1
|
Sabater L, Locatelli L, Oakley F, Hardy T, French J, Robinson SM, Sen G, Mann DA, Mann J. RNA sequencing reveals changes in the microRNAome of transdifferentiating hepatic stellate cells that are conserved between human and rat. Sci Rep 2020; 10:21708. [PMID: 33303921 PMCID: PMC7728773 DOI: 10.1038/s41598-020-78776-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Accepted: 11/26/2020] [Indexed: 12/19/2022] Open
Abstract
MicroRNAs are small (~ 22nt long) noncoding RNAs (ncRNAs) that regulate gene expression at the post-transcriptional level. Over 2000 microRNAs have been described in humans and many are implicated in human pathologies including tissue fibrosis. Hepatic stellate cells (HSC) are the major cellular contributors to excess extracellular matrix deposition in the diseased liver and as such are important in the progression of liver fibrosis. We employed next generation sequencing to map alterations in the expression of microRNAs occurring across a detailed time course of culture-induced transdifferentiation of primary human HSC, this a key event in fibrogenesis. Furthermore, we compared profiling of human HSC microRNAs with that of rat HSC so as to identify those molecules that are conserved with respect to modulation of expression. Our analysis reveals that a total of 229 human microRNAs display altered expression as a consequence of HSC transdifferentiation and of these 104 were modulated early during the initiation phase. Typically modulated microRNAs were targeting kinases, transcription factors, chromatin factors, cell cycle regulators and growth factors. 162 microRNAs changed in expression during transdifferentiation of rat HSC, however only 17 underwent changes that were conserved in human HSC. Our study therefore identifies widespread changes in the expression of HSC microRNAs in fibrogenesis, but suggests a need for caution when translating data obtained from rodent HSC to events occurring in human cells.
Collapse
Affiliation(s)
- Laura Sabater
- Newcastle Fibrosis Research Group, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Luigi Locatelli
- Newcastle Fibrosis Research Group, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Fiona Oakley
- Newcastle Fibrosis Research Group, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Timothy Hardy
- Newcastle Fibrosis Research Group, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jeremy French
- Department of Hepatobiliary Surgery, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Stuart M Robinson
- Department of Hepatobiliary Surgery, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - Gourab Sen
- Department of Hepatobiliary Surgery, Newcastle Upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne, UK
| | - D A Mann
- Newcastle Fibrosis Research Group, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jelena Mann
- Newcastle Fibrosis Research Group, Bioscience Institute, Faculty of Medical Sciences, Newcastle University, 4th Floor, William Leech Building, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
| |
Collapse
|
2
|
Cui Z, Huang N, Liu L, Li X, Li G, Chen Y, Wu Q, Zhang J, Long S, Wang M, Sun F, Shi Y, Pan Q. Dynamic analysis of m6A methylation spectroscopy during progression and reversal of hepatic fibrosis. Epigenomics 2020; 12:1707-1723. [PMID: 33174480 DOI: 10.2217/epi-2019-0365] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Aim: To dynamically analyze the differential m6A methylation during the progression and reversal of hepatic fibrosis. Materials & methods: We induced hepatic fibrosis in C57/BL6 mice by intraperitoneal injection of CCl4. The reversal model of hepatic fibrosis was established by stopping drug after continuous injection of CCl4. Dynamic m6A methylation was evaluated using MeRIP-Seq in the progression and reversal of hepatic fibrosis at different stages. Result: During the hepatic fibrosis, differential m6A methylation was mainly enriched in processes associated with oxidative stress and cytochrome metabolism, while differential m6A methylation was mainly enriched in processes associated with immune response and apoptosis in the hepatic fibrosis reversal. Conclusion: m6A methylation plays an important role in the progression and reversal of hepatic fibrosis.
Collapse
Affiliation(s)
- Zhongqi Cui
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Nan Huang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Li Liu
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Xue Li
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Guohui Li
- Institute of Life Sciences, Jiangsu University, 301# Xuefu Road, Zhenjiang 212013, China
| | - Yan Chen
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Qi Wu
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Jie Zhang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Shuping Long
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Minyi Wang
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Fenyong Sun
- Department of Clinical Laboratory, Shanghai Tenth People's Hospital, Tongji University, Shanghai 200072, China
| | - Yi Shi
- Department of Clinical Laboratory, Shanghai Fourth People's Hospital affiliated to Tongji University School of Medicine, Shanghai 200081, China
| | - Qiuhui Pan
- Department of Laboratory Medicine, Shanghai Children's Medical Center, Shanghai Jiaotong University School of Medicine, Shanghai 200127, China
| |
Collapse
|
3
|
Targeting chromatin dysregulation in organ fibrosis. Cytokine Growth Factor Rev 2020; 57:64-72. [PMID: 32900600 DOI: 10.1016/j.cytogfr.2020.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/24/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022]
Abstract
Fibrosis leads to destruction of organ architecture accompanied by chronic inflammation and loss of function. Fibrosis affects nearly every organ in the body and accounts for ∼45% of total deaths worldwide. Over the past decade, tremendous progress has been made in understanding the basic mechanisms leading to organ fibrosis. However, we are limited with therapeutic options and there is a significant need to develop highly effective anti-fibrotic therapies. Recent advances in sequencing technologies have advanced the burgeoning field of epigenetics towards molecular understanding at a higher resolution. Here we provide a comprehensive review of the recent advances in chromatin regulatory processes, specifically DNA methylation, post-translational modification of histones, and chromatin remodeling complexes in kidney, liver and lung fibrosis. Although this research field is young, we discuss new strategies for potential therapeutic interventions for treating organ fibrosis.
Collapse
|
4
|
Jones DL, Haak AJ, Caporarello N, Choi KM, Ye Z, Yan H, Varelas X, Ordog T, Ligresti G, Tschumperlin DJ. TGFβ-induced fibroblast activation requires persistent and targeted HDAC-mediated gene repression. J Cell Sci 2019; 132:jcs.233486. [PMID: 31527052 DOI: 10.1242/jcs.233486] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Accepted: 09/06/2019] [Indexed: 12/11/2022] Open
Abstract
Tissue fibrosis is a chronic disease driven by persistent fibroblast activation that has recently been linked to epigenetic modifications. Here, we screened a small library of epigenetic small-molecule modulators to identify compounds capable of inhibiting or reversing TGFβ-mediated fibroblast activation. We identified pracinostat, an HDAC inhibitor, as a potent attenuator of lung fibroblast activation and confirmed its efficacy in patient-derived fibroblasts isolated from fibrotic lung tissue. Mechanistically, we found that HDAC-dependent transcriptional repression was an early and essential event in TGFβ-mediated fibroblast activation. Treatment of lung fibroblasts with pracinostat broadly attenuated TGFβ-mediated epigenetic repression and promoted fibroblast quiescence. We confirmed a specific role for HDAC-dependent histone deacetylation in the promoter region of the anti-fibrotic gene PPARGC1A (PGC1α) in response to TGFβ stimulation. Finally, we identified HDAC7 as a key factor whose siRNA-mediated knockdown attenuates fibroblast activation without altering global histone acetylation. Together, these results provide novel mechanistic insight into the essential role HDACs play in TGFβ-mediated fibroblast activation via targeted gene repression.
Collapse
Affiliation(s)
- Dakota L Jones
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Andrew J Haak
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Nunzia Caporarello
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Kyoung M Choi
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenqing Ye
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Huihuang Yan
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN 55905, USA
| | - Xaralabos Varelas
- Department of Biochemistry, Boston University, Boston, MA 02118, USA
| | - Tamas Ordog
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Giovanni Ligresti
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| | - Daniel J Tschumperlin
- Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN 55905, USA
| |
Collapse
|
5
|
Dietary supplementation with hybrid palm oil alters liver function in the common Marmoset. Sci Rep 2018; 8:2765. [PMID: 29426919 PMCID: PMC5807430 DOI: 10.1038/s41598-018-21151-0] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2017] [Accepted: 01/26/2018] [Indexed: 12/13/2022] Open
Abstract
Hybrid palm oil, which contains higher levels of oleic acid and lower saturated fatty acids in comparison with African palm oil, has been proposed to be somehow equivalent to extra virgin olive oil. However, the biological effects of its consumption are poorly described. Here we have explored the effects of its overconsumption on lipid metabolism in a non-human primate model, the common marmoset. Dietary supplementation of marmoset with hyperlipidic diet containing hybrid palm oil for 3 months did not modify plasma lipids levels, but increased glucose levels as compared to the supplementation with African palm oil. Liver volume was unexpectedly found to be more increased in marmosets consuming hybrid palm oil than in those consuming African palm oil. Hepatic total lipid content and circulating transaminases were dramatically increased in animals consuming hybrid palm oil, as well as an increased degree of fibrosis. Analysis of liver miRNAs showed a selective modulation of certain miRNAs by hybrid palm oil, some of which were predicted to target genes involved in cell adhesion molecules and peroxisomal pathways. Our data suggest that consumption of hybrid palm oil should be monitored carefully, as its overconsumption compared to that of African palm oil could involve important alterations to hepatic metabolism.
Collapse
|
6
|
Boyle M, Mann J. WITHDRAWN: Epigenetics in Chronic Liver Disease. J Hepatol 2017:S0168-8278(17)32255-9. [PMID: 28855099 DOI: 10.1016/j.jhep.2017.08.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 08/17/2017] [Accepted: 08/18/2017] [Indexed: 12/04/2022]
Abstract
This article has been withdrawn at the request of the editors. The Publisher apologizes for any inconvenience this may cause. The full Elsevier Policy on Article Withdrawal can be found at https://www.elsevier.com/about/our-business/policies/article-withdrawal.
Collapse
Affiliation(s)
- Marie Boyle
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4(th) Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK
| | - Jelena Mann
- Institute of Cellular Medicine, Faculty of Medical Sciences, 4(th) Floor, William Leech Building, Newcastle University, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK.
| |
Collapse
|
7
|
El Taghdouini A, van Grunsven LA. Epigenetic regulation of hepatic stellate cell activation and liver fibrosis. Expert Rev Gastroenterol Hepatol 2016; 10:1397-1408. [PMID: 27762150 DOI: 10.1080/17474124.2016.1251309] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Chronic liver injury to hepatocytes or cholangiocytes, when left unmanaged, leads to the development of liver fibrosis, a condition characterized by the excessive intrahepatic deposition of extracellular matrix proteins. Activated hepatic stellate cells constitute the predominant source of extracellular matrix in fibrotic livers and their transition from a quiescent state during fibrogenesis is associated with important alterations in their transcriptional and epigenetic landscape. Areas covered: We briefly describe the processes involved in hepatic stellate cell activation and discuss our current understanding of alterations in the epigenetic landscape, i.e DNA methylation, histone modifications and the functional role of non-coding RNAs that accompany this key event in the development of chronic liver disease. Expert commentary: Although great progress has been made, our understanding of the epigenetic regulation of hepatic stellate cell activation is limited and, thus far, insufficient to allow the development of epigenetic drugs that can selectively interrupt liver fibrosis.
Collapse
Affiliation(s)
- Adil El Taghdouini
- a Institut de Recherche Expérimentale et Clinique (IREC), Laboratory of Pediatric Hepatology and Cell Therapy , Université Catholique de Louvain , Brussels , Belgium.,b Liver Cell Biology Laboratory , Vrije Universiteit Brussel (VUB) , Brussels , Belgium
| | - Leo A van Grunsven
- b Liver Cell Biology Laboratory , Vrije Universiteit Brussel (VUB) , Brussels , Belgium
| |
Collapse
|