GEO series
Chromatin accessibility and gene expression profiling of primary and metastatic ER+ breast cancer [ATAC-seq]
GSE316389
Homo sapiens
Genome binding/occupancy profiling by high throughput sequencing
36 samples
Submitted 2026/07/15
Platform GPL30173
Summary
In this project, we generated a resource dataset that includes ATAC-seq and RNA-seq data from ER positive primary breast tumors and matched liver and lung metastases. We collected samples from four patients at diagnosis in addition to samples from eight patients at autopsy following cancer-related death, allowing us to gain insights into the molecular mechanisms driving metastasis. Our research centered on the hypothesis that breast cancer metastasis is driven by tissue-specific enhancer programs, where differential transcription factor motif activity orchestrates distinct gene regulatory networks in metastatic sites. Peaks with divergent TF motif activity between tissues may define key regulatory nodes that control metastatic colonization and tissue adaptation. For ATAC-seq, reads were processed using the PEPATAC pipeline, and DiffBind was applied to identify differentially accessible regions, with ChIPseeker used to annotate metastatic-specific peaks. RNA-seq reads were aligned with STAR and quantified using HTSeq, and DESeq2 was employed to identify differentially expressed genes while controlling for batch effects. We established peak-to-gene correlations within a 0.5 Mbp window between chromatin accessibility and gene expression, assessing significance using a conservative null model. To investigate transcription factor (TF) activity, we applied TOBIAS footprinting, which infers TF occupancy by integrating chromatin accessibility with motif information. Leveraging footprinting scores together with RNA-seq expression, we computed a Total Functional Score of Enhancer Elements to identify the most relevant TFs per tissue. Using this approach, we linked TF motif activity at each peak with gene expression correlations, revealing peaks with tissue-specific TF activity and contrasting motif patterns between Liver and Breast. By connecting ATAC-seq peaks to RNA-seq expression, we identified putative metastasis driver genes, including 99 genes in Liver and 9 in Lung, as well as 23 genes shared across both metastatic sites, such as CCNF, SPINT1, and SLC2A1, which may play critical roles in metastatic progression. Notably, we discovered that the majority of these genes are correlated 3 or more enhancers in the metastatic tissue but not in the primary tissue.
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE316389_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 36 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA999001. Searching any of these in the dataset finder brings you back here.
Study design
16 conditions, mostly in duplicate
A18LIV ×2
A18LUN ×2
A23LIV ×2
A23LUN ×2
A33LIV ×2
A33LUN ×2
A36LIV ×2
A36LUN ×2
+12 more
Supports a between-group comparison across 32 samples.
16 replicated groups read from 36 sample titles; they account for 32 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM9451483 A18LIV_1
- GSM9451484 A18LIV_2
- GSM9451485 A18LUN_1
- GSM9451486 A18LUN_2
- GSM9451487 A23LIV_1
- GSM9451488 A23LIV_2
- GSM9451489 A23LUN_1
- GSM9451490 A23LUN_2
- GSM9451491 A33LIV_1
- GSM9451492 A33LIV_2
- GSM9451493 A33LUN_1
- GSM9451494 A33LUN_2
- GSM9451495 A36LIV_1
- GSM9451496 A36LIV_2
- GSM9451497 A36LUN_1
- GSM9451498 A36LUN_2
- GSM9451499 A39BR_1
- GSM9451500 A39LIV_1
- GSM9451501 A39LIV_2
- GSM9451502 A49BR_1
- GSM9451503 A49BR_2
- GSM9451504 A49LIV_1
- GSM9451505 A49LIV_2
- GSM9451506 A49LUN_1
- GSM9451507 A49LUN_2
- GSM9451508 A8BR_1
- GSM9451509 A8BR_2
- GSM9451510 A8LIV_1
- GSM9451511 A8LIV_2
- GSM9451512 A8LUN_1
- GSM9451513 A8LUN_2
- GSM9451514 A_1D91L
- GSM9451515 A_345CDL
- GSM9451516 A_3E0C8L
- GSM9451517 A35B65L1
- GSM9451518 A35B65L2
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