GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE223182 Query DataSets for GSE223182
Status Public on Sep 27, 2023
Title Integrated chromatin accessibility and gene expression landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry [Bulk ATAC-seq]
Organism Homo sapiens
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary African American (AA) women are at increased risk of developing and dying from Triple-Negative Breast Cancer (TNBC), an aggressive breast cancer subtype, compared to European American (EA) women in the United States. In addition to social determinants, further investigation into biologic factors that contribute to these disparities is needed to fully understand this multi-factorial problem. In particular, the epigenetics of racial/population diversity and its influence on breast cancer incidence and outcomes remains underexplored. Using ATAC-sequencing and RNA-sequencing, we characterized differences in chromatin accessibility and gene expression between EA-derived versus AA-derived TNBC cell lines (N=9). Our analyses revealed significant differences in transcription factor binding and downstream gene expression associated with cancer stemness, resistance, and epithelial to mesenchymal transition. Differences were exacerbated under conditions of hypoxia. Together, these data suggest a differential chromatin and transcriptomic landscape that may contribute to worsened TNBC biology in women of African ancestry. Additionally, as many of these cell lines are used routinely in biomedical research, these findings also indicate that the ancestral origin of patient derived cell lines matters and may contribute to biologic variation in experimental data, suggesting that inclusion of diversely sourced cell lines should be considered in experimental design. 
Overall design Cell revival, cell lysis, transposition, and DNA extraction were done using a published method by Corces et al., 2017 (PMID: 28846090) with some modifications for cryopreserved cell processing (Caravaca et al., 2022). The peaks (open chromatin regions) of the above breast cancel cell lines were generated by sequencing using Illumina  NextSeq 2000  P2.
Contributor(s) Harris AR, Panigrahi G, Liu H, Koparde V, Bailey-Whyte M, Dorsey TH, Yates C, Ambs S
Citation(s) 37732899
Submission date Jan 18, 2023
Last update date Oct 19, 2023
Contact name Stefan Ambs
Phone 240-760-6836
Organization name NCI
Department CCR
Street address Building 37, Room 3050B
City Bethesda
State/province MD
ZIP/Postal code 20892-4258
Country USA
Platforms (1)
GPL30173 NextSeq 2000 (Homo sapiens)
Samples (50)
GSM6940703 MDAMB468_Norm_1 
GSM6940704 MDAMB157_Norm_1 
GSM6940705 HCC1806_Norm_1 
This SubSeries is part of SuperSeries:
GSE223183 Integrated chromatin accessibility and gene expression landscape of human triple-negative breast cancer cell lines reveals variation by patient donor ancestry
BioProject PRJNA925199

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE223182_ccbr1005_project1_chromVAR.tnbc_only.results.xlsx 142.1 Kb (ftp)(http) XLSX
GSE223182_ccbr1181_ChromVAR_results.xlsx 507.4 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap