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Clinical implications of chromatin accessibility in human cancers
Assay for transposase-accessible chromatin using sequencing (ATAC-seq) has not yet been widely used in cancer research. Clinical implications of chromatin accessibility assessed by ATAC-seq profiling in human cancers especially in a large patient cohort is largely unknown. In this study, we analyzed...
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Impact Journals LLC
2020
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210018/ https://www.ncbi.nlm.nih.gov/pubmed/32405341 http://dx.doi.org/10.18632/oncotarget.27584 |
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author | Liu, Yuexin |
author_facet | Liu, Yuexin |
author_sort | Liu, Yuexin |
collection | PubMed |
description | Assay for transposase-accessible chromatin using sequencing (ATAC-seq) has not yet been widely used in cancer research. Clinical implications of chromatin accessibility assessed by ATAC-seq profiling in human cancers especially in a large patient cohort is largely unknown. In this study, we analyzed ATAC-seq data in 404 cancer patients from the Cancer Genome Atlas, representing the largest cancer patient cohort with ATAC-seq data, and correlated chromatin accessibility with patient demographics, tumor histology, molecular subtypes, and survival. Our results showed that chromatin accessibility varies from chromosome to chromosome, and is different in different genomic regions along the same chromosome. Chromatin accessibility especially on the X chromosome is strongly dependent on patient sex, but not much on patient age or tumor stage. Striking difference in chromatin accessibility is observed between lung adenocarcinoma and lung squamous cell carcinoma, the two most common histological subgroups in lung cancer. Furthermore, chromatin accessibility was different between basal and non-basal breast cancer. Finally, we identified prognostic peaks in the promoter regions that were significantly correlated with survival. In particular, we identified six peaks in the ESR1 gene promoter region in the ATAC-seq profiling and found that the peak about 247 bp away from the transcription start site was significantly associated with better survival. In conclusion, our study provides an alternative mechanism underlying tumor prognosis. |
format | Online Article Text |
id | pubmed-7210018 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | Impact Journals LLC |
record_format | MEDLINE/PubMed |
spelling | pubmed-72100182020-05-13 Clinical implications of chromatin accessibility in human cancers Liu, Yuexin Oncotarget Research Paper Assay for transposase-accessible chromatin using sequencing (ATAC-seq) has not yet been widely used in cancer research. Clinical implications of chromatin accessibility assessed by ATAC-seq profiling in human cancers especially in a large patient cohort is largely unknown. In this study, we analyzed ATAC-seq data in 404 cancer patients from the Cancer Genome Atlas, representing the largest cancer patient cohort with ATAC-seq data, and correlated chromatin accessibility with patient demographics, tumor histology, molecular subtypes, and survival. Our results showed that chromatin accessibility varies from chromosome to chromosome, and is different in different genomic regions along the same chromosome. Chromatin accessibility especially on the X chromosome is strongly dependent on patient sex, but not much on patient age or tumor stage. Striking difference in chromatin accessibility is observed between lung adenocarcinoma and lung squamous cell carcinoma, the two most common histological subgroups in lung cancer. Furthermore, chromatin accessibility was different between basal and non-basal breast cancer. Finally, we identified prognostic peaks in the promoter regions that were significantly correlated with survival. In particular, we identified six peaks in the ESR1 gene promoter region in the ATAC-seq profiling and found that the peak about 247 bp away from the transcription start site was significantly associated with better survival. In conclusion, our study provides an alternative mechanism underlying tumor prognosis. Impact Journals LLC 2020-05-05 /pmc/articles/PMC7210018/ /pubmed/32405341 http://dx.doi.org/10.18632/oncotarget.27584 Text en Copyright: © 2020 Liu. http://creativecommons.org/licenses/by/3.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/) 3.0 (CC BY 3.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. |
spellingShingle | Research Paper Liu, Yuexin Clinical implications of chromatin accessibility in human cancers |
title | Clinical implications of chromatin accessibility in human cancers |
title_full | Clinical implications of chromatin accessibility in human cancers |
title_fullStr | Clinical implications of chromatin accessibility in human cancers |
title_full_unstemmed | Clinical implications of chromatin accessibility in human cancers |
title_short | Clinical implications of chromatin accessibility in human cancers |
title_sort | clinical implications of chromatin accessibility in human cancers |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7210018/ https://www.ncbi.nlm.nih.gov/pubmed/32405341 http://dx.doi.org/10.18632/oncotarget.27584 |
work_keys_str_mv | AT liuyuexin clinicalimplicationsofchromatinaccessibilityinhumancancers |