DNA Methylation Analysis in Nonalcoholic Fatty Liver Disease Suggests Distinct Disease-Specific and Remodeling Signatures after Bariatric Surgery

Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specifi...

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Published inCell metabolism Vol. 18; no. 2; pp. 296 - 302
Main Authors Ahrens, Markus, Ammerpohl, Ole, von Schönfels, Witigo, Kolarova, Julia, Bens, Susanne, Itzel, Timo, Teufel, Andreas, Herrmann, Alexander, Brosch, Mario, Hinrichsen, Holger, Erhart, Wiebke, Egberts, Jan, Sipos, Bence, Schreiber, Stefan, Häsler, Robert, Stickel, Felix, Becker, Thomas, Krawczak, Michael, Röcken, Christoph, Siebert, Reiner, Schafmayer, Clemens, Hampe, Jochen
Format Journal Article
LanguageEnglish
Published United States Elsevier Inc 06.08.2013
Subjects
Online AccessGet full text
ISSN1550-4131
1932-7420
1932-7420
DOI10.1016/j.cmet.2013.07.004

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Abstract Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, and PLCG1) and insulin/insulin-like signaling (including IGF1, IGFBP2, and PRKCE) and replicated by bisulfite pyrosequening (independent n = 39). Transcription factor binding sites at NAFLD-specific CpG sites were >1,000-fold enriched for ZNF274, PGC1A, and SREBP2. Intraindividual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Postbariatric and NAFLD-specific methylation signatures were clearly distinct both in gene ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1, and ESRRA sites. Our findings provide an example of treatment-induced epigenetic organ remodeling in humans. •Nonalcoholic fatty liver disease has a specific methylation signature•Consistent expression and methylation may point to epigenetic drivers of disease•The epigenetic signature after bariatric surgery is distinct from disease patterns•ENCODE analysis points to candidate transcription factors for liver remodeling
AbstractList Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, and PLCG1) and insulin/insulin-like signaling (including IGF1, IGFBP2, and PRKCE) and replicated by bisulfite pyrosequening (independent n = 39). Transcription factor binding sites at NAFLD-specific CpG sites were >1,000-fold enriched for ZNF274, PGC1A, and SREBP2. Intraindividual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Postbariatric and NAFLD-specific methylation signatures were clearly distinct both in gene ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1, and ESRRA sites. Our findings provide an example of treatment-induced epigenetic organ remodeling in humans.
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, and PLCG1) and insulin/insulin-like signaling (including IGF1, IGFBP2, and PRKCE) and replicated by bisulfite pyrosequening (independent n = 39). Transcription factor binding sites at NAFLD-specific CpG sites were >1,000-fold enriched for ZNF274, PGC1A, and SREBP2. Intraindividual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Postbariatric and NAFLD-specific methylation signatures were clearly distinct both in gene ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1, and ESRRA sites. Our findings provide an example of treatment-induced epigenetic organ remodeling in humans.Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, and PLCG1) and insulin/insulin-like signaling (including IGF1, IGFBP2, and PRKCE) and replicated by bisulfite pyrosequening (independent n = 39). Transcription factor binding sites at NAFLD-specific CpG sites were >1,000-fold enriched for ZNF274, PGC1A, and SREBP2. Intraindividual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Postbariatric and NAFLD-specific methylation signatures were clearly distinct both in gene ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1, and ESRRA sites. Our findings provide an example of treatment-induced epigenetic organ remodeling in humans.
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n = 45) with all stages of NAFLD and controls (n = 18) were analyzed by array-based DNA methylation and mRNA expression profiling. NAFLD-specific expression and methylation differences were seen for nine genes coding for key enzymes in intermediate metabolism (including PC, ACLY, and PLCG1) and insulin/insulin-like signaling (including IGF1, IGFBP2, and PRKCE) and replicated by bisulfite pyrosequening (independent n = 39). Transcription factor binding sites at NAFLD-specific CpG sites were >1,000-fold enriched for ZNF274, PGC1A, and SREBP2. Intraindividual comparison of liver biopsies before and after bariatric surgery showed NAFLD-associated methylation changes to be partially reversible. Postbariatric and NAFLD-specific methylation signatures were clearly distinct both in gene ontology and transcription factor binding site analyses, with >400-fold enrichment of NRF1, HSF1, and ESRRA sites. Our findings provide an example of treatment-induced epigenetic organ remodeling in humans. •Nonalcoholic fatty liver disease has a specific methylation signature•Consistent expression and methylation may point to epigenetic drivers of disease•The epigenetic signature after bariatric surgery is distinct from disease patterns•ENCODE analysis points to candidate transcription factors for liver remodeling
Author Sipos, Bence
Egberts, Jan
Ahrens, Markus
Brosch, Mario
Siebert, Reiner
Röcken, Christoph
Hampe, Jochen
von Schönfels, Witigo
Kolarova, Julia
Krawczak, Michael
Stickel, Felix
Becker, Thomas
Ammerpohl, Ole
Herrmann, Alexander
Bens, Susanne
Itzel, Timo
Erhart, Wiebke
Schreiber, Stefan
Teufel, Andreas
Häsler, Robert
Schafmayer, Clemens
Hinrichsen, Holger
Author_xml – sequence: 1
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  organization: Department of General and Thoracic Surgery, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 2
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  surname: Ammerpohl
  fullname: Ammerpohl, Ole
  organization: Institute of Human Genetics, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 3
  givenname: Witigo
  surname: von Schönfels
  fullname: von Schönfels, Witigo
  organization: Department of General and Thoracic Surgery, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 4
  givenname: Julia
  surname: Kolarova
  fullname: Kolarova, Julia
  organization: Institute of Human Genetics, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
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  givenname: Susanne
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  organization: Institute of Human Genetics, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
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  fullname: Itzel, Timo
  organization: Department of Internal Medicine I, University Hospital Regensburg, 93053 Regensburg, Germany
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  surname: Teufel
  fullname: Teufel, Andreas
  organization: Department of Internal Medicine I, University Hospital Regensburg, 93053 Regensburg, Germany
– sequence: 8
  givenname: Alexander
  surname: Herrmann
  fullname: Herrmann, Alexander
  organization: Department of Internal Medicine I, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 9
  givenname: Mario
  surname: Brosch
  fullname: Brosch, Mario
  organization: Department of Internal Medicine I, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 10
  givenname: Holger
  surname: Hinrichsen
  fullname: Hinrichsen, Holger
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  givenname: Wiebke
  surname: Erhart
  fullname: Erhart, Wiebke
  organization: Department of Internal Medicine I, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 12
  givenname: Jan
  surname: Egberts
  fullname: Egberts, Jan
  organization: Department of General and Thoracic Surgery, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 13
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  surname: Sipos
  fullname: Sipos, Bence
  organization: Institute of Pathology, University Hospital Tübingen, 72074 Tübingen, Germany
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  givenname: Stefan
  surname: Schreiber
  fullname: Schreiber, Stefan
  organization: Department of Internal Medicine I, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 15
  givenname: Robert
  surname: Häsler
  fullname: Häsler, Robert
  organization: Institute for Clinical Molecular Biology, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
– sequence: 16
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  surname: Stickel
  fullname: Stickel, Felix
  organization: Department of Clinical Research - Hepatology, University of Berne, CH-3010 Berne, Switzerland
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  givenname: Thomas
  surname: Becker
  fullname: Becker, Thomas
  organization: Department of General and Thoracic Surgery, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
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  givenname: Michael
  surname: Krawczak
  fullname: Krawczak, Michael
  organization: Institute for Medical Statistics and Informatics, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
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  givenname: Christoph
  surname: Röcken
  fullname: Röcken, Christoph
  organization: Institute of Pathology, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
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  givenname: Reiner
  surname: Siebert
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  organization: Institute of Human Genetics, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
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  organization: Department of Internal Medicine I, Christian-Albrechts-University Kiel/University Hospital Schleswig-Holstein, 24015 Kiel, Germany
BackLink https://www.ncbi.nlm.nih.gov/pubmed/23931760$$D View this record in MEDLINE/PubMed
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Snippet Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n =...
Nonalcoholic fatty liver disease (NAFLD) is the most common chronic liver disorder in industrialized countries. Liver samples from morbidly obese patients (n =...
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SubjectTerms Adult
Aged
bariatric surgery
Bariatric Surgery - adverse effects
binding sites
biopsy
developed countries
DNA methylation
DNA Methylation - genetics
enzymes
epigenetics
fatty liver
Fatty Liver - genetics
Female
gene expression
Gene Expression Regulation
genes
Humans
Insulin - metabolism
liver
Liver - metabolism
Male
messenger RNA
metabolism
Middle Aged
Non-alcoholic Fatty Liver Disease
Obesity, Morbid - genetics
Obesity, Morbid - metabolism
Obesity, Morbid - surgery
patients
Signal Transduction - genetics
transcription factors
Title DNA Methylation Analysis in Nonalcoholic Fatty Liver Disease Suggests Distinct Disease-Specific and Remodeling Signatures after Bariatric Surgery
URI https://dx.doi.org/10.1016/j.cmet.2013.07.004
https://www.ncbi.nlm.nih.gov/pubmed/23931760
https://www.proquest.com/docview/1420163935
https://www.proquest.com/docview/1560104074
https://www.proquest.com/docview/1733555862
Volume 18
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