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Besli N, Ercin N, Carmena-Bargueño M, Sarikamis B, Kalkan Cakmak R, Yenmis G, Pérez-Sánchez H, Beker M, Kilic U. Research into how carvacrol and metformin affect several human proteins in a hyperglycemic condition: A comparative study in silico and in vitro. Arch Biochem Biophys 2024; 758:110062. [PMID: 38880320 DOI: 10.1016/j.abb.2024.110062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2024] [Revised: 04/30/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Carvacrol (CV) is an organic compound found in the essential oils of many aromatic herbs. It is nearly unfeasible to analyze all the current human proteins for a query ligand using in vitro and in vivo methods. This study aimed to clarify whether CV possesses an anti-diabetic feature via Docking-based inverse docking and molecular dynamic (MD) simulation and in vitro characterization against a set of novel human protein targets. Herein, the best poses of CV docking simulations according to binding energy ranged from -7.9 to -3.5 (kcal/mol). After pathway analysis of the protein list through GeneMANIA and WebGestalt, eight interacting proteins (DPP4, FBP1, GCK, HSD11β1, INSR, PYGL, PPARA, and PPARG) with CV were determined, and these proteins exhibited stable structures during the MD process with CV. In vitro application, statistically significant results were achieved only in combined doses with CV or metformin. Considering all these findings, PPARG and INSR, among these target proteins of CV, are FDA-approved targets for treating diabetes. Therefore, CV may be on its way to becoming a promising therapeutic compound for treating Diabetes Mellitus (DM). Our outcomes expose formerly unexplored potential target human proteins, whose association with diabetic disorders might guide new potential treatments for DM.
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Affiliation(s)
- Nail Besli
- Department of Medical Biology, Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey.
| | - Nilufer Ercin
- Department of Medical Biology, Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey.
| | - Miguel Carmena-Bargueño
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Guadalupe, Spain.
| | - Bahar Sarikamis
- Department of Medical Biology, Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey.
| | - Rabia Kalkan Cakmak
- Department of Medical Biology, Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey; Department of Medical Biology, Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey.
| | - Guven Yenmis
- Department of Medical Biology, Faculty of Medicine, Biruni University, Istanbul, Turkey.
| | - Horacio Pérez-Sánchez
- Structural Bioinformatics and High Performance Computing Research Group (BIO-HPC), Computer Engineering Department, UCAM Universidad Católica de Murcia, Guadalupe, Spain.
| | - Merve Beker
- Department of Medical Biology, International School of Medicine, University of Health Sciences, Istanbul, Turkey.
| | - Ulkan Kilic
- Department of Medical Biology, Hamidiye School of Medicine, University of Health Sciences, Istanbul, Turkey; Department of Medical Biology, Institute of Health Sciences, University of Health Sciences, Istanbul, Turkey.
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Kumar KK, Aburawi EH, Ljubisavljevic M, Leow MKS, Feng X, Ansari SA, Emerald BS. Exploring histone deacetylases in type 2 diabetes mellitus: pathophysiological insights and therapeutic avenues. Clin Epigenetics 2024; 16:78. [PMID: 38862980 PMCID: PMC11167878 DOI: 10.1186/s13148-024-01692-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Accepted: 06/04/2024] [Indexed: 06/13/2024] Open
Abstract
Diabetes mellitus is a chronic disease that impairs metabolism, and its prevalence has reached an epidemic proportion globally. Most people affected are with type 2 diabetes mellitus (T2DM), which is caused by a decline in the numbers or functioning of pancreatic endocrine islet cells, specifically the β-cells that release insulin in sufficient quantity to overcome any insulin resistance of the metabolic tissues. Genetic and epigenetic factors have been implicated as the main contributors to the T2DM. Epigenetic modifiers, histone deacetylases (HDACs), are enzymes that remove acetyl groups from histones and play an important role in a variety of molecular processes, including pancreatic cell destiny, insulin release, insulin production, insulin signalling, and glucose metabolism. HDACs also govern other regulatory processes related to diabetes, such as oxidative stress, inflammation, apoptosis, and fibrosis, revealed by network and functional analysis. This review explains the current understanding of the function of HDACs in diabetic pathophysiology, the inhibitory role of various HDAC inhibitors (HDACi), and their functional importance as biomarkers and possible therapeutic targets for T2DM. While their role in T2DM is still emerging, a better understanding of the role of HDACi may be relevant in improving insulin sensitivity, protecting β-cells and reducing T2DM-associated complications, among others.
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Affiliation(s)
- Kukkala Kiran Kumar
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 15551, Al Ain, Abu Dhabi, United Arab Emirates
| | - Elhadi Husein Aburawi
- Department of Pediatrics, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
| | - Milos Ljubisavljevic
- Department of Physiology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Program, Singapore, Singapore
| | - Melvin Khee Shing Leow
- LKC School of Medicine, Nanyang Technological University, Singapore, Singapore
- Dept of Endocrinology, Tan Tock Seng Hospital, Singapore, Singapore
- Duke-NUS Medical School, Cardiovascular and Metabolic Disorders Program, Singapore, Singapore
| | - Xu Feng
- Department of Biochemistry, YLL School of Medicine, National University of Singapore, Singapore, Singapore
| | - Suraiya Anjum Ansari
- Department of Biochemistry, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, Abu Dhabi, United Arab Emirates
- Zayed Center for Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates
- ASPIRE Precision Medicine Research Institute, Abu Dhabi, United Arab Emirates
| | - Bright Starling Emerald
- Department of Anatomy, College of Medicine and Health Sciences, United Arab Emirates University, PO Box 15551, Al Ain, Abu Dhabi, United Arab Emirates.
- Zayed Center for Health Sciences, United Arab Emirates University, Abu Dhabi, United Arab Emirates.
- ASPIRE Precision Medicine Research Institute, Abu Dhabi, United Arab Emirates.
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3
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Kabaliei A, Palchyk V, Izmailova O, Shynkevych V, Shlykova O, Kaidashev I. Long-Term Administration of Omeprazole-Induced Hypergastrinemia and Changed Glucose Homeostasis and Expression of Metabolism-Related Genes. BIOMED RESEARCH INTERNATIONAL 2024; 2024:7747599. [PMID: 38884019 PMCID: PMC11178409 DOI: 10.1155/2024/7747599] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 04/23/2024] [Accepted: 05/10/2024] [Indexed: 06/18/2024]
Abstract
Introduction PPIs, or proton pump inhibitors, are the most widely prescribed drugs. There is a debate regarding the relationship between long-term PPI use and the risk of type 2 diabetes mellitus (T2DM). A potential connection between T2DM and PPIs could be an elevated gastrin concentration. This study is aimed at investigating the long-term effects of PPI omeprazole (OZ) on glucose homeostasis and pancreatic gene expression profile in mice. Methods Healthy adult male BALB/c mice were randomly divided into three equal groups (n = 10 in each one): (1) experimental mice that received OZ 20 mg/kg; (2) control mice that received 30 μl saline per os; (3) intact mice without any interventions. Mice were treated for 30 weeks. Glucose homeostasis was investigated by fasting blood glucose level, oral glucose tolerance test (GTT), insulin tolerance test (ITT), and basal insulin resistance (HOMA-IR). Serum gastrin and insulin concentration were determined by ELISA. Expressions of Sirt1, Pparg, Nfκb1 (p105), Nfe2l2, Cxcl5, Smad3, H2a.z, and H3f3b were measured by RT-PCR. Result The ROC analysis revealed an increase in fasting blood glucose levels in OZ-treated mice in comparison with control and intact groups during the 30-week experiment. A slight but statistically significant increase in glucose tolerance and insulin sensitivity was observed in OZ-treated mice within 30 weeks of the experiment. The mice treated with OZ exhibited significant increases in serum insulin and gastrin levels, accompanied by a rise in the HOMA-IR level. These animals had a statistically significant increase in Sirt1, Pparg, and Cxcl5 mRNA expression. There were no differences in β-cell numbers between groups. Conclusion Long-term OZ treatment induced hypergastrin- and hyperinsulinemia and increased expression of Sirt1, Pparg, and Cxcl5 in mouse pancreatic tissues accompanied by specific changes in glucose metabolism. The mechanism of omeprazole-induced Cxcl5 mRNA expression and its association with pancreatic cancer risk should be investigated.
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4
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Ageeli Hakami M. Diabetes and diabetic associative diseases: An overview of epigenetic regulations of TUG1. Saudi J Biol Sci 2024; 31:103976. [PMID: 38510528 PMCID: PMC10951089 DOI: 10.1016/j.sjbs.2024.103976] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/29/2024] [Accepted: 03/08/2024] [Indexed: 03/22/2024] Open
Abstract
The epigenetic regulation of lncRNA TUG1 has garnered significant attention in the context of diabetes and its associated disorders. TUG1's multifaceted roles in gene expression modulation, and cellular differentiation, and it plays a major role in the growth of diabetes and the issues that are related to it due to pathological processes. In diabetes, aberrant epigenetic modifications can lead to dysregulation of TUG1 expression, contributing to disrupted insulin signaling, impaired glucose metabolism, and beta-cell dysfunction. Moreover, it has been reported that TUG1 contributes to the development of problems linked to diabetes, such as nephropathy, retinopathy, and cardiovascular complications, through epigenetically mediated mechanisms. Understanding the epigenetic regulations of TUG1 offers novel insights into the primary molecular mechanisms of diabetes and provides a possible path for healing interventions. Targeting epigenetic modifications associated with TUG1 holds promise for restoring proper gene expression patterns, ameliorating insulin sensitivity, and mitigating the inception and development of diabetic associative diseases. This review highlights the intricate epigenetic landscape that governs TUG1 expression in diabetes, encompassing DNA methylation and alterations in histone structure, as well as microRNA interactions.
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Affiliation(s)
- Mohammed Ageeli Hakami
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Shaqra University, Al-Quwayiyah, Riyadh, Saudi Arabia
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Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian noisy logic model for inference of transcription factor activity from single cell and bulk transcriptomic data. NAR Genom Bioinform 2023; 5:lqad106. [PMID: 38094309 PMCID: PMC10716740 DOI: 10.1093/nargab/lqad106] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/12/2023] [Accepted: 11/24/2023] [Indexed: 12/20/2023] Open
Abstract
The advent of high-throughput sequencing has made it possible to measure the expression of genes at relatively low cost. However, direct measurement of regulatory mechanisms, such as transcription factor (TF) activity is still not readily feasible in a high-throughput manner. Consequently, there is a need for computational approaches that can reliably estimate regulator activity from observable gene expression data. In this work, we present a noisy Boolean logic Bayesian model for TF activity inference from differential gene expression data and causal graphs. Our approach provides a flexible framework to incorporate biologically motivated TF-gene regulation logic models. Using simulations and controlled over-expression experiments in cell cultures, we demonstrate that our method can accurately identify TF activity. Moreover, we apply our method to bulk and single cell transcriptomics measurements to investigate transcriptional regulation of fibroblast phenotypic plasticity. Finally, to facilitate usage, we provide user-friendly software packages and a web-interface to query TF activity from user input differential gene expression data: https://umbibio.math.umb.edu/nlbayes/.
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Affiliation(s)
- Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
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6
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Li B, Li X, Zeng Y, Zhou Z, Zhao D, Qin F, Zhang B, Yao W, Mao Y, Zhou L, Li K, Zhu Q, Rong X, Guo J. Network pharmacology combined with molecular docking and experimental verification to elucidate functional mechanism of Fufang Zhenzhu Tiaozhi against type 2 diabetes mellitus. J Biomol Struct Dyn 2023:1-17. [PMID: 37942992 DOI: 10.1080/07391102.2023.2278082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2023] [Accepted: 09/29/2023] [Indexed: 11/10/2023]
Abstract
Fufang Zhenzhu Tiaozhi (FTZ) capsules have been prescribed for treating glucose and lipid metabolism disorders such as type 2 diabetes mellitus (T2DM). However, the underlying mechanism remains unknown. In this study, network pharmacology and experimental verification were combined to investigate the mechanisms of FTZ in treating T2DM. A total of 176 active ingredients and 1169 corresponding targets were screened using biological databases. 598 potential targets of T2DM were retrieved from GeneCards, PharmGKB, OMIM, Drugbank, and TTD. The Venn diagram was employed to identify the 194 intersection targets, which were employed to construct the "Herb-Compound-Target" interacting networks. These common targets were also used to prepare a protein-protein interaction (PPI) network to uncover potential targets. The four core targets were docked to their corresponding targets for binding analysis. Additionally, the top-ranked poses of ingredients and the positive compounds from each protein were evaluated for stability using molecular dynamics. Our results suggest that core active ingredients such as kaempferol, luteolin, and baicalein have high binding affinity and stability with AKT1, PTGS2 (also known as COX-2), DPP4, and PAPRG. GO and KEGG analyses indicated that the treatment T2DM by FTZ might be related to different pathway like AMPK and EGFR pathways. The experimental validation results proved that kaempferol, luteolin, and baicalein could significantly inhibit the activity of DPP4 and COX-2, kaempferol and luteolin were also able to activate AKT and AMPK signaling pathway. This study further validated previous findings and enhanced our understanding of the potential effects of FTZ on T2DM.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Bo Li
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xinying Li
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Youyan Zeng
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Zhenhua Zhou
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Dongyu Zhao
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Fei Qin
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Bin Zhang
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Weiwei Yao
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Yongxin Mao
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Li Zhou
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Kunping Li
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Qing Zhu
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Xianglu Rong
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
| | - Jiao Guo
- Institute of Chinese Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong Metabolic Diseases Research, Center of Integrated Chinese and Western Medicine, Guangdong Pharmaceutical University, Guangzhou, China
- Ministry of Education, Key Laboratory of Glucolipid Metabolic Disorder, Guangdong Pharmaceutical University, Guangzhou, China
- Guangdong TCM Key Laboratory for Metabolic Diseases, Guangdong Pharmaceutical University, Guangzhou, China
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7
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Schuermans N, El Chehadeh S, Hemelsoet D, Gautheron J, Vantyghem MC, Nouioua S, Tazir M, Vigouroux C, Auclair M, Bogaert E, Dufour S, Okawa F, Hilbert P, Van Doninck N, Taquet MC, Rosseel T, De Clercq G, Debackere E, Van Haverbeke C, Cherif FR, Urtizberea JA, Chanson JB, Funalot B, Authier FJ, Kaya S, Terryn W, Callens S, Depypere B, Van Dorpe J, Poppe B, Impens F, Mizushima N, Depienne C, Jéru I, Dermaut B. Loss of phospholipase PLAAT3 causes a mixed lipodystrophic and neurological syndrome due to impaired PPARγ signaling. Nat Genet 2023; 55:1929-1940. [PMID: 37919452 DOI: 10.1038/s41588-023-01535-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 09/16/2023] [Indexed: 11/04/2023]
Abstract
Phospholipase A/acyltransferase 3 (PLAAT3) is a phospholipid-modifying enzyme predominantly expressed in neural and white adipose tissue (WAT). It is a potential drug target for metabolic syndrome, as Plaat3 deficiency in mice protects against diet-induced obesity. We identified seven patients from four unrelated consanguineous families, with homozygous loss-of-function variants in PLAAT3, who presented with a lipodystrophy syndrome with loss of fat varying from partial to generalized and associated with metabolic complications, as well as variable neurological features including demyelinating neuropathy and intellectual disability. Multi-omics analysis of mouse Plaat3-/- and patient-derived WAT showed enrichment of arachidonic acid-containing membrane phospholipids and a strong decrease in the signaling of peroxisome proliferator-activated receptor gamma (PPARγ), the master regulator of adipocyte differentiation. Accordingly, CRISPR-Cas9-mediated PLAAT3 inactivation in human adipose stem cells induced insulin resistance, altered adipocyte differentiation with decreased lipid droplet formation and reduced the expression of adipogenic and mature adipocyte markers, including PPARγ. These findings establish PLAAT3 deficiency as a hereditary lipodystrophy syndrome with neurological manifestations, caused by a PPARγ-dependent defect in WAT differentiation and function.
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Affiliation(s)
- Nika Schuermans
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Salima El Chehadeh
- Service de Génétique Médicale, Institut de Génétique Médicale d'Alsace (IGMA), Hôpitaux Universitaires de Strasbourg, Strasbourg, France
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Laboratoire de Génétique Médicale, UMRS_1112, Institut de Génétique Médicale d'Alsace (IGMA), Université de Strasbourg et INSERM, Strasbourg, France
| | | | - Jérémie Gautheron
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
| | - Marie-Christine Vantyghem
- Endocrinology, Diabetology, Metabolism Department, National Competence Centre for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Lille University Hospital, Lille, France
- University of Lille, INSERM U1190, European Genomic Institute for Diabetes, Lille, France
| | - Sonia Nouioua
- Department of Neurology of the EHS of Cherchell, University Centre of Blida, Tipaza, Algeria
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
| | - Meriem Tazir
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
- Department of Neurology, CHU Algiers (Mustapha Pacha Hospital), Algiers, Algeria
| | - Corinne Vigouroux
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, National Reference Center for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Department of Endocrinology, Diabetology and Reproductive Endocrinology, and Department of Molecular Biology and Genetics, Paris, France
| | - Martine Auclair
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Assistance Publique-Hôpitaux de Paris, Saint-Antoine University Hospital, National Reference Center for Rare Diseases of Insulin Secretion and Insulin Sensitivity (PRISIS), Department of Endocrinology, Diabetology and Reproductive Endocrinology, and Department of Molecular Biology and Genetics, Paris, France
| | - Elke Bogaert
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Sara Dufour
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Fumiya Okawa
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Pascale Hilbert
- Department of Molecular and Cellular Biology, Institute of Pathology and Genetics, Charleroi, Belgium
| | - Nike Van Doninck
- Department of Endocrinology and Diabetology, General Hospital VITAZ, Sint-Niklaas, Belgium
| | - Marie-Caroline Taquet
- Department of Internal Medicine and Nutrition, Hopitaux Universitaires Strasbourg, Strasbourg, France
| | - Toon Rosseel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Griet De Clercq
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Elke Debackere
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | | | - Ferroudja Ramdane Cherif
- Department of Neurology of the EHS of Cherchell, University Centre of Blida, Tipaza, Algeria
- NeuroSciences Research Laboratory, University of Algiers Benyoucef Benkhedda, Algiers, Algeria
| | | | - Jean-Baptiste Chanson
- Service de Neurologie et Centre de Référence Neuromusculaire Nord/Est/Ile de France, Hôpital de Hautepierre, Strasbourg, France
| | - Benoit Funalot
- Department of Medical Genetics, Hôpital Henri Mondor, Université Paris-Est-Créteil, Créteil, France
- INSERM UMR955, Team Relaix, Faculty of Medicine, Créteil, France
| | - François-Jérôme Authier
- INSERM UMR955, Team Relaix, Faculty of Medicine, Créteil, France
- Centre Expert de Pathologie Neuromusculaire/Histologie, Département de Pathologie, Hôpital Henri Mondor, Université Paris-Est-Créteil, Créteil, France
| | - Sabine Kaya
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Wim Terryn
- Department of Nephrology, Jan Yperman Hospital, Ieper, Belgium
| | - Steven Callens
- Department of General Internal Medicine, Ghent University Hospital, Ghent, Belgium
| | - Bernard Depypere
- Department of Plastic and Reconstructive Surgery, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Bruce Poppe
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
| | - Francis Impens
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium
- VIB-UGent Center for Medical Biotechnology, VIB, Ghent, Belgium
- VIB Proteomics Core, VIB, Ghent, Belgium
| | - Noboru Mizushima
- Department of Biochemistry and Molecular Biology, Graduate School and Faculty of Medicine, The University of Tokyo, Bunkyo, Japan
| | - Christel Depienne
- Institut de Génétique et de Biologie Moléculaire et Cellulaire (IGBMC), INSERM U1258, CNRS-UMR7104, Université de Strasbourg, Strasbourg, France
- Institut für Humangenetik, Universitätsklinikum Essen, Essen, Germany
| | - Isabelle Jéru
- Sorbonne Université, INSERM UMRS_938, Centre de Recherche Saint-Antoine (CRSA), Paris, France
- Department of Medical Genetics, DMU BioGeM, Sorbonne Université, AP-HP, Pitié-Salpêtrière Hospital, Paris, France
| | - Bart Dermaut
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium.
- Department of Biomolecular Medicine, Faculty of Medicine and Health Sciences, Ghent University, Ghent, Belgium.
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8
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Liu J, Li X, Wang H, Ren Y, Li Y, Guo F. Bavachinin selectively modulates PPAR γ and maintains bone homeostasis in Type 2 Diabetes. Phytother Res 2023; 37:4457-4472. [PMID: 37308719 DOI: 10.1002/ptr.7912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 04/25/2023] [Accepted: 05/19/2023] [Indexed: 06/14/2023]
Abstract
Full peroxisome proliferator-activated receptor (PPAR) γ agonists, Thiazolidinediones (TZDs), effectively prevent the process of Type 2 Diabetes Mellitus (T2DM), but their side effects have curtailed use in the clinic, including weight gain and bone loss. Here, we identified that a selective PPAR γ modulator, Bavachinin (BVC), isolated from the seeds of Psoralea Corylifolia L., could potently regulate bone homeostasis. MC3T3-E1 pre-osteoblast cells and C3H10T1/2 mesenchymal stem cells were assessed for osteogenic differentiation activities, and receptor activator of NF-κB ligand (RANKL)-induced RAW 264.7 cells were assessed osteoclasts formation. Leptin receptor-deficient mice and diet-induced obesity mice were applied to evaluate the effect of BVC on bone homeostasis in vivo. Compared to full PPAR γ agonist rosiglitazone, BVC significantly increased the osteogenesis differentiation activities under normal and high glucose conditions in MC3T3-E1 cells. Moreover, BVC could alleviate osteoclast differentiation in RANKL-induced RAW 264.7 cells. In vivo, synthesized BVC prodrug (BN) has been applied to improve water solubility, increase the extent of oral absorption of BVC and prolong its residence time in blood circulation. BN could prevent weight gain, ameliorate lipid metabolism disorders, improve insulin sensitivity, and maintain bone mass and bone biomechanical properties. BVC, a unique PPAR γ selective modulator, could maintain bone homeostasis, and its prodrug (BN) exhibits insulin sensitizer activity while circumventing the side effects of the TZDs, including bone loss and undesirable weight gain.
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Affiliation(s)
- Jingwen Liu
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Xiaoye Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Hong Wang
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Yan Ren
- Experiment Center for Science and Technology, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Yiming Li
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
| | - Fujiang Guo
- School of Pharmacy, Shanghai University of Traditional Chinese Medicine, Shanghai, People's Republic of China
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9
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Kurek JM, Mikołajczyk-Stecyna J, Krejpcio Z. Steviol glycosides from Stevia rebaudiana Bertoni mitigate lipid metabolism abnormalities in diabetes by modulating selected gene expression - An in vivo study. Biomed Pharmacother 2023; 166:115424. [PMID: 37677968 DOI: 10.1016/j.biopha.2023.115424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2023] [Revised: 08/29/2023] [Accepted: 08/30/2023] [Indexed: 09/09/2023] Open
Abstract
In diabetes, in parallel to hyperglycaemia, elevated serum lipids are also diagnosed, representing a high-risk factor for coronary heart disease and cardiovascular complications. The objective of this study was to unravel the mechanisms that underlie the potential of steviol glycosides (stevioside or rebaudioside A) administered at two doses (500 or 2500 mg/kg body weight for 5 weeks) to regulate lipid metabolism. In this paper, the expression of selected genes responsible for glucose and lipid metabolism (Glut4, Pparγ, Cebpa, Fasn, Lpl and Egr1) in the peripheral tissues (adipose, liver and muscle tissue) was determined using quantitative real-time PCR method. It was found that the supplementation of steviol glycosides affected the expression of Glut4, Cebpa and Fasn genes, depending on the type of the glycoside and its dose, as well as the type of tissue, whish in part may explain the lipid-regulatory potential of steviol glycosides in hyperglycaemic conditions. Nevertheless, more in-depth studies, including human trials, are needed to confirm these effects, before steviol glycosides can be used in the therapy of type 2 diabetes.
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Affiliation(s)
- Jakub Michał Kurek
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland.
| | - Joanna Mikołajczyk-Stecyna
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland.
| | - Zbigniew Krejpcio
- Department of Human Nutrition and Dietetics, Poznań University of Life Sciences, Wojska Polskiego 31, 60-624 Poznań, Poland.
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10
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Luan J, Ji X, Liu L. PPARγ in Atherosclerotic Endothelial Dysfunction: Regulatory Compounds and PTMs. Int J Mol Sci 2023; 24:14494. [PMID: 37833942 PMCID: PMC10572723 DOI: 10.3390/ijms241914494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 09/20/2023] [Accepted: 09/22/2023] [Indexed: 10/15/2023] Open
Abstract
The formation of atherosclerotic plaques is one of the main sources of cardiovascular disease. In addition to known risk factors such as dyslipidemia, diabetes, obesity, and hypertension, endothelial dysfunction has been shown to play a key role in the formation and progression of atherosclerosis. Peroxisome proliferator-activated receptor-gamma (PPARγ), a transcription factor belonging to the steroid superfamily, is expressed in the aorta and plays a critical role in protecting endothelial function. It thereby serves as a target for treating both diabetes and atherosclerosis. Although many studies have examined endothelial cell disorders in atherosclerosis, the role of PPARγ in endothelial dysfunction is still not well understood. In this review, we summarize the possible mechanisms of action behind PPARγ regulatory compounds and post-translational modifications (PTMs) of PPARγ in the control of endothelial function. We also explore the potential use of endothelial PPARγ-targeted agents in the prevention and treatment of atherosclerosis.
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Affiliation(s)
| | | | - Longhua Liu
- School of Exercise and Health, Shanghai University of Sport, Shanghai 200082, China
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11
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Guo T, Pan Y, Yang L, Chen G, Deng J, Zhu L. Flavonoid compound from Agrimonia pilosa Ledeb improves adipose insulin resistance by alleviating oxidative stress and inflammation. BMC Complement Med Ther 2023; 23:322. [PMID: 37710214 PMCID: PMC10503054 DOI: 10.1186/s12906-023-04114-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2022] [Accepted: 08/02/2023] [Indexed: 09/16/2023] Open
Abstract
BACKGROUND Researches and practice of traditional Chinese medicine indicated that Agrimonia pilosa Ledeb could improve insulin resistance (IR) and treat type 2 diabetes (T2DM). To reveal its underling mechanisms, we isolated Flavonoid component (FC) from Agrimonia pilosa Ledeb and elucidated its effects on glucose metabolism to improve IR by suppressing oxidative stress and inflammation. METHODS Adipocytes or mice IR model was established with overdosed glucose and insulin or high-fat diet. The uptake of 2-NBDG and glucose consumption were measured to verify insulin sensitivity in vitro and vivo. Reactive oxidative species (ROS) were detected by flow cytometry, and superoxide dismutase (SOD) activity as well as the malondialdehyde (MDA) content were also measured. Meanwhile, factors associated with insulin signal pathway including PPARγ, insulin receptor substrate-1 (IRS-1), GLUT4, and oxidative stress including NF-E2-related factor 2 (Nrf2), as well as the related inflammatory cytokines such as NF-κB, IL-1β, IL-6 and TNF-α were tested. Furthermore, the JNK/PI3K/Akt signal pathway was also explored. RESULTS FC extracted from Agrimonia pilosa Ledeb ameliorated the impaired glucose metabolism significantly. Further study indicated that FC could regulate the insulin signal pathway to improve insulin resistance. Moreover, it could upregulate PPARγ with the similar efficacy as pioglitazone (Piog) straightway. FC also decreased the endogenous ROS and MDA content, increased SOD activity and Nrf2 expression to facilitate oxidative homeostasis. It attenuated expression and secretion of inflammatory cytokines obviously. At last, our results indicated JNK/PI3K/Akt pathway was regulated by FC in adipocytes and adipose tissue. CONCLUSION FC could ameliorate glucose metabolism and improve IR. It exerted these effects by suppressing oxidative stress and inflammation. FC from Agrimonia pilosa Ledeb has a good prospect to be drugs or functional foods for IR and T2DM.
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Affiliation(s)
- Tingwang Guo
- Department of Gastroenterology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing, China
| | - Yun Pan
- Department of Gastroenterology, Children's Hospital of Chongqing Medical University, National Clinical Research Center for Child Health and Disorders, Ministry of Education Key Laboratory of Child Development and Disorders, Chongqing Key Laboratory of Pediatrics, Chongqing, China.
| | - Lin Yang
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing, China
| | - Gang Chen
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing, China
| | - Jia Deng
- College of Environment and Resources, Chongqing Technology and Business University, Chongqing, China
| | - Liancai Zhu
- Key Laboratory of Biorheological Science and Technology, Ministry of Education, College of Bioengineering, Chongqing University, Chongqing, China.
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12
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Yu L, Gao Y, Aaron N, Qiang L. A glimpse of the connection between PPARγ and macrophage. Front Pharmacol 2023; 14:1254317. [PMID: 37701041 PMCID: PMC10493289 DOI: 10.3389/fphar.2023.1254317] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Accepted: 07/31/2023] [Indexed: 09/14/2023] Open
Abstract
Nuclear receptors are ligand-regulated transcription factors that regulate vast cellular activities and serve as an important class of drug targets. Among them, peroxisome proliferator-activated receptors (PPARs) are members of the nuclear receptor family and have been extensively studied for their roles in metabolism, differentiation, development, and cancer, among others. Recently, there has been considerable interest in understanding and defining the function of PPARs and their agonists in regulating innate and adaptive immune responses and their pharmacological potential in combating chronic inflammatory diseases. In this review, we focus on emerging evidence for the potential role of PPARγ in macrophage biology, which is the prior innate immune executive in metabolic and tissue homeostasis. We also discuss the role of PPARγ as a regulator of macrophage function in inflammatory diseases. Lastly, we discuss the possible application of PPARγ antagonists in metabolic pathologies.
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Affiliation(s)
- Lexiang Yu
- Naomi Berrie Diabetes Center, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Yuen Gao
- Department of Physiology, Michigan State University, East Lansing, MI, United States
| | - Nicole Aaron
- Naomi Berrie Diabetes Center, Columbia University, New York, NY, United States
- Department of Molecular Pharmacology and Therapeutics, Columbia University, New York, NY, United States
| | - Li Qiang
- Naomi Berrie Diabetes Center, Columbia University, New York, NY, United States
- Department of Pathology and Cell Biology, Columbia University, New York, NY, United States
- Department of Medicine, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States
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13
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Sun WX, Shu YP, Yang XY, Huang W, Chen J, Yu NN, Zhao M. Effects of folic acid supplementation in pregnant mice on glucose metabolism disorders in male offspring induced by lipopolysaccharide exposure during pregnancy. Sci Rep 2023; 13:7984. [PMID: 37198280 DOI: 10.1038/s41598-023-31690-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 03/15/2023] [Indexed: 05/19/2023] Open
Abstract
The DOHaD theory suggests that adverse environmental factors in early life may lead to the development of metabolic diseases including diabetes and hypertension in adult offspring through epigenetic mechanisms such as DNA methylation. Folic acid (FA) is an important methyl donor in vivo and participates in DNA replication and methylation. The preliminary experimental results of our group demonstrated that lipopolysaccharide (LPS, 50 µg/kg/d) exposure during pregnancy could lead to glucose metabolism disorders in male offspring, but not female offspring; however, the effect of folic acid supplementation on glucose metabolism disorders in male offspring induced by LPS exposure remains unclear. Therefore, in this study, pregnant mice were exposed to LPS on gestational day (GD) 15-17 and were given three doses of FA supplementation (2 mg/kg, 5 mg/kg, or 40 mg/kg) from mating to lactation to explore its effect on glucose metabolism in male offspring and the potential mechanism. This study confirmed that FA supplementation of 5 mg/kg in pregnant mice improved glucose metabolism in LPS-exposed offspring during pregnancy by regulating gene expression.
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Affiliation(s)
- Wan-Xiao Sun
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- Anhui Medical College, Hefei, 230601, Anhui, China
| | - Yi-Ping Shu
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
| | - Xin-Yu Yang
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Wei Huang
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
| | - Jing Chen
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- Anhui Provincial Hospital, Hefei, 230022, Anhui, China
| | - Ning-Ning Yu
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China
- The First Affiliated Hospital of Anhui Medical University, Hefei, 230601, Anhui, China
| | - Mei Zhao
- Department of Basic Nursing, School of Nursing, Anhui Medical University, 81 Meishan Road, Hefei, 230032, Anhui, China.
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14
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Arriojas A, Patalano S, Macoska J, Zarringhalam K. A Bayesian Noisy Logic Model for Inference of Transcription Factor Activity from Single Cell and Bulk Transcriptomic Data. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.03.539308. [PMID: 37205561 PMCID: PMC10187261 DOI: 10.1101/2023.05.03.539308] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
The advent of high-throughput sequencing has made it possible to measure the expression of genes at relatively low cost. However, direct measurement of regulatory mechanisms, such as Transcription Factor (TF) activity is still not readily feasible in a high-throughput manner. Consequently, there is a need for computational approaches that can reliably estimate regulator activity from observable gene expression data. In this work, we present a noisy Boolean logic Bayesian model for TF activity inference from differential gene expression data and causal graphs. Our approach provides a flexible framework to incorporate biologically motivated TF-gene regulation logic models. Using simulations and controlled over-expression experiments in cell cultures, we demonstrate that our method can accurately identify TF activity. Moreover, we apply our method to bulk and single cell transcriptomics measurements to investigate transcriptional regulation of fibroblast phenotypic plasticity. Finally, to facilitate usage, we provide user-friendly software packages and a web-interface to query TF activity from user input differential gene expression data: https://umbibio.math.umb.edu/nlbayes/.
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Affiliation(s)
- Argenis Arriojas
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Department of Physics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Susan Patalano
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Jill Macoska
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
| | - Kourosh Zarringhalam
- Department of Mathematics, University of Massachusetts Boston, Boston, MA 02125, USA
- Center for Personalized Cancer Therapy, University of Massachusetts Boston, Boston, MA 02125, USA
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15
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Vourdoumpa A, Paltoglou G, Charmandari E. The Genetic Basis of Childhood Obesity: A Systematic Review. Nutrients 2023; 15:1416. [PMID: 36986146 PMCID: PMC10058966 DOI: 10.3390/nu15061416] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2023] [Revised: 03/05/2023] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
Overweight and obesity in childhood and adolescence represents one of the most challenging public health problems of our century owing to its epidemic proportions and the associated significant morbidity, mortality, and increase in public health costs. The pathogenesis of polygenic obesity is multifactorial and is due to the interaction among genetic, epigenetic, and environmental factors. More than 1100 independent genetic loci associated with obesity traits have been currently identified, and there is great interest in the decoding of their biological functions and the gene-environment interaction. The present study aimed to systematically review the scientific evidence and to explore the relation of single-nucleotide polymorphisms (SNPs) and copy number variants (CNVs) with changes in body mass index (BMI) and other measures of body composition in children and adolescents with obesity, as well as their response to lifestyle interventions. Twenty-seven studies were included in the qualitative synthesis, which consisted of 7928 overweight/obese children and adolescents at different stages of pubertal development who underwent multidisciplinary management. The effect of polymorphisms in 92 different genes was assessed and revealed SNPs in 24 genetic loci significantly associated with BMI and/or body composition change, which contribute to the complex metabolic imbalance of obesity, including the regulation of appetite and energy balance, the homeostasis of glucose, lipid, and adipose tissue, as well as their interactions. The decoding of the genetic and molecular/cellular pathophysiology of obesity and the gene-environment interactions, alongside with the individual genotype, will enable us to design targeted and personalized preventive and management interventions for obesity early in life.
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Affiliation(s)
- Aikaterini Vourdoumpa
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, ‘Aghia Sophia’ Children’s Hospital, 11527 Athens, Greece
| | - George Paltoglou
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, ‘Aghia Sophia’ Children’s Hospital, 11527 Athens, Greece
| | - Evangelia Charmandari
- Division of Endocrinology, Metabolism and Diabetes, First Department of Pediatrics, National and Kapodistrian University of Athens Medical School, ‘Aghia Sophia’ Children’s Hospital, 11527 Athens, Greece
- Division of Endocrinology and Metabolism, Center for Clinical, Experimental Surgery and Translational Research, Biomedical Research Foundation of the Academy of Athens, 11527 Athens, Greece
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16
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Hasankhani A, Bahrami A, Tavakoli-Far B, Iranshahi S, Ghaemi F, Akbarizadeh MR, Amin AH, Abedi Kiasari B, Mohammadzadeh Shabestari A. The role of peroxisome proliferator-activated receptors in the modulation of hyperinflammation induced by SARS-CoV-2 infection: A perspective for COVID-19 therapy. Front Immunol 2023; 14:1127358. [PMID: 36875108 PMCID: PMC9981974 DOI: 10.3389/fimmu.2023.1127358] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Accepted: 02/08/2023] [Indexed: 02/19/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19) is a severe respiratory disease caused by infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that affects the lower and upper respiratory tract in humans. SARS-CoV-2 infection is associated with the induction of a cascade of uncontrolled inflammatory responses in the host, ultimately leading to hyperinflammation or cytokine storm. Indeed, cytokine storm is a hallmark of SARS-CoV-2 immunopathogenesis, directly related to the severity of the disease and mortality in COVID-19 patients. Considering the lack of any definitive treatment for COVID-19, targeting key inflammatory factors to regulate the inflammatory response in COVID-19 patients could be a fundamental step to developing effective therapeutic strategies against SARS-CoV-2 infection. Currently, in addition to well-defined metabolic actions, especially lipid metabolism and glucose utilization, there is growing evidence of a central role of the ligand-dependent nuclear receptors and peroxisome proliferator-activated receptors (PPARs) including PPARα, PPARβ/δ, and PPARγ in the control of inflammatory signals in various human inflammatory diseases. This makes them attractive targets for developing therapeutic approaches to control/suppress the hyperinflammatory response in patients with severe COVID-19. In this review, we (1) investigate the anti-inflammatory mechanisms mediated by PPARs and their ligands during SARS-CoV-2 infection, and (2) on the basis of the recent literature, highlight the importance of PPAR subtypes for the development of promising therapeutic approaches against the cytokine storm in severe COVID-19 patients.
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Affiliation(s)
- Aliakbar Hasankhani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Faculty of Agricultural Sciences and Engineering, University of Tehran, Karaj, Iran
| | - Bahareh Tavakoli-Far
- Dietary Supplements and Probiotic Research Center, Alborz University of Medical Sciences, Karaj, Iran
- Department of Physiology and Pharmacology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Setare Iranshahi
- School of Pharmacy, Shahid Beheshty University of Medical Sciences, Tehran, Iran
| | - Farnaz Ghaemi
- Department of Biochemistry, Faculty of Advanced Sciences and Technology, Tehran Medical Sciences, Islamic Azad University, Tehran, Iran
| | - Majid Reza Akbarizadeh
- Department of Pediatric, School of Medicine, Amir al momenin Hospital, Zabol University of Medical Sciences, Zabol, Iran
| | - Ali H. Amin
- Zoology Department, Faculty of Science, Mansoura University, Mansoura, Egypt
| | - Bahman Abedi Kiasari
- Virology Department, Faculty of Veterinary Medicine, University of Tehran, Tehran, Iran
| | - Alireza Mohammadzadeh Shabestari
- Department of Dental Surgery, Mashhad University of Medical Sciences, Mashhad, Iran
- Khorasan Covid-19 Scientific Committee, Mashhad, Iran
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17
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Ma L, Tang J, Cai G, Chen F, Liu Q, Zhou Z, Zhang S, Liu X, Hou N, Yi W. Structure-based screening and biological validation of the anti-thrombotic drug-dicoumarol as a novel and potent PPARγ-modulating ligand. Bioorg Chem 2022; 129:106191. [DOI: 10.1016/j.bioorg.2022.106191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Revised: 09/17/2022] [Accepted: 09/30/2022] [Indexed: 11/16/2022]
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18
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Miyamoto A, Tomotaka U, Takaaki K, Kenichi M, Chimi M. Molecular characterization of two pedigrees with maternally inherited diabetes mellitus. Mitochondrial DNA B Resour 2022. [DOI: 10.1080/23802359.2022.2050474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Akira Miyamoto
- Faculty of Rehabilitation, Kobe International University, Hyogo, Japan
| | - Ueda Tomotaka
- Faculty of Rehabilitation, Nishikyushu University, Saga, Japan
| | - Kubo Takaaki
- Faculty of health science, Kumamoto Health Science University, Kumamoto, Japan
| | - Mori Kenichi
- Omote Orthopedic Osteoporosis Clinic, Toyonaka, Japan
| | - Miyamoto Chimi
- Department of Occupational Therapy, Faculty of Health Science, Aino University, Osaka, Japan
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19
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Soluble Epoxide Hydrolase and Diabetes Complications. Int J Mol Sci 2022; 23:ijms23116232. [PMID: 35682911 PMCID: PMC9180978 DOI: 10.3390/ijms23116232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Revised: 05/28/2022] [Accepted: 05/30/2022] [Indexed: 02/04/2023] Open
Abstract
Type 2 diabetes mellitus (T2DM) can result in microvascular complications such as neuropathy, retinopathy, nephropathy, and cerebral small vessel disease, and contribute to macrovascular complications, such as heart failure, peripheral arterial disease, and large vessel stroke. T2DM also increases the risks of depression and dementia for reasons that remain largely unclear. Perturbations in the cytochrome P450-soluble epoxide hydrolase (CYP-sEH) pathway have been implicated in each of these diabetes complications. Here we review evidence from the clinical and animal literature suggesting the involvement of the CYP-sEH pathway in T2DM complications across organ systems, and highlight possible mechanisms (e.g., inflammation, fibrosis, mitochondrial function, endoplasmic reticulum stress, the unfolded protein response and autophagy) that may be relevant to the therapeutic potential of the pathway. These mechanisms may be broadly relevant to understanding, preventing and treating microvascular complications affecting the brain and other organ systems in T2DM.
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20
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Queiroz-Glauss CP, Vieira MS, Gonçalves-Pereira MH, Almeida SS, Freire RH, Gomes MA, Alvarez-Leite JI, Santiago HC. Helminth infection modulates number and function of adipose tissue Tregs in high fat diet-induced obesity. PLoS Negl Trop Dis 2022; 16:e0010105. [PMID: 35499991 PMCID: PMC9098094 DOI: 10.1371/journal.pntd.0010105] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2021] [Revised: 05/12/2022] [Accepted: 04/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background Epidemiological and experimental studies have shown a protective effect of helminth infections in weight gain and against the development of metabolic dysfunctions in the host. However, the mechanisms Treg cells exert in the helminth-obesity interface has been poorly investigated. The present study aimed to verify the influence of Heligmosomoides polygyrus infection in early stages of high fat diet-induced obesity. Principal findings The presence of infection was able to prevent exacerbated weight gain in mice fed with high fat diet when compared to non-infected controls. In addition, infected animals displayed improved insulin sensitivity and decreased fat accumulation in the liver. Obesity-associated inflammation was reduced in the presence of infection, demonstrated by lower levels of leptin and resistin, lower infiltration of Th1 and Th17 cells in adipose tissue, higher expression of IL10 and adiponectin, increased infiltration of Th2 and eosinophils in adipose tissue of infected animals. Of note, the parasite infection was associated with increased Treg frequency in adipose tissue which showed higher expression of cell surface markers of function and activation, like LAP and CD134. The infection could also increase adipose Treg suppressor function in animals on high fat diet. Conclusion These data suggest that H. polygyrus modulates adipose tissue Treg cells with implication for weight gain and metabolic syndrome. Helminth infections are known to modulate the immune system being responsible for protecting the host from developing allergic and autoimmune disorders (Hygiene Hypothesis). We hypothesized that the same immunomodulatory effect could have an impact on immunometabolic diseases, such as obesity and its linked diseases such as type 2 diabetes. Weight disorders have reached epidemic levels, nearly tripling since 1975 and being responsible for almost 5 million premature deaths each year, but have been spared in areas of high helminth prevalence. To test our hypothesis C57BL/6 male mice were fed control or high fat diet, for five weeks, in the presence or not of infection with the worm Heligmosomoides polygyrus. Weight gain, development of metabolic disorders, inflammation and cellular migration to the adipose tissue were evaluated. In accordance with our hypothesis, we found that the presence of infection prevented the exacerbated weight gain and also improved metabolic parameters in animals fed a high fat diet. This was associated with the infection’s ability to modulate parameters of a cell responsible for regulatory functions: Tregs. In the light of these findings, helminth infection could be protective against weight gain and metabolic disturbances.
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Affiliation(s)
- Camila P. Queiroz-Glauss
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mariana S. Vieira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Marcela Helena Gonçalves-Pereira
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Stephanie S. Almeida
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rachel H. Freire
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Maria A. Gomes
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Jacqueline I. Alvarez-Leite
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Helton C. Santiago
- Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
- * E-mail:
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21
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Song Y, Li S, He C. PPARγ Gene Polymorphisms, Metabolic Disorders, and Coronary Artery Disease. Front Cardiovasc Med 2022; 9:808929. [PMID: 35402540 PMCID: PMC8984027 DOI: 10.3389/fcvm.2022.808929] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 02/22/2022] [Indexed: 01/14/2023] Open
Abstract
Being activated by endogenous and exogenous ligands, nuclear receptor peroxisome proliferator-activated receptor gamma (PPARγ) enhances insulin sensitivity, promotes adipocyte differentiation, stimulates adipogenesis, and has the properties of anti-atherosclerosis, anti-inflammation, and anti-oxidation. The Human PPARγ gene (PPARG) contains thousands of polymorphic loci, among them two polymorphisms (rs10865710 and rs7649970) in the promoter region and two polymorphisms (rs1801282 and rs3856806) in the exonic region were widely reported to be significantly associated with coronary artery disease (CAD). Mechanistically, PPARG polymorphisms lead to abnormal expression of PPARG gene and/or dysfunction of PPARγ protein, causing metabolic disorders such as hypercholesterolemia and hypertriglyceridemia, and thereby increasing susceptibility to CAD.
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Affiliation(s)
- Yongyan Song
- Central Laboratory, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
| | - Shujin Li
- Central Laboratory, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
| | - Chuan He
- Department of Cardiology, Clinical Medical College and Affiliated Hospital of Chengdu University, Chengdu, China
- *Correspondence: Chuan He,
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22
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Vales-Villamarín C, de Dios O, Pérez-Nadador I, Gavela-Pérez T, Soriano-Guillén L, Garcés C. PPARγ2 Pro12Ala Polymorphism is Associated in Children With Traits Related to Susceptibility to Type 2 Diabetes. Front Pharmacol 2021; 12:763853. [PMID: 34887761 PMCID: PMC8650059 DOI: 10.3389/fphar.2021.763853] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Accepted: 11/10/2021] [Indexed: 12/16/2022] Open
Abstract
Peroxisome proliferator-activated receptor gamma (PPARγ) is a ligand-activated nuclear receptor that regulates glucose and lipid metabolism. Pharmacological activators of PPARγ are being used as a treatment of obesity related disorders such as dyslipidaemia and type 2 diabetes, but questions remain open regarding the effects of PPARγ on traits related to the development of type 2 diabetes. In our study, we have analyzed the relationship of the common variant Pro12Ala in the human PPARγ2 gene with the presence of obesity and with insulin, HOMA and lipid profile in a representative sample of 6-to 8-year-old children free from the confounding factors associated with adults. We found that Ala12Ala genotype was significantly more frequent in females with obesity than in those without obesity, with Ala12Ala carriers having significantly higher weight and body mass index (BMI), however the association disappeared when adjusting by leptin concentrations. The Ala12Ala genotype was associated with significantly higher HDL-cholesterol and apoA-I levels in males but not in females, independently of BMI. In a recessive model, in females, leptin levels appeared higher in Ala12Ala carriers. Although no apparent differences were observed in any sex when analyzing insulin levels and HOMA among genotypes without adjusting, lower insulin levels and lower HOMA appeared associated with Ala12Ala carriers when adjusting for BMI and leptin levels. In summary, our data showed that leptin seems to be having an effect on the association between the PPARγ2 Pro12Ala and BMI. Besides, after controlling for BMI and leptin, a protective effect of the Ala12Ala variant of the PPARγ2 Pro12Ala polymorphism on insulin sensitivity is evident already in prepubertal children.
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Affiliation(s)
| | - Olaya de Dios
- Lipid Research Laboratory, IIS-Fundación Jiménez Díaz UAM, Madrid, Spain
| | - Iris Pérez-Nadador
- Lipid Research Laboratory, IIS-Fundación Jiménez Díaz UAM, Madrid, Spain
| | | | | | - Carmen Garcés
- Lipid Research Laboratory, IIS-Fundación Jiménez Díaz UAM, Madrid, Spain
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23
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PPARs-Orchestrated Metabolic Homeostasis in the Adipose Tissue. Int J Mol Sci 2021; 22:ijms22168974. [PMID: 34445679 PMCID: PMC8396609 DOI: 10.3390/ijms22168974] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/17/2021] [Accepted: 08/17/2021] [Indexed: 01/12/2023] Open
Abstract
It has been more than three decades since peroxisome proliferator-activated receptors (PPARs) were first discovered. Many investigations have revealed the central regulators of PPARs in lipid and glucose homeostasis in response to different nutrient conditions. PPARs have attracted much attention due to their ability to improve metabolic syndromes, and they have also been proposed as classical drug targets for the treatment of hyperlipidemia and type 2 diabetes (T2D) mellitus. In parallel, adipose tissue is known to play a unique role in the pathogenesis of insulin resistance and metabolic syndromes due to its ability to “safely” store lipids and secrete cytokines that regulate whole-body metabolism. Adipose tissue relies on a complex and subtle network of transcription factors to maintain its normal physiological function, by coordinating various molecular events, among which PPARs play distinctive and indispensable roles in adipocyte differentiation, lipid metabolism, adipokine secretion, and insulin sensitivity. In this review, we discuss the characteristics of PPARs with special emphasis on the roles of the different isotypes in adipocyte biology.
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