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Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers
BACKGROUND: Quantification of circulating organ-specific cell-free DNA (cfDNA) provides a sensitive measure of ongoing cell death that could benefit evaluation of the cholestatic liver diseases primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC), which lack reliable non-invasi...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2021
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8017778/ https://www.ncbi.nlm.nih.gov/pubmed/33794792 http://dx.doi.org/10.1186/s12876-021-01741-5 |
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author | Punia, Sohan Juran, Brian D. Ali, Ahmad H. Schlicht, Erik M. Moore, Raymond M. Sun, Zhifu Lazaridis, Konstantinos N. |
author_facet | Punia, Sohan Juran, Brian D. Ali, Ahmad H. Schlicht, Erik M. Moore, Raymond M. Sun, Zhifu Lazaridis, Konstantinos N. |
author_sort | Punia, Sohan |
collection | PubMed |
description | BACKGROUND: Quantification of circulating organ-specific cell-free DNA (cfDNA) provides a sensitive measure of ongoing cell death that could benefit evaluation of the cholestatic liver diseases primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC), which lack reliable non-invasive biomarkers. Our goal in this pilot study was to determine whether liver-specific cfDNA levels are increased in PBC and PSC patients relative to controls and in advanced versus early disease, to evaluate their potential as novel disease biomarkers. METHODS: Peripheral blood derived bisulfite-treated DNA was PCR amplified from patients with PBC (n = 48), PSC (n = 48) and controls (n = 96) to evaluate methylation status at 16 CpG sites reported to be specifically unmethylated in liver tissue near the genes IGF2R, ITIH4 and VTN. Amplicons were used to prepare paired end libraries which were sequenced on a MiSeq sequencer. Trimmed reads were aligned and used to determine unmethylation ratios and to calculate concentration of liver-specific cfDNA. Comparisons between groups were performed using the two-tailed Mann–Whitney Test and relationships between variables were evaluated using Pearson’s Correlation. RESULTS: Levels of liver-specific cfDNA, as measured at the 3 genetic loci, were increased in PBC and PSC patients relative to controls and in late-stage relative to early-stage patients. As well, cfDNA levels were correlated with levels of alkaline phosphatase, a commonly used biochemical test to evaluate disease severity in liver disease, in patients, but not in controls. CONCLUSIONS: cfDNA offers promise as a non-invasive liquid-biopsy to evaluate liver-specific cell-death in patients with cholestatic liver diseases. |
format | Online Article Text |
id | pubmed-8017778 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-80177782021-04-02 Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers Punia, Sohan Juran, Brian D. Ali, Ahmad H. Schlicht, Erik M. Moore, Raymond M. Sun, Zhifu Lazaridis, Konstantinos N. BMC Gastroenterol Research Article BACKGROUND: Quantification of circulating organ-specific cell-free DNA (cfDNA) provides a sensitive measure of ongoing cell death that could benefit evaluation of the cholestatic liver diseases primary biliary cholangitis (PBC) and primary sclerosing cholangitis (PSC), which lack reliable non-invasive biomarkers. Our goal in this pilot study was to determine whether liver-specific cfDNA levels are increased in PBC and PSC patients relative to controls and in advanced versus early disease, to evaluate their potential as novel disease biomarkers. METHODS: Peripheral blood derived bisulfite-treated DNA was PCR amplified from patients with PBC (n = 48), PSC (n = 48) and controls (n = 96) to evaluate methylation status at 16 CpG sites reported to be specifically unmethylated in liver tissue near the genes IGF2R, ITIH4 and VTN. Amplicons were used to prepare paired end libraries which were sequenced on a MiSeq sequencer. Trimmed reads were aligned and used to determine unmethylation ratios and to calculate concentration of liver-specific cfDNA. Comparisons between groups were performed using the two-tailed Mann–Whitney Test and relationships between variables were evaluated using Pearson’s Correlation. RESULTS: Levels of liver-specific cfDNA, as measured at the 3 genetic loci, were increased in PBC and PSC patients relative to controls and in late-stage relative to early-stage patients. As well, cfDNA levels were correlated with levels of alkaline phosphatase, a commonly used biochemical test to evaluate disease severity in liver disease, in patients, but not in controls. CONCLUSIONS: cfDNA offers promise as a non-invasive liquid-biopsy to evaluate liver-specific cell-death in patients with cholestatic liver diseases. BioMed Central 2021-04-01 /pmc/articles/PMC8017778/ /pubmed/33794792 http://dx.doi.org/10.1186/s12876-021-01741-5 Text en © The Author(s) 2021 Open AccessThis article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Research Article Punia, Sohan Juran, Brian D. Ali, Ahmad H. Schlicht, Erik M. Moore, Raymond M. Sun, Zhifu Lazaridis, Konstantinos N. Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers |
title | Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers |
title_full | Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers |
title_fullStr | Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers |
title_full_unstemmed | Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers |
title_short | Evaluation of circulating cell-free DNA in cholestatic liver disease using liver-specific methylation markers |
title_sort | evaluation of circulating cell-free dna in cholestatic liver disease using liver-specific methylation markers |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8017778/ https://www.ncbi.nlm.nih.gov/pubmed/33794792 http://dx.doi.org/10.1186/s12876-021-01741-5 |
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