Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer

Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer

As a noninvasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma has raised an increasing interest due to diagnostic applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. In this study, we investigated the cfDN...

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Main Authors: Wei Xu, Jun Lu, Qiang Zhao, Jun Wu, Jielin Sun, Baohui Han, Xiaodong Zhao, Yani Kang
Format: Article
Language:English
Published: Hindawi Limited 2019-01-01
Series:Disease Markers
Online Access:http://dx.doi.org/10.1155/2019/4108474
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spelling doaj-f069ac32cb674f59b5ed6abe62ab9f492020-11-24T21:42:59ZengHindawi LimitedDisease Markers0278-02401875-86302019-01-01201910.1155/2019/41084744108474Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung CancerWei Xu0Jun Lu1Qiang Zhao2Jun Wu3Jielin Sun4Baohui Han5Xiaodong Zhao6Yani Kang7School of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, ChinaDepartment of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200240, ChinaSchool of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, ChinaSchool of Life Sciences, East China Normal University, Shanghai 200240, ChinaShanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, ChinaDepartment of Pulmonary Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai 200240, ChinaShanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, ChinaSchool of Biomedical Engineering, Bio-ID Center, Shanghai Jiao Tong University, Shanghai 200240, ChinaAs a noninvasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma has raised an increasing interest due to diagnostic applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. Compared with the healthy individuals, 330 differentially methylated regions (DMRs) at gene promoters were identified in lung cancer patients with 33 hypermethylated and 297 hypomethylated regions, respectively. Moreover, these hypermethylated genes were validated with the publicly available DNA methylation data, yielding a set of ten significant differentially methylated genes in lung cancer, including B3GAT2, BCAR1, HLF, HOPX, HOXD11, MIR1203, MYL9, SLC9A3R2, SYT5, and VTRNA1-3. Our study demonstrated MeDIP-seq could be effectively used for cfDNA methylation profiling and identified a set of potential biomarker genes with clinical application for lung cancer.http://dx.doi.org/10.1155/2019/4108474
collection DOAJ
language English
format Article
sources DOAJ
author Wei Xu
Jun Lu
Qiang Zhao
Jun Wu
Jielin Sun
Baohui Han
Xiaodong Zhao
Yani Kang
spellingShingle Wei Xu
Jun Lu
Qiang Zhao
Jun Wu
Jielin Sun
Baohui Han
Xiaodong Zhao
Yani Kang
Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
Disease Markers
author_facet Wei Xu
Jun Lu
Qiang Zhao
Jun Wu
Jielin Sun
Baohui Han
Xiaodong Zhao
Yani Kang
author_sort Wei Xu
title Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
title_short Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
title_full Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
title_fullStr Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
title_full_unstemmed Genome-Wide Plasma Cell-Free DNA Methylation Profiling Identifies Potential Biomarkers for Lung Cancer
title_sort genome-wide plasma cell-free dna methylation profiling identifies potential biomarkers for lung cancer
publisher Hindawi Limited
series Disease Markers
issn 0278-0240
1875-8630
publishDate 2019-01-01
description As a noninvasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma has raised an increasing interest due to diagnostic applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. Compared with the healthy individuals, 330 differentially methylated regions (DMRs) at gene promoters were identified in lung cancer patients with 33 hypermethylated and 297 hypomethylated regions, respectively. Moreover, these hypermethylated genes were validated with the publicly available DNA methylation data, yielding a set of ten significant differentially methylated genes in lung cancer, including B3GAT2, BCAR1, HLF, HOPX, HOXD11, MIR1203, MYL9, SLC9A3R2, SYT5, and VTRNA1-3. Our study demonstrated MeDIP-seq could be effectively used for cfDNA methylation profiling and identified a set of potential biomarker genes with clinical application for lung cancer.
url http://dx.doi.org/10.1155/2019/4108474
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