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Li P, Ma X, Huang D, Gu X. Exploring the roles of non-coding RNAs in liver regeneration. Noncoding RNA Res 2024; 9:945-953. [PMID: 38680418 PMCID: PMC11046251 DOI: 10.1016/j.ncrna.2024.04.003] [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: 02/14/2024] [Revised: 03/26/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Liver regeneration (LR) is a complex process encompassing three distinct phases: priming, proliferation phase and restoration, all influenced by various regulatory factors. After liver damage or partial resection, the liver tissue demonstrates remarkable restorative capacity, driven by cellular proliferation and repair mechanisms. The essential roles of non-coding RNAs (ncRNAs), predominantly microRNAs (miRNAs), long non-coding RNAs (lncRNAs) and circular RNA (circRNA), in regulating LR have been vastly studied. Additionally, the impact of ncRNAs on LR and their abnormal expression profiles during this process have been extensively documented. Mechanistic investigations have revealed that ncRNAs interact with genes involved in proliferation to regulate hepatocyte proliferation, apoptosis and differentiation, along with liver progenitor cell proliferation and migration. Given the significant role of ncRNAs in LR, an in-depth exploration of their involvement in the liver's self-repair capacity can reveal promising therapeutic strategies for LR and liver-related diseases. Moreover, understanding the unique regenerative potential of the adult liver and the mechanisms and regulatory factors of ncRNAs in LR are crucial for improving current treatment strategies and exploring new therapeutic approaches for various liver-related diseases. This review provides a brief overview of the LR process and the ncRNA expression profiles during this process. Furthermore, we also elaborate on the specific molecular mechanisms through which multiple key ncRNAs regulate the LR process. Finally, based on the expression characteristics of ncRNAs and their interactions with proliferation-associated genes, we explore their potential clinical application, such as developing predictive indicators reflecting liver regenerative activity and manipulating LR processes for therapeutic purposes.
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Affiliation(s)
- Penghui Li
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
| | - Xiao Ma
- Zhejiang University School of Medicine, Hangzhou, 310000, Zhejiang, China
| | - Di Huang
- Department of Child Health Care, The Third Affiliated Hospital of Zhengzhou University, Zhengzhou, 450000, Henan, China
| | - Xinyu Gu
- Department of Oncology, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, 471000, Henan, China
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2
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Christ B, Collatz M, Dahmen U, Herrmann KH, Höpfl S, König M, Lambers L, Marz M, Meyer D, Radde N, Reichenbach JR, Ricken T, Tautenhahn HM. Hepatectomy-Induced Alterations in Hepatic Perfusion and Function - Toward Multi-Scale Computational Modeling for a Better Prediction of Post-hepatectomy Liver Function. Front Physiol 2021; 12:733868. [PMID: 34867441 PMCID: PMC8637208 DOI: 10.3389/fphys.2021.733868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/26/2021] [Indexed: 01/17/2023] Open
Abstract
Liver resection causes marked perfusion alterations in the liver remnant both on the organ scale (vascular anatomy) and on the microscale (sinusoidal blood flow on tissue level). These changes in perfusion affect hepatic functions via direct alterations in blood supply and drainage, followed by indirect changes of biomechanical tissue properties and cellular function. Changes in blood flow impose compression, tension and shear forces on the liver tissue. These forces are perceived by mechanosensors on parenchymal and non-parenchymal cells of the liver and regulate cell-cell and cell-matrix interactions as well as cellular signaling and metabolism. These interactions are key players in tissue growth and remodeling, a prerequisite to restore tissue function after PHx. Their dysregulation is associated with metabolic impairment of the liver eventually leading to liver failure, a serious post-hepatectomy complication with high morbidity and mortality. Though certain links are known, the overall functional change after liver surgery is not understood due to complex feedback loops, non-linearities, spatial heterogeneities and different time-scales of events. Computational modeling is a unique approach to gain a better understanding of complex biomedical systems. This approach allows (i) integration of heterogeneous data and knowledge on multiple scales into a consistent view of how perfusion is related to hepatic function; (ii) testing and generating hypotheses based on predictive models, which must be validated experimentally and clinically. In the long term, computational modeling will (iii) support surgical planning by predicting surgery-induced perfusion perturbations and their functional (metabolic) consequences; and thereby (iv) allow minimizing surgical risks for the individual patient. Here, we review the alterations of hepatic perfusion, biomechanical properties and function associated with hepatectomy. Specifically, we provide an overview over the clinical problem, preoperative diagnostics, functional imaging approaches, experimental approaches in animal models, mechanoperception in the liver and impact on cellular metabolism, omics approaches with a focus on transcriptomics, data integration and uncertainty analysis, and computational modeling on multiple scales. Finally, we provide a perspective on how multi-scale computational models, which couple perfusion changes to hepatic function, could become part of clinical workflows to predict and optimize patient outcome after complex liver surgery.
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Affiliation(s)
- Bruno Christ
- Cell Transplantation/Molecular Hepatology Lab, Department of Visceral, Transplant, Thoracic and Vascular Surgery, University of Leipzig Medical Center, Leipzig, Germany
| | - Maximilian Collatz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
- Optisch-Molekulare Diagnostik und Systemtechnologié, Leibniz Institute of Photonic Technology (IPHT), Jena, Germany
- InfectoGnostics Research Campus Jena, Jena, Germany
| | - Uta Dahmen
- Experimental Transplantation Surgery, Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena, Germany
| | - Karl-Heinz Herrmann
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany
| | - Sebastian Höpfl
- Faculty of Engineering Design, Production Engineering and Automotive Engineering, Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany
| | - Matthias König
- Systems Medicine of the Liver Lab, Institute for Theoretical Biology, Humboldt-University Berlin, Berlin, Germany
| | - Lena Lambers
- Faculty of Aerospace Engineering and Geodesy, Institute of Mechanics, Structural Analysis and Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Daria Meyer
- RNA Bioinformatics and High-Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany
| | - Nicole Radde
- Faculty of Engineering Design, Production Engineering and Automotive Engineering, Institute for Systems Theory and Automatic Control, University of Stuttgart, Stuttgart, Germany
| | - Jürgen R. Reichenbach
- Medical Physics Group, Institute of Diagnostic and Interventional Radiology, Jena University Hospital, Jena, Germany
| | - Tim Ricken
- Faculty of Aerospace Engineering and Geodesy, Institute of Mechanics, Structural Analysis and Dynamics, University of Stuttgart, Stuttgart, Germany
| | - Hans-Michael Tautenhahn
- Department of General, Visceral and Vascular Surgery, Jena University Hospital, Jena, Germany
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Zhang Y, Li Z, Zhao W, Hu H, Zhao L, Zhu Y, Yang X, Gao B, Yang H, Huang Y, Song X. WD repeat and SOCS box containing protein 2 in the proliferation, cycle progression, and migration of melanoma cells. Biomed Pharmacother 2019; 116:108974. [DOI: 10.1016/j.biopha.2019.108974] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Revised: 05/06/2019] [Accepted: 05/08/2019] [Indexed: 02/02/2023] Open
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Diaz de Cerio O, Bilbao E, Izagirre U, Etxebarria N, Moreno G, Díez G, Cajaraville MP, Cancio I. Toxicology tailored low density oligonucleotide microarray for the thicklip grey mullets (Chelon labrosus): Biomarker gene transcription profile after caging in a polluted harbour. MARINE ENVIRONMENTAL RESEARCH 2018; 140:265-277. [PMID: 30042060 DOI: 10.1016/j.marenvres.2018.06.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Revised: 06/06/2018] [Accepted: 06/11/2018] [Indexed: 06/08/2023]
Abstract
In aquatic organisms inhabiting polluted waters genes are activated to build an adaptive/compensatory defence against the possible effects of pollutants. Such responses can be used as biomarkers of exposure to chemical compounds, outlining the molecular mechanisms activated under specific pollution scenarios. With the aim of exploiting such approach in environmental health assessment, toxicologically relevant gene fragments were sequenced in the thicklip grey mullet (Chelon labrosus) and a toxicologically tailored low-density (160 genes) oligonucleotide microarray was customised. The tool was validated comparing organ/sex specific gene expression profiles and characterising responses under laboratory exposure to model chemicals. Finally, juvenile mullets were caged in a polluted harbour and hepatic gene expression profiles analysed after 5 and 21 days of deployment. Cages were deployed in the inner (IH) and outer (OH) Pasaia harbour, Bay of Biscay. Mussels (Mytilus galloprovincialis) were also caged as biological matrix for chemical bioaccumulation analysis and stress biomarkers measurements. Slightly higher concentrations of chemicals (metals, tributyltin, PAHs, phthalates) were quantified in IH than in OH, fish bile metabolites also revealing higher availability of PAHs in IH. Lysosome membrane stability in mussels was reduced, indicating stress condition in both sites. The developed microarray discriminated mullets showing distinctive expression profiles depending on site and deployment time. Genes related to immune and hypoxia responses were regulated comparing IH and OH at day 5. Phase I and II biotransformation genes, such as cyp2, cyp3 and ugt, were up-regulated in IH, together with the aryl hydrocarbon receptor 2 (ahr2) and the ahr repressor. Similarly, TBT-binding proteins and genes involved in lipid metabolism (pparγ, cyp7) were up-regulated with deployment time. Even if nowadays higher throughput approaches for gene expression analyses are available, the developed mullet tool constitutes a comprehensive tool to assess molecular responses of mullets exposed to pollutants, although it remains to be explored whether it can be applied to assess pollutant exposure in active pollution monitorings and in environmental health assessment.
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Affiliation(s)
- O Diaz de Cerio
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - E Bilbao
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - U Izagirre
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - N Etxebarria
- IBEA Res Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Analytical Chemistry Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - G Moreno
- International Seafood Sustainability Foundation (ISSF), 805 15th Street NW, Washington, DC, 20005, USA
| | - G Díez
- AZTI, Marine Research Division, Txatxarramendi irla z/g, 48395, Sukarrieta, Bizkaia, Spain
| | - M P Cajaraville
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain
| | - I Cancio
- CBET Res. Group. Centre for Experimental Marine Biology and Biotechnology (PiE-UPV/EHU) and Zoology and Cell Biology Dept. (Fac. Science and Technology), University of the Basque Country (UPV/EHU), E-48080, Bilbao, PO Box 644, Basque Country, Spain.
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Yagi S, Shiojiri N. Identification of novel genetic markers for mouse yolk sac cells by using microarray analyses. Placenta 2017; 49:68-71. [DOI: 10.1016/j.placenta.2016.11.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/27/2016] [Revised: 11/07/2016] [Accepted: 11/22/2016] [Indexed: 11/26/2022]
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Yan IK, Wang X, Asmann YW, Haga H, Patel T. Circulating Extracellular RNA Markers of Liver Regeneration. PLoS One 2016; 11:e0155888. [PMID: 27415797 PMCID: PMC4945050 DOI: 10.1371/journal.pone.0155888] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Accepted: 05/05/2016] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND AND AIMS Although a key determinant of hepatic recovery after injury is active liver regeneration, the ability to detect ongoing regeneration is lacking. The restoration of liver mass after hepatectomy involves systemic changes with coordinated changes in gene expression guiding regenerative responses, activation of progenitor cells, and proliferation of quiescent hepatocytes. We postulated that these responses involve intercellular communication involving extracellular RNA and that these could represent biomarkers of active regenerative responses. METHODS RNA sequencing was performed to identify temporal changes in serum extracellular non-coding RNA after partial hepatectomy in C57BL/6 male mice. Tissue expression of selected RNA was performed by microarray analysis and validated using qRT-PCR. Digital PCR was used to detect and quantify serum expression of selected RNA. RESULTS A peak increase in extracellular RNA content occurred six hours after hepatectomy. RNA sequencing identified alterations in several small non-coding RNA including known and novel microRNAs, snoRNAs, tRNA, antisense and repeat elements after partial hepatectomy. Combinatorial effects and network analyses identified signal regulation, protein complex assembly, and signal transduction as the most common biological processes targeted by miRNA that altered. miR-1A and miR-181 were most significantly altered microRNA in both serum and in hepatic tissues, and their presence in serum was quantitated using digital PCR. CONCLUSIONS Extracellular RNA selectively enriched during acute regeneration can be detected within serum and represent biomarkers of ongoing liver regeneration in mice. The ability to detect ongoing active regeneration would improve the assessment of hepatic recovery from liver injury.
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Affiliation(s)
- Irene K. Yan
- Department of Transplantation, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
- Department of Cancer Biology, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
| | - Xue Wang
- Department of Health Sciences Research, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
| | - Yan W. Asmann
- Department of Health Sciences Research, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
| | - Hiroaki Haga
- Department of Transplantation, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
- Department of Cancer Biology, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
| | - Tushar Patel
- Department of Transplantation, Mayo Clinic, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
- Department of Cancer Biology, 4500 San Pablo Road South, Jacksonville, FL 32224, United States of America
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Li D, Mackowiak B, Brayman TG, Mitchell M, Zhang L, Huang SM, Wang H. Genome-wide analysis of human constitutive androstane receptor (CAR) transcriptome in wild-type and CAR-knockout HepaRG cells. Biochem Pharmacol 2015; 98:190-202. [PMID: 26275810 DOI: 10.1016/j.bcp.2015.08.087] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Accepted: 08/07/2015] [Indexed: 10/23/2022]
Abstract
The constitutive androstane receptor (CAR) modulates the transcription of numerous genes involving drug metabolism, energy homeostasis, and cell proliferation. Most functions of CAR however were defined from animal studies. Given the known species difference of CAR and the significant cross-talk between CAR and the pregnane X receptor (PXR), it is extremely difficult to decipher the exact role of human CAR (hCAR) in gene regulation, relying predominantly on pharmacological manipulations. Here, utilizing a newly generated hCAR-knockout (KO) HepaRG cell line, we carried out RNA-seq analysis of the global transcriptomes in wild-type (WT) and hCAR-KO HepaRG cells treated with CITCO, a selective hCAR agonist, phenobarbital (PB), a dual activator of hCAR and hPXR, or vehicle control. Real-time PCR assays in separate experiments were used to validate RNA-seq findings. Our results indicate that genes encoding drug-metabolizing enzymes are among the main clusters altered by both CITCO and PB. Specifically, CITCO significantly changed the expression of 135 genes in an hCAR-dependent manner, while PB altered the expression of 227 genes in WT cells of which 94 were simultaneously modulated in both cell lines reflecting dual effects of PB on hCAR/PXR. Notably, we found that many genes promoting cell proliferation and tumorigenesis were up-regulated in hCAR-KO cells, suggesting that hCAR may play an important role in cell growth that differs from mouse CAR. Together, our results reveal both novel and known targets of hCAR and support the role of hCAR in maintaining the homeostasis of metabolism and cell proliferation in the liver.
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Affiliation(s)
- Daochuan Li
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, United States
| | - Bryan Mackowiak
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, United States
| | - Timothy G Brayman
- Sigma Life Sciences, 2909 Laclede Ave, St. Louis, MO 63103, United States
| | - Michael Mitchell
- Sigma Life Sciences, 2909 Laclede Ave, St. Louis, MO 63103, United States
| | - Lei Zhang
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20901, United States
| | - Shiew-Mei Huang
- Office of Clinical Pharmacology, Office of Translational Sciences, Center for Drug Evaluation and Research, Food and Drug Administration, Silver Spring, MD 20901, United States
| | - Hongbing Wang
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy, 20 Penn Street, Baltimore, MD 21201, United States.
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Chiba M. Differential expression of natural antisense transcripts during liver development in embryonic mice. Biomed Rep 2014; 2:918-922. [PMID: 25279170 DOI: 10.3892/br.2014.363] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Accepted: 09/08/2014] [Indexed: 01/22/2023] Open
Abstract
The mature adult liver is a metabolizing and synthesizing organ consisting of hepatic lobules. The liver development during fetal stages is induced by the interaction between hepatoblast cells derived from the endoderm and stellate cells and/or endothelial cells derived from the mesoderm. Recently, the association of non-coding RNAs, such as microRNAs, in the liver development process has been reported. In the present study, the gene expression changes were investigated of natural antisense transcripts (NATs), a type of non-coding RNA, during the liver development using livers from embryonic day (E) 14, E17, E19 and newborn (NB). The upregulated NATs of 87 genes and the downregulated NATs of 26 genes were identified when the expression was >5.0-fold up/downregulated NATs at E17, E19 or NB compared to those at E14, as examined by microarray analysis. Among these NATs, strand-specific reverse transcription-quantitative polymerase chain reaction analyses validated that the NAT expression of Fga, Fgb, Fgg, F2, Apoa1, Fabp1, C3 and Proc, which have metabolic and synthesizing functions in the adult liver, increased, whereas the NAT expression of Ermap and Tfrc, which function in the hematopoiesis, decreased during the developmental stages. These results indicate that the differential expression of several NATs is induced during the process of liver development, suggesting that these NATs may be involved in the regulation of gene expression and functional conversion from a hematopoietic to a metabolic organ in the developmental stages of the liver.
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Affiliation(s)
- Mitsuru Chiba
- Department of Biomedical Sciences, Division of Medical Life Sciences, Hirosaki University Graduate School of Health Sciences, Hirosaki, Aomori 036-8564, Japan
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