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Caballero-Solares A, Eslamloo K, Hall JR, Katan T, Emam M, Xue X, Taylor RG, Balder R, Parrish CC, Rise ML. Vegetable omega-3 and omega-6 fatty acids differentially modulate the antiviral and antibacterial immune responses of Atlantic salmon. Sci Rep 2024; 14:10947. [PMID: 38740811 DOI: 10.1038/s41598-024-61144-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 05/02/2024] [Indexed: 05/16/2024] Open
Abstract
The immunomodulatory effects of omega-3 and omega-6 fatty acids are a crucial subject of investigation for sustainable fish aquaculture, as fish oil is increasingly replaced by terrestrial vegetable oils in aquafeeds. Unlike previous research focusing on fish oil replacement with vegetable alternatives, our study explored how the omega-6 to omega-3 polyunsaturated fatty acid (PUFA) ratio in low-fish oil aquafeeds influences Atlantic salmon's antiviral and antibacterial immune responses. Atlantic salmon were fed aquafeeds rich in soy oil (high in omega-6) or linseed oil (high in omega-3) for 12 weeks and then challenged with bacterial (formalin-killed Aeromonas salmonicida) or viral-like (polyriboinosinic polyribocytidylic acid) antigens. The head kidneys of salmon fed high dietary omega-3 levels exhibited a more anti-inflammatory fatty acid profile and a restrained induction of pro-inflammatory and neutrophil-related genes during the immune challenges. The high-omega-3 diet also promoted a higher expression of genes associated with the interferon-mediated signaling pathway, potentially enhancing antiviral immunity. This research highlights the capacity of vegetable oils with different omega-6 to omega-3 PUFA ratios to modulate specific components of fish immune responses, offering insights for future research on the intricate lipid nutrition-immunity interplay and the development of novel sustainable low-fish oil clinical aquaculture feeds.
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Affiliation(s)
| | - Khalil Eslamloo
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
- Centre for Marine Applied Research, Dartmouth, NS, Canada
| | - Jennifer R Hall
- Aquatic Research Cluster, CREAIT Network, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Tomer Katan
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
- Stantec Inc., St. John's, NL, Canada
| | - Mohamed Emam
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | | | - Rachel Balder
- Cargill Animal Nutrition and Health, Elk River, MN, USA
| | - Christopher C Parrish
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
| | - Matthew L Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John's, NL, Canada
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2
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Muhammad T, Pastore SF, Good K, Ausió J, Vincent JB. Chromatin gatekeeper and modifier CHD proteins in development, and in autism and other neurological disorders. Psychiatr Genet 2023; 33:213-232. [PMID: 37851134 DOI: 10.1097/ypg.0000000000000353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2023]
Abstract
Chromatin, a protein-DNA complex, is a dynamic structure that stores genetic information within the nucleus and responds to molecular/cellular changes in its structure, providing conditional access to the genetic machinery. ATP-dependent chromatin modifiers regulate access of transcription factors and RNA polymerases to DNA by either "opening" or "closing" the structure of chromatin, and its aberrant regulation leads to a variety of neurodevelopmental disorders. The chromodomain helicase DNA-binding (CHD) proteins are ATP-dependent chromatin modifiers involved in the organization of chromatin structure, act as gatekeepers of genomic access, and deposit histone variants required for gene regulation. In this review, we first discuss the structural and functional domains of the CHD proteins, and their binding sites, and phosphorylation, acetylation, and methylation sites. The conservation of important amino acids in SWItch/sucrose non-fermenting (SWI/SNF) domains, and their protein and mRNA tissue expression profiles are discussed. Next, we convey the important binding partners of CHD proteins, their protein complexes and activities, and their involvements in epigenetic regulation. We also show the ChIP-seq binding dynamics for CHD1, CHD2, CHD4, and CHD7 proteins at promoter regions of histone genes, as well as several genes that are critical for neurodevelopment. The role of CHD proteins in development is also discussed. Finally, this review provides information about CHD protein mutations reported in autism and neurodevelopmental disorders, and their pathogenicity. Overall, this review provides information on the progress of research into CHD proteins, their structural and functional domains, epigenetics, and their role in stem cell, development, and neurological disorders.
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Affiliation(s)
- Tahir Muhammad
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Stephen F Pastore
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
| | - Katrina Good
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - Juan Ausió
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC
| | - John B Vincent
- Molecular Neuropsychiatry & Development (MiND) Lab, Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health
- Institute of Medical Science, University of Toronto, Toronto, ON
- Department of Psychiatry, University of Toronto, Toronto, ON, Canada
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3
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Huntzinger E, Sinteff J, Morlet B, Séraphin B. HELZ2: a new, interferon-regulated, human 3'-5' exoribonuclease of the RNB family is expressed from a non-canonical initiation codon. Nucleic Acids Res 2023; 51:9279-9293. [PMID: 37602378 PMCID: PMC10516660 DOI: 10.1093/nar/gkad673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2023] [Revised: 07/27/2023] [Accepted: 08/10/2023] [Indexed: 08/22/2023] Open
Abstract
Proteins containing a RNB domain, originally identified in Escherichia coli RNase II, are widely present throughout the tree of life. Many RNB proteins have 3'-5' exoribonucleolytic activity but some have lost catalytic activity during evolution. Database searches identified a new RNB domain-containing protein in human: HELZ2. Analysis of genomic and expression data combined with evolutionary information suggested that the human HELZ2 protein is produced from an unforeseen non-canonical initiation codon in Hominidae. This unusual property was confirmed experimentally, extending the human protein by 247 residues. Human HELZ2 was further shown to be an active ribonuclease despite the substitution of a key residue in its catalytic center. HELZ2 RNase activity is lost in cells from some cancer patients as a result of somatic mutations. HELZ2 harbors also two RNA helicase domains and several zinc fingers and its expression is induced by interferon treatment. We demonstrate that HELZ2 is able to degrade structured RNAs through the coordinated ATP-dependent displacement of duplex RNA mediated by its RNA helicase domains and its 3'-5' ribonucleolytic action. The expression characteristics and biochemical properties of HELZ2 support a role for this factor in response to viruses and/or mobile elements.
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Affiliation(s)
- Eric Huntzinger
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Jordan Sinteff
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bastien Morlet
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
| | - Bertrand Séraphin
- Institut de Génétique et de Biologie Moléculaire et cellulaire (IGBMC), Centre National de Recherche scientifique (CNRS) UMR 7104 - Institut National de santé et de Recherche Médicale (Inserm) U1258 - Université de Strasbourg, 1 rue Laurent Fries, Illkirch, France
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4
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Egusa G, Ohno H, Nagano G, Sagawa J, Shinjo H, Yamamoto Y, Himeno N, Morita Y, Kanai A, Baba R, Kobuke K, Oki K, Yoneda M, Hattori N. Selective activation of PPARα maintains thermogenic capacity of beige adipocytes. iScience 2023; 26:107143. [PMID: 37456852 PMCID: PMC10338232 DOI: 10.1016/j.isci.2023.107143] [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: 09/30/2022] [Revised: 04/17/2023] [Accepted: 06/12/2023] [Indexed: 07/18/2023] Open
Abstract
Beige adipocytes are inducible thermogenic adipocytes used for anti-obesity treatment. Beige adipocytes rapidly lose their thermogenic capacity once external cues are removed. However, long-term administration of stimulants, such as PPARγ and β-adrenergic receptor agonists, is unsuitable due to various side effects. Here, we reported that PPARα pharmacological activation was the preferred target for maintaining induced beige adipocytes. Pemafibrate used in clinical practice for dyslipidemia was developed as a selective PPARα modulator (SPPARMα). Pemafibrate administration regulated the thermogenic capacity of induced beige adipocytes, repressed body weight gain, and ameliorated impaired glucose tolerance in diet-induced obese mouse models. The transcriptome analysis revealed that the E-twenty-six transcription factor ELK1 acted as a cofactor of PPARα. ELK1 was mobilized to the Ucp1 transcription regulatory region with PPARα and modulated its expression by pemafibrate. These results suggest that selective activation of PPARα by pemafibrate is advantageous to maintain the function of beige adipocytes.
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Affiliation(s)
- Gentaro Egusa
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Haruya Ohno
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Gaku Nagano
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Junji Sagawa
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Hiroko Shinjo
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yutaro Yamamoto
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Natsumi Himeno
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Yoshimi Morita
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Akinori Kanai
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Ryuta Baba
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kazuhiro Kobuke
- Department of Preventive Medicine for Diabetes and Lifestyle-related Diseases, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Kenji Oki
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Masayasu Yoneda
- Department of Preventive Medicine for Diabetes and Lifestyle-related Diseases, Graduate School of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Noboru Hattori
- Department of Molecular and Internal Medicine, Graduate School of Biomedical & Health Sciences, Hiroshima University, Hiroshima, Japan
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5
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Weber LM, Jia Y, Stielow B, Gisselbrecht S, Cao Y, Ren Y, Rohner I, King J, Rothman E, Fischer S, Simon C, Forné I, Nist A, Stiewe T, Bulyk M, Wang Z, Liefke R. The histone acetyltransferase KAT6A is recruited to unmethylated CpG islands via a DNA binding winged helix domain. Nucleic Acids Res 2023; 51:574-594. [PMID: 36537216 PMCID: PMC9881136 DOI: 10.1093/nar/gkac1188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Revised: 11/04/2022] [Accepted: 11/29/2022] [Indexed: 12/24/2022] Open
Abstract
The lysine acetyltransferase KAT6A (MOZ, MYST3) belongs to the MYST family of chromatin regulators, facilitating histone acetylation. Dysregulation of KAT6A has been implicated in developmental syndromes and the onset of acute myeloid leukemia (AML). Previous work suggests that KAT6A is recruited to its genomic targets by a combinatorial function of histone binding PHD fingers, transcription factors and chromatin binding interaction partners. Here, we demonstrate that a winged helix (WH) domain at the very N-terminus of KAT6A specifically interacts with unmethylated CpG motifs. This DNA binding function leads to the association of KAT6A with unmethylated CpG islands (CGIs) genome-wide. Mutation of the essential amino acids for DNA binding completely abrogates the enrichment of KAT6A at CGIs. In contrast, deletion of a second WH domain or the histone tail binding PHD fingers only subtly influences the binding of KAT6A to CGIs. Overexpression of a KAT6A WH1 mutant has a dominant negative effect on H3K9 histone acetylation, which is comparable to the effects upon overexpression of a KAT6A HAT domain mutant. Taken together, our work revealed a previously unrecognized chromatin recruitment mechanism of KAT6A, offering a new perspective on the role of KAT6A in gene regulation and human diseases.
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Affiliation(s)
- Lisa Marie Weber
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Yulin Jia
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Bastian Stielow
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Stephen S Gisselbrecht
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Yinghua Cao
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Yanpeng Ren
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Iris Rohner
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Jessica King
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Elisabeth Rothman
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Sabrina Fischer
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Clara Simon
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
| | - Ignasi Forné
- Protein Analysis Unit, Biomedical Center (BMC), Faculty of Medicine, Ludwig-Maximilians-University (LMU) Munich, Martinsried 82152, Germany
| | - Andrea Nist
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Thorsten Stiewe
- Genomics Core Facility, Institute of Molecular Oncology, Member of the German Center for Lung Research (DZL), Philipps University of Marburg, Marburg 35043, Germany
| | - Martha L Bulyk
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
- Department of Pathology, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Zhanxin Wang
- Key Laboratory of Cell Proliferation and Regulation Biology of Ministry of Education, College of Life Sciences, Beijing Normal University, Beijing 100875, China
| | - Robert Liefke
- Institute of Molecular Biology and Tumor Research (IMT), Philipps University of Marburg, Marburg 35043, Germany
- Department of Hematology, Oncology, and Immunology, University Hospital Giessen and Marburg, Marburg 35043, Germany
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6
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Luqman-Fatah A, Watanabe Y, Uno K, Ishikawa F, Moran JV, Miyoshi T. The interferon stimulated gene-encoded protein HELZ2 inhibits human LINE-1 retrotransposition and LINE-1 RNA-mediated type I interferon induction. Nat Commun 2023; 14:203. [PMID: 36639706 PMCID: PMC9839780 DOI: 10.1038/s41467-022-35757-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Accepted: 12/23/2022] [Indexed: 01/15/2023] Open
Abstract
Some interferon stimulated genes (ISGs) encode proteins that inhibit LINE-1 (L1) retrotransposition. Here, we use immunoprecipitation followed by liquid chromatography-tandem mass spectrometry to identify proteins that associate with the L1 ORF1-encoded protein (ORF1p) in ribonucleoprotein particles. Three ISG proteins that interact with ORF1p inhibit retrotransposition: HECT and RLD domain containing E3 ubiquitin-protein ligase 5 (HERC5); 2'-5'-oligoadenylate synthetase-like (OASL); and helicase with zinc finger 2 (HELZ2). HERC5 destabilizes ORF1p, but does not affect its cellular localization. OASL impairs ORF1p cytoplasmic foci formation. HELZ2 recognizes sequences and/or structures within the L1 5'UTR to reduce L1 RNA, ORF1p, and ORF1p cytoplasmic foci levels. Overexpression of WT or reverse transcriptase-deficient L1s lead to a modest induction of IFN-α expression, which is abrogated upon HELZ2 overexpression. Notably, IFN-α expression is enhanced upon overexpression of an ORF1p RNA binding mutant, suggesting ORF1p binding might protect L1 RNA from "triggering" IFN-α induction. Thus, ISG proteins can inhibit retrotransposition by different mechanisms.
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Affiliation(s)
- Ahmad Luqman-Fatah
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Yuzo Watanabe
- Proteomics Facility, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - Kazuko Uno
- Division of Basic Research, Louis Pasteur Center for Medical Research, Kyoto, 606-8225, Japan
| | - Fuyuki Ishikawa
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan
| | - John V Moran
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
- Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, 48109-5618, USA
| | - Tomoichiro Miyoshi
- Department of Gene Mechanisms, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Radiation Biology Center, Graduate School of Biostudies, Kyoto University, Kyoto, 606-8501, Japan.
- Laboratory for Retrotransposon Dynamics, RIKEN Center for Integrative Medical Sciences, Yokohama, 230-0045, Japan.
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7
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Estefanía González-Alvarez M, Severin A, Sayadi M, Keating AF. PFOA-Induced Ovotoxicity Differs Between Lean and Obese Mice With Impacts on Ovarian Reproductive and DNA Damage Sensing and Repair Proteins. Toxicol Sci 2022; 190:173-188. [PMID: 36214631 PMCID: PMC9789752 DOI: 10.1093/toxsci/kfac104] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Perfluorooctanoic acid (PFOA) is an environmentally persistent perfluoroalkyl substance that is widely used in consumer products. Exposure to PFOA is associated with reproductive and developmental effects including endocrine disruption, delayed puberty in girls, and decreased fetal growth. In the United States, obesity affects 40% of women and 20% of girls, with higher rates in minority females. Obesity causes infertility, poor oocyte quality, miscarriage, and offspring defects. This study proposed that PFOA exposure would impact estrous cyclicity, ovarian steroid hormones, and the ovarian proteome and further hypothesized that obesity would impact PFOA-induced ovotoxicity. Female wild type (KK.Cg-a/a; lean) or KK.Cg-Ay/J mice (obese) received saline (CT) or PFOA (2.5 mg/kg) per os for 15 days beginning at 7 weeks of age. There were no effects on food intake, body weight, estrous cyclicity, serum progesterone, and heart, spleen, kidney, or uterus weight (p > .05). Ovary weight was decreased (p < .05) by PFOA exposure relative to vehicle control-treated mice in lean but not obese mice. Liquid chromatography-tandem mass spectrometry was performed on isolated ovarian protein and PFOA exposure altered the ovarian abundance of proteins involved in DNA damage sensing and repair pathways and reproduction pathways (p < .05) differentially in lean and obese mice. The data suggest that PFOA exposure alters ovary weight and differentially targets ovarian proteins in lean and obese females in ways that might reduce female fecundity.
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Affiliation(s)
| | - Andrew Severin
- Department of Animal Science and Interdepartmental Toxicology Graduate Program, Iowa State University, Ames, Iowa 50011, USA
| | - Maryam Sayadi
- Department of Animal Science and Interdepartmental Toxicology Graduate Program, Iowa State University, Ames, Iowa 50011, USA
| | - Aileen F Keating
- To whom correspondence should be addressed at Department of Animal Science and Interdepartmental Toxicology Graduate Program, Iowa State University, 2356H Kildee Hall, 806 Stange Road, Ames, IA 50011, USA. E-mail:
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8
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Kohzaki M. Mammalian Resilience Revealed by a Comparison of Human Diseases and Mouse Models Associated With DNA Helicase Deficiencies. Front Mol Biosci 2022; 9:934042. [PMID: 36032672 PMCID: PMC9403131 DOI: 10.3389/fmolb.2022.934042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Accepted: 06/23/2022] [Indexed: 12/01/2022] Open
Abstract
Maintaining genomic integrity is critical for sustaining individual animals and passing on the genome to subsequent generations. Several enzymes, such as DNA helicases and DNA polymerases, are involved in maintaining genomic integrity by unwinding and synthesizing the genome, respectively. Indeed, several human diseases that arise caused by deficiencies in these enzymes have long been known. In this review, the author presents the DNA helicases associated with human diseases discovered to date using recent analyses, including exome sequences. Since several mouse models that reflect these human diseases have been developed and reported, this study also summarizes the current knowledge regarding the outcomes of DNA helicase deficiencies in humans and mice and discusses possible mechanisms by which DNA helicases maintain genomic integrity in mammals. It also highlights specific diseases that demonstrate mammalian resilience, in which, despite the presence of genomic instability, patients and mouse models have lifespans comparable to those of the general population if they do not develop cancers; finally, this study discusses future directions for therapeutic applications in humans that can be explored using these mouse models.
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9
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Guixé‐Muntet S, Biquard L, Szabo G, Dufour J, Tacke F, Francque S, Rautou P, Gracia‐Sancho J. Review article: vascular effects of PPARs in the context of NASH. Aliment Pharmacol Ther 2022; 56:209-223. [PMID: 35661191 PMCID: PMC9328268 DOI: 10.1111/apt.17046] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/04/2021] [Accepted: 05/08/2022] [Indexed: 12/12/2022]
Abstract
BACKGROUND Peroxisome proliferator-activated receptors (PPARs) are ligand-activated transcription factors known to regulate glucose and fatty acid metabolism, inflammation, endothelial function and fibrosis. PPAR isoforms have been extensively studied in metabolic diseases, including type 2 diabetes and cardiovascular diseases. Recent data extend the key role of PPARs to liver diseases coursing with vascular dysfunction, including nonalcoholic fatty liver disease (NAFLD) and nonalcoholic steatohepatitis (NASH). AIM This review summarises and discusses the pathobiological role of PPARs in cardiovascular diseases with a special focus on their impact and therapeutic potential in NAFLD and NASH. RESULTS AND CONCLUSIONS PPARs may be attractive for the treatment of NASH due to their liver-specific effects but also because of their efficacy in improving cardiovascular outcomes, which may later impact liver disease. Assessment of cardiovascular disease in the context of NASH trials is, therefore, of the utmost importance, both from a safety and efficacy perspective.
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Affiliation(s)
- Sergi Guixé‐Muntet
- Liver Vascular Biology Research GroupIDIBAPS Biomedical Research Institute & CIBEREHDBarcelonaSpain
| | - Louise Biquard
- Université de Paris, Inserm, CNRSCentre de recherche sur l'InflammationUMR1149ParisFrance
| | - Gyongyi Szabo
- Beth Israel Deaconess Medical CenterHarvard Medical SchoolBostonMassachusettsUSA
| | - Jean‐François Dufour
- Department of Visceral Surgery and Medicine & Department for Biomedical ResearchInselspital, University of BernBernSwitzerland
| | - Frank Tacke
- Department of Hepatology & GastroenterologyCharité Universitätsmedizin Berlin, Campus Virchow‐Klinikum (CVK) and Campus Charité Mitte (CCM)BerlinGermany
| | - Sven Francque
- Department of Gastroenterology and HepatologyAntwerp University HospitalAntwerpBelgium,Translational Sciences in Inflammation and ImmunologyInflaMed Centre of Excellence, Laboratory of Experimental Medicine and Paediatrics, Faculty of Medicine and Health Sciences, University of AntwerpAntwerpBelgium
| | - Pierre‐Emmanuel Rautou
- Université de Paris, AP‐HP, Hôpital Beaujon, Service d'Hépatologie, DMU DIGESTCentre de Référence des Maladies Vasculaires du Foie, FILFOIE, ERN RARE‐LIVER, Centre de recherche sur l'inflammationParisFrance
| | - Jordi Gracia‐Sancho
- Liver Vascular Biology Research GroupIDIBAPS Biomedical Research Institute & CIBEREHDBarcelonaSpain,Department of Visceral Surgery and Medicine & Department for Biomedical ResearchInselspital, University of BernBernSwitzerland
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10
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Lin Y, Wang Y, Li PF. PPARα: An emerging target of metabolic syndrome, neurodegenerative and cardiovascular diseases. Front Endocrinol (Lausanne) 2022; 13:1074911. [PMID: 36589809 PMCID: PMC9800994 DOI: 10.3389/fendo.2022.1074911] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/20/2022] [Accepted: 11/23/2022] [Indexed: 12/23/2022] Open
Abstract
Peroxisome proliferator-activated receptor α (PPARα) is a ligand-activated transcription factor that is involved in lipid metabolism of various tissues. Different metabolites of fatty acids and agonists like fibrates activate PPARα for its transactivative or repressive function. PPARα is known to affect diverse human diseases, and we focus on advanced studies of its transcriptional regulation in these diseases. In MAFLD, PPARα shows a protective function with its upregulation of lipid oxidation and mitochondrial biogenesis and transcriptional repression of inflammatory genes, which is similar in Alzheimer's disease and cardiovascular disease. Activation of PPARα also prevents the progress of diabetes complications; however, its role in diabetes and cancers remains uncertain. Some PPARα-specific agonists, such as Wy14643 and fenofibrate, have been applied in metabolic syndrome treatment, which might own potential in wider application. Future studies may further explore the functions and interventions of PPARα in cancer, diabetes, immunological diseases, and neurodegenerative disease.
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Affiliation(s)
- Yijun Lin
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen, China
- *Correspondence: Yijun Lin, ; Yan Wang, ; Pei-feng Li,
| | - Yan Wang
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen, China
- *Correspondence: Yijun Lin, ; Yan Wang, ; Pei-feng Li,
| | - Pei-feng Li
- Xiamen Cardiovascular Hospital of Xiamen University, School of Medicine, Xiamen University, Xiamen, China
- Xiamen Key Laboratory of Cardiovascular Disease, Xiamen, China
- *Correspondence: Yijun Lin, ; Yan Wang, ; Pei-feng Li,
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11
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Dixit G, Prabhu A. The pleiotropic peroxisome proliferator activated receptors: Regulation and therapeutics. Exp Mol Pathol 2021; 124:104723. [PMID: 34822814 DOI: 10.1016/j.yexmp.2021.104723] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 11/15/2021] [Indexed: 02/07/2023]
Abstract
The Peroxisome proliferator-activated receptors (PPARs) are key regulators of metabolic events in our body. Owing to their implication in maintenance of homeostasis, both PPAR agonists and antagonists assume therapeutic significance. Understanding the molecular mechanisms of each of the PPAR isotypes in the healthy body and during disease is crucial to exploiting their full therapeutic potential. This article is an attempt to present a rational analysis of the multifaceted therapeutic effects and underlying mechanisms of isotype-specific PPAR agonists, dual PPAR agonists, pan PPAR agonists as well as PPAR antagonists. A holistic understanding of the mechanistic dimensions of these key metabolic regulators will guide future efforts to identify novel molecules in the realm of metabolic, inflammatory and immunotherapeutic diseases.
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Affiliation(s)
- Gargi Dixit
- Department of Pharmaceutical Chemistry & Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India
| | - Arati Prabhu
- Department of Pharmaceutical Chemistry & Quality Assurance, SVKM's Dr. Bhanuben Nanavati College of Pharmacy, Mumbai, India.
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12
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Abstract
Chromatin is highly dynamic, undergoing continuous global changes in its structure and type of histone and DNA modifications governed by processes such as transcription, repair, replication, and recombination. Members of the chromodomain helicase DNA-binding (CHD) family of enzymes are ATP-dependent chromatin remodelers that are intimately involved in the regulation of chromatin dynamics, altering nucleosomal structure and DNA accessibility. Genetic studies in yeast, fruit flies, zebrafish, and mice underscore essential roles of CHD enzymes in regulating cellular fate and identity, as well as proper embryonic development. With the advent of next-generation sequencing, evidence is emerging that these enzymes are subjected to frequent DNA copy number alterations or mutations and show aberrant expression in malignancies and other human diseases. As such, they might prove to be valuable biomarkers or targets for therapeutic intervention.
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Affiliation(s)
- Andrej Alendar
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
| | - Anton Berns
- Division of Molecular Genetics, The Netherlands Cancer Institute, Amsterdam 1066CX, The Netherlands
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13
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Tahri-Joutey M, Andreoletti P, Surapureddi S, Nasser B, Cherkaoui-Malki M, Latruffe N. Mechanisms Mediating the Regulation of Peroxisomal Fatty Acid Beta-Oxidation by PPARα. Int J Mol Sci 2021; 22:ijms22168969. [PMID: 34445672 PMCID: PMC8396561 DOI: 10.3390/ijms22168969] [Citation(s) in RCA: 58] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Revised: 08/14/2021] [Accepted: 08/15/2021] [Indexed: 12/12/2022] Open
Abstract
In mammalian cells, two cellular organelles, mitochondria and peroxisomes, share the ability to degrade fatty acid chains. Although each organelle harbors its own fatty acid β-oxidation pathway, a distinct mitochondrial system feeds the oxidative phosphorylation pathway for ATP synthesis. At the same time, the peroxisomal β-oxidation pathway participates in cellular thermogenesis. A scientific milestone in 1965 helped discover the hepatomegaly effect in rat liver by clofibrate, subsequently identified as a peroxisome proliferator in rodents and an activator of the peroxisomal fatty acid β-oxidation pathway. These peroxisome proliferators were later identified as activating ligands of Peroxisome Proliferator-Activated Receptor α (PPARα), cloned in 1990. The ligand-activated heterodimer PPARα/RXRα recognizes a DNA sequence, called PPRE (Peroxisome Proliferator Response Element), corresponding to two half-consensus hexanucleotide motifs, AGGTCA, separated by one nucleotide. Accordingly, the assembled complex containing PPRE/PPARα/RXRα/ligands/Coregulators controls the expression of the genes involved in liver peroxisomal fatty acid β-oxidation. This review mobilizes a considerable number of findings that discuss miscellaneous axes, covering the detailed expression pattern of PPARα in species and tissues, the lessons from several PPARα KO mouse models and the modulation of PPARα function by dietary micronutrients.
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Affiliation(s)
- Mounia Tahri-Joutey
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences & Techniques, University Hassan I, BP 577, 26000 Settat, Morocco;
| | - Pierre Andreoletti
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
| | - Sailesh Surapureddi
- Office of Pollution Prevention and Toxics, United States Environmental Protection Agency, Washington, DC 20460, USA;
| | - Boubker Nasser
- Laboratory of Biochemistry, Neurosciences, Natural Resources and Environment, Faculty of Sciences & Techniques, University Hassan I, BP 577, 26000 Settat, Morocco;
| | - Mustapha Cherkaoui-Malki
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
| | - Norbert Latruffe
- Bio-PeroxIL Laboratory, University of Bourgogne Franche-Comté, 21000 Dijon, France; (M.T.-J.); (P.A.); (M.C.-M.)
- Correspondence:
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14
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Katan T, Xue X, Caballero-Solares A, Taylor RG, Parrish CC, Rise ML. Influence of Varying Dietary ω6 to ω3 Fatty Acid Ratios on the Hepatic Transcriptome, and Association with Phenotypic Traits (Growth, Somatic Indices, and Tissue Lipid Composition), in Atlantic Salmon ( Salmo salar). BIOLOGY 2021; 10:biology10070578. [PMID: 34202562 PMCID: PMC8301090 DOI: 10.3390/biology10070578] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Revised: 06/18/2021] [Accepted: 06/21/2021] [Indexed: 11/24/2022]
Abstract
Simple Summary Plant oils are routinely used in fish feeds as a fish oil replacement. However, these terrestrial alternatives typically contain high levels of ω6 fatty acids (FA) and, thus, high ω6 to ω3 (ω6:ω3) FA ratios, which influence farmed fish and their consumers. The ω6:ω3 ratio is known to affect many biological processes (e.g., inflammation, FA metabolism) and human diseases; however, its impacts on fish physiology and the underlying molecular mechanisms are less well understood. In this study, we used 44 K microarrays to examine which genes and molecular pathways are altered by variation in dietary ω6:ω3 in Atlantic salmon. Our microarray study showed that several genes related to immune response, lipid metabolism, cell proliferation, and translation were differentially expressed between the two extreme ω6:ω3 dietary treatments. We also revealed that the PPARα activation-related transcript helz2 is a potential novel molecular biomarker of tissue variation in ω6:ω3. Further, correlation analyses illustrated the relationships between liver transcript expression and tissue (liver, muscle) lipid composition, and other phenotypic traits in salmon fed low levels of fish oil. This nutrigenomic study enhanced the current understanding of Atlantic salmon gene expression response to varying dietary ω6:ω3. Abstract The importance of dietary omega-6 to omega-3 (ω6:ω3) fatty acid (FA) ratios for human health has been extensively examined. However, its impact on fish physiology, and the underlying molecular mechanisms, are less well understood. This study investigated the influence of plant-based diets (12-week exposure) with varying ω6:ω3 (0.4–2.7) on the hepatic transcriptome of Atlantic salmon. Using 44 K microarray analysis, genes involved in immune and inflammatory response (lect2a, itgb5, helz2a, p43), lipid metabolism (helz2a), cell proliferation (htra1b), control of muscle and neuronal development (mef2d) and translation (eif2a, eif4b1, p43) were identified; these were differentially expressed between the two extreme ω6:ω3 dietary treatments (high ω6 vs. high ω3) at week 12. Eight out of 10 microarray-identified transcripts showed an agreement in the direction of expression fold-change between the microarray and qPCR studies. The PPARα activation-related transcript helz2a was confirmed by qPCR to be down-regulated by high ω6 diet compared with high ω3 diet. The transcript expression of two helz2 paralogues was positively correlated with ω3, and negatively with ω6 FA in both liver and muscle, thus indicating their potential as biomarkers of tissue ω6:ω3 variation. Mef2d expression in liver was suppressed in the high ω6 compared to the balanced diet (ω6:ω3 of 2.7 and 0.9, respectively) fed fish, and showed negative correlations with ω6:ω3 in both tissues. The hepatic expression of two lect2 paralogues was negatively correlated with viscerosomatic index, while htra1b correlated negatively with salmon weight gain and condition factor. Finally, p43 and eif2a were positively correlated with liver Σω3, while these transcripts and eif4b2 showed negative correlations with 18:2ω6 in the liver. This suggested that some aspects of protein synthesis were influenced by dietary ω6:ω3. In summary, this nutrigenomic study identified hepatic transcripts responsive to dietary variation in ω6:ω3, and relationships of transcript expression with tissue (liver, muscle) lipid composition and other phenotypic traits.
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Affiliation(s)
- Tomer Katan
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (X.X.); (C.C.P.); (M.L.R.)
- Correspondence: (T.K.); (A.C.-S.); Tel.: +1-709-7703846 (T.K.); Tel.: +1-709-3251598 (A.C.-S.)
| | - Xi Xue
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (X.X.); (C.C.P.); (M.L.R.)
| | - Albert Caballero-Solares
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (X.X.); (C.C.P.); (M.L.R.)
- Correspondence: (T.K.); (A.C.-S.); Tel.: +1-709-7703846 (T.K.); Tel.: +1-709-3251598 (A.C.-S.)
| | - Richard G. Taylor
- Cargill Animal Nutrition, 10383 165th Avenue NW, Elk River, MN 55330, USA;
| | - Christopher C. Parrish
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (X.X.); (C.C.P.); (M.L.R.)
| | - Matthew L. Rise
- Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada; (X.X.); (C.C.P.); (M.L.R.)
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15
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Thulasi Raman SN, Latreille E, Gao J, Zhang W, Wu J, Russell MS, Walrond L, Cyr T, Lavoie JR, Safronetz D, Cao J, Sauve S, Farnsworth A, Chen W, Shi PY, Wang Y, Wang L, Rosu-Myles M, Li X. Dysregulation of Ephrin receptor and PPAR signaling pathways in neural progenitor cells infected by Zika virus. Emerg Microbes Infect 2020; 9:2046-2060. [PMID: 32873194 PMCID: PMC7534353 DOI: 10.1080/22221751.2020.1818631] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 08/28/2020] [Indexed: 12/13/2022]
Abstract
Zika virus (ZIKV) infection is a serious public threat with cases reported in about 70 countries and territories. One of the most serious consequences of ZIKV infection is congenital microcephaly in babies. Congenital microcephaly has been suggested to result from infection of neural progenitor cells (NPCs) in the developing fetal brain. However, the molecular and cellular mechanisms underlying microcephaly development remains to be fully elucidated. In this study, we employed quantitative proteomics to determine protein expression profile that occur during viral replication in NPCs. Bioinformatics analysis of the protein expression changes resulted in the identification of a wide range of cell signaling pathways. Specifically, pathways involved in neurogenesis and embryonic development were markedly altered, along with those associated with cell cycle, apoptosis, lipid metabolism and oxidative stress. Notably, the differential regulation of Ephrin Receptor and PPAR signaling pathways, as revealed by quantitative proteomics and validated by qPCR array, underscores the need to explore these pathways in disease development. Collectively, these results indicate that ZIKV-induced pathogenesis involves complex virus-host reactions; the findings reported here could help shed light on the mechanisms underlying ZIKV-induced microcephaly and ZIKV replication in NPCs.
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Affiliation(s)
- Sathya N. Thulasi Raman
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Elyse Latreille
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Jun Gao
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Wanyue Zhang
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jianguo Wu
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Marsha S. Russell
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Lisa Walrond
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Terry Cyr
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Jessie R. Lavoie
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - David Safronetz
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Jingxin Cao
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Simon Sauve
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Aaron Farnsworth
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
| | - Wangxue Chen
- National Research Council of Canada, Human Health Therapeutics, Ottawa, ON, Canada
| | - Pei-Yong Shi
- Department of Biochemistry & Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Youchun Wang
- National Institute for Food and Drug Control and WHO Collaborating Center for Standardization and Evaluation of Biologicals, Beijing, People’s Republic of China
| | - Lisheng Wang
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Michael Rosu-Myles
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Xuguang Li
- Centre for Biologics Evaluation, Biologics and Radiopharmaceutical Drugs Directorate, HPFB, Health Canada and WHO Collaborating Centre for Standardization and Evaluation of Biologicals, Ottawa, ON, Canada
- Department of Biochemistry, Microbiology and Immunology, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
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16
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Ríos-Castro E, Souza GHMF, Delgadillo-Álvarez DM, Ramírez-Reyes L, Torres-Huerta AL, Velasco-Suárez A, Cruz-Cruz C, Hernández-Hernández JM, Tapia-Ramírez J. Quantitative Proteomic Analysis of MARC-145 Cells Infected with a Mexican Porcine Reproductive and Respiratory Syndrome Virus Strain Using a Label-Free Based DIA approach. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2020; 31:1302-1312. [PMID: 32379441 DOI: 10.1021/jasms.0c00134] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is an infectious disease characterized by severe reproductive failure in sows, acute respiratory disorders in growing pigs, and high mortality in piglets. The causative agent of this syndrome is the PRRS virus (PRRSV), an RNA virus belonging to the Arteriviridae family. To date, several quantitative approaches of proteomics have been applied to analyze the gene expression profiles during PRRSV infection in PAMs and MARC-145 cells, and few proteins have been consistent among independent studies, probably due to the differences in the levels of virulence of different PRRSV strains used and/or due to analytical conditions. In this study, total proteins isolated from noninfected and infected MARC-145 cells with a Mexican PRRSV strain were relatively quantified using label-free based DIA approach in combination with ion-mobility separation. As a result, 1456 quantified proteins were found to be shared between the control and infected samples. Afterward, these proteins were filtered, and 699 of them were considered without change. Also, 17 proteins were up-regulated and 19 proteins were down-regulated during the PRSSV infection. Bioinformatic analysis revealed that many of the differentially expressed proteins are involved in processes like antigen processing, presentation of antigens, response to viruses, response to IFNs, and innate immune response, among others. The present work is the first one which provides a detailed proteomic analysis through label-free based DIA approach in MARC-145 cells during the infection with a Mexican PRRSV strain.
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Affiliation(s)
- Emmanuel Ríos-Castro
- Unidad de Genómica, Proteómica y Metabolómica (UGPM), LaNSE, Cinvestav-IPN, Ciudad de México C.P. 07360, México
| | | | | | - Lorena Ramírez-Reyes
- Unidad de Genómica, Proteómica y Metabolómica (UGPM), LaNSE, Cinvestav-IPN, Ciudad de México C.P. 07360, México
| | - Ana Laura Torres-Huerta
- Unidad de Desarrollo e Innovación (UDI), LaNSE, Cinvestav-IPN, Ciudad de México, C.P. 07360, México
| | - Andrea Velasco-Suárez
- Unidad de Genómica, Proteómica y Metabolómica (UGPM), LaNSE, Cinvestav-IPN, Ciudad de México C.P. 07360, México
| | - Carlos Cruz-Cruz
- Departamento de Genética y Biologı́a Molecular, Cinvestav-IPN, Ciudad de México, C.P. 07360, México
| | | | - José Tapia-Ramírez
- Departamento de Genética y Biologı́a Molecular, Cinvestav-IPN, Ciudad de México, C.P. 07360, México
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17
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Gene Expression Profiles Induced by a Novel Selective Peroxisome Proliferator-Activated Receptor α Modulator (SPPARMα) Pemafibrate. Int J Mol Sci 2019; 20:ijms20225682. [PMID: 31766193 PMCID: PMC6888257 DOI: 10.3390/ijms20225682] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Revised: 11/05/2019] [Accepted: 11/11/2019] [Indexed: 12/16/2022] Open
Abstract
Pemafibrate is the first clinically-available selective peroxisome proliferator-activated receptor α modulator (SPPARMα) that has been shown to effectively improve hypertriglyceridemia and low high-density lipoprotein cholesterol (HDL-C) levels. Global gene expression analysis reveals that the activation of PPARα by pemafibrate induces fatty acid (FA) uptake, binding, and mitochondrial or peroxisomal oxidation as well as ketogenesis in mouse liver. Pemafibrate most profoundly induces HMGCS2 and PDK4, which regulate the rate-limiting step of ketogenesis and glucose oxidation, respectively, compared to other fatty acid metabolic genes in human hepatocytes. This suggests that PPARα plays a crucial role in nutrient flux in the human liver. Additionally, pemafibrate induces clinically favorable genes, such as ABCA1, FGF21, and VLDLR. Furthermore, pemafibrate shows anti-inflammatory effects in vascular endothelial cells. Pemafibrate is predicted to exhibit beneficial effects in patients with atherogenic dyslipidemia and diabetic microvascular complications.
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18
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Lin B, Dutta B, Fraser IDC. Systematic Investigation of Multi-TLR Sensing Identifies Regulators of Sustained Gene Activation in Macrophages. Cell Syst 2019; 5:25-37.e3. [PMID: 28750197 DOI: 10.1016/j.cels.2017.06.014] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Revised: 04/26/2017] [Accepted: 06/22/2017] [Indexed: 12/22/2022]
Abstract
A typical pathogen presents a combination of Toll-like receptor (TLR) ligands during infection. Although individual TLR pathways have been well characterized, the nature of this "combinatorial code" in pathogen sensing remains unclear. Here, we conducted a comprehensive transcriptomic analysis of primary macrophages stimulated with all possible pairwise combinations of four different TLR ligands to understand the requirements, kinetics, and outcome of combined pathway engagement. We find that signal integration between TLR pathways leads to non-additive responses for a subset of immune mediators with sustained expression (>6 hr) properties and T cell polarizing function. To identify the underlying regulators, we conducted a focused RNAi screen and identified four genes-Helz2, Phf11d, Sertad3, and Zscan12-which preferentially affect the late phase response of TLR-induced immune effector expression. This study reveals key molecular details of how contemporaneous signaling through multiple TLRs, as would often be the case with pathogen infection, produce biological outcomes distinct from the single ligands typically used to characterize TLR pathways.
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Affiliation(s)
- Bin Lin
- Signaling Systems Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Bhaskar Dutta
- Bioinformatics Group, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Iain D C Fraser
- Signaling Systems Unit, Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA.
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19
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Cai M, Liang X, Sun X, Chen H, Dong Y, Wu L, Gu S, Han S. Nuclear Receptor Coactivator 2 Promotes Human Breast Cancer Cell Growth by Positively Regulating the MAPK/ERK Pathway. Front Oncol 2019; 9:164. [PMID: 30941313 PMCID: PMC6434718 DOI: 10.3389/fonc.2019.00164] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/25/2019] [Indexed: 01/20/2023] Open
Abstract
As a member of the p160 steroid receptor coactivator (SRC) family, nuclear receptor coactivator 2 (NCOA2) is known to play essential roles in many physiological and pathological processes, including development, endocrine regulation, and tumorigenesis. However, the biological function of NCOA2 in breast cancer is not fully understood. We found that the copy number of the NCOA2 gene was frequently amplified in four breast cancers datasets, varying from 6 to 10%, and the mRNA levels of NCOA2 were also upregulated in 11% of the sequenced cases/patients (TCGA provisional dataset). Next, we confirmed that NCOA2 silencing significantly suppressed cell proliferation in different breast cancer cell lines, by inducing cell cycle arrest and apoptosis. Mechanistically, whole-transcriptome sequencing (RNA-Seq) analysis showed that NCOA2 depletion leads to downregulation of the MAPK/ERK signaling cascade, possibly via downregulating NCOA2's downstream target RASEF. In conclusion, our results suggest NCOA2 as a potential target of therapeutics against breast cancer.
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Affiliation(s)
- Mengjiao Cai
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Xin Liang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.,National Center for Protein Sciences, Beijing, China
| | - Xiao Sun
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.,State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Huan Chen
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China
| | - Yiping Dong
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Lingzhi Wu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center, Beijing Institute of Radiation Medicine, Beijing, China.,National Center for Protein Sciences, Beijing, China
| | - Suxi Gu
- Orthopeadic Department, Beijing Tsinghua Changgung Hospital, School of Clinical Medcine, Tsinghua University, Beijing, China
| | - Suxia Han
- Department of Oncology, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
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20
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Bougarne N, Weyers B, Desmet SJ, Deckers J, Ray DW, Staels B, De Bosscher K. Molecular Actions of PPARα in Lipid Metabolism and Inflammation. Endocr Rev 2018; 39:760-802. [PMID: 30020428 DOI: 10.1210/er.2018-00064] [Citation(s) in RCA: 407] [Impact Index Per Article: 67.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2018] [Accepted: 07/10/2018] [Indexed: 12/13/2022]
Abstract
Peroxisome proliferator-activated receptor α (PPARα) is a nuclear receptor of clinical interest as a drug target in various metabolic disorders. PPARα also exhibits marked anti-inflammatory capacities. The first-generation PPARα agonists, the fibrates, have however been hampered by drug-drug interaction issues, statin drop-in, and ill-designed cardiovascular intervention trials. Notwithstanding, understanding the molecular mechanisms by which PPARα works will enable control of its activities as a drug target for metabolic diseases with an underlying inflammatory component. Given its role in reshaping the immune system, the full potential of this nuclear receptor subtype as a versatile drug target with high plasticity becomes increasingly clear, and a novel generation of agonists may pave the way for novel fields of applications.
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Affiliation(s)
- Nadia Bougarne
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Receptor Research Laboratories, Nuclear Receptor Laboratory, VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Basiel Weyers
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Receptor Research Laboratories, Nuclear Receptor Laboratory, VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Sofie J Desmet
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Receptor Research Laboratories, Nuclear Receptor Laboratory, VIB Center for Medical Biotechnology, Ghent, Belgium
| | - Julie Deckers
- Department of Internal Medicine, Ghent University, Ghent, Belgium
- Laboratory of Immunoregulation, VIB Center for Inflammation Research, Ghent (Zwijnaarde), Belgium
| | - David W Ray
- Division of Metabolism and Endocrinology, Faculty of Biology, Medicine, and Health, University of Manchester, Manchester, United Kingdom
| | - Bart Staels
- Université de Lille, U1011-European Genomic Institute for Diabetes, Lille, France
- INSERM, U1011, Lille, France
- Centre Hospitalier Universitaire de Lille, Lille, France
- Institut Pasteur de Lille, Lille, France
| | - Karolien De Bosscher
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- Receptor Research Laboratories, Nuclear Receptor Laboratory, VIB Center for Medical Biotechnology, Ghent, Belgium
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miR-22/KAT6B axis is a chemotherapeutic determiner via regulation of PI3k-Akt-NF-kB pathway in tongue squamous cell carcinoma. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2018; 37:164. [PMID: 30041677 PMCID: PMC6056941 DOI: 10.1186/s13046-018-0834-z] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/07/2018] [Accepted: 06/26/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Tongue squamous cell carcinoma (TSCC) is the most common oral cancer. Neoadjuvant systemic treatment before or after surgery for advanced TSCC is considered one of the most crucial factors in reducing mortality. However, the therapeutic benefits of chemotherapy are usually attenuated due to intrinsic and/or acquired drug resistance, and a large proportion of TSCC are resistant to chemotherapy, which may result in more aggressive tumor behavior and an even worse clinical outcome. Recently, the potential application of using miRNAs to predict therapeutic response to cancer treatment holds high promise, but miRNAs with predictive value remain to be identified and underlying mechanisms remain to be understood in TSCC. METHODS The expression of miR-22 in tissues from patients diagnosed with TSCC was analyzed using real-time PCR. The effects of miR-22 on cell proliferation and tumorigenesis in TSCC cells were analyzed by MTS assay, and flow cytometry. The tumor growth in vivo was observed in xenograft model. Luciferase reporter assay, real-time PCR and western blot were performed to validate a potential target of miR-22 in TC. The correlation between miR-22 expression and KAT6B expression, as well as the mechanisms by which miR-22 regulates PI3k-Akt-NF-kB pathway in TSCC were also addressed. RESULTS We found a strong correlation between miR-22 expression and chemosensitivity to cisplatin (CDDP) in TSCC patients. Ectopic overexpression of miR-22 enhanced TSCC cells apoptosis in response to CDDP in experimental models performed in vitro and in vivo. Moreover, we found that KAT6B is a direct functional target of miR-22. Ectopic expression of KAT6B attenuated the efficiency of miR-22 in TSCC cells upon CDDP treatment. Mechanistically, miR-22 overexpression or KAT6B knockdown inhibited PI3K/Akt/NF-κB signaling in TSCC cells, possibly via downregulating the activators of PI3K/Akt/NF-κB signaling, such as S100A8, PDGF and VEGF. Furthermore, the activation of miR-22 depended on the intensity of the stresses in the presence of p53 activation. CONCLUSIONS Our findings define miR-22 as an intrinsic molecular switch that determines p53-dependent cellular fate through KAT6B/ PI3K-Akt/ NF-kB pathway.
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Functional pharmacogenomics and toxicity of PolyPurine Reverse Hoogsteen hairpins directed against survivin in human cells. Biochem Pharmacol 2018; 155:8-20. [PMID: 29940174 DOI: 10.1016/j.bcp.2018.06.020] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 06/14/2018] [Indexed: 01/27/2023]
Abstract
PolyPurine Reverse Hoogsteen (PPRH) hairpins constitute a relatively new pharmacological agent for gene silencing that has been applied for a growing number of gene targets. Previously we reported that specific PPRHs against the antiapoptotic gene survivin were able to decrease viability of PC3 prostate cancer cells by increasing apoptosis, while not acting on HUVEC non-tumoral cells. These PPRHs were efficient both in vitro and in vivo. In the present work, we performed a functional pharmacogenomics study on the effects of specific and unspecific hairpins against survivin. Incubation of PC3 cells with the specific HpsPr-C-WT led to 244 differentially expressed genes when applying the p < 0.05, FC > 2, Benjamini-Hochberg filtering. Importantly, the unspecific or control Hp-WC did not originate differentially expressed genes using the same settings. Gene Set Enrichment Analysis (GSEA) revealed that the differentially expressed genes clustered very significantly within the gene sets of Regulation of cell proliferation, Cellular response to stress, Apoptosis and Prostate cancer. Network analyses using STRING identified important interacting gene-nodes within the response of PC3 cells to treatment with the PPRH against survivin, mainly POLR2G, PAK1IP1, SMC3, SF3A1, PPARGC1A, NCOA6, UGT2B7, ALG5, VAMP7 and HIST1H2BE, the former six present in the Gene Sets detected in the GSEA. Additionally, HepG2 and 786-O cell lines were used to carry out in vitro experiments of hepatotoxicity and nephrotoxicity, respectively. The unspecific hairpin did not cause toxicity in cell survival assays (MTT) and produced minor changes in gene expression for selected genes in RT-qPCR arrays specifically developed for hepatic and renal toxicity screening.
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Genome-wide DNA methylation profiles altered by Helicobacter pylori in gastric mucosa and blood leukocyte DNA. Oncotarget 2018; 7:37132-37144. [PMID: 27206798 PMCID: PMC5095064 DOI: 10.18632/oncotarget.9469] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Accepted: 04/24/2016] [Indexed: 01/28/2023] Open
Abstract
Purpose To investigate Helicobacter pylori (H.pylori) associated genome-wide aberrant methylation patterns in gastric mucosa and blood leukocyte DNA, a population-based study was conducted in Linqu County. Results A total of 3000 and 386 CpGs were differentially methylated after successful H.pylori eradication in gastric mucosa and blood leukocyte DNA respectively, and 17 were the same alteration trend in the both tissues. The differentially methylated CpGs were located more frequently in promoters or CpG islands for gastric mucosa and gene body or open sea for blood leukocyte DNA. In eradicated gastric mucosa, the hypermethylated CpGs were enriched across inflammatory pathways, while the hypomethylated CpGs in tube morphogenesis, development and so on. The final validation found lower SPI1, PRIC285 and S1PR4 methylation levels in H.pylori positive subjects by case-control comparison, and increased methylation levels in H.pylori eradicated gastric mucosa by self-comparison. The Cancer Genome Atlas (TCGA) database analysis suggested that the up-regulation of the three genes by hypomethylation might be associated with gastric carcinogenesis. Experimental Design Infinium HumanMethylation 450K BeadChip was used to compare methylation profiles prior to and after eradication treatment. The methylation levels of identified candidate differentially methylated genes before and after H.pylori eradication were further validated by two stages (Stage I: self-comparison of 16 subjects before and after anti-H.pylori treatment; Stage II: case-control comparison of 25 H.pylori positive and 25 negative subjects and self-comparison of 50 anti-H.pylori treated subjects). Conclusions Novel H.pylori associated aberrant methylated genes were identified across the whole genome both in gastric mucosa and blood leukocyte DNA.
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Fusco DN, Pratt H, Kandilas S, Cheon SSY, Lin W, Cronkite DA, Basavappa M, Jeffrey KL, Anselmo A, Sadreyev R, Yapp C, Shi X, O'Sullivan JF, Gerszten RE, Tomaru T, Yoshino S, Satoh T, Chung RT. HELZ2 Is an IFN Effector Mediating Suppression of Dengue Virus. Front Microbiol 2017; 8:240. [PMID: 28265266 PMCID: PMC5316548 DOI: 10.3389/fmicb.2017.00240] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Accepted: 02/03/2017] [Indexed: 01/07/2023] Open
Abstract
Flaviviral infections including dengue virus are an increasing clinical problem worldwide. Dengue infection triggers host production of the type 1 IFN, IFN alpha, one of the strongest and broadest acting antivirals known. However, dengue virus subverts host IFN signaling at early steps of IFN signal transduction. This subversion allows unbridled viral replication which subsequently triggers ongoing production of IFN which, again, is subverted. Identification of downstream IFN antiviral effectors will provide targets which could be activated to restore broad acting antiviral activity, stopping the signal to produce endogenous IFN at toxic levels. To this end, we performed a targeted functional genomic screen for IFN antiviral effector genes (IEGs), identifying 56 IEGs required for antiviral effects of IFN against fully infectious dengue virus. Dengue IEGs were enriched for genes encoding nuclear receptor interacting proteins, including HELZ2, MAP2K4, SLC27A2, HSP90AA1, and HSP90AB1. We focused on HELZ2 (Helicase With Zinc Finger 2), an IFN stimulated gene and IEG which encodes a promiscuous nuclear factor coactivator that exists in two isoforms. The two unique HELZ2 isoforms are both IFN responsive, contain ISRE elements, and gene products increase in the nucleus upon IFN stimulation. Chromatin immunoprecipitation-sequencing revealed that the HELZ2 complex interacts with triglyceride-regulator LMF1. Mass spectrometry revealed that HELZ2 knockdown cells are depleted of triglyceride subsets. We thus sought to determine whether HELZ2 interacts with a nuclear receptor known to regulate immune response and lipid metabolism, AHR, and identified HELZ2:AHR interactions via co-immunoprecipitation, found that AHR is a dengue IEG, and that an AHR ligand, FICZ, exhibits anti-dengue activity. Primary bone marrow derived macrophages from HELZ2 knockout mice, compared to wild type controls, exhibit enhanced dengue infectivity. Overall, these findings reveal that IFN antiviral response is mediated by HELZ2 transcriptional upregulation, enrichment of HELZ2 protein levels in the nucleus, and activation of a transcriptional program that appears to modulate intracellular lipid state. IEGs identified in this study may serve as both (1) potential targets for host directed antiviral design, downstream of the common flaviviral subversion point, as well as (2) possible biomarkers, whose variation, natural, or iatrogenic, could affect host response to viral infections.
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Affiliation(s)
- Dahlene N. Fusco
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
- Division of Infectious Diseases, Vaccine and Immunotherapy Center, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
- Laboratory for Systems Pharmacology, Harvard Medical SchoolBoston, MA, USA
| | - Henry Pratt
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Stephen Kandilas
- Division of Infectious Diseases, Vaccine and Immunotherapy Center, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
- Department of Medicine, Athens University Medical SchoolAthens, Greece
| | | | - Wenyu Lin
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - D. Alex Cronkite
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Megha Basavappa
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Kate L. Jeffrey
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Anthony Anselmo
- Department of Molecular Biology, Massachusetts General HospitalBoston, MA, USA
| | - Ruslan Sadreyev
- Department of Molecular Biology, Massachusetts General HospitalBoston, MA, USA
| | - Clarence Yapp
- Laboratory for Systems Pharmacology, Harvard Medical SchoolBoston, MA, USA
| | - Xu Shi
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical CenterBoston, MA, USA
| | - John F. O'Sullivan
- Division of Cardiology, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Robert E. Gerszten
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical CenterBoston, MA, USA
- Division of Cardiology, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
| | - Takuya Tomaru
- Department of Medicine and Molecular Science, Gunma University Graduate School of MedicineMaebashi, Japan
| | - Satoshi Yoshino
- Department of Medicine and Molecular Science, Gunma University Graduate School of MedicineMaebashi, Japan
| | - Tetsurou Satoh
- Department of Medicine and Molecular Science, Gunma University Graduate School of MedicineMaebashi, Japan
| | - Raymond T. Chung
- Gastrointestinal Division, Department of Medicine, Massachusetts General HospitalBoston, MA, USA
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Racimo F, Marnetto D, Huerta-Sánchez E. Signatures of Archaic Adaptive Introgression in Present-Day Human Populations. Mol Biol Evol 2017; 34:296-317. [PMID: 27756828 PMCID: PMC5400396 DOI: 10.1093/molbev/msw216] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
Comparisons of DNA from archaic and modern humans show that these groups interbred, and in some cases received an evolutionary advantage from doing so. This process-adaptive introgression-may lead to a faster rate of adaptation than is predicted from models with mutation and selection alone. Within the last couple of years, a series of studies have identified regions of the genome that are likely examples of adaptive introgression. In many cases, once a region was ascertained as being introgressed, commonly used statistics based on both haplotype as well as allele frequency information were employed to test for positive selection. Introgression by itself, however, changes both the haplotype structure and the distribution of allele frequencies, thus confounding traditional tests for detecting positive selection. Therefore, patterns generated by introgression alone may lead to false inferences of positive selection. Here we explore models involving both introgression and positive selection to investigate the behavior of various statistics under adaptive introgression. In particular, we find that the number and allelic frequencies of sites that are uniquely shared between archaic humans and specific present-day populations are particularly useful for detecting adaptive introgression. We then examine the 1000 Genomes dataset to characterize the landscape of uniquely shared archaic alleles in human populations. Finally, we identify regions that were likely subject to adaptive introgression and discuss some of the most promising candidate genes located in these regions.
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Affiliation(s)
- Fernando Racimo
- Department of Integrative Biology, University of California Berkeley, Berkeley, CA
| | - Davide Marnetto
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Turin, Italy
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Olivares AM, Moreno-Ramos OA, Haider NB. Role of Nuclear Receptors in Central Nervous System Development and Associated Diseases. J Exp Neurosci 2016; 9:93-121. [PMID: 27168725 PMCID: PMC4859451 DOI: 10.4137/jen.s25480] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 01/06/2016] [Accepted: 01/07/2016] [Indexed: 11/13/2022] Open
Abstract
The nuclear hormone receptor (NHR) superfamily is composed of a wide range of receptors involved in a myriad of important biological processes, including development, growth, metabolism, and maintenance. Regulation of such wide variety of functions requires a complex system of gene regulation that includes interaction with transcription factors, chromatin-modifying complex, and the proper recognition of ligands. NHRs are able to coordinate the expression of genes in numerous pathways simultaneously. This review focuses on the role of nuclear receptors in the central nervous system and, in particular, their role in regulating the proper development and function of the brain and the eye. In addition, the review highlights the impact of mutations in NHRs on a spectrum of human diseases from autism to retinal degeneration.
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Affiliation(s)
- Ana Maria Olivares
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
| | - Oscar Andrés Moreno-Ramos
- Departamento de Ciencias Biológicas, Facultad de Ciencias, Universidad de los Andes, Bogotá, Colombia
| | - Neena B Haider
- Department of Ophthalmology, Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, USA
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Li P, Lu G, Wang L, Cui Y, Wu Z, Chen S, Li J, Wen X, Zhang H, Mu S, Zhang F, Li Y. A rare nonsynonymous variant in the lipid metabolic gene HELZ2 related to primary biliary cirrhosis in Chinese Han. Allergy Asthma Clin Immunol 2016; 12:14. [PMID: 27047549 PMCID: PMC4819269 DOI: 10.1186/s13223-016-0120-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2015] [Accepted: 02/17/2016] [Indexed: 02/01/2023] Open
Abstract
Background Several genome-wide association studies of primary biliary cirrhosis (PBC) in European and Japanese origins have shown significant association of dozens of genetic loci contributive to the susceptibility of PBC. Most of the loci were related to immune response pathway. In this study, we tested whether the lipid metabolic gene HELZ2 was associated with the pathogenesis of PBC. Methods In 586 PBC cases (358 in case 1 group and 201 in case 2 group) and 726 healthy controls of Chinese Han, six nonsynonymous SNPs were genotyped by MassArray iPLEX. The same control were used for the two groups of PBC cases. Allele frequencies were calculated by χ2 test based on 2 × 2 contingency tables. All data were analyzed using the PLINK tool set. The odds ratio (OR) and 95 % confidence interval (95 % CI) were calculated, and p values (corrected for multiple testing by Bonferroni adjustment) less than 0.05 were considered statistically significant. Results The A allele of rs79267778 was significantly associated with PBC (ORcombined = 4.204 [1.670–10.582], pcombined = 1.87E−04). It changed the amino acid at position 1904 (NM_001037335) from Threonine (ACG) to Methionine (ATG). This site was highly conserved in mammals and predicted to be POSSIBLY DAMAGING with a score of 0.469 by PolyPhen-2. It’s further predicted that T1904 M could INCREASE the protein stability with a confidence at 25.18 % under the condition of pH 7.0 and 37 °C. Conclusion The result was the first time to show evidence of the lipid metabolic gene HELZ2 related to autoimmune disease, at least in PBC of Chinese Han.
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Affiliation(s)
- Ping Li
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Guanting Lu
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China.,Department of Blood Transfusion, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Li Wang
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Ying Cui
- Department of Blood Transfusion, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Ziyan Wu
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Si Chen
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Jing Li
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Xiaoting Wen
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Haoze Zhang
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Shijie Mu
- Department of Blood Transfusion, Tangdu Hospital, The Fourth Military Medical University, Xi'an, China
| | - Fengchun Zhang
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
| | - Yongzhe Li
- Key Laboratory of Rheumatology and Clinical Immunology, Department of Rheumatology and Clinical Immunology, Peking Union Medical College Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Ministry of Education, Beijing, China
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Youssef J, Badr M. Peroxisome Proliferator-Activated Receptors Features, Functions, and Future. NUCLEAR RECEPTOR RESEARCH 2015. [DOI: 10.11131/2015/101188] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Lee B, Duz MB, Sagong B, Koparir A, Lee KY, Choi JY, Seven M, Yuksel A, Kim UK, Ozen M. Revealing the function of a novel splice-site mutation of CHD7 in CHARGE syndrome. Gene 2015; 576:776-81. [PMID: 26551301 DOI: 10.1016/j.gene.2015.11.006] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 09/24/2015] [Accepted: 11/04/2015] [Indexed: 11/27/2022]
Abstract
Most cases of CHARGE syndrome are sporadic and autosomal dominant. CHD7 is a major causative gene of CHARGE syndrome. In this study, we screened CHD7 in two Turkish patients demonstrating symptoms of CHARGE syndrome such as coloboma, heart defect, choanal atresia, retarded growth, genital abnomalities and ear anomalies. Two mutations of CHD7 were identified including a novel splice-site mutation (c.2443-2A>G) and a previously known frameshift mutation (c.2504_2508delATCTT). We performed exon trapping analysis to determine the effect of the c.2443-2A>G mutation at the transcriptional level, and found that it caused a complete skip of exon 7 and splicing at a cryptic splice acceptor site. Our current study is the second study demonstrating an exon 7 deficit in CHD7. Results of previous studies suggest that the c.2443-2A>G mutation affects the formation of nasal tissues and the neural retina during early development, resulting in choanal atresia and coloboma, respectively. The findings of the present study will improve our understanding of the genetic causes of CHARGE syndrome.
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Affiliation(s)
- Byeonghyeon Lee
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Mehmet Bugrahan Duz
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Borum Sagong
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea
| | - Asuman Koparir
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Kyu-Yup Lee
- Department of Otorhinolaryngology-Head and Neck Surgery, School of Medicine, Kyungpook National University, Daegu, South Korea
| | - Jae Young Choi
- Department of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, South Korea
| | - Mehmet Seven
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey
| | - Adnan Yuksel
- Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey
| | - Un-Kyung Kim
- Department of Biology, College of Natural Sciences, Kyungpook National University, Daegu, South Korea; School of Life Sciences, BK21 Plus KNU Creative BioResearch Group, Kyungpook National University, Daegu, South Korea.
| | - Mustafa Ozen
- Department of Medical Genetics, Istanbul University Cerrahpasa Medical School, Istanbul, Turkey; Department of Medical Genetics, Biruni University Medical School, Istanbul, Turkey; Department of Pathology & Immunology, Baylor College of Medicine, Michael E. DeBakey VAMC, Houston, TX, United States.
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Renauer P, Coit P, Jeffries MA, Merrill JT, McCune WJ, Maksimowicz-McKinnon K, Sawalha AH. DNA methylation patterns in naïve CD4+ T cells identify epigenetic susceptibility loci for malar rash and discoid rash in systemic lupus erythematosus. Lupus Sci Med 2015; 2:e000101. [PMID: 26405558 PMCID: PMC4577980 DOI: 10.1136/lupus-2015-000101] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2015] [Revised: 07/08/2015] [Accepted: 07/24/2015] [Indexed: 11/13/2022]
Abstract
Objective Systemic lupus erythematosus (SLE) is a complex autoimmune disease characterised by heterogeneous clinical manifestations, autoantibody production and epigenetic dysregulation in T cells. We sought to investigate the epigenetic contribution to the development of cutaneous manifestations in SLE. Methods We performed genome-wide DNA methylation analyses in patients with SLE stratified by a history of malar rash, discoid rash or neither cutaneous manifestation, and age, sex and ethnicity matched healthy controls. We characterised differentially methylated regions (DMRs) in naïve CD4+ T cells unique to each disease subset, and assessed functional relationships between DMRs using bioinformatic approaches. Results We identified 36 and 37 unique DMRs that contribute to the epigenetic susceptibility to malar rash and discoid rash, respectively. These DMRs were primarily localised to genes mediating cell proliferation and apoptosis. Hypomethylation of MIR886 and TRIM69, and hypermethylation of RNF39 were specific to patients with SLE with a history of malar rash. Hypomethylation of the cytoskeleton-related gene RHOJ was specific to patients with SLE with a history of discoid rash. In addition, discoid rash-specific hypomethylated DMRs were found in genes involved in antigen-processing and presentation such as TAP1 and PSMB8. Network analyses showed that DMRs in patients with SLE with but not without a history of cutaneous manifestations are associated with TAP-dependent processing and major histocompatibility-class I antigen cross-presentation (p=3.66×10−18 in malar rash, and 3.67×10−13 in discoid rash). Conclusions We characterised DNA methylation changes in naïve CD4+ T cells specific to malar rash and discoid rash in patients with SLE. These data suggest unique epigenetic susceptibility loci that predispose to or are associated with the development of cutaneous manifestations in SLE.
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Affiliation(s)
- Paul Renauer
- Division of Rheumatology, Department of Internal Medicine , University of Michigan , Ann Arbor, Michigan , USA
| | - Patrick Coit
- Division of Rheumatology, Department of Internal Medicine , University of Michigan , Ann Arbor, Michigan , USA
| | - Matlock A Jeffries
- Department of Internal Medicine , University of Oklahoma Health Sciences Center , Oklahoma City, Oklahoma , USA
| | - Joan T Merrill
- Clinical Pharmacology Program , Oklahoma Medical Research Foundation , Oklahoma City, Oklahoma , USA
| | - W Joseph McCune
- Division of Rheumatology, Department of Internal Medicine , University of Michigan , Ann Arbor, Michigan , USA
| | | | - Amr H Sawalha
- Division of Rheumatology, Department of Internal Medicine , University of Michigan , Ann Arbor, Michigan , USA ; Center for Computational Medicine and Bioinformatics, University of Michigan , Ann Arbor, Michigan , USA
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Pawlak M, Lefebvre P, Staels B. Molecular mechanism of PPARα action and its impact on lipid metabolism, inflammation and fibrosis in non-alcoholic fatty liver disease. J Hepatol 2015; 62:720-33. [PMID: 25450203 DOI: 10.1016/j.jhep.2014.10.039] [Citation(s) in RCA: 964] [Impact Index Per Article: 107.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2014] [Revised: 09/22/2014] [Accepted: 10/26/2014] [Indexed: 02/07/2023]
Abstract
Peroxisome proliferator-activated receptor α (PPARα) is a ligand-activated transcription factor belonging, together with PPARγ and PPARβ/δ, to the NR1C nuclear receptor subfamily. Many PPARα target genes are involved in fatty acid metabolism in tissues with high oxidative rates such as muscle, heart and liver. PPARα activation, in combination with PPARβ/δ agonism, improves steatosis, inflammation and fibrosis in pre-clinical models of non-alcoholic fatty liver disease, identifying a new potential therapeutic area. In this review, we discuss the transcriptional activation and repression mechanisms by PPARα, the spectrum of target genes and chromatin-binding maps from recent genome-wide studies, paying particular attention to PPARα-regulation of hepatic fatty acid and plasma lipoprotein metabolism during nutritional transition, and of the inflammatory response. The role of PPARα, together with other PPARs, in non-alcoholic steatohepatitis will be discussed in light of available pre-clinical and clinical data.
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Affiliation(s)
- Michal Pawlak
- European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France; Université Lille 2, F-59000 Lille, France; Inserm UMR 1011, F-59000 Lille, France; Institut Pasteur de Lille, F-59000 Lille, France
| | - Philippe Lefebvre
- European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France; Université Lille 2, F-59000 Lille, France; Inserm UMR 1011, F-59000 Lille, France; Institut Pasteur de Lille, F-59000 Lille, France
| | - Bart Staels
- European Genomic Institute for Diabetes (EGID), FR 3508, F-59000 Lille, France; Université Lille 2, F-59000 Lille, France; Inserm UMR 1011, F-59000 Lille, France; Institut Pasteur de Lille, F-59000 Lille, France.
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Englert NA, Luo G, Goldstein JA, Surapureddi S. Epigenetic modification of histone 3 lysine 27: mediator subunit MED25 is required for the dissociation of polycomb repressive complex 2 from the promoter of cytochrome P450 2C9. J Biol Chem 2014; 290:2264-78. [PMID: 25391650 DOI: 10.1074/jbc.m114.579474] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The Mediator complex is vital for the transcriptional regulation of eukaryotic genes. Mediator binds to nuclear receptors at target response elements and recruits chromatin-modifying enzymes and RNA polymerase II. Here, we examine the involvement of Mediator subunit MED25 in the epigenetic regulation of human cytochrome P450 2C9 (CYP2C9). MED25 is recruited to the CYP2C9 promoter through association with liver-enriched HNF4α, and we show that MED25 influences the H3K27 status of the HNF4α binding region. This region was enriched for the activating marker H3K27ac and histone acetyltransferase CREBBP after MED25 overexpression but was trimethylated when MED25 expression was silenced. The epigenetic regulator Polycomb repressive complex (PRC2), which represses expression by methylating H3K27, plays an important role in target gene regulation. Silencing MED25 correlated with increased association of PRC2 not only with the promoter region chromatin but with HNF4α itself. We confirmed the involvement of MED25 for fully functional preinitiation complex recruitment and transcriptional output in vitro. Formaldehyde-assisted isolation of regulatory elements (FAIRE) revealed chromatin conformation changes that were reliant on MED25, indicating that MED25 induced a permissive chromatin state that reflected increases in CYP2C9 mRNA. For the first time, we showed evidence that a functionally relevant human gene is transcriptionally regulated by HNF4α via MED25 and PRC2. CYP2C9 is important for the metabolism of many exogenous chemicals including pharmaceutical drugs as well as endogenous substrates. Thus, MED25 is important for regulating the epigenetic landscape resulting in transcriptional activation of a highly inducible gene, CYP2C9.
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Affiliation(s)
- Neal A Englert
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - George Luo
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Joyce A Goldstein
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
| | - Sailesh Surapureddi
- From the Laboratory of Toxicology and Pharmacology, NIEHS, National Institutes of Health, Research Triangle Park, North Carolina 27709
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Yoshino S, Satoh T, Yamada M, Hashimoto K, Tomaru T, Katano-Toki A, Kakizaki S, Okada S, Shimizu H, Ozawa A, Tuchiya T, Ikota H, Nakazato Y, Mori M, Matozaki T, Sasaki T, Kitamura T, Mori M. Protection against high-fat diet-induced obesity in Helz2-deficient male mice due to enhanced expression of hepatic leptin receptor. Endocrinology 2014; 155:3459-72. [PMID: 25004093 DOI: 10.1210/en.2013-2160] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Obesity arises from impaired energy balance, which is centrally coordinated by leptin through activation of the long form of leptin receptor (Leprb). Obesity causes central leptin resistance. However, whether enhanced peripheral leptin sensitivity could overcome central leptin resistance remains obscure. A peripheral metabolic organ targeted by leptin is the liver, with low Leprb expression. We here show that mice fed a high-fat diet (HFD) and obese patients with hepatosteatosis exhibit increased expression of hepatic helicase with zinc finger 2, a transcriptional coactivator (Helz2), which functions as a transcriptional coregulator of several nuclear receptors, including peroxisome proliferator-activated receptor γ in vitro. To explore the physiological importance of Helz2, we generated Helz2-deficient mice and analyzed their metabolic phenotypes. Helz2-deficient mice showing hyperleptinemia associated with central leptin resistance were protected against HFD-induced obesity and had significantly up-regulated hepatic Leprb expression. Helz2 deficiency and adenovirus-mediated liver-specific exogenous Leprb overexpression in wild-type mice significantly stimulated hepatic AMP-activated protein kinase on HFD, whereas Helz2-deficient db/db mice lacking functional Leprb did not. Fatty acid-β oxidation was increased in Helz2-deficeint hepatocytes, and Helz2-deficient mice revealed increased oxygen consumption and decreased respiratory quotient in calorimetry analyses. The enhanced hepatic AMP-activated protein kinase energy-sensing pathway in Helz2-deficient mice ameliorated hyperlipidemia, hepatosteatosis, and insulin resistance by reducing lipogenic gene expression and stimulating lipid-burning gene expression in the liver. These findings together demonstrate that Helz2 deficiency ameliorates HFD-induced metabolic abnormalities by stimulating endogenous hepatic Leprb expression, despite central leptin resistance. Hepatic HELZ2 might be a novel target molecule for the treatment of obesity with hepatosteatosis.
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Affiliation(s)
- Satoshi Yoshino
- Departments of Medicine and Molecular Science (S.Y., T.Sat., M.Y., K.H., T.To., A.K.-T., S.K., S.O., H.S., A.O., T.Tu., Ma.Mori) and Human Pathology (H.I., Y.N.), Gunma University Graduate School of Medicine, Maebashi, 371-8511 Japan; Laboratory of Biosignal Sciences (Mu.Mori, T.Ma.) and Metabolic Signal Research Center, Institute for Molecular and Cellular Regulation (T.Sas., T.K.), Gunma University, Maebashi, 371-8512 Japan; and Kitakanto Molecular Novel Research Institute for Obesity and Metabolism (Ma.Mori), Midori, 379-2311 Japan
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Irvin MR, Zhi D, Aslibekyan S, Claas SA, Absher DM, Ordovas JM, Tiwari HK, Watkins S, Arnett DK. Genomics of post-prandial lipidomic phenotypes in the Genetics of Lipid lowering Drugs and Diet Network (GOLDN) study. PLoS One 2014; 9:e99509. [PMID: 24905834 PMCID: PMC4048279 DOI: 10.1371/journal.pone.0099509] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 05/15/2014] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Increased postprandial lipid (PPL) response to dietary fat intake is a heritable risk factor for cardiovascular disease (CVD). Variability in postprandial lipids results from the complex interplay of dietary and genetic factors. We hypothesized that detailed lipid profiles (eg, sterols and fatty acids) may help elucidate specific genetic and dietary pathways contributing to the PPL response. METHODS AND RESULTS We used gas chromatography mass spectrometry to quantify the change in plasma concentration of 35 fatty acids and 11 sterols between fasting and 3.5 hours after the consumption of a high-fat meal (PPL challenge) among 40 participants from the GOLDN study. Correlations between sterols, fatty acids and clinical measures were calculated. Mixed linear regression was used to evaluate associations between lipidomic profiles and genomic markers including single nucleotide polymorphisms (SNPs) and methylation markers derived from the Affymetrix 6.0 array and the Illumina Methyl450 array, respectively. After the PPL challenge, fatty acids increased as well as sterols associated with cholesterol absorption, while sterols associated with cholesterol synthesis decreased. PPL saturated fatty acids strongly correlated with triglycerides, very low-density lipoprotein, and chylomicrons. Two SNPs (rs12247017 and rs12240292) in the sorbin and SH3 domain containing 1 (SORBS1) gene were associated with b-Sitosterol after correction for multiple testing (P≤4.5*10(-10)). SORBS1 has been linked to obesity and insulin signaling. No other markers reached the genome-wide significance threshold, yet several other biologically relevant loci are highlighted (eg, PRIC285, a co-activator of PPARa). CONCLUSIONS Integration of lipidomic and genomic data has the potential to identify new biomarkers of CVD risk.
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Affiliation(s)
- Marguerite R. Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- * E-mail:
| | - Degui Zhi
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Stella Aslibekyan
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Steven A. Claas
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Devin M. Absher
- HudsonAlpha Institute for Biotechnology, Huntsville, Alabama, United States of America
| | - Jose M. Ordovas
- Department of Epidemiology, Atherothrombosis and Imaging, Centro Nacional de Investigaciones Cardiovasculares, Madrid, Spain
- Instituto Madrileño de Estudios Avanzados Alimentacion, Madrid, Spain
- Jean Mayer USDA Human Nutrition Research Center on Aging, Tufts University, Boston, Massachusetts, United States of America
| | - Hemant K. Tiwari
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Steve Watkins
- Metabolon, Lipomics Division, Research Triangle Park, North Carolina, United States of America
| | - Donna K. Arnett
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
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Lien F, Berthier A, Bouchaert E, Gheeraert C, Alexandre J, Porez G, Prawitt J, Dehondt H, Ploton M, Colin S, Lucas A, Patrice A, Pattou F, Diemer H, Van Dorsselaer A, Rachez C, Kamilic J, Groen AK, Staels B, Lefebvre P. Metformin interferes with bile acid homeostasis through AMPK-FXR crosstalk. J Clin Invest 2014; 124:1037-51. [PMID: 24531544 DOI: 10.1172/jci68815] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 12/05/2013] [Indexed: 12/24/2022] Open
Abstract
The nuclear bile acid receptor farnesoid X receptor (FXR) is an important transcriptional regulator of bile acid, lipid, and glucose metabolism. FXR is highly expressed in the liver and intestine and controls the synthesis and enterohepatic circulation of bile acids. However, little is known about FXR-associated proteins that contribute to metabolic regulation. Here, we performed a mass spectrometry-based search for FXR-interacting proteins in human hepatoma cells and identified AMPK as a coregulator of FXR. FXR interacted with the nutrient-sensitive kinase AMPK in the cytoplasm of target cells and was phosphorylated in its hinge domain. In cultured human and murine hepatocytes and enterocytes, pharmacological activation of AMPK inhibited FXR transcriptional activity and prevented FXR coactivator recruitment to promoters of FXR-regulated genes. Furthermore, treatment with AMPK activators, including the antidiabetic biguanide metformin, inhibited FXR agonist induction of FXR target genes in mouse liver and intestine. In a mouse model of intrahepatic cholestasis, metformin treatment induced FXR phosphorylation, perturbed bile acid homeostasis, and worsened liver injury. Together, our data indicate that AMPK directly phosphorylates and regulates FXR transcriptional activity to precipitate liver injury under conditions favoring cholestasis.
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Jia Y, Viswakarma N, Reddy JK. Med1 subunit of the mediator complex in nuclear receptor-regulated energy metabolism, liver regeneration, and hepatocarcinogenesis. Gene Expr 2014; 16:63-75. [PMID: 24801167 PMCID: PMC4093800 DOI: 10.3727/105221614x13919976902219] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Several nuclear receptors regulate diverse metabolic functions that impact on critical biological processes, such as development, differentiation, cellular regeneration, and neoplastic conversion. In the liver, some members of the nuclear receptor family, such as peroxisome proliferator-activated receptors (PPARs), constitutive androstane receptor (CAR), farnesoid X receptor (FXR), liver X receptor (LXR), pregnane X receptor (PXR), glucocorticoid receptor (GR), and others, regulate energy homeostasis, the formation and excretion of bile acids, and detoxification of xenobiotics. Excess energy burning resulting from increases in fatty acid oxidation systems in liver generates reactive oxygen species, and the resulting oxidative damage influences liver regeneration and liver tumor development. These nuclear receptors are important sensors of exogenous activators as well as receptor-specific endogenous ligands. In this regard, gene knockout mouse models revealed that some lipid-metabolizing enzymes generate PPARα-activating ligands, while others such as ACOX1 (fatty acyl-CoA oxidase1) inactivate these endogenous PPARα activators. In the absence of ACOX1, the unmetabolized ACOX1 substrates cause sustained activation of PPARα, and the resulting increase in energy burning leads to hepatocarcinogenesis. Ligand-activated nuclear receptors recruit the multisubunit Mediator complex for RNA polymerase II-dependent gene transcription. Evidence indicates that the Med1 subunit of the Mediator is essential for PPARα, PPARγ, CAR, and GR signaling in liver. Med1 null hepatocytes fail to respond to PPARα activators in that these cells do not show induction of peroxisome proliferation and increases in fatty acid oxidation enzymes. Med1-deficient hepatocytes show no increase in cell proliferation and do not give rise to liver tumors. Identification of nuclear receptor-specific coactivators and Mediator subunits should further our understanding of the complexities of metabolic diseases associated with increased energy combustion in liver.
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Affiliation(s)
- Yuzhi Jia
- *Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Navin Viswakarma
- †Department of Molecular Pharmacology and Therapeutics, Loyola University Chicago, Maywood, IL, USA
| | - Janardan K. Reddy
- *Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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Kuklin A, Tokovenko B, Makogon N, Oczko-Wojciechowska M, Jarząb B, Obolenskaya M. Hepatocytes response to interferon alpha levels recorded after liver resection. J Interferon Cytokine Res 2013; 34:90-9. [PMID: 24107099 DOI: 10.1089/jir.2012.0125] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Extensive damage of liver parenchyma stimulates hepatic cells to transit from quiescence to proliferation with eventual restoration of liver mass and function. Our recent studies have revealed upregulated expression of interferon (IFN)-α and its antiviral activity during the early hours after partial hepatectomy. In this study, we analyzed the response of primary hepatocytes from intact liver to IFN-α mimicking its levels (250 U/mL) during the transition period of liver restoration. The gene expression profile was analyzed with rat genome array 230 2.0 (Affymetrix). After 3- and 6-h treatment we identified respectively 28 and 124 differentially expressed genes responsible for autonomous changes in hepatocytes and those involving non-parenchymal cells in a concerted response to IFN-α. The response has an energy sparing character and affects all levels of gene expression. The factors activating T cells and apoptosis are opposed by those restricting the signal propagation, inhibiting T cells activation, and promoting survival. The partial resemblance between the specific in vitro response to IFN-α and the processes in regenerating liver is discussed. Our study opens the way to a more focused investigation of the liver cell response to quasiphysiological dose of IFN-α.
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Affiliation(s)
- Andrii Kuklin
- 1 Institute of Molecular Biology and Genetics , National Academy of Sciences of Ukraine, Kyiv, Ukraine
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Vamecq J, Cherkaoui-Malki M, Andreoletti P, Latruffe N. The human peroxisome in health and disease: the story of an oddity becoming a vital organelle. Biochimie 2013; 98:4-15. [PMID: 24075875 DOI: 10.1016/j.biochi.2013.09.019] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2013] [Accepted: 09/18/2013] [Indexed: 12/18/2022]
Abstract
Since the first report by Rhodin in 1954, our knowledge on mammalian microbodies/peroxisomes has known several periods. An initial two decades period (1954-1973) has contributed to the biochemical individualisation of peroxisomes as a new class of subcellular organelles (de Duve, 1965). The corresponding research period failed to define a clear role of mammalian peroxisomes in vital functions and intermediary metabolism, explaining why feeling that peroxisomes might be in the human cell oddities has prevailed during several decades. The period standing from 1973 to nowadays has progressively removed this cell oddity view of peroxisomes by highlighting vital function and metabolic role of peroxisomes in health and disease along with genetic and metabolic regulation of peroxisomal protein content, organelle envelope formation and protein signal targeting mechanisms. Research on peroxisomes and their response to various drugs and metabolites, dietary and physiological conditions has also played a key role in the discovery of peroxisome proliferator activated receptors (PPARs) belonging to the nuclear hormone receptor superfamily and for which impact in science and medicine goes now by far beyond that of the peroxisomes.
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Affiliation(s)
- Joseph Vamecq
- INSERM, Laboratory of Biochemistry and Molecular Biology, Hormonology-Metabolism-Nutrition-Oncology, Centre of Biology and Pathology (CBP), CHU Lille, France.
| | - Mustapha Cherkaoui-Malki
- Laboratory of Biochemistry of Peroxisome, Inflammation & Lipids Metabolism (BioPeroxIL-EA7270), University of Burgundy, 21000 Dijon, France
| | - Pierre Andreoletti
- Laboratory of Biochemistry of Peroxisome, Inflammation & Lipids Metabolism (BioPeroxIL-EA7270), University of Burgundy, 21000 Dijon, France
| | - Norbert Latruffe
- Laboratory of Biochemistry of Peroxisome, Inflammation & Lipids Metabolism (BioPeroxIL-EA7270), University of Burgundy, 21000 Dijon, France
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Worsham MJ, Chen KM, Ghanem T, Stephen JK, Divine G. Epigenetic modulation of signal transduction pathways in HPV-associated HNSCC. Otolaryngol Head Neck Surg 2013; 149:409-16. [PMID: 23736812 DOI: 10.1177/0194599813490895] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
OBJECTIVE Human papilloma virus (HPV) positive and HPV negative head and neck squamous cell cancer (HNSCC) are biologically distinct with a prognostic advantage for HPV positive patients compared to HPV negative cases. DNA promoter methylation is central to human diseases such as cancer, including HNSCC, with reported genome-wide hypomethylaton and promoter hypermethylation in HPV positive HNSCC tumors. The goal of this study was to identify differentially methylated genes in HPV positive versus HPV negative primary HNSCC genomes with clues to signaling networks. STUDY DESIGN Laboratory-based study. SETTING Primary care academic health care system. SUBJECTS AND METHODS DNA from 4 HPV positive and 4 HPV negative freshly frozen primary HNSCC were subject to comprehensive genome-wide methylation profiling. Differentially methylated gene lists were examined using the Signal Transduction Pathways (canonical) filter in the Genomatix Pathway System (GePS). RESULTS Twofold methylation differences were observed between HPV positive and HPV negative cases for 1168 genes. Pathway analysis applied to investigate the biological role of the 1168 differentially methylated genes revealed 8 signal transduction pathways forming a network of 66 genes, of which 62% are hypermethylated. CONCLUSION Our study reveals a predominant hypermethylation profile for genes in signal transduction pathways of HPV positive HNSCC tumor genomes. Because signaling events in the cell play a critical role in the execution of key biological functions, insights into how complex cellular signaling cascades and networks may be programmed in HNSCC are likely to be critical in the development of new biological agents designed to hit multiple targets.
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Affiliation(s)
- Maria J Worsham
- Department of Otolaryngology/Head and Neck Research, Henry Ford Hospital, Detroit, Michigan 48202, USA.
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Fusco DN, Brisac C, John SP, Huang YW, Chin CR, Xie T, Zhao H, Zhang L, Chevalier S, Wambua D, Lin W, Peng L, Chung RT, Brass AL. A genetic screen identifies interferon-α effector genes required to suppress hepatitis C virus replication. Gastroenterology 2013; 144:1438-49, 1449.e1-9. [PMID: 23462180 PMCID: PMC3665646 DOI: 10.1053/j.gastro.2013.02.026] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2012] [Revised: 01/15/2013] [Accepted: 02/12/2013] [Indexed: 01/26/2023]
Abstract
BACKGROUND & AIMS Hepatitis C virus (HCV) infection is a leading cause of end-stage liver disease. Interferon-α (IFNα) is an important component of anti-HCV therapy; it up-regulates transcription of IFN-stimulated genes, many of which have been investigated for their antiviral effects. However, all of the genes required for the antiviral function of IFNα (IFN effector genes [IEGs]) are not known. IEGs include not only IFN-stimulated genes, but other nontranscriptionally induced genes that are required for the antiviral effect of IFNα. In contrast to candidate approaches based on analyses of messenger RNA (mRNA) expression, identification of IEGs requires a broad functional approach. METHODS We performed an unbiased genome-wide small interfering RNA screen to identify IEGs that inhibit HCV. Huh7.5.1 hepatoma cells were transfected with small interfering RNAs incubated with IFNα and then infected with JFH1 HCV. Cells were stained using HCV core antibody, imaged, and analyzed to determine the percent infection. Candidate IEGs detected in the screen were validated and analyzed further. RESULTS The screen identified 120 previously unreported IEGs. From these, we more fully evaluated the following: asparagine-linked glycosylation 10 homolog (yeast, α-1,2-glucosyltransferase); butyrylcholinesterase; dipeptidyl-peptidase 4 (CD26, adenosine deaminase complexing protein 2); glucokinase (hexokinase 4) regulator; guanylate cyclase 1, soluble, β 3; MYST histone acetyltransferase 1; protein phosphatase 3 (formerly 2B), catalytic subunit, β isoform; peroxisomal proliferator-activated receptor-γ-DBD-interacting protein 1; and solute carrier family 27 (fatty acid transporter), member 2; and demonstrated that they enabled IFNα-mediated suppression of HCV at multiple steps of its life cycle. Expression of these genes had more potent effects against flaviviridae because a subset was required for IFNα to suppress dengue virus but not influenza A virus. In addition, many of the host genes detected in this screen (92%) were not transcriptionally stimulated by IFNα; these genes represent a heretofore unknown class of non-IFN-stimulated gene IEGs. CONCLUSIONS We performed a whole-genome loss-of-function screen to identify genes that mediate the effects of IFNα against human pathogenic viruses. We found that IFNα restricts HCV via actions of general and specific IEGs.
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Affiliation(s)
- Dahlene N. Fusco
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Cynthia Brisac
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Sinu P. John
- Laboratory of Systems Biology, NIAID/NIH, Bethesda, MD
| | - Yi-Wen Huang
- Department of Internal Medicine, National Taiwan University College of, Medicine and Hospital, Liver Center, Cathay General Hospital Medical Center &, School of Medicine, Taipei Medical University, No. 280, Sec. 4, Jen-Ai Road, Taipei-10630, Taiwan
| | - Christopher R. Chin
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester MA 01605
| | - Tiao Xie
- Harvard Medical School Image and Data Analysis Core, 240 Longwood Avenue, Boston, MA 02115
| | - Hong Zhao
- Department of Infectious Diseases, Peking University First Hospital, Beijing, China, 100034
| | - Leiliang Zhang
- MOH Key Laboratory of Systems Biology of Pathogens; Institute of Pathogen Biology; Chinese Academy of Medical Sciences & Peking Union Medical College; Beijing, China
| | - Stephane Chevalier
- Hospital University Henri Mondor, Department of Virology, Université Paris-Est, Créteil, France, Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Daniel Wambua
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Wenyu Lin
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Lee Peng
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Raymond T. Chung
- Gastrointestinal Unit, Massachusetts General Hospital, 55 Fruit Street Boston MA 02114
| | - Abraham L. Brass
- Ragon Institute, 149 13th Street Charlestown, MA 02129, Current Address: Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, 55 Lake Avenue North, Worcester MA 01605
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Katano-Toki A, Satoh T, Tomaru T, Yoshino S, Ishizuka T, Ishii S, Ozawa A, Shibusawa N, Tsuchiya T, Saito T, Shimizu H, Hashimoto K, Okada S, Yamada M, Mori M. THRAP3 interacts with HELZ2 and plays a novel role in adipocyte differentiation. Mol Endocrinol 2013; 27:769-80. [PMID: 23525231 DOI: 10.1210/me.2012-1332] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Using yeast two-hybrid screen, we previously isolated HELZ2 (helicase with zinc finger 2, transcriptional coactivator) that functions as a coregulator of peroxisome proliferator-activated receptorγ (PPARγ). To further delineate its molecular function, we here identified thyroid hormone receptor-associated protein3 (THRAP3), a putative component of the Mediator complex, as a protein stably associating with HELZ2 using immunoprecipitation coupled with mass spectrometry analyses. In immunoprecipitation assays, Thrap3 could associate with endogenous Helz2 as well as Pparg in differentiated 3T3-L1 cells. HELZ2 interacts with the serine/arginine-rich domain and Bcl2 associated transcription factor1-homologous region in THRAP3, whereas THRAP3 directly binds 2 helicase motifs in HELZ2. HELZ2 and THRAP3 synergistically augment transcriptional activation mediated by PPARγ, whereas knockdown of endogenous THRAP3 abolished the enhancement by HELZ2 in reporter assays. Thrap3, similar to Helz2, is evenly expressed in the process of adipogenic differentiation in 3T3-L1 cells. Knockdown of Thrap3 in 3T3-L1 preadipocytes using short-interfering RNA did not influence the expression of Krox20, Klf5, Cebpb, or Cebpd during early stages of adipocyte differentiation, but significantly attenuated the expression of Pparg, Cebpa, and Fabp4/aP2 and accumulation of lipid droplets. Pharmacologic activation of Pparg by troglitazone could not fully restore the differentiation of Thrap3-knockdown adipocytes. In chromatin immunoprecipitation assays, endogenous Helz2 and Thrap3 could be co-recruited, in a ligand-dependent manner, to the PPARγ-response elements in Fabp4/aP2 and Adipoq gene enhancers in differentiated 3T3-L1 cells. These findings collectively suggest that Thrap3 could play indispensable roles in terminal differentiation of adipocytes by enhancing PPARγ-mediated gene activation cooperatively with Helz2.
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Affiliation(s)
- Akiko Katano-Toki
- Department of Medicine and Molecular Science, Gunma University Graduate School of Medicine, Maebashi, Japan
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Jia Y, Viswakarma N, Crawford SE, Sarkar J, Sambasiva Rao M, Karpus WJ, Kanwar YS, Zhu YJ, Reddy JK. Early embryonic lethality of mice with disrupted transcription cofactor PIMT/NCOA6IP/Tgs1 gene. Mech Dev 2012; 129:193-207. [PMID: 22982455 DOI: 10.1016/j.mod.2012.08.002] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2012] [Revised: 08/09/2012] [Accepted: 08/27/2012] [Indexed: 11/29/2022]
Abstract
PIMT (also known as PIPMT/NCOA6IP/Tgs1), first isolated as a transcription coactivator PRIP (NCOA6)-interacting 96-kDa protein with RNA-binding property, possesses RNA methyltransferase activity. As a transcription coactivator binding protein, PIMT enhances the nuclear receptor transcriptional activity and its methyltransferase property is involved in the formation of the 2,2,7-trimethylguanosine cap of non-coding small RNAs, but the in vivo functions of this gene have not been fully explored. To elucidate the biological functions, we used gene targeting to generate mice with a disrupted PIMT/Tgs1 gene. Disruption of PIMT gene results in early embryonic lethality due to impairment of development around the blastocyst and uterine implantation stages. We show that PIMT is expressed in all cells of the E3.5day blastocyst in the mouse. PIMT null mutation abolished PIMT expression in all cells of the blastocyst and caused a reduction in the expression of Oct4 and Nanog transcription factor proteins in the E3.5 blastocyst resulting in the near failure to form inner cell mass (ICM). With conditional deletion of PIMT gene, mouse embryonic fibroblasts (MEFs) exhibit defective wound healing in the scratch assay and a reduction in cell proliferation due to decreased G₀/G₁ transition and G₂/M phase cell cycle arrest. We conclude that PIMT/NCOA6IP, which is expressed in all cells of the 3.5 day stage blastocyst, is indispensable for early embryonic development.
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Affiliation(s)
- Yuzhi Jia
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611-3008, USA
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Campeau PM, Lu JT, Dawson BC, Fokkema IFAC, Robertson SP, Gibbs RA, Lee BH. The KAT6B-related disorders genitopatellar syndrome and Ohdo/SBBYS syndrome have distinct clinical features reflecting distinct molecular mechanisms. Hum Mutat 2012; 33:1520-5. [PMID: 22715153 DOI: 10.1002/humu.22141] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2012] [Accepted: 06/03/2012] [Indexed: 01/29/2023]
Abstract
Genitopatellar syndrome (GPS) and Say-Barber-Biesecker-Young-Simpson syndrome (SBBYSS or Ohdo syndrome) have both recently been shown to be caused by distinct mutations in the histone acetyltransferase KAT6B (a.k.a. MYST4/MORF). All variants are de novo dominant mutations that lead to protein truncation. Mutations leading to GPS occur in the proximal portion of the last exon and lead to the expression of a protein without a C-terminal domain. Mutations leading to SBBYSS occur either throughout the gene, leading to nonsense-mediated decay, or more distally in the last exon. Features present only in GPS are contractures, anomalies of the spine, ribs and pelvis, renal cysts, hydronephrosis, and agenesis of the corpus callosum. Features present only in SBBYSS include long thumbs and long great toes and lacrimal duct abnormalities. Several features occur in both, such as intellectual disability, congenital heart defects, and genital and patellar anomalies. We propose that haploinsufficiency or loss of a function mediated by the C-terminal domain causes the common features, whereas gain-of-function activities would explain the features unique to GPS. Further molecular studies and the compilation of mutations in a database for genotype-phenotype correlations (www.LOVD.nl/KAT6B) might help tease out answers to these questions and understand the developmental programs dysregulated by the different truncations.
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Affiliation(s)
- Philippe M Campeau
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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Campeau PM, Kim JC, Lu JT, Schwartzentruber JA, Abdul-Rahman OA, Schlaubitz S, Murdock DM, Jiang MM, Lammer EJ, Enns GM, Rhead WJ, Rowland J, Robertson SP, Cormier-Daire V, Bainbridge MN, Yang XJ, Gingras MC, Gibbs RA, Rosenblatt DS, Majewski J, Lee BH. Mutations in KAT6B, encoding a histone acetyltransferase, cause Genitopatellar syndrome. Am J Hum Genet 2012; 90:282-9. [PMID: 22265014 DOI: 10.1016/j.ajhg.2011.11.023] [Citation(s) in RCA: 97] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2011] [Revised: 11/14/2011] [Accepted: 11/22/2011] [Indexed: 01/15/2023] Open
Abstract
Genitopatellar syndrome (GPS) is a skeletal dysplasia with cerebral and genital anomalies for which the molecular basis has not yet been determined. By exome sequencing, we found de novo heterozygous truncating mutations in KAT6B (lysine acetyltransferase 6B, formerly known as MYST4 and MORF) in three subjects; then by Sanger sequencing of KAT6B, we found similar mutations in three additional subjects. The mutant transcripts do not undergo nonsense-mediated decay in cells from subjects with GPS. In addition, human pathological analyses and mouse expression studies point to systemic roles of KAT6B in controlling organismal growth and development. Myst4 (the mouse orthologous gene) is expressed in mouse tissues corresponding to those affected by GPS. Phenotypic differences and similarities between GPS, the Say-Barber-Biesecker variant of Ohdo syndrome (caused by different mutations of KAT6B), and Rubinstein-Taybi syndrome (caused by mutations in other histone acetyltransferases) are discussed. Together, the data support an epigenetic dysregulation of the limb, brain, and genital developmental programs.
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Affiliation(s)
- Philippe M Campeau
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
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Peroxisome Proliferator-Activated Receptor Delta: A Conserved Director of Lipid Homeostasis through Regulation of the Oxidative Capacity of Muscle. PPAR Res 2011; 2008:172676. [PMID: 18815630 PMCID: PMC2547483 DOI: 10.1155/2008/172676] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2008] [Revised: 07/10/2008] [Accepted: 08/13/2008] [Indexed: 12/13/2022] Open
Abstract
The peroxisome proliferator-activated receptors (PPARs), which are ligand-inducible transcription factors expressed in a variety of tissues, have been shown to perform key roles in lipid homeostasis. In physiological situations such as fasting and physical exercise, one PPAR subtype, PPARδ, triggers a transcriptional program in skeletal muscle leading to a switch in fuel usage from glucose/fatty acids to solely fatty acids, thereby drastically increasing its oxidative capacity. The metabolic action of PPARδ has also been verified in humans. In addition, it has become clear that the action of PPARδ is not restricted to skeletal muscle. Indeed, PPARδ has been shown to play a crucial role in whole-body lipid homeostasis as well as in insulin sensitivity, and it is active not only in skeletal muscle (as an activator of fat burning) but also in the liver (where it can activate glycolysis/lipogenesis, with the produced fat being oxidized in muscle) and in the adipose tissue (by incrementing lipolysis). The main aim of this review is to highlight the central role for activated PPARδ in the reversal of any tendency toward the development of insulin resistance.
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Powell E, Kuhn P, Xu W. Nuclear Receptor Cofactors in PPARgamma-Mediated Adipogenesis and Adipocyte Energy Metabolism. PPAR Res 2011; 2007:53843. [PMID: 17389765 PMCID: PMC1783724 DOI: 10.1155/2007/53843] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2006] [Revised: 10/17/2006] [Accepted: 10/17/2006] [Indexed: 01/18/2023] Open
Abstract
Transcriptional cofactors are integral to the proper function and regulation of nuclear receptors. Members of the peroxisome proliferator-activated receptor (PPAR) family of nuclear receptors are involved in the regulation of lipid and carbohydrate metabolism. They modulate gene transcription in response to a wide variety of ligands, a process that is mediated by transcriptional coactivators and corepressors. The mechanisms by which these cofactors mediate transcriptional regulation of nuclear receptor function are still being elucidated. The rapidly increasing array of cofactors has brought into focus the need for a clear understanding of how these cofactors interact in ligand- and cell-specific manners. This review highlights the differential effects of the assorted cofactors regulating the transcriptional action of PPARγ and summarizes the recent advances in understanding the physiological functions of corepressors and coactivators.
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Affiliation(s)
- Emily Powell
- McArdle Laboratory for Cancer Research, University of Wisconsin, 1400 University Avenue, Madison, WI 53706, USA
| | - Peter Kuhn
- McArdle Laboratory for Cancer Research, University of Wisconsin, 1400 University Avenue, Madison, WI 53706, USA
| | - Wei Xu
- McArdle Laboratory for Cancer Research, University of Wisconsin, 1400 University Avenue, Madison, WI 53706, USA
- *Wei Xu:
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Gaudel C, Grimaldi PA. Metabolic Functions of Peroxisome Proliferator-Activated Receptor beta/delta in Skeletal Muscle. PPAR Res 2011; 2007:86394. [PMID: 17389772 PMCID: PMC1783743 DOI: 10.1155/2007/86394] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2006] [Revised: 11/16/2006] [Accepted: 11/21/2006] [Indexed: 12/31/2022] Open
Abstract
Peroxisome proliferator-activated receptors (PPARs) are transcription factors that act as lipid sensors and adapt the metabolic rates of various tissues to the concentration of dietary lipids. PPARs are pharmacological targets for the treatment of metabolic disorders. PPARα and PPARγ are activated by hypolipidemic and insulin-sensitizer compounds, such as fibrates and thiazolidinediones. The roles of PPARβ/δ in metabolic regulations remained unclear until recently. Treatment of obese monkeys and rodents by specific PPARβ/δ agonists promoted normalization of metabolic parameters and reduction of adiposity. Recent evidences strongly suggested that some of these beneficial actions are related to activation of fatty acid catabolism in skeletal muscle and also that PPARβ/δ is involved in the adaptive responses of skeletal muscle to environmental changes, such as long-term fasting or physical exercise, by controlling the number of oxidative myofibers. These observations indicated that PPARβ/δ agonists might have therapeutic usefulness in metabolic syndrome by increasing fatty acid consumption in skeletal muscle and reducing obesity.
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Affiliation(s)
- Céline Gaudel
- INSERM U636, Centre de Biochimie, UFR Sciences, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice, France
| | - Paul A. Grimaldi
- INSERM U636, Centre de Biochimie, UFR Sciences, Université de Nice Sophia Antipolis, Parc Valrose, 06108 Nice, France
- *Paul A. Grimaldi:
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Bai L, Jia Y, Viswakarma N, Huang J, Vluggens A, Wolins NE, Jafari N, Rao MS, Borensztajn J, Yang G, Reddy JK. Transcription coactivator mediator subunit MED1 is required for the development of fatty liver in the mouse. Hepatology 2011; 53:1164-74. [PMID: 21480322 PMCID: PMC3076129 DOI: 10.1002/hep.24155] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
UNLABELLED Peroxisome proliferator-activated receptor-γ (PPARγ), a nuclear receptor, when overexpressed in liver stimulates the induction of adipocyte-specific and lipogenesis-related genes and causes hepatic steatosis. We report here that Mediator 1 (MED1; also known as PBP or TRAP220), a key subunit of the Mediator complex, is required for high-fat diet-induced hepatic steatosis as well as PPARγ-stimulated adipogenic hepatic steatosis. Mediator forms the bridge between transcriptional activators and RNA polymerase II. MED1 interacts with nuclear receptors such as PPARγ and other transcriptional activators. Liver-specific MED1 knockout (MED1(ΔLiv) ) mice, when fed a high-fat (60% kcal fat) diet for up to 4 months failed to develop fatty liver. Similarly, MED1(ΔLiv) mice injected with adenovirus-PPARγ (Ad/PPARγ) by tail vein also did not develop fatty liver, whereas mice with MED1 (MED1(fl/fl) ) fed a high-fat diet or injected with Ad/PPARγ developed severe hepatic steatosis. Gene expression profiling and northern blot analyses of Ad/PPARγ-injected mouse livers showed impaired induction in MED1(ΔLiv) mouse liver of adipogenic markers, such as aP2, adipsin, adiponectin, and lipid droplet-associated genes, including caveolin-1, CideA, S3-12, and others. These adipocyte-specific and lipogenesis-related genes are strongly induced in MED1(fl/fl) mouse liver in response to Ad/PPARγ. Re-expression of MED1 using adenovirally-driven MED1 (Ad/MED1) in MED1(ΔLiv) mouse liver restored PPARγ-stimulated hepatic adipogenic response. These studies also demonstrate that disruption of genes encoding other coactivators such as SRC-1, PRIC285, PRIP, and PIMT had no effect on hepatic adipogenesis induced by PPARγ overexpression. CONCLUSION We conclude that transcription coactivator MED1 is required for high-fat diet-induced and PPARγ-stimulated fatty liver development, which suggests that MED1 may be considered a potential therapeutic target for hepatic steatosis. (HEPATOLOGY 2011;).
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Affiliation(s)
- Liang Bai
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
,Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Shaanxi 712100, China
| | - Yuzhi Jia
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Navin Viswakarma
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jiansheng Huang
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Aurore Vluggens
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Nathan E. Wolins
- Center for Human Nutrition, Department of Medicine, Washington University School of Medicine, St. Louis, MO 63110
| | - Nadereh Jafari
- Genomics Core Facility Center for Genetic Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - M. Sambasiva Rao
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Jayme Borensztajn
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
| | - Gongshe Yang
- Laboratory of Animal Fat Deposition and Muscle Development, College of Animal Science and Technology, Northwest A & F University, Shaanxi 712100, China
| | - Janardan K. Reddy
- Department of Pathology, Feinberg School of Medicine, Northwestern University, Chicago, IL 60611, USA
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PRIC295, a Nuclear Receptor Coactivator, Identified from PPARα-Interacting Cofactor Complex. PPAR Res 2010; 2010. [PMID: 20885938 PMCID: PMC2946606 DOI: 10.1155/2010/173907] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2010] [Accepted: 07/22/2010] [Indexed: 01/22/2023] Open
Abstract
The peroxisome proliferator-activated receptor-α (PPARα) plays a key role in lipid metabolism and energy combustion. Chronic activation of PPARα in rodents leads to the development of hepatocellular carcinomas. The ability of PPARα to induce expression of its target genes depends on Mediator, an evolutionarily conserved complex of cofactors and, in particular, the subunit 1 (Med1) of this complex. Here, we report the identification and characterization of PPARα-interacting cofactor (PRIC)-295 (PRIC295), a novel coactivator protein, and show that it interacts with the Med1 and Med24 subunits of the Mediator complex. PRIC295 contains 10 LXXLL signature motifs that facilitate nuclear receptor binding and interacts with PPARα and five other members of the nuclear receptor superfamily in a ligand-dependent manner. PRIC295 enhances the transactivation function of PPARα, PPARγ, and ERα. These data demonstrate that PRIC295 interacts with nuclear receptors such as PPARα and functions as a transcription coactivator under in vitro conditions and may play an important role in mediating the effects in vivo as a member of the PRIC complex with Med1 and Med24.
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50
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Molecular Mechanisms and Genome-Wide Aspects of PPAR Subtype Specific Transactivation. PPAR Res 2010; 2010. [PMID: 20862367 PMCID: PMC2938449 DOI: 10.1155/2010/169506] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2010] [Accepted: 06/27/2010] [Indexed: 12/13/2022] Open
Abstract
The peroxisome proliferator-activated receptors (PPARs) are central regulators of fat metabolism, energy homeostasis, proliferation, and inflammation. The three PPAR subtypes, PPARα, β/δ, and γ activate overlapping but also very different target gene programs. This review summarizes the insights into PPAR subtype-specific transactivation provided by genome-wide studies and discusses the recent advances in the understanding of the molecular mechanisms underlying PPAR subtype specificity with special focus on the regulatory role of AF-1.
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