ArticleOncotarget2020
Clinical implications of chromatin accessibility in human cancers.
Article in Oncotarget, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed, 15 citations in OpenAlex.
- Sex and gender differences in cancer pathogenesis and pharmacology.Clinical & translational oncology : official publication of the Federation of Spanish Oncology Societies and of the National Cancer Institute of Mexico · 2025Review
- Exploring Chromoanagenesis with DAFCA (Dam Assisted Fluorescent Tagging of Chromatin Accessibility): Integrating Chromatin Accessibility and Optical Genome Mapping for Enhanced Structural Variant Detection.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Article
- Proteasome Inhibition Reprograms Chromatin Landscape in Breast Cancer.Cancer research communications · 2024Article
- Advancing immunotherapy for melanoma: the critical role of single-cell analysis in identifying predictive biomarkers.Frontiers in immunology · 2024Review
- Ancestry-related differences in chromatin accessibility and gene expression of APOE ε4 are associated with Alzheimer's disease risk.Alzheimer's & dementia : the journal of the Alzheimer's Association · 2023Article
- Dam Assisted Fluorescent Tagging of Chromatin Accessibility (DAFCA) for Optical Genome Mapping in Nanochannel Arrays.ACS nano · 2023Article
- ATAC-seq Optimization for Cancer Epigenetics Research.Journal of visualized experiments : JoVE · 2022Article
- One-pot universal NicE-seq: all enzymatic downstream processing of 4% formaldehyde crosslinked cells for chromatin accessibility genomics.Epigenetics & chromatin · 2021Article
- An Information Theoretical Multilayer Network Approach to Breast Cancer Transcriptional Regulation.Frontiers in genetics · 2021Article
- Genome-Wide Sex and Gender Differences in Cancer.Frontiers in oncology · 2020Review
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
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.
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