Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
Details
Serval ID
serval:BIB_B29AA6B6D436
Type
Article: article from journal or magazin.
Collection
Publications
Institution
Title
Robust estimation of cancer and immune cell-type proportions from bulk tumor ATAC-Seq data.
Journal
eLife
ISSN
2050-084X (Electronic)
ISSN-L
2050-084X
Publication state
Published
Issued date
09/10/2024
Peer-reviewed
Oui
Volume
13
Pages
RP94833
Language
english
Notes
Publication types: Journal Article
Publication Status: epublish
Publication Status: epublish
Abstract
Assay for Transposase-Accessible Chromatin sequencing (ATAC-Seq) is a widely used technique to explore gene regulatory mechanisms. For most ATAC-Seq data from healthy and diseased tissues such as tumors, chromatin accessibility measurement represents a mixed signal from multiple cell types. In this work, we derive reliable chromatin accessibility marker peaks and reference profiles for most non-malignant cell types frequently observed in the microenvironment of human tumors. We then integrate these data into the EPIC deconvolution framework (Racle et al., 2017) to quantify cell-type heterogeneity in bulk ATAC-Seq data. Our EPIC-ATAC tool accurately predicts non-malignant and malignant cell fractions in tumor samples. When applied to a human breast cancer cohort, EPIC-ATAC accurately infers the immune contexture of the main breast cancer subtypes.
Keywords
Humans, Breast Neoplasms/genetics, Breast Neoplasms/immunology, Chromatin Immunoprecipitation Sequencing/methods, Tumor Microenvironment, Female, Chromatin/metabolism, Chromatin/genetics, Neoplasms/genetics, Neoplasms/immunology, ATAC-Seq, bulk deconvolution, cancer biology, chromatin accessibility, computational biology, human, systems biology, tumor microenvironment
Pubmed
Open Access
Yes
Create date
11/10/2024 12:53
Last modification date
11/10/2024 19:15