SI, Sakaki T, Ikari A, Miwa M. Nutritional status affects fluvastatin-induced hepatotoxicity and myopathy in rats. Drug Metab Dispos 2010; 38:1655-64. [PMID: 20587623 DOI: 10.1124/dmd.110.034090] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Rats that consumed a high-fat and high-sucrose diet (HF diet) developed hepatic steatosis. Treatment of HF diet-fed rats with fluvastatin (8 mg/kg) was lethal, followed by an elevation in levels of plasma aspartate aminotransferase and creatine kinase activities and skeletal muscle toxicity. This study was conducted to determine whether nutritional status affects statin-induced adverse effects in rats. Fluvastatin treatment of rats fed the HF diet led to an increase in systemic exposure, suggesting altered metabolism and elimination. In fact, although hepatic multidrug resistance-associated protein (Mrp) 2 and multidrug resistance (Mdr) 1b protein levels were not significantly changed by fluvastatin treatment for 8 days of rats fed a HF diet, the organic anion-transporting protein (Oatp) 1, Mrp3, CYP1A, CYP2C, UDP-glucuronosyltransferase (UGT) 1A1, and UGT1A5 protein levels were moderately decreased and the Oatp2, CYP3A, and UGT2B1 protein levels were markedly suppressed. No significant difference in the baseline level of Oatp1, Oatp2, Mrp2, Mrp3, Mdr1b, CYP1A, CYP2C, CYP3A, UGT1A1, UGT1A5, or UGT2B1 protein was found between the standard diet- and HF diet-fed groups. In addition, the mRNA levels of Oatp2, CYP2C11, and CYP3A1/2 were markedly decreased in HF diet-fed and fluvastatin-treated rats. There was no significant difference in the glucuronidation activities against fluvastatin among the four groups. In liver cell nuclei, levels of constitutive androstane receptor, pregnane X receptor, and hepatocyte nuclear factor 4α proteins were decreased in fluvastatin-treated HF diet-fed rats, which correlated with the decrease in Oatp2, CYP2C, and CYP3A. Taken together, these results indicate that nutritional status may influence adverse effects of fluvastatin by increasing systemic exposure through modulation of hepatic uptake and elimination.
Collapse
Affiliation(s)
- Junko Sugatani
- School of Pharmaceutical Sciences, University of Shizuoka, 52-1 Yada, Shizuoka, Japan.
| | | | | | | | | | | | | |
Collapse
|
37
|
Bolotin E, Liao H, Chi Ta T, Yang C, Hwang-Verslues W, Evans JR, Jiang T, Sladek FM. Integrated approach for the identification of human hepatocyte nuclear factor 4alpha target genes using protein binding microarrays. Hepatology 2010; 51:642-53. [PMID: 20054869 PMCID: PMC3581146 DOI: 10.1002/hep.23357] [Citation(s) in RCA: 142] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
UNLABELLED Hepatocyte nuclear factor 4 alpha (HNF4alpha), a member of the nuclear receptor superfamily, is essential for liver function and is linked to several diseases including diabetes, hemophilia, atherosclerosis, and hepatitis. Although many DNA response elements and target genes have been identified for HNF4alpha, the complete repertoire of binding sites and target genes in the human genome is unknown. Here, we adapt protein binding microarrays (PBMs) to examine the DNA-binding characteristics of two HNF4alpha species (rat and human) and isoforms (HNF4alpha2 and HNF4alpha8) in a high-throughput fashion. We identified approximately 1400 new binding sequences and used this dataset to successfully train a Support Vector Machine (SVM) model that predicts an additional approximately 10,000 unique HNF4alpha-binding sequences; we also identify new rules for HNF4alpha DNA binding. We performed expression profiling of an HNF4alpha RNA interference knockdown in HepG2 cells and compared the results to a search of the promoters of all human genes with the PBM and SVM models, as well as published genome-wide location analysis. Using this integrated approach, we identified approximately 240 new direct HNF4alpha human target genes, including new functional categories of genes not typically associated with HNF4alpha, such as cell cycle, immune function, apoptosis, stress response, and other cancer-related genes. CONCLUSION We report the first use of PBMs with a full-length liver-enriched transcription factor and greatly expand the repertoire of HNF4alpha-binding sequences and target genes, thereby identifying new functions for HNF4alpha. We also establish a web-based tool, HNF4 Motif Finder, that can be used to identify potential HNF4alpha-binding sites in any sequence.
Collapse
Affiliation(s)
- Eugene Bolotin
- Genetics, Genomics and Bioinformatics Graduate Program, University of California Riverside, Riverside, CA
| | - Hailing Liao
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA
| | - Tuong Chi Ta
- Cell, Molecular, and Developmental Biology Graduate Program, University of California Riverside, Riverside, CA
| | - Chuhu Yang
- Genetics, Genomics and Bioinformatics Graduate Program, University of California Riverside, Riverside, CA
| | - Wendy Hwang-Verslues
- Environmental Toxicology Graduate Program, University of California Riverside, Riverside, CA
| | - Jane R. Evans
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA
| | - Tao Jiang
- Department of Computer Science and Engineering, University of California Riverside, Riverside, CA,Institute for Integrated Genome Biology (also at UCR)
| | - Frances M. Sladek
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, CA,Institute for Integrated Genome Biology (also at UCR)
| |
Collapse
|
38
|
Cross-Talk between PPARs and the Partners of RXR: A Molecular Perspective. PPAR Res 2009; 2009:925309. [PMID: 20052392 PMCID: PMC2801013 DOI: 10.1155/2009/925309] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2009] [Accepted: 09/07/2009] [Indexed: 11/23/2022] Open
Abstract
The PPARs are integral parts of the RXR-dependent signaling networks. Many other nuclear receptor subfamily 1 members also require RXR as their obligatory heterodimerization partner and they are often co-expressed in any given tissue. Therefore, the PPARs often complete with other RXR-dependent nuclear receptors and this competition has important biological implications. Thorough understanding of this cross-talk at the molecular level is crucial to determine the detailed functional roles of the PPARs. At the level of DNA binding, most RXR heterodimers bind selectively to the well-known “DR1 to 5” DNA response elements. As a result, many heterodimers share the same DR element and must complete with each other for DNA binding. At the level of heterodimerization, the partners of RXR share the same RXR dimerization interface. As a result, individual nuclear receptors must complete with each other for RXR to form functional heterodimers. Cross-talk through DNA binding and RXR heterodimerization present challenges to the study of these nuclear receptors that cannot be adequately addressed by current experimental approaches. Novel tools, such as engineered nuclear receptors with altered dimerization properties, are currently being developed. These tools will enable future studies to dissect specific RXR heterodimers and their signaling pathways.
Collapse
|
39
|
Rha GB, Wu G, Shoelson SE, Chi YI. Multiple binding modes between HNF4alpha and the LXXLL motifs of PGC-1alpha lead to full activation. J Biol Chem 2009; 284:35165-76. [PMID: 19846556 DOI: 10.1074/jbc.m109.052506] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Hepatocyte nuclear factor 4alpha (HNF4alpha) is a novel nuclear receptor that participates in a hierarchical network of transcription factors regulating the development and physiology of such vital organs as the liver, pancreas, and kidney. Among the various transcriptional coregulators with which HNF4alpha interacts, peroxisome proliferation-activated receptor gamma (PPARgamma) coactivator 1alpha (PGC-1alpha) represents a novel coactivator whose activation is unusually robust and whose binding mode appears to be distinct from that of canonical coactivators such as NCoA/SRC/p160 family members. To elucidate the potentially unique molecular mechanism of PGC-1alpha recruitment, we have determined the crystal structure of HNF4alpha in complex with a fragment of PGC-1alpha containing all three of its LXXLL motifs. Despite the presence of all three LXXLL motifs available for interactions, only one is bound at the canonical binding site, with no additional contacts observed between the two proteins. However, a close inspection of the electron density map indicates that the bound LXXLL motif is not a selected one but an averaged structure of more than one LXXLL motif. Further biochemical and functional studies show that the individual LXXLL motifs can bind but drive only minimal transactivation. Only when more than one LXXLL motif is involved can significant transcriptional activity be measured, and full activation requires all three LXXLL motifs. These findings led us to propose a model wherein each LXXLL motif has an additive effect, and the multiple binding modes by HNF4alpha toward the LXXLL motifs of PGC-1alpha could account for the apparent robust activation by providing a flexible mechanism for combinatorial recruitment of additional coactivators and mediators.
Collapse
Affiliation(s)
- Geun Bae Rha
- Department of Molecular and Cellular Biochemistry, Center for Structural Biology, University of Kentucky, Lexington, Kentucky 40536, USA
| | | | | | | |
Collapse
|
40
|
Takahashi H, Martin-Brown S, Washburn MP, Florens L, Conaway JW, Conaway RC. Proteomics reveals a physical and functional link between hepatocyte nuclear factor 4alpha and transcription factor IID. J Biol Chem 2009; 284:32405-12. [PMID: 19805548 DOI: 10.1074/jbc.m109.017954] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Proteomic analyses have contributed substantially to our understanding of diverse cellular processes. Improvements in the sensitivity of mass spectrometry approaches are enabling more in-depth analyses of protein-protein networks and, in some cases, are providing surprising new insights into well established, longstanding problems. Here, we describe such a proteomic analysis that exploits MudPIT mass spectrometry and has led to the discovery of a physical and functional link between the orphan nuclear receptor hepatocyte nuclear factor 4alpha (HNF4alpha) and transcription factor IID (TFIID). A systematic characterization of the HNF4alpha-TFIID link revealed that the HNF4alpha DNA-binding domain binds directly to the TATA box-binding protein (TBP) and, through this interaction, can target TBP or TFIID to promoters containing HNF4alpha-binding sites in vitro. Supporting the functional significance of this interaction, an HNF4alpha mutation that blocks binding of TBP to HNF4alpha interferes with HNF4alpha transactivation activity in cells. These findings identify an unexpected role for the HNF4alpha DNA-binding domain in mediating key regulatory interactions and provide new insights into the roles of HNF4alpha and TFIID in RNA polymerase II transcription.
Collapse
Affiliation(s)
- Hidehisa Takahashi
- Stowers Institute for Medical Research, Kansas City, Missouri 64110, USA
| | | | | | | | | | | |
Collapse
|
41
|
Le Guével R, Oger F, Lecorgne A, Dudasova Z, Chevance S, Bondon A, Barath P, Simonneaux G, Salbert G. Identification of small molecule regulators of the nuclear receptor HNF4alpha based on naphthofuran scaffolds. Bioorg Med Chem 2009; 17:7021-30. [PMID: 19729315 DOI: 10.1016/j.bmc.2009.07.079] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2009] [Revised: 07/24/2009] [Accepted: 07/26/2009] [Indexed: 01/01/2023]
Abstract
Nuclear receptors are ligand-activated transcription factors involved in all major physiological functions of complex organisms. In this respect, they are often described as drugable targets for a number of pathological states including hypercholesterolemia and atherosclerosis. HNF4alpha (NR2A1) is a recently 'deorphanized' nuclear receptor which is bound in vivo by linoleic acid, although this natural ligand does not seem to promote transcriptional activation. In mouse, HNF4alpha is a major regulator of liver development and hepatic lipid metabolism and mutations in human have been linked to diabetes. Here, we have used a yeast one-hybrid system to identify small molecule activators of HNF4alpha in a library of synthetic compounds and found one hit bearing a methoxy group branched on a nitronaphthofuran backbone. A collection of molecules deriving from the discovered hit was generated and tested for activity toward HNF4alpha in yeast one-hybrid system. It was found that both the nitro group and a complete naphthofuran backbone were required for full activity of the compounds. Furthermore, adding a hydroxy group at position 7 of the minimal backbone led to the most active compound of the collection. Accordingly, a direct interaction of the hydroxylated compound with the ligand binding domain of HNF4alpha was detected by NMR and thermal denaturation assays. When used in mammalian cell culture systems, these compounds proved to be highly toxic, except when methylated on the furan ring. One such compound was able to modulate HNF4alpha-driven transcription in transfected HepG2C3A cells. These data indicate that HNF4alpha activity can be modulated by small molecules and suggest new routes for targeting the receptor in humans.
Collapse
Affiliation(s)
- Rémy Le Guével
- Equipe SPARTE, Université de Rennes 1, UMR6026 CNRS, Campus de Beaulieu, Bat 13, 35042 Rennes Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
The Caenorhabditis elegans HNF4alpha Homolog, NHR-31, mediates excretory tube growth and function through coordinate regulation of the vacuolar ATPase. PLoS Genet 2009; 5:e1000553. [PMID: 19668342 PMCID: PMC2720251 DOI: 10.1371/journal.pgen.1000553] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2008] [Accepted: 06/09/2009] [Indexed: 12/29/2022] Open
Abstract
Nuclear receptors of the Hepatocyte Nuclear Factor-4 (HNF4) subtype have been linked to a host of developmental and metabolic functions in animals ranging from worms to humans; however, the full spectrum of physiological activities carried out by this nuclear receptor subfamily is far from established. We have found that the Caenorhabditis elegans nuclear receptor NHR-31, a homolog of mammalian HNF4 receptors, is required for controlling the growth and function of the nematode excretory cell, a multi-branched tubular cell that acts as the C. elegans renal system. Larval specific RNAi knockdown of nhr-31 led to significant structural abnormalities along the length of the excretory cell canal, including numerous regions of uncontrolled growth at sites near to and distant from the cell nucleus. nhr-31 RNAi animals were sensitive to acute challenge with ionic stress, implying that the osmoregulatory function of the excretory cell was also compromised. Gene expression profiling revealed a surprisingly specific role for nhr-31 in the control of multiple genes that encode subunits of the vacuolar ATPase (vATPase). RNAi of these vATPase genes resulted in excretory cell defects similar to those observed in nhr-31 RNAi animals, demonstrating that the influence of nhr-31 on excretory cell growth is mediated, at least in part, through coordinate regulation of the vATPase. Sequence analysis revealed a stunning enrichment of HNF4α type binding sites in the promoters of both C. elegans and mouse vATPase genes, arguing that coordinate regulation of the vATPase by HNF4 receptors is likely to be conserved in mammals. Our study establishes a new pathway for regulation of excretory cell growth and reveals a novel role for HNF4-type nuclear receptors in the development and function of a renal system. The function of many important biological structures requires the construction of very complex cellular shapes. For example, mammalian kidneys or related renal systems in other animals rely on the formation of elongated tubes that maximize surface area to facilitate the exchange of ions between the body and excreted fluid. Defects in kidney development or function may lead to kidney failure or polycystic kidney disease. Mechanisms involved in orchestrating the formation and function of the elaborate tube structures in renal systems are still poorly characterized. Here, we show a novel transcription factor involved in the growth and elongation of an excretory tube in C. elegans. This factor helps manage tube development by regulating genes involved in ion transport and membrane fusion, likely helping to balance the growth of the inner and outer portions of the excretory tube as this structure elongates. This transcription factor shares significant homology with a mammalian protein that participates in hormone signaling and is present in the kidney tubules, suggesting that elongation and growth of tube structures may rely on a new kind of hormonal communication that occurs between distant parts of the cell; this signaling mechanism may be important for appropriate kidney development in humans.
Collapse
|
43
|
Plengvidhya N, Boonyasrisawat W, Chongjaroen N, Jungtrakoon P, Sriussadaporn S, Vannaseang S, Banchuin N, Yenchitsomanus PT. Mutations of maturity-onset diabetes of the young (MODY) genes in Thais with early-onset type 2 diabetes mellitus. Clin Endocrinol (Oxf) 2009; 70:847-53. [PMID: 18811724 DOI: 10.1111/j.1365-2265.2008.03397.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
OBJECTIVE Six known genes responsible for maturity-onset diabetes of the young (MODY) were analysed to evaluate the prevalence of their mutations in Thai patients with MODY and early-onset type 2 diabetes. PATIENTS AND METHODS Fifty-one unrelated probands with early-onset type 2 diabetes, 21 of them fitted into classic MODY criteria, were analysed for nucleotide variations in promoters, exons, and exon-intron boundaries of six known MODY genes, including HNF-4alpha, GCK, HNF-1alpha, IPF-1, HNF-1beta, and NeuroD1/beta2, by the polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP) method followed by direct DNA sequencing. Missense mutations or mutations located in regulatory region, which were absent in 130 chromosomes of non-diabetic controls, were classified as potentially pathogenic mutations. RESULTS We found that mutations of the six known MODY genes account for a small proportion of classic MODY (19%) and early-onset type 2 diabetes (10%) in Thais. Five of these mutations are novel including GCK R327H, HNF-1alpha P475L, HNF-1alphaG554fsX556, NeuroD1-1972 G > A and NeuroD1 A322N. Mutations of IPF-1 and HNF-1beta were not identified in the studied probands. CONCLUSIONS Mutations of the six known MODY genes may not be a major cause of MODY and early-onset type 2 diabetes in Thais. Therefore, unidentified genes await discovery in a majority of Thai patients with MODY and early-onset type 2 diabetes.
Collapse
Affiliation(s)
- Nattachet Plengvidhya
- Department of Medicine, Division of Endocrinology and Metabolism, Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand.
| | | | | | | | | | | | | | | |
Collapse
|
44
|
Yuan X, Ta TC, Lin M, Evans JR, Dong Y, Bolotin E, Sherman MA, Forman BM, Sladek FM. Identification of an endogenous ligand bound to a native orphan nuclear receptor. PLoS One 2009; 4:e5609. [PMID: 19440305 PMCID: PMC2680617 DOI: 10.1371/journal.pone.0005609] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2009] [Accepted: 04/22/2009] [Indexed: 12/25/2022] Open
Abstract
Orphan nuclear receptors have been instrumental in identifying novel signaling pathways and therapeutic targets. However, identification of ligands for these receptors has often been based on random compound screens or other biased approaches. As a result, it remains unclear in many cases if the reported ligands are the true endogenous ligands, – i.e., the ligand that is bound to the receptor in an unperturbed in vivo setting. Technical limitations have limited our ability to identify ligands based on this rigorous definition. The orphan receptor hepatocyte nuclear factor 4 α (HNF4α) is a key regulator of many metabolic pathways and linked to several diseases including diabetes, atherosclerosis, hemophilia and cancer. Here we utilize an affinity isolation/mass-spectrometry (AIMS) approach to demonstrate that HNF4α is selectively occupied by linoleic acid (LA, C18:2ω6) in mammalian cells and in the liver of fed mice. Receptor occupancy is dramatically reduced in the fasted state and in a receptor carrying a mutation derived from patients with Maturity Onset Diabetes of the Young 1 (MODY1). Interestingly, however, ligand occupancy does not appear to have a significant effect on HNF4α transcriptional activity, as evidenced by genome-wide expression profiling in cells derived from human colon. We also use AIMS to show that LA binding is reversible in intact cells, indicating that HNF4α could be a viable drug target. This study establishes a general method to identify true endogenous ligands for nuclear receptors (and other lipid binding proteins), independent of transcriptional function, and to track in vivo receptor occupancy under physiologically relevant conditions.
Collapse
Affiliation(s)
- Xiaohui Yuan
- Department of Gene Regulation and Drug Discovery, Gonda Diabetes Research Center, The Beckman Research Institute at the City of Hope National Medical Center, Duarte, California, United States of America
| | - Tuong Chi Ta
- Cell, Molecular and Developmental Biology Graduate Program, University of California Riverside, Riverside, California, United States of America
| | - Min Lin
- Department of Gene Regulation and Drug Discovery, Gonda Diabetes Research Center, The Beckman Research Institute at the City of Hope National Medical Center, Duarte, California, United States of America
| | - Jane R. Evans
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, California, United States of America
| | - Yinchen Dong
- Department of Gene Regulation and Drug Discovery, Gonda Diabetes Research Center, The Beckman Research Institute at the City of Hope National Medical Center, Duarte, California, United States of America
| | - Eugene Bolotin
- Genetics, Genomics and Bioinformatics Graduate Program, University of California Riverside, Riverside, California, United States of America
| | - Mark A. Sherman
- Department of Biomedical Informatics, The Beckman Research Institute at the City of Hope National Medical Center, Duarte, California, United States of America
| | - Barry M. Forman
- Department of Gene Regulation and Drug Discovery, Gonda Diabetes Research Center, The Beckman Research Institute at the City of Hope National Medical Center, Duarte, California, United States of America
- * E-mail: (BMF); (FMS)
| | - Frances M. Sladek
- Department of Cell Biology and Neuroscience, University of California Riverside, Riverside, California, United States of America
- * E-mail: (BMF); (FMS)
| |
Collapse
|
45
|
Lu P, Rha GB, Melikishvili M, Wu G, Adkins BC, Fried MG, Chi YI. Structural basis of natural promoter recognition by a unique nuclear receptor, HNF4alpha. Diabetes gene product. J Biol Chem 2008; 283:33685-97. [PMID: 18829458 DOI: 10.1074/jbc.m806213200] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
HNF4alpha (hepatocyte nuclear factor 4alpha) plays an essential role in the development and function of vertebrate organs, including hepatocytes and pancreatic beta-cells by regulating expression of multiple genes involved in organ development, nutrient transport, and diverse metabolic pathways. As such, HNF4alpha is a culprit gene product for a monogenic and dominantly inherited form of diabetes, known as maturity onset diabetes of the young (MODY). As a unique member of the nuclear receptor superfamily, HNF4alpha recognizes target genes containing two hexanucleotide direct repeat DNA-response elements separated by one base pair (DR1) by exclusively forming a cooperative homodimer. We describe here the 2.0 angstroms crystal structure of human HNF4alpha DNA binding domain in complex with a high affinity promoter element of another MODY gene, HNF1alpha, which reveals the molecular basis of unique target gene selection/recognition, DNA binding cooperativity, and dysfunction caused by diabetes-causing mutations. The predicted effects of MODY mutations have been tested by a set of biochemical and functional studies, which show that, in contrast to other MODY gene products, the subtle disruption of HNF4alpha molecular function can cause significant effects in afflicted MODY patients.
Collapse
Affiliation(s)
- Peng Lu
- Department of Molecular and Cellular Biochemistry, University of Kentucky, Lexington, Kentucky 40536, USA
| | | | | | | | | | | | | |
Collapse
|
46
|
Skafar DF, Zhao C. The multifunctional estrogen receptor-alpha F domain. Endocrine 2008; 33:1-8. [PMID: 18363044 DOI: 10.1007/s12020-008-9054-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/27/2007] [Revised: 02/04/2008] [Accepted: 03/04/2008] [Indexed: 10/22/2022]
Abstract
The members of the nuclear receptor superfamily act as transcriptional regulatory factors and exhibit a multidomain structure characterized as domains A-E/F. This review focuses on a small, relatively understudied region at the extreme carboxy-terminus of the estrogen receptor (ER) alpha, the F domain. The F domain contributes to differences in the activity of ER alpha and beta subtypes; it is required for tamoxifen's agonist activity on an estrogen response element, and it modifies the receptor's interactions with coregulators including steroid receptor coactivator-1. The differences between the F domains of the ER alpha and beta subtypes and among the other members of the nuclear hormone receptor superfamily may offer opportunities for selective control of the activity of these proteins.
Collapse
Affiliation(s)
- Debra F Skafar
- Department of Physiology, Wayne State University School of Medicine, 540 E. Canfield, Detroit, MI, 48201, USA.
| | | |
Collapse
|
47
|
Schroeder F, Petrescu AD, Huang H, Atshaves BP, McIntosh AL, Martin GG, Hostetler HA, Vespa A, Landrock D, Landrock KK, Payne HR, Kier AB. Role of fatty acid binding proteins and long chain fatty acids in modulating nuclear receptors and gene transcription. Lipids 2007; 43:1-17. [PMID: 17882463 DOI: 10.1007/s11745-007-3111-z] [Citation(s) in RCA: 171] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2007] [Accepted: 07/26/2007] [Indexed: 12/16/2022]
Abstract
Abnormal energy regulation may significantly contribute to the pathogenesis of obesity, diabetes mellitus, cardiovascular disease, and cancer. For rapid control of energy homeostasis, allosteric and posttranslational events activate or alter activity of key metabolic enzymes. For longer impact, transcriptional regulation is more effective, especially in response to nutrients such as long chain fatty acids (LCFA). Recent advances provide insights into how poorly water-soluble lipid nutrients [LCFA; retinoic acid (RA)] and their metabolites (long chain fatty acyl Coenzyme A, LCFA-CoA) reach nuclei, bind their cognate ligand-activated receptors, and regulate transcription for signaling lipid and glucose catabolism or storage: (i) while serum and cytoplasmic LCFA levels are in the 200 mircroM-mM range, real-time imaging recently revealed that LCFA and LCFA-CoA are also located within nuclei (nM range); (ii) sensitive fluorescence binding assays show that LCFA-activated nuclear receptors [peroxisome proliferator-activated receptor-alpha (PPARalpha) and hepatocyte nuclear factor 4alpha (HNF4alpha)] exhibit high affinity (low nM KdS) for LCFA (PPARalpha) and/or LCFA-CoA (PPARalpha, HNF4alpha)-in the same range as nuclear levels of these ligands; (iii) live and fixed cell immunolabeling and imaging revealed that some cytoplasmic lipid binding proteins [liver fatty acid binding protein (L-FABP), acyl CoA binding protein (ACBP), cellular retinoic acid binding protein-2 (CRABP-2)] enter nuclei, bind nuclear receptors (PPARalpha, HNF4alpha, CRABP-2), and activate transcription of genes in fatty acid and glucose metabolism; and (iv) studies with gene ablated mice provided physiological relevance of LCFA and LCFA-CoA binding proteins in nuclear signaling. This led to the hypothesis that cytoplasmic lipid binding proteins transfer and channel lipidic ligands into nuclei for initiating nuclear receptor transcriptional activity to provide new lipid nutrient signaling pathways that affect lipid and glucose catabolism and storage.
Collapse
Affiliation(s)
- Friedhelm Schroeder
- Department of Physiology and Pharmacology, Texas A&M University, TVMC, College Station, TX 77843-4466, USA.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Leng S, Lu S, Yao Y, Kan Z, Morris GS, Stair BR, Cherny MA, Black DD. Hepatocyte nuclear factor-4 mediates apolipoprotein A-IV transcriptional regulation by fatty acid in newborn swine enterocytes. Am J Physiol Gastrointest Liver Physiol 2007; 293:G475-83. [PMID: 17556588 DOI: 10.1152/ajpgi.00072.2007] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
Hepatocyte nuclear factor-4alpha (HNF-4alpha) regulates transcription of several genes involved in lipid metabolism, including that of apolipoprotein (apo) A-IV, which is tightly regulated by lipid absorption and enhances enterocyte chylomicron secretion. Studies were performed to define the role of HNF-4alpha in the regulation of apo A-IV gene transcription by dietary fatty acid in neonatal swine small intestine. HNF-4alpha mRNA was expressed in liver > intestine > kidney in suckling, weanling, and weaned pigs. Jejunal HNF-4alpha mRNA and protein and apo A-IV and swine microsomal triglyceride transfer protein (MTP) large subunit mRNA expression were induced in parallel in 2-day-old swine by a 24-h high-fat intraduodenal infusion. In IPEC-1 cells, incubation with oleic acid (OA) resulted in coordinate induction of both HNF-4alpha, apo A-IV, and MTP mRNA, similar to that observed in vivo. When HNF-4alpha expression was driven by doxycycline by using the TET-On system in the absence of OA to observe the effect of HNF-4alpha directly on apo A-IV and MTP mRNA levels in the absence of other factors that might be concomitantly induced by fatty acid absorption, apo A-IV and MTP expression were increased. In luciferase reporter gene assays in IPEC-1 cells using apo A-IV/C-III intergenic region constructs, TET-On-regulated HNF-4alpha expression without OA increased luciferase activity, and incubation with OA did not further increase activity. These data suggest that acute induction of the apo A-IV and MTP genes by dietary lipid in newborn intestine occurs, at least in part, via ligand-independent transactivation by HNF-4alpha that is itself induced by a lipid-mediated mechanism.
Collapse
Affiliation(s)
- Shuangying Leng
- Children's Foundation Research Center of Memphis, Le Bonheur Children's Medical Center, Department of Pediatrics, University of Tennessee Health Science Center, Memphis, TN 38103, USA
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Xu Z, Tavares-Sanchez OL, Li Q, Fernando J, Rodriguez CM, Studer EJ, Pandak WM, Hylemon PB, Gil G. Activation of bile acid biosynthesis by the p38 mitogen-activated protein kinase (MAPK): hepatocyte nuclear factor-4alpha phosphorylation by the p38 MAPK is required for cholesterol 7alpha-hydroxylase expression. J Biol Chem 2007; 282:24607-14. [PMID: 17603092 PMCID: PMC3291957 DOI: 10.1074/jbc.m611481200] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Bile acids are required for intestinal absorption and biliary solubilization of cholesterol and lipids. In addition, bile acids play a crucial role in cholesterol homeostasis. One of the key enzymes in the bile acid biosynthetic pathways is cholesterol 7alpha-hydroxylase/cytochrome P450 7alpha-hydroxylase (7alpha-hydroxylase), which is the rate-limiting and regulatory step of the "classic" pathway. Transcription of the 7alpha-hydroxylase gene is highly regulated. Two nuclear receptors, hepatocyte nuclear factor 4alpha (HNF-4alpha) and alpha(1)-fetoprotein transcription factor, are required for both transcription and regulation by different physiological events. It has been shown that some mitogen-activated protein kinases, such as the c-Jun N-terminal kinase and the ERK, play important roles in the regulation of 7alpha-hydroxylase transcription. In this study, we show evidence that the p38 kinase pathway plays an important role in 7alpha-hydroxylase expression and hence in bile acid synthesis. Inhibition of p38 kinase activity in primary hepatocytes results in approximately 5-10-fold reduction of 7alpha-hydroxylase mRNA. This suppression is mediated, at least in part, through HNF-4alpha. Inhibition of p38 kinase activity diminishes HNF-4alpha nuclear protein levels and its phosphorylation in vivo and in vitro, and it renders a less stable protein. Induction of the p38 kinase pathway by insulin results in an increase in HNF-4alpha protein and a concomitant induction of 7alpha-hydroxylase expression that is blocked by inhibiting the p38 pathway. These studies show a functional link between the p38 signaling pathway, HNF-4alpha, and bile acid synthesis.
Collapse
Affiliation(s)
- Zhumei Xu
- Department of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Olga L. Tavares-Sanchez
- Department of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Quanzhong Li
- Department of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Josephine Fernando
- Department of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Carmen M. Rodriguez
- Department of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Elaine J. Studer
- Department of Microbiology and Immunology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - William M. Pandak
- Department of Medicine, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Phillip B. Hylemon
- Department of Microbiology and Immunology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
| | - Gregorio Gil
- Department of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, Richmond, Virginia 23298-0614
- To whom correspondence should be addressed: Dept. of Biochemistry and Molecular Biology, Medical College of Virginia at Virginia Commonwealth University, P. O. Box 980614, Richmond, VA 23298-0614. Tel.: 804-828-0140; Fax: 804-828-0144;
| |
Collapse
|
50
|
Chan LS, Wells RA. Manipulation of reciprocal salt bridges at the heterodimerization interface alters the dimerization properties of mouse RXRalpha and PPARgamma1. Biochem Biophys Res Commun 2007; 358:1080-5. [PMID: 17521607 DOI: 10.1016/j.bbrc.2007.05.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2007] [Accepted: 05/07/2007] [Indexed: 10/23/2022]
Abstract
Heterodimerization with RXR is essential for the high-affinity specific binding of multiple nuclear receptors to their cognate DNA sequences. NR dimerization is a two-step process, initiated in solution by interaction between amino acid residues with helices 9 and 10 of the ligand binding domains of RXR and its NR partners. Studies of the orphan nuclear receptor HNF4alpha, which forms homodimers exclusively, have indicated that two charged residues in this region, HNF4alpha(K300) and HNF4alpha(E327), are key mediators of dimerization. We have analyzed the contribution of the homologous residues in RXRalpha (RXRalpha(E395), RXRalpha(K422)) and PPARgamma (PPARgamma(E405), PPARgamma(K432)) to the formation of the RXRalpha-PPARgamma heterodimer. Charge reversal mutants of RXRalpha (RXRalpha(E395K), RXRalpha(K422E)) and PPARgamma (PPARgamma(E405K), PPARgamma(K432E)) show impaired ability to form heterodimers with wild-type PPARgamma and RXRalpha, respectively. However, pairs of mutants with balanced charge changes, i.e., RXRalpha(E395K) with PPARgamma(K432E) and RXRalpha(K422E) with PPARgamma(E405K), are able to form dimers. Ligand response is preserved in the PPARgamma mutants, indicating the mutation does not result in major structural derangement of the protein. These results establish the importance of salt bridges between these residues in the heterodimerization of nuclear receptors, and offer a technical approach to generating functional NR mutants with directed heterodimerization specificity. Such mutants will be valuable tools in the genetic analysis of NR function.
Collapse
Affiliation(s)
- Lap Shu Chan
- Molecular and Cellular Biology, Sunnybrook Research Institute, 2075 Bayview Avenue, T2-058 Toronto, Ont., Canada M4N 2M5
| | | |
Collapse
|