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Ramezani M, Zobeiry M, Abdolahi S, Hatami B, Zali MR, Baghaei K. A crosstalk between epigenetic modulations and non-alcoholic fatty liver disease progression. Pathol Res Pract 2023; 251:154809. [PMID: 37797383 DOI: 10.1016/j.prp.2023.154809] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 09/08/2023] [Accepted: 09/08/2023] [Indexed: 10/07/2023]
Abstract
Non-alcoholic fatty liver disease (NAFLD) has recently emerged as a major public health concern worldwide due to its rapidly rising prevalence and its potential to progress into end-stage liver disease. While the precise pathophysiology underlying NAFLD remains incompletely understood, it is strongly associated with various environmental triggers and other metabolic disorders. Epigenetics examines changes in gene expression that are not caused by alterations in the DNA sequence itself. There is accumulating evidence that epigenetics plays a key role in linking environmental cues to the onset and progression of NAFLD. Our understanding of how epigenetic mechanisms contribute to NAFLD pathophysiology has expanded considerably in recent years as research on the epigenetics of NAFLD has developed. This review summarizes recent insights into major epigenetic processes that have been implicated in NAFLD pathogenesis including DNA methylation, histone acetylation, and microRNAs that have emerged as promising targets for further investigation. Elucidating epigenetic mechanisms in NAFLD may uncover novel diagnostic biomarkers and therapeutic targets for this disease. However, many questions have remained unanswered regarding how epigenetics promotes NAFLD onset and progression. Additional studies are needed to further characterize the epigenetic landscape of NAFLD and validate the potential of epigenetic markers as clinical tools. Nevertheless, an enhanced understanding of the epigenetic underpinnings of NAFLD promises to provide key insights into disease mechanisms and pave the way for novel prognostic and therapeutic approaches.
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Affiliation(s)
- Meysam Ramezani
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | | | - Shahrokh Abdolahi
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Behzad Hatami
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Kaveh Baghaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Gastroenterology and Liver Diseases Research center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
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Bayraktar A, Li X, Kim W, Zhang C, Turkez H, Shoaie S, Mardinoglu A. Drug repositioning targeting glutaminase reveals drug candidates for the treatment of Alzheimer's disease patients. J Transl Med 2023; 21:332. [PMID: 37210557 DOI: 10.1186/s12967-023-04192-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/11/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Despite numerous clinical trials and decades of endeavour, there is still no effective cure for Alzheimer's disease. Computational drug repositioning approaches may be employed for the development of new treatment strategies for Alzheimer's patients since an extensive amount of omics data has been generated during pre-clinical and clinical studies. However, targeting the most critical pathophysiological mechanisms and determining drugs with proper pharmacodynamics and good efficacy are equally crucial in drug repurposing and often imbalanced in Alzheimer's studies. METHODS Here, we investigated central co-expressed genes upregulated in Alzheimer's disease to determine a proper therapeutic target. We backed our reasoning by checking the target gene's estimated non-essentiality for survival in multiple human tissues. We screened transcriptome profiles of various human cell lines perturbed by drug induction (for 6798 compounds) and gene knockout using data available in the Connectivity Map database. Then, we applied a profile-based drug repositioning approach to discover drugs targeting the target gene based on the correlations between these transcriptome profiles. We evaluated the bioavailability, functional enrichment profiles and drug-protein interactions of these repurposed agents and evidenced their cellular viability and efficacy in glial cell culture by experimental assays and Western blotting. Finally, we evaluated their pharmacokinetics to anticipate to which degree their efficacy can be improved. RESULTS We identified glutaminase as a promising drug target. Glutaminase overexpression may fuel the glutamate excitotoxicity in neurons, leading to mitochondrial dysfunction and other neurodegeneration hallmark processes. The computational drug repurposing revealed eight drugs: mitoxantrone, bortezomib, parbendazole, crizotinib, withaferin-a, SA-25547 and two unstudied compounds. We demonstrated that the proposed drugs could effectively suppress glutaminase and reduce glutamate production in the diseased brain through multiple neurodegeneration-associated mechanisms, including cytoskeleton and proteostasis. We also estimated the human blood-brain barrier permeability of parbendazole and SA-25547 using the SwissADME tool. CONCLUSIONS This study method effectively identified an Alzheimer's disease marker and compounds targeting the marker and interconnected biological processes by use of multiple computational approaches. Our results highlight the importance of synaptic glutamate signalling in Alzheimer's disease progression. We suggest repurposable drugs (like parbendazole) with well-evidenced activities that we linked to glutamate synthesis hereby and novel molecules (SA-25547) with estimated mechanisms for the treatment of Alzheimer's patients.
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Affiliation(s)
- Abdulahad Bayraktar
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Xiangyu Li
- Bash Biotech Inc, 600 West Broadway, Suite 700, San Diego, CA, 92101, USA
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121, Stockholm, Sweden
| | - Woonghee Kim
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121, Stockholm, Sweden
| | - Cheng Zhang
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121, Stockholm, Sweden
| | - Hasan Turkez
- Department of Medical Biology, Faculty of Medicine, Atatürk University, Erzurum, Turkey
| | - Saeed Shoaie
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK
| | - Adil Mardinoglu
- Centre for Host-Microbiome Interactions, Faculty of Dentistry, Oral & Craniofacial Sciences, King's College London, London, SE1 9RT, UK.
- Science for Life Laboratory, KTH-Royal Institute of Technology, SE-17121, Stockholm, Sweden.
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Xu Z, Wu FW, Niu X, Lu XP, Li YR, Zhang ST, Ou JZ, Wang XM. Integrated strategy of RNA-sequencing and network pharmacology for exploring the protective mechanism of Shen-Shi-Jiang-Zhuo formula in rat with non-alcoholic fatty liver disease. PHARMACEUTICAL BIOLOGY 2022; 60:1819-1838. [PMID: 36124995 PMCID: PMC9518293 DOI: 10.1080/13880209.2022.2106250] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 07/08/2022] [Accepted: 07/22/2022] [Indexed: 06/15/2023]
Abstract
CONTEXT Shen-Shi-Jiang-Zhuo formula (SSJZF) exhibits a definite curative effect in the clinical treatment of non-alcoholic fatty liver disease (NAFLD). OBJECTIVE To explore the therapeutic effect and mechanism of SSJZF on NAFLD. MATERIALS AND METHODS Sprague Dawley rats were randomly divided into control, NAFLD, positive drug (12 mg/kg/day), SSJZF high-dose (200 mg/kg/day), SSJZF middle-dose (100 mg/kg/day), and SSJZF low-dose (50 mg/kg/day) groups. After daily intragastric administration of NAFLD rats for 8 weeks, lipid metabolism and hepatic fibrosis were evaluated by biochemical indices and histopathology. Then we uncovered the main active compounds and mechanism of SSJZF against NAFLD by integrating RNA-sequencing and network pharmacology, and PI3K/AKT pathway activity was verified by western blot. RESULTS High dose SSJZF had the best inhibitory effect on hepatic lipid accumulation and fibrosis in rats with NAFLD, which significantly down-regulated total triglycerides (58%), cholesterol (62%), aspartate aminotransferase (57%), alanine aminotransferase (41%) andγ-glutamyl transpeptidase (36%), as well as the expression of ACC (5.3-fold), FAS (12.1-fold), SREBP1C (2.3-fold), and CD36 (4.4-fold), and significantly reduced collagen deposition (67%). Then we identified 23 compounds of SSJZF that acted on 25 key therapeutic targets of NAFLD by integrating RNA-sequencing and network pharmacology. Finally, we also confirmed that high dose SSJZF increased p-PI3K/PI3K (1.6-fold) and p-AKT/AKT (1.6-fold) in NAFLD rats. DISCUSSION AND CONCLUSION We found for first time that SSJZF improved NAFLD in rats by activating the PI3K/Akt pathway. These findings provide scientific support for SSJZF in the clinical treatment of NAFLD and contribute to the development of new NAFLD drugs.
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Affiliation(s)
- Zheng Xu
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- School of Basic Medical Sciences, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fan-Wei Wu
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xuan Niu
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Xiao-Peng Lu
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
| | - Yan-Rong Li
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Shu-Ting Zhang
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- Guangdong Agriculture and Reclamation Central Hospital, Zhanjiang, Guangdong
| | - Jun-Zhao Ou
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Xue-Mei Wang
- Liu Pai Chinese Medical Center, The Seventh Clinical Medical College of Guangzhou University of Chinese Medicine, Shenzhen, China
- Graduate School, Guangzhou University of Chinese Medicine, Guangzhou, China
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Vachher M, Bansal S, Kumar B, Yadav S, Burman A. Deciphering the role of aberrant DNA methylation in NAFLD and NASH. Heliyon 2022; 8:e11119. [PMID: 36299516 PMCID: PMC9589178 DOI: 10.1016/j.heliyon.2022.e11119] [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: 05/05/2022] [Revised: 07/30/2022] [Accepted: 10/12/2022] [Indexed: 11/15/2022] Open
Abstract
The global incidence of nonalcoholic fatty liver disease (NAFLD) is mounting incessantly, and it is emerging as the most frequent cause of chronic and end stage liver disorders. It is the starting point for a range of conditions from simple steatosis to more progressive nonalcoholic steatohepatitis (NASH) and associated hepatocellular carcinoma (HCC). Dysregulation of insulin secretion and dyslipidemia due to obesity and other lifestyle variables are the primary contributors to establishment of NAFLD. Onset and progression of NAFLD is orchestrated by an interplay of metabolic environment with genetic and epigenetic factors. An incompletely understood mechanism of NAFLD progression has greatly hampered the progress in identification of novel prognostic and therapeutic strategies. Emerging evidence suggests altered DNA methylation pattern as a key determinant of NAFLD pathogenesis. Environmental and lifestyle factors can manipulate DNA methylation patterns in a reversible manner, which manifests as changes in gene expression. In this review we attempt to highlight the importance of DNA methylation in establishment and progression of NAFLD. Development of novel diagnostic, prognostic and therapeutic strategies centered around DNA methylation signatures and modifiers has also been explored.
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Lefever DE, Miedel MT, Pei F, DiStefano JK, Debiasio R, Shun TY, Saydmohammed M, Chikina M, Vernetti LA, Soto-Gutierrez A, Monga SP, Bataller R, Behari J, Yechoor VK, Bahar I, Gough A, Stern AM, Taylor DL. A Quantitative Systems Pharmacology Platform Reveals NAFLD Pathophysiological States and Targeting Strategies. Metabolites 2022; 12:528. [PMID: 35736460 PMCID: PMC9227696 DOI: 10.3390/metabo12060528] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/28/2022] [Accepted: 06/03/2022] [Indexed: 11/17/2022] Open
Abstract
Non-alcoholic fatty liver disease (NAFLD) has a high global prevalence with a heterogeneous and complex pathophysiology that presents barriers to traditional targeted therapeutic approaches. We describe an integrated quantitative systems pharmacology (QSP) platform that comprehensively and unbiasedly defines disease states, in contrast to just individual genes or pathways, that promote NAFLD progression. The QSP platform can be used to predict drugs that normalize these disease states and experimentally test predictions in a human liver acinus microphysiology system (LAMPS) that recapitulates key aspects of NAFLD. Analysis of a 182 patient-derived hepatic RNA-sequencing dataset generated 12 gene signatures mirroring these states. Screening against the LINCS L1000 database led to the identification of drugs predicted to revert these signatures and corresponding disease states. A proof-of-concept study in LAMPS demonstrated mitigation of steatosis, inflammation, and fibrosis, especially with drug combinations. Mechanistically, several structurally diverse drugs were predicted to interact with a subnetwork of nuclear receptors, including pregnane X receptor (PXR; NR1I2), that has evolved to respond to both xenobiotic and endogenous ligands and is intrinsic to NAFLD-associated transcription dysregulation. In conjunction with iPSC-derived cells, this platform has the potential for developing personalized NAFLD therapeutic strategies, informing disease mechanisms, and defining optimal cohorts of patients for clinical trials.
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Affiliation(s)
- Daniel E. Lefever
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
| | - Mark T. Miedel
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
| | - Fen Pei
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
| | - Johanna K. DiStefano
- Diabetes and Fibrotic Disease Unit, Translational Genomics Research Institute TGen, Phoenix, AZ 85004, USA;
| | - Richard Debiasio
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
| | - Tong Ying Shun
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
| | - Manush Saydmohammed
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
| | - Maria Chikina
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Lawrence A. Vernetti
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
| | - Alejandro Soto-Gutierrez
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
- McGowan Institute for Regenerative Medicine, University of Pittsburgh, Pittsburgh, PA 15203, USA
| | - Satdarshan P. Monga
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
- Department of Pathology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Ramon Bataller
- Division of Gastroenterology Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; (R.B.); (J.B.)
| | - Jaideep Behari
- Division of Gastroenterology Hepatology and Nutrition, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15261, USA; (R.B.); (J.B.)
- UPMC Liver Clinic, University of Pittsburgh Medical Center, Pittsburgh, PA 15213, USA
| | - Vijay K. Yechoor
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Division of Endocrinology and Metabolism, Department of Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15203, USA
| | - Ivet Bahar
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
| | - Albert Gough
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
| | - Andrew M. Stern
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
| | - D. Lansing Taylor
- Drug Discovery Institute, University of Pittsburgh, Pittsburgh, PA 15261, USA; (D.E.L.); (M.T.M.); (R.D.); (T.Y.S.); (M.S.); (L.A.V.); (A.S.-G.); (S.P.M.); (V.K.Y.); (I.B.); (A.G.)
- Department of Computational and Systems Biology, School of Medicine, University of Pittsburgh, Pittsburgh, PA 15260, USA; (F.P.); (M.C.)
- Pittsburgh Liver Research Center, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Tian Y, Guan L, Qian Y, Wu Y, Gu Z. Effect of PPP1R14D gene high expression in lung adenocarcinoma knocked out on proliferation and apoptosis of DMS53 cell. Clin Transl Oncol 2022; 24:1914-1923. [PMID: 35579727 DOI: 10.1007/s12094-022-02842-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/13/2022] [Indexed: 12/24/2022]
Abstract
PURPOSE Globally, lung cancer remains the most commonly diagnosed cancer and the leading cause of cancer-related mortality. Lung adenocarcinoma (LUAD) is a common subtype of lung cancer and carries a poor prognosis. Treatment outcomes biomarkers in LUAD are critical, and there is currently a paucity of data; therefore, there is a need for novel biomarkers and newer therapeutic targets. METHODS Bayesian analysis was used to obtain the whole-genome t value of LUAD. Gene set enrichment analysis (GSEA) was conducted to obtain the normalized enrichment scores (NES) of the whole genome, and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway was analyzed using the Gene Set Analysis Toolkit. Herein, we investigated the PPP1R14D expression level at the protein level in LUAD and the impact of PPP1R14D knockdown on the proliferation and apoptosis of LUAD cells in vitro. RESULTS A total of 483 LUAD samples and 59 normal control samples were included, and 904 differentially expressed genes (DEGs) and 504 LUAD-related genes reported in the literature were obtained. The DEGs showed that PPP1R14D was the most significantly up-regulated gene. Western blot of 30 cases of LUAD tissue and adjacent normal tissue also found that PPP1R14D was significantly highly expressed in cancer tissues. Lentivirus-mediated shRNA strategy effectively inhibited PPP1R14D expression in human LUAD cells DMS53, while PPP1R14D knockdown induced apoptosis and cell proliferation in DMS53 cells. CONCLUSION Abnormally up-regulated PPP1R14D promotes the survival and proliferation of tumor cells in human LUAD and may serve as a therapeutic and diagnostic target for LUAD.
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Affiliation(s)
- Ye Tian
- Ward 2, Department of Respiratory Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Liguo Guan
- Department of Traditional Chinese Medicine, Jianhua District Hospital of Traditional Chinese Medicine, Qiqihar, 161000, China
| | - Yuting Qian
- Ward 2, Department of Respiratory Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Yue Wu
- Ward 2, Department of Respiratory Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China
| | - Zexin Gu
- Ward 2, Department of Respiratory Medicine, The Second Affiliated Hospital of Qiqihar Medical University, Qiqihar, 161000, China.
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LPS-induced lipid alterations in microglia revealed by MALDI mass spectrometry-based cell fingerprinting in neuroinflammation studies. Sci Rep 2022; 12:2908. [PMID: 35190595 PMCID: PMC8861089 DOI: 10.1038/s41598-022-06894-1] [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: 11/05/2021] [Accepted: 02/03/2022] [Indexed: 12/17/2022] Open
Abstract
Pathological microglia activation can promote neuroinflammation in many neurodegenerative diseases, and it has therefore emerged as a potential therapeutic target. Increasing evidence suggests alterations in lipid metabolism as modulators and indicators in microglia activation and its effector functions. Yet, how lipid dynamics in activated microglia is affected by inflammatory stimuli demands additional investigation to allow development of more effective therapies. Here, we report an extensive matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS) whole cell fingerprinting workflow to investigate inflammation-associated lipid patterns in SIM-A9 microglial cells. By combining a platform of three synergistic MALDI MS technologies we could detect substantial differences in lipid profiles of lipopolysaccharide (LPS)- stimulated and unstimulated microglia-like cells leading to the identification of 21 potential inflammation-associated lipid markers. LPS-induced lipids in SIM-A9 microglial cells include phosphatidylcholines, lysophosphatidylcholines (LysoPC), sphingolipids, diacylglycerols and triacylglycerols. Moreover, MALDI MS-based cell lipid fingerprinting of LPS-stimulated SIM-A9 microglial cells pre-treated with the non-selective histone deacetylase inhibitor suberoylanilide hydroxamic acid revealed specific modulation of LPS-induced-glycerolipids and LysoPC(18:0) with a significant reduction of microglial inflammation response. Our study introduces MALDI MS as a complementary technology for fast and label-free investigation of stimulus-dependent changes in lipid patterns and their modulation by pharmaceutical agents.
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Abstract
Introduction: Nonalcoholic fatty liver disease (NAFLD) is a group of diseases related to metabolic abnormalities, which severely impairs the life and health of patients, and brings great pressure to the society and medical resources. Currently, there is no specific treatment. Histone deacetylases (HDACs) have recently been reported to be involved in the pathogenesis of NAFLD and are considered as new targets for the treatment of NAFLD.Area covered: In this review, we summarized the role of HDACs in the pathogenesis of NAFLD and proposed possible therapeutic targets in order to provide new strategies for the treatment of NAFLD.Expert commentary: HDACs and related signal pathways are widely involved in the pathogenesis of NAFLD and have the potential to become therapeutic targets. However, based on current research alone, HDACs cannot be practical applied to the treatment of NAFLD. Therefore, more research on the pathogenesis of NAFLD and the mechanism of HDACs is what we need most now.
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Affiliation(s)
- Shifeng Fu
- Department of Gastroenterology, the Second Xiangya Hospital, Central South University, Changsha, Hunan China.,Research Center of Digestive Disease, Central South University, Changsha, HunanChina
| | - Meihong Yu
- Department of Gastroenterology, the Second Xiangya Hospital, Central South University, Changsha, Hunan China.,Research Center of Digestive Disease, Central South University, Changsha, HunanChina
| | - Yuyong Tan
- Department of Gastroenterology, the Second Xiangya Hospital, Central South University, Changsha, Hunan China.,Research Center of Digestive Disease, Central South University, Changsha, HunanChina
| | - Dengliang Liu
- Department of Gastroenterology, the Second Xiangya Hospital, Central South University, Changsha, Hunan China.,Research Center of Digestive Disease, Central South University, Changsha, HunanChina
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Perakakis N, Stefanakis K, Mantzoros CS. The role of omics in the pathophysiology, diagnosis and treatment of non-alcoholic fatty liver disease. Metabolism 2020; 111S:154320. [PMID: 32712221 PMCID: PMC7377759 DOI: 10.1016/j.metabol.2020.154320] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/02/2020] [Revised: 07/15/2020] [Accepted: 07/18/2020] [Indexed: 12/12/2022]
Abstract
Non-alcoholic fatty liver disease (NAFLD) is a multifaceted metabolic disorder, whose spectrum covers clinical, histological and pathophysiological developments ranging from simple steatosis to non-alcoholic steatohepatitis (NASH) and liver fibrosis, potentially evolving into cirrhosis, hepatocellular carcinoma and liver failure. Liver biopsy remains the gold standard for diagnosing NAFLD, while there are no specific treatments. An ever-increasing number of high-throughput Omics investigations on the molecular pathobiology of NAFLD at the cellular, tissue and system levels produce comprehensive biochemical patient snapshots. In the clinical setting, these applications are considerably enhancing our efforts towards obtaining a holistic insight on NAFLD pathophysiology. Omics are also generating non-invasive diagnostic modalities for the distinct stages of NAFLD, that remain though to be validated in multiple, large, heterogenous and independent cohorts, both cross-sectionally as well as prospectively. Finally, they aid in developing novel therapies. By tracing the flow of information from genomics to epigenomics, transcriptomics, proteomics, metabolomics, lipidomics and glycomics, the chief contributions of these techniques in understanding, diagnosing and treating NAFLD are summarized herein.
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Affiliation(s)
- Nikolaos Perakakis
- Department of Internal Medicine, Boston VA Healthcare system and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA..
| | - Konstantinos Stefanakis
- Department of Internal Medicine, Boston VA Healthcare system and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Christos S Mantzoros
- Department of Internal Medicine, Boston VA Healthcare system and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
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Xu F, Guo W. The progress of epigenetics in the development and progression of non-alcoholic fatty liver disease. LIVER RESEARCH 2020. [DOI: 10.1016/j.livres.2020.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
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Bayoumi A, Grønbæk H, George J, Eslam M. The Epigenetic Drug Discovery Landscape for Metabolic-associated Fatty Liver Disease. Trends Genet 2020; 36:429-441. [PMID: 32396836 DOI: 10.1016/j.tig.2020.03.003] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/05/2020] [Accepted: 03/09/2020] [Indexed: 02/07/2023]
Abstract
Despite decades of research, effective therapies for metabolic (dysfunction)-associated fatty liver disease (MAFLD) are lacking. An increasing body of evidence suggests that epigenetic dysregulation is frequent in MAFLD, and orchestrates many aspects of its development and progression. Furthermore, the high plasticity of epigenetic modifications in response to environmental cues renders epigenetics a novel area for therapeutic drug discovery. Over recent years, several epigenetics-based drugs and diagnostic biomarkers have entered clinical development and/or obtained regulatory approval. Here, we review recent advances in our understanding of epigenetic regulation and programming during MAFLD, including DNA methylation, histone modifications, chromatin remodelling, transcriptional control, and noncoding (nc)RNAs. We also discuss the potential translational implications and challenges of epigenetics in the context of MAFLD.
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Affiliation(s)
- Ali Bayoumi
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Henning Grønbæk
- Department of Hepatology and Gastroenterology, Aarhus University Hospital, Aarhus, Denmark
| | - Jacob George
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia
| | - Mohammed Eslam
- Storr Liver Centre, Westmead Institute for Medical Research, Westmead Hospital and University of Sydney, NSW, Australia.
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