Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis
Neonatal liver-derived rat epithelial cells (rLEC) from biliary origin are liver progenitor cells that acquire a hepatocyte-like phenotype upon sequential exposure to hepatogenic growth factors and cytokines. Undifferentiated rLEC express several liver-enriched transcription factors, including the h...
Main Authors: | , , , , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
MDPI AG
2020-04-01
|
Series: | Genes |
Subjects: | |
Online Access: | https://www.mdpi.com/2073-4425/11/5/486 |
id |
doaj-afcd2ba5d8bd41f383363b46a45e9573 |
---|---|
record_format |
Article |
spelling |
doaj-afcd2ba5d8bd41f383363b46a45e95732020-11-25T03:03:16ZengMDPI AGGenes2073-44252020-04-011148648610.3390/genes11050486Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile AnalysisJennifer Bolleyn0Matthias Rombaut1Nisha Nair2Steven Branson3Anja Heymans4Marinee Chuah5Thierry VandenDriessche6Vera Rogiers7Joery De Kock8Tamara Vanhaecke9Department of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of Gene Therapy and Regenerative Medicine (GTRM), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of Gene Therapy and Regenerative Medicine (GTRM), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of Gene Therapy and Regenerative Medicine (GTRM), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumDepartment of In Vitro Toxicology and Dermato-cosmetology (IVTD), Vrije Universiteit Brussel (VUB), Laarbeeklaan 103, B-1090 Brussels, BelgiumNeonatal liver-derived rat epithelial cells (rLEC) from biliary origin are liver progenitor cells that acquire a hepatocyte-like phenotype upon sequential exposure to hepatogenic growth factors and cytokines. Undifferentiated rLEC express several liver-enriched transcription factors, including the hepatocyte nuclear factors (HNF) 3β and HNF6, but not the hepatic master regulator HNF4α. In this study, we first investigated the impact of the ectopic expression of HNF4α in rLEC on both mRNA and microRNA (miR) level by means of microarray technology. We found that HNF4α transduction did not induce major changes to the rLEC phenotype. However, we next investigated the influence of DNA methyl transferase (DNMT) inhibition on the phenotype of undifferentiated naïve rLEC by exposure to 5' azacytidine (AZA), which was found to have a significant impact on rLEC gene expression. The transduction of HNF4α or AZA treatment resulted both in significantly downregulated C/EBPα expression levels, while the exposure of the cells to AZA had a significant effect on the expression of HNF3β. Computationally, dysregulated miRNAs were linked to target mRNAs using the microRNA Target Filter function of Ingenuity Pathway Analysis. We found that differentially regulated miRNA–mRNA target associations predict ectopic HNF4α expression in naïve rLEC to interfere with cell viability and cellular maturation (miR-19b-3p/<i>NR4A2</i>, miR30C-5p/<i>P4HA2</i>, miR328-3p/<i>CD44</i>) while it predicts AZA exposure to modulate epithelial/hepatic cell proliferation, apoptosis, cell cycle progression and the differentiation of stem cells (miR-18a-5p/<i>ESR1</i>, miR-503-5p/<i>CCND1</i>). Finally, our computational analysis predicts that the combination of HNF4α transduction with subsequent AZA treatment might cause changes in hepatic cell proliferation and maturation (miR-18a-5p/<i>ESR1</i>, miR-503-5p/<i>CCND1</i>, miR-328-3p/<i>CD44</i>) as well as the apoptosis (miR-16-5p/BCL2, miR-17-5p/BCL2, miR-34a-5p/<i>BCL2</i> and miR-494-3p/<i>HMOX1</i>) of naïve rLEC.https://www.mdpi.com/2073-4425/11/5/486liver-enriched transcription factorazacytidinemicroRNAliver progenitor celllentiviral transductiongene expression |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Jennifer Bolleyn Matthias Rombaut Nisha Nair Steven Branson Anja Heymans Marinee Chuah Thierry VandenDriessche Vera Rogiers Joery De Kock Tamara Vanhaecke |
spellingShingle |
Jennifer Bolleyn Matthias Rombaut Nisha Nair Steven Branson Anja Heymans Marinee Chuah Thierry VandenDriessche Vera Rogiers Joery De Kock Tamara Vanhaecke Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis Genes liver-enriched transcription factor azacytidine microRNA liver progenitor cell lentiviral transduction gene expression |
author_facet |
Jennifer Bolleyn Matthias Rombaut Nisha Nair Steven Branson Anja Heymans Marinee Chuah Thierry VandenDriessche Vera Rogiers Joery De Kock Tamara Vanhaecke |
author_sort |
Jennifer Bolleyn |
title |
Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis |
title_short |
Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis |
title_full |
Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis |
title_fullStr |
Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis |
title_full_unstemmed |
Genetic and Epigenetic Modification of Rat Liver Progenitor Cells via HNF4α Transduction and 5’ Azacytidine Treatment: An Integrated miRNA and mRNA Expression Profile Analysis |
title_sort |
genetic and epigenetic modification of rat liver progenitor cells via hnf4α transduction and 5’ azacytidine treatment: an integrated mirna and mrna expression profile analysis |
publisher |
MDPI AG |
series |
Genes |
issn |
2073-4425 |
publishDate |
2020-04-01 |
description |
Neonatal liver-derived rat epithelial cells (rLEC) from biliary origin are liver progenitor cells that acquire a hepatocyte-like phenotype upon sequential exposure to hepatogenic growth factors and cytokines. Undifferentiated rLEC express several liver-enriched transcription factors, including the hepatocyte nuclear factors (HNF) 3β and HNF6, but not the hepatic master regulator HNF4α. In this study, we first investigated the impact of the ectopic expression of HNF4α in rLEC on both mRNA and microRNA (miR) level by means of microarray technology. We found that HNF4α transduction did not induce major changes to the rLEC phenotype. However, we next investigated the influence of DNA methyl transferase (DNMT) inhibition on the phenotype of undifferentiated naïve rLEC by exposure to 5' azacytidine (AZA), which was found to have a significant impact on rLEC gene expression. The transduction of HNF4α or AZA treatment resulted both in significantly downregulated C/EBPα expression levels, while the exposure of the cells to AZA had a significant effect on the expression of HNF3β. Computationally, dysregulated miRNAs were linked to target mRNAs using the microRNA Target Filter function of Ingenuity Pathway Analysis. We found that differentially regulated miRNA–mRNA target associations predict ectopic HNF4α expression in naïve rLEC to interfere with cell viability and cellular maturation (miR-19b-3p/<i>NR4A2</i>, miR30C-5p/<i>P4HA2</i>, miR328-3p/<i>CD44</i>) while it predicts AZA exposure to modulate epithelial/hepatic cell proliferation, apoptosis, cell cycle progression and the differentiation of stem cells (miR-18a-5p/<i>ESR1</i>, miR-503-5p/<i>CCND1</i>). Finally, our computational analysis predicts that the combination of HNF4α transduction with subsequent AZA treatment might cause changes in hepatic cell proliferation and maturation (miR-18a-5p/<i>ESR1</i>, miR-503-5p/<i>CCND1</i>, miR-328-3p/<i>CD44</i>) as well as the apoptosis (miR-16-5p/BCL2, miR-17-5p/BCL2, miR-34a-5p/<i>BCL2</i> and miR-494-3p/<i>HMOX1</i>) of naïve rLEC. |
topic |
liver-enriched transcription factor azacytidine microRNA liver progenitor cell lentiviral transduction gene expression |
url |
https://www.mdpi.com/2073-4425/11/5/486 |
work_keys_str_mv |
AT jenniferbolleyn geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT matthiasrombaut geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT nishanair geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT stevenbranson geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT anjaheymans geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT marineechuah geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT thierryvandendriessche geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT verarogiers geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT joerydekock geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis AT tamaravanhaecke geneticandepigeneticmodificationofratliverprogenitorcellsviahnf4atransductionand5azacytidinetreatmentanintegratedmirnaandmrnaexpressionprofileanalysis |
_version_ |
1724686624221036544 |