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You H, Wang L, Bu F, Meng H, Pan X, Li J, Zhang Y, Wang A, Yin N, Huang C, Li J. The miR-455-3p/HDAC2 axis plays a pivotal role in the progression and reversal of liver fibrosis and is regulated by epigenetics. FASEB J 2021; 35:e21700. [PMID: 34105828 DOI: 10.1096/fj.202002319rrr] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 01/29/2021] [Accepted: 05/11/2021] [Indexed: 12/29/2022]
Abstract
Histone deacetylases (HDACs), especially HDAC2, play a role in alleviating liver fibrosis; however, the specific upstream regulation mechanism is unknown. Herein, TargetScan was used to predict the potential upstream targets of HDAC2, and the role of miR-455-3p was explored. The dual luciferase reporter assay showed that miR-455-3p binds to the 3' UTR of HDAC2 mRNA. Additionally, miR-455-3p was downregulated in the liver tissues of patients with cirrhosis and mice with liver fibrosis, as well as in primary HSCs isolated from fibrotic mouse livers and TGF-β-treated LX-2 cells. In contrast, it is highly expressed in the reversal stage of hepatic fibrosis and MDI-cultured LX-2 cells. Our functional analyses showed that miR-455-3p overexpression facilitated apoptosis and reduced the expression of pro-fibrotic markers and the proliferation of activated LX-2 cells. On the contrary, miR-455-3p inhibition converted inactivated LX-2 cells into activated, proliferative, fibrogenic cells. Interestingly, restoration of HDAC2 expression partially blocked the function of miR-455-3p. Downregulated miR-455-3p expression can be restored by DNA methyltransferases in activated LX-2 cells. Methylation-specific PCR, bisulfite sequencing PCR, and chromatin immunoprecipitation assays indicated that the methylation level of miR-455-3p promoter CpG islands was elevated in TGF-β-treated LX-2 cells and that miR-455-3p was downregulated in activated LX-2 cells by DNA hypermethylation, which is mediated by DNMT3b and DNMT1. In conclusion, miR-455-3p acts as a liver fibrosis suppressor by targeting HDAC2, and its deficiency further aggravates the reversal phase of fibrosis. Thus, the epigenetics mediated miR-455-3p/HDAC2 axis may serve as a novel potential therapeutic target for clinical treatment of hepatic fibrosis.
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Affiliation(s)
- Hongmei You
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Ling Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Fangtian Bu
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Hongwu Meng
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Xueyin Pan
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Juanjuan Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Yafei Zhang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Ao Wang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Nana Yin
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Cheng Huang
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
| | - Jun Li
- Inflammation and Immune Mediated Diseases Laboratory of Anhui Province, Anhui Institute of Innovative Drugs, School of Pharmacy, Anhui Medical University, Hefei, China
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2
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Liu YR, Wang JQ, Huang ZG, Chen RN, Cao X, Zhu DC, Yu HX, Wang XR, Zhou HY, Xia Q, Li J. Histone deacetylase‑2: A potential regulator and therapeutic target in liver disease (Review). Int J Mol Med 2021; 48:131. [PMID: 34013366 PMCID: PMC8136123 DOI: 10.3892/ijmm.2021.4964] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 04/12/2021] [Indexed: 12/12/2022] Open
Abstract
Histone acetyltransferases are responsible for histone acetylation, while histone deacetylases (HDACs) counteract histone acetylation. An unbalanced dynamic between histone acetylation and deacetylation may lead to aberrant chromatin landscape and chromosomal function. HDAC2, a member of class I HDAC family, serves a crucial role in the modulation of cell signaling, immune response and gene expression. HDAC2 has emerged as a promising therapeutic target for liver disease by regulating gene transcription, chromatin remodeling, signal transduction and nuclear reprogramming, thus receiving attention from researchers and clinicians. The present review introduces biological information of HDAC2 and its physiological and biochemical functions. Secondly, the functional roles of HDAC2 in liver disease are discussed in terms of hepatocyte apoptosis and proliferation, liver regeneration, hepatocellular carcinoma, liver fibrosis and non-alcoholic steatohepatitis. Moreover, abnormal expression of HDAC2 may be involved in the pathogenesis of liver disease, and its expression levels and pharmacological activity may represent potential biomarkers of liver disease. Finally, research on selective HDAC2 inhibitors and non-coding RNAs relevant to HDAC2 expression in liver disease is also reviewed. The aim of the present review was to improve understanding of the multifunctional role and potential regulatory mechanism of HDAC2 in liver disease.
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Affiliation(s)
- Ya-Ru Liu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Jie-Quan Wang
- Department of Pharmacy, Affiliated Psychological Hospital of Anhui Medical University, Hefei, Anhui 230000, P.R. China
| | - Zhao-Gang Huang
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Ruo-Nan Chen
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xi Cao
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Dong-Chun Zhu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Hai-Xia Yu
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Xiu-Rong Wang
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Hai-Yun Zhou
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Quan Xia
- Department of Pharmacy, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui 230022, P.R. China
| | - Jun Li
- The Key Laboratory of Anti‑inflammatory Immune Medicines, School of Pharmacy, Anhui Medical University, Ministry of Education, Hefei, Anhui 230032, P.R. China
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3
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Rahman L, Williams A, Gelda K, Nikota J, Wu D, Vogel U, Halappanavar S. 21st Century Tools for Nanotoxicology: Transcriptomic Biomarker Panel and Precision-Cut Lung Slice Organ Mimic System for the Assessment of Nanomaterial-Induced Lung Fibrosis. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2020; 16:e2000272. [PMID: 32347014 DOI: 10.1002/smll.202000272] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Revised: 03/23/2020] [Accepted: 03/24/2020] [Indexed: 06/11/2023]
Abstract
There is an urgent need for reliable toxicity assays to support the human health risk assessment of an ever increasing number of engineered nanomaterials (ENMs). Animal testing is not a suitable option for ENMs. Sensitive in vitro models and mechanism-based targeted in vitro assays that enable accurate prediction of in vivo responses are not yet available. In this proof-of-principle study, publicly available mouse lung transcriptomics data from studies investigating xenobiotic-induced lung diseases are used and a 17-gene biomarker panel (PFS17) applicable to the assessment of lung fibrosis is developed. The PFS17 is validated using a limited number of in vivo mouse lung transcriptomics datasets from studies investigating ENM-induced responses. In addition, an ex vivo precision-cut lung slice (PCLS) model is optimized for screening of potentially inflammogenic and pro-fibrotic ENMs. Using bleomycin and a multiwalled carbon nanotube, the practical application of the PCLS method as a sensitive alternative to whole animal tests to screen ENMs that may potentially induce inhalation toxicity is shown. Conditional to further optimization and validation, it is established that a combination of PFS17 and the ex vivo PCLS method will serve as a robust and sensitive approach to assess lung inflammation and fibrosis induced by ENMs.
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Affiliation(s)
- Luna Rahman
- Environmental Health Science and Research Bureau, Health Canada, Sir Frederick G Banting Research Centre, 251 Sir Frederick Banting Driveway, Building 22, Ottawa, ON, K1A 0K9, Canada
| | - Andrew Williams
- Environmental Health Science and Research Bureau, Health Canada, Sir Frederick G Banting Research Centre, 251 Sir Frederick Banting Driveway, Building 22, Ottawa, ON, K1A 0K9, Canada
| | - Krishna Gelda
- Environmental Health Science and Research Bureau, Health Canada, Sir Frederick G Banting Research Centre, 251 Sir Frederick Banting Driveway, Building 22, Ottawa, ON, K1A 0K9, Canada
| | - Jake Nikota
- Environmental Health Science and Research Bureau, Health Canada, Sir Frederick G Banting Research Centre, 251 Sir Frederick Banting Driveway, Building 22, Ottawa, ON, K1A 0K9, Canada
| | - Dongmei Wu
- Environmental Health Science and Research Bureau, Health Canada, Sir Frederick G Banting Research Centre, 251 Sir Frederick Banting Driveway, Building 22, Ottawa, ON, K1A 0K9, Canada
| | - Ulla Vogel
- National Research Centre for the Working Environment, Lersø Parkallé 105, Copenhagen, 2100, Denmark
- Department of Micro- and Nanotechnology, Technical University of Denmark, Building 101A 2800 Copenhagen, Lyngby, Denmark
| | - Sabina Halappanavar
- Environmental Health Science and Research Bureau, Health Canada, Sir Frederick G Banting Research Centre, 251 Sir Frederick Banting Driveway, Building 22, Ottawa, ON, K1A 0K9, Canada
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4
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Chen G, Chen J, Liu H, Chen S, Zhang Y, Li P, Thierry-Mieg D, Thierry-Mieg J, Mattes W, Ning B, Shi T. Comprehensive Identification and Characterization of Human Secretome Based on Integrative Proteomic and Transcriptomic Data. Front Cell Dev Biol 2019; 7:299. [PMID: 31824949 PMCID: PMC6881247 DOI: 10.3389/fcell.2019.00299] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2019] [Accepted: 11/07/2019] [Indexed: 12/25/2022] Open
Abstract
Secreted proteins (SPs) play important roles in diverse important biological processes; however, a comprehensive and high-quality list of human SPs is still lacking. Here we identified 6,943 high-confidence human SPs (3,522 of them are novel) based on 330,427 human proteins derived from databases of UniProt, Ensembl, AceView, and RefSeq. Notably, 6,267 of 6,943 (90.3%) SPs have the supporting evidences from a large amount of mass spectrometry (MS) and RNA-seq data. We found that the SPs were broadly expressed in diverse tissues as well as human body fluid, and a significant portion of them exhibited tissue-specific expression. Moreover, 14 cancer-specific SPs that their expression levels were significantly associated with the patients’ survival of eight different tumors were identified, which could be potential prognostic biomarkers. Strikingly, 89.21% of 6,943 SPs (2,927 novel SPs) contain known protein domains. Those novel SPs we mainly enriched with the known domains regarding immunity, such as Immunoglobulin V-set and C1-set domain. Specifically, we constructed a user-friendly and freely accessible database, SPRomeDB (www.unimd.org/SPRomeDB), to catalog those SPs. Our comprehensive SP identification and characterization gain insights into human secretome and provide valuable resource for future researches.
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Affiliation(s)
- Geng Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Jiwei Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Huanlong Liu
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Shuangguan Chen
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Yang Zhang
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Peng Li
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
| | - Danielle Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - Jean Thierry-Mieg
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, United States
| | - William Mattes
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Baitang Ning
- National Center for Toxicological Research, Food and Drug Administration, Jefferson City, AR, United States
| | - Tieliu Shi
- The Center for Bioinformatics and Computational Biology, Shanghai Key Laboratory of Regulatory Biology, The Institute of Biomedical Sciences and School of Life Sciences, East China Normal University, Shanghai, China
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5
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Metabolic Signature of Hepatic Fibrosis: From Individual Pathways to Systems Biology. Cells 2019; 8:cells8111423. [PMID: 31726658 PMCID: PMC6912636 DOI: 10.3390/cells8111423] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2019] [Revised: 11/08/2019] [Accepted: 11/10/2019] [Indexed: 02/06/2023] Open
Abstract
Hepatic fibrosis is a major cause of morbidity and mortality worldwide, as it ultimately leads to cirrhosis, which is estimated to affect up to 2% of the global population. Hepatic fibrosis is confirmed by liver biopsy, and the erroneous nature of this technique necessitates the search for noninvasive alternatives. However, current biomarker algorithms for hepatic fibrosis have many limitations. Given that the liver is the largest organ and a major metabolic hub in the body, probing the metabolic signature of hepatic fibrosis holds promise for the discovery of new markers and therapeutic targets. Regarding individual metabolic pathways, accumulating evidence shows that hepatic fibrosis leads to alterations in carbohydrate metabolism, as aerobic glycolysis is aggravated in activated hepatic stellate cells (HSCs) and the whole fibrotic liver; in amino acid metabolism, as Fischer’s ratio (branched-chain amino acids/aromatic amino acids) decreases in patients with hepatic fibrosis; and in lipid metabolism, as HSCs lose vitamin A-containing lipid droplets during transdifferentiation, and cirrhotic patients have decreased serum lipids. The current review also summarizes recent findings of metabolic alterations relevant to hepatic fibrosis based on systems biology approaches, including transcriptomics, proteomics, and metabolomics in vitro, in animal models and in humans.
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6
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Kim HS, Yoon YM, Meang MK, Park YE, Lee JY, Lee TH, Lee JE, Kim IH, Youn BS. Reversion of in vivo fibrogenesis by novel chromone scaffolds. EBioMedicine 2019; 39:484-496. [PMID: 30611717 PMCID: PMC6355727 DOI: 10.1016/j.ebiom.2018.12.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 12/10/2018] [Accepted: 12/10/2018] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Myofibroblasts are known to play a key role in the development of idiopathic pulmonary fibrosis (IPF). Two drugs, pirfenidone and nintedanib, are the only approved therapeutic options for IPF, but their applications are limited due to their side effects. Thus, curative IPF drugs represent a huge unmet medical need. METHODS A mouse hepatic stellate cell (HSC) line was established that could robustly differentiate into myofibroblasts upon treatment with TGF-β. Eupatilin was assessed in diseased human lung fibroblasts from IPF patients (DHLFs) as well as in human lung epithelial cells (HLECs). The drug's performance was extensively tested in a bleomycin-induced lung fibrosis model (BLM). Global gene expression studies and proteome analysis were performed. FINDINGS Eupatilin attenuated disease severity of BLM in both preventative and therapeutic studies. The drug inhibited the in vitro transdifferantiation of DHLFs to myofibroblasts upon stimulation with TGF-β. No such induction of the in vitro transdifferantiation was observed in TGF-β treated HLECs. Specific carbons of eupatilin were essential for its anti-fibrotic activity. Eupatilin was capable of dismantling latent TGF-β complex, specifically by eliminating expression of the latent TGF-β binding protein 1 (LTBP1), in ECM upon actin depolymerization. Unlike eupatilin, pirfenidone was unable to block fibrosis of DHLFs or HSCs stimulated with TGF-β. Eupatilin attenuated phosphorylation of Smad3 by TGF-β. Eupatilin induced myofibroblasts to dedifferentiate into intermediate HCS-like cells. INTERPRETATION Eupatilin may act directly on pathogenic myofibroblasts, disarming them, whereas the anti-fibrotic effect of pirfenidone may be indirect. Eupatilin could increase the efficacy of IPF treatment to curative levels.
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Affiliation(s)
- Han-Soo Kim
- Department of Biomedical Sciences, Catholic Kwandong University College of Medicine, Gangneung-si, Gangwon-do 25601, Republic of Korea; Basic Research Division, Biomedical Institute of Mycological Resource, College of Medicine,Catholic Kwandong University, Gangneung-si, Gangwon-do, 25601, Republic of Korea
| | | | - Moon Kee Meang
- OsteoNeuroGenInc, Seoul 08501, Republic of Korea; Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
| | - Yae Eun Park
- Center for Theragnosis, Biomedical Research Institute, Korean Institute of Science and Technology, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea; College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ji Yong Lee
- Department of Anatomy, Yonsei University Wonju College of Medicine, Wonju-si, Gangwon-do 26426, Republic of Korea
| | - Tae Hee Lee
- School of Oriental Medicine, Formulae Pharmacology Department, Gachon University, Seongnam-si 13120, Republic of Korea
| | - Ji Eun Lee
- Center for Theragnosis, Biomedical Research Institute, Korean Institute of Science and Technology, Department of Biochemistry, College of Life Science and Biotechnology, Yonsei University, Seoul 03722, Republic of Korea
| | - Ik-Hwan Kim
- Department of Biotechnology, Korea University, Seoul 02841, Republic of Korea
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7
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Anjo SI, Manadas B. A translational view of cells' secretome analysis - from untargeted proteomics to potential circulating biomarkers. Biochimie 2018; 155:37-49. [DOI: 10.1016/j.biochi.2018.05.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 05/16/2018] [Indexed: 02/06/2023]
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8
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Giraudi PJ, Gambaro SE, Ornelas Arroyo S, Chackelevicius CM, Giuricin M, Silvestri M, Macor D, Crocé LS, Bonazza D, Soardo G, de Manzini N, Zanconati F, Tiribelli C, Palmisano S, Rosso N. A simple in silico strategy identifies candidate biomarkers for the diagnosis of liver fibrosis in morbidly obese subjects. Liver Int 2018. [PMID: 28650518 DOI: 10.1111/liv.13505] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND & AIMS Non-alcoholic fatty liver disease (NAFLD) is a chronic liver disorder, tightly associated with obesity. The histological spectrum of the disease ranges from simple steatosis to steatohepatitis, with different stages of fibrosis, and fibrosis stage is the most significant predictor of mortality in NAFLD. Liver biopsy continues to be the gold standard for its diagnosis and reliable non-invasive diagnostic tools are unavailable. We investigated the accuracy of candidate proteins, identified by an in silico approach, as biomarkers for diagnosis of fibrosis. METHODS Seventy-one morbidly obese (MO) subjects with biopsy-proven NAFLD were enrolled, and the cohort was subdivided according to minimal (F0/F1) or moderate (F2/F3) fibrosis. The plasmatic level of CD44 antigen (CD44), secreted protein acidic and rich in cysteine (SPARC), epidermal growth factor receptor (EGFR) and insulin-like growth factor 2 (IGF2) were determined by ELISA. Significant associations between plasmatic levels and histological fibrosis were determined by correlation analysis and the diagnostic accuracy by the area under receiver operating characteristic curves (AUROC). RESULTS Eighty-two percentage of the subjects had F0/F1 and 18% with F2/F3 fibrosis. Plasmatic levels of IGF2, EGFR and their ratio (EGFR/IGF2) were associated with liver fibrosis, correlating inversely for IGF2 (P < .006) and directly (P < .018; P < .0001) for EGFR and EGFR/IGF2 respectively. The IGF2 marker had the best diagnostic accuracy for moderate fibrosis (AUROC 0.83), followed by EGFR/IGF2 ratio (AUROC 0.79) and EGFR (AUROC 0.71). CONCLUSIONS Our study supports the potential utility of IGF2 and EGFR as non-invasive diagnostic biomarkers for liver fibrosis in morbidly obese subjects.
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Affiliation(s)
- Pablo J Giraudi
- Fondazione Italiana Fegato, Centro Studi Fegato, Trieste, Italy
| | | | | | | | - Michela Giuricin
- Chirurgia Generale, Ospedale di Cattinara, Università degli Studi di Trieste, Trieste, Italy
| | - Marta Silvestri
- Chirurgia Generale, Ospedale di Cattinara, Università degli Studi di Trieste, Trieste, Italy.,Dipartimento Universitario Clinico di Scienze Mediche Chirurgiche e della Salute, Università degli Studi di Trieste, Trieste, Italy
| | - Daniele Macor
- Clinica Patologie del Fegato, Dip. Medicina Ospedale Cattinara, Università degli Studi di Trieste, Trieste, Italy
| | - Lory S Crocé
- Clinica Patologie del Fegato, Dip. Medicina Ospedale Cattinara, Università degli Studi di Trieste, Trieste, Italy
| | - Deborah Bonazza
- Dipartimento Universitario Clinico di Scienze Mediche Chirurgiche e della Salute, Università degli Studi di Trieste, Trieste, Italy.,School of Anatomic Pathology, University of Udine and Trieste, Trieste, Italy
| | - Giorgio Soardo
- Dipartimento di Scienze Mediche Sperimentali e Cliniche, Azienda Ospedaliero Universitaria Santa Maria della Misericordia di Udine, Trieste, Italy
| | - Nicolò de Manzini
- Chirurgia Generale, Ospedale di Cattinara, Università degli Studi di Trieste, Trieste, Italy.,Dipartimento Universitario Clinico di Scienze Mediche Chirurgiche e della Salute, Università degli Studi di Trieste, Trieste, Italy
| | - Fabrizio Zanconati
- Dipartimento Universitario Clinico di Scienze Mediche Chirurgiche e della Salute, Università degli Studi di Trieste, Trieste, Italy.,School of Anatomic Pathology, University of Udine and Trieste, Trieste, Italy
| | | | - Silvia Palmisano
- Chirurgia Generale, Ospedale di Cattinara, Università degli Studi di Trieste, Trieste, Italy.,Dipartimento Universitario Clinico di Scienze Mediche Chirurgiche e della Salute, Università degli Studi di Trieste, Trieste, Italy
| | - Natalia Rosso
- Fondazione Italiana Fegato, Centro Studi Fegato, Trieste, Italy
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9
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Zhao F, Fang L, Wang D, Song T, Wang T, Xin Y, Chen H, Xiao S. SILAC-based quantitative proteomic analysis of secretome of Marc-145 cells infected with porcine reproductive and respiratory syndrome virus. Proteomics 2016; 16:2678-2687. [PMID: 27493009 DOI: 10.1002/pmic.201500486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Revised: 07/26/2016] [Accepted: 08/03/2016] [Indexed: 12/17/2022]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is the causative agent of PRRS, which causes severe reproductive failure in sows, respiratory disease in young and growing pigs, and enormous economic losses to the global swine industry. In this study, SILAC combined with MS/MS was used to quantitatively identify the secretory proteins differentially expressed in PRRSV-infected Marc-145 cells compared with mock-infected controls. In total, we identified 204 secretory proteins showing significant differences in infected cells (163 upregulated, 41 downregulated). Intensive bioinformatic analysis of secretome data revealed that PRRSV infection strongly activated nonclassical protein secretion, especially vesicle-mediated release of exosomal proteins, including different danger-associated molecular pattern molecules and the majority of secreted proteins involved in protein binding and transport, regulation of response to stimulus, metabolic processes, and immune responses. According to the functional proteins analysis, we speculate that proteins functioning in binding, transport, and the immune response are exploited by PRRSV to facilitate virus replication and immune evasion. Our study for the first time analyzes the secretory protein profile of PRRSV-infected Marc-145 cells and provides valuable insight into the host response to PRRSV infection.
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Affiliation(s)
- Fuwei Zhao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Liurong Fang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Dang Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Tao Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Ting Wang
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Yinghao Xin
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Huanchun Chen
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China
| | - Shaobo Xiao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, Hubei, P. R. China. .,Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, Hubei, P. R. China.
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10
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Yu H, Wang F, Lin L, Cao W, Liu Y, Qin L, Lu H, He F, Shen H, Yang P. Mapping and analyzing the human liver proteome: progress and potential. Expert Rev Proteomics 2016; 13:833-43. [PMID: 27448621 DOI: 10.1080/14789450.2016.1213132] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION The liver is an important organ in humans. Hepatocellular carcinoma (HCC) is one of the deadliest cancers in the world. Progress in the Human Liver Proteome Project (HLPP) has improved understanding of the liver and the liver cancer proteome. AREAS COVERED Here, we summarize the recent progress in liver proteome modification profiles, proteomic studies in liver cancer, proteomic study in the search for novel liver cancer biomarkers and drug targets, and progress of the Chromosome Centric Human Proteome Project (CHPP) in the past five years in the Institutes of Biomedical Sciences (IBS) of Fudan University. Expert commentary: Recent advances and findings discussed here provide great promise of improving the outcome of patients with liver cancer.
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Affiliation(s)
- Hongxiu Yu
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Fang Wang
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Ling Lin
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Weiqian Cao
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China
| | - Yinkun Liu
- c China Liver Cancer Institute, Zhongshan Hospital , Fudan University , Shanghai , China
| | - Lunxiu Qin
- c China Liver Cancer Institute, Zhongshan Hospital , Fudan University , Shanghai , China
| | - Haojie Lu
- b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Fuchu He
- d State Key Laboratory of Proteomics, Beijing Proteome Research Center , Beijing Institute of Radiation Medicine , Beijing , China
| | - Huali Shen
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
| | - Pengyuan Yang
- a Department of Systems Biology for Medicine, School of Basic Medical Sciences , Fudan University , Shanghai , China.,b Minhang Hospital and Institutes of Biomedical Sciences , Fudan University , Shanghai , China
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Proteomic analysis of the secretome of HepG2 cells indicates differential proteolytic processing after infection with dengue virus. J Proteomics 2016; 151:106-113. [PMID: 27427332 DOI: 10.1016/j.jprot.2016.07.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2016] [Revised: 06/27/2016] [Accepted: 07/13/2016] [Indexed: 01/04/2023]
Abstract
Secretome analysis can be described as a subset of proteomics studies consisting in the analysis of the molecules secreted by cells or tissues. Dengue virus (DENV) infection can lead to a broad spectrum of clinical manifestations, with the severe forms of the disease characterized by hemostasis abnormalities and liver injury. The hepatocytes are a relevant site of viral replication and a major source of plasma proteins. Until now, we had limited information on the small molecules secreted by hepatic cells after infection by DENV. In the present study, we analysed a fraction of the secretome of mock- and DENV-infected hepatic cells (HepG2 cells) containing molecules with <10kDa, using different proteomic approaches. We identified 175 proteins, with 57 detected only in the samples from mock-infected cells, 59 only in samples from DENV-infected cells, and 59 in both conditions. Most of the peptides identified were derived from proteins larger than 10kDa, suggesting a proteolytic processing of the secreted molecules. Using in silico analysis, we predicted consistent differences between the proteolytic processing occurring in mock and DENV-infected samples, raising, for the first time, the hypothesis that differential proteolysis of secreted molecules would be involved in the pathogenesis of dengue. BIOLOGICAL SIGNIFICANCE Since the liver, one of the targets of DENV infection, is responsible for producing molecules involved in distinct biological processes, the identification of proteins and peptides secreted by hepatocytes after infection would help to a better understanding of the physiopathology of dengue. Proteomic analyses of molecules with <10kDa secreted by HepG2 cells after infection with DENV revealed differential proteolytic processing as an effect of DENV infection.
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Li X, Wu XQ, Xu T, Li XF, Yang Y, Li WX, Huang C, Meng XM, Li J. Role of histone deacetylases(HDACs) in progression and reversal of liver fibrosis. Toxicol Appl Pharmacol 2016; 306:58-68. [PMID: 27396813 DOI: 10.1016/j.taap.2016.07.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Revised: 06/19/2016] [Accepted: 07/06/2016] [Indexed: 01/10/2023]
Abstract
Liver fibrosis refers to a reversible wound healing process response to chronic liver injuries. Activation of hepatic stellate cells (HSCs) is closely correlated with the development of liver fibrosis. Histone deacetylases(HDACs) determine the acetylation levels of core histones to modulate expression of genes. To demonstrate the link between HDACs and liver fibrosis, CCl4-induced mouse liver fibrosis model and its spontaneous reversal model were established. Results of the current study demonstrated that deregulation of liver HDACs may involved in the development of liver fibrosis. Among 11 HDACs tested in our study (Class I, II, and IV HDACs), expression of HDAC2 was maximally increased in CCl4-induced fibrotic livers but decreased after spontaneous recovery. Moreover, expression of HDAC2 was elevated in human liver fibrotic tissues. In this regard, the potential role of HDAC2 in liver fibrosis was further evaluated. Our results showed that administration of HSC-T6 cells with transforming growth factor-beta1 (TGF-β1) resulted in an increase of HDAC2 protein expression in dose- and time-dependent manners. Moreover, HDAC2 deficiency inhibited HSC-T6 cell proliferation and activation induced by TGF-β1. More importantly, the present study showed HDAC2 may regulate HSCs activation by suppressing expression of Smad7, which is a negative modulator in HSCs activation and liver fibrosis. Collectively, these observations revealed that HDAC2 may play a pivotal role in HSCs activation and liver fibrosis while deregulation of HDACs may serve as a novel mechanism underlying liver fibrosis.
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Affiliation(s)
- Xing Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Xiao-Qin Wu
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Tao Xu
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Xiao-Feng Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Yang Yang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Wan-Xia Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Cheng Huang
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Xiao-Ming Meng
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China
| | - Jun Li
- School of Pharmacy, Anhui Medical University, Hefei 230032, China; Anhui Key Laboratory of Bioactivity of Natural Products, Anhui Medical University, Hefei 230032, China; The Key Laboratory of Anti-inflammatory and Immune Medicine, Anhui Medical University, Ministry of Education, Hefei 230032, China; Institute for Liver Diseases of Anhui Medical University (ILD-AMU), Anhui Medical University, Hefei 230032, China.
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Liu X, Wu Y, Yang Y, Li W, Huang C, Meng X, Li J. Role of NLRC5 in progression and reversal of hepatic fibrosis. Toxicol Appl Pharmacol 2016; 294:43-53. [DOI: 10.1016/j.taap.2016.01.012] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2015] [Revised: 01/15/2016] [Accepted: 01/19/2016] [Indexed: 12/15/2022]
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Chen PJ, Cai SP, Yang Y, Li WX, Huang C, Meng XM, Li J. PTP1B confers liver fibrosis by regulating the activation of hepatic stellate cells. Toxicol Appl Pharmacol 2016; 292:8-18. [DOI: 10.1016/j.taap.2015.12.021] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2015] [Revised: 12/23/2015] [Accepted: 12/24/2015] [Indexed: 01/21/2023]
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Zhang X, Xu L, Yin L, Qi Y, Xu Y, Han X, Peng J. Quantitative chemical proteomics for investigating the biomarkers of dioscin against liver fibrosis caused by CCl4 in rats. Chem Commun (Camb) 2015; 51:11064-7. [DOI: 10.1039/c4cc09160d] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
2D-DIGE technology was used for screening the biomarkers and drug-targets of dioscin against liver fibrosis in rats caused by CCl4.
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Affiliation(s)
- Xiaoling Zhang
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
| | - Lina Xu
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
| | - Lianhong Yin
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
| | - Yan Qi
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
| | - Youwei Xu
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
| | - Xu Han
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
| | - Jinyong Peng
- College of Pharmacy
- Dalian Medical University
- Dalian 116044
- China
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