GEO series

DAB2IP Loss in Luminal A Breast Cancer Leads to NF-kB- Associated Aggressive Oncogenic Phenotypes

GSE227875 Homo sapiens (human) ChIP-seq / ATAC-seq (genome binding and open chromatin) 16 samples Submitted 2024/12/18 Platform GPL24676

At a glance

ChIP-seq / ATAC-seq (genome binding and open chromatin) · human · 16 samples

What it is: ChIP-seq / ATAC-seq (genome binding and open chromatin)Where proteins bind the genome, or which regions are open and active.
Organism: Homo sapiens (human)
Samples: 16 samples: 8 conditions, mostly in duplicateGroups are read from the sample names, not from the paper. Check the list below.
Data you can get: A processed table (series matrix) and supplementary files from NCBI; the raw sequencing reads from ENA. Which of these hold counts depends on the study, so check the file list.
Paper: DAB2IP loss in luminal a breast cancer leads to NF-κB-associated aggressive oncogenic phenotypesJCI insight · 2024

Summary (written by the submitters)

Despite proven therapy options for estrogen receptor (ER)-positive tumors, a significant number of patients with these cancers exhibit relapse with associated metastasis. Studies have shown that the loss of expression of RasGAPs leads to aggressive phenotypes and poor outcomes in several cancers including breast cancer. In our study, mining TCGA gene expression profiles of ER-positive breast tumors, we found that low expression of the RasGAP, DAB2IP is associated with a significant decrease in relapse-free survival in patients with Luminal A breast tumors.

Read the full summary ↓

Immunostaining found that DAB2IP loss occurs in grade 2 tumors and higher. Consistent with this, genes upregulated in low DAB2IP Luminal A tumors are shared with more aggressive tumor subtypes, and are associated with proliferation, metastasis, and enhanced ER-signaling. In addition, cell-based studies reveal that low DAB2IP expression in ER-positive breast cancer cells is associated with increased proliferation, enhanced stemness phenotypes, and activation of IKK, the upstream regulator of the NF-B signaling pathway. Further, integrating cell-based ChIP-seq with motif analysis and TCGA RNA-seq data, we identify a candidate set of NF-B target genes that are upregulated with loss of DAB2IP and are proposed to regulate several oncogenic phenotypes, including altered RNA processing. This study provides new insight into mechanisms associated with aggressiveness and recurrence within a subset of Luminal A breast cancers that are otherwise typically less aggressive.

Published in

DAB2IP loss in luminal a breast cancer leads to NF-κB-associated aggressive oncogenic phenotypes

Mukherjee A, Kakati RT, Van Alsten S et al. · JCI insight 2024 · PMID 39418101 · doi:10.1172/jci.insight.171705

This dataset

Open GSE227875 in finder → Find more human ChIP / ATAC / CUT&Tag datasets →

Download · which file do I need?

Direct links to NCBI and ENA, no account and no request form. Pick by what you want to do: take the small processed table to look, the supplementary files to re-analyse, or the original raw data to start over.

1 · Just have a look

Processed table

The series matrix: one table of values per sample as the submitters processed it. The smallest download, and it opens in Excel or R. Start here to see what the data look like.

Series matrix ↓

2 · Re-analyse it

Supplementary files

The count tables and other files the authors uploaded. Take only the samples you need, or the whole study as GSE227875_RAW.tar (it can run to tens of gigabytes).

All supplementary files ↗ Whole study · RAW.tar ↓

3 · Start from the raw reads

Raw sequencing reads

The original FASTQ files, straight from the sequencer, held at ENA. Large, and you align them yourself, so only choose this if you need to re-process the study from scratch.

Raw reads on ENA ↗

What the files usually look like: Look for peak files (.bed, .narrowPeak) and signal tracks (.bigWig) among the supplementary files; the raw reads are on ENA.

Also filed as BioProject PRJNA947220 and SRA study SRP428481. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 39418101) ↗

Study design

8 conditions, mostly in duplicate

DAB2IP KD_Input ×2 DAB2IP KD_P65 ×2 DAB2IP KD_RelB ×2 DAB2IP KD_NFkB2 ×2 Control_Input ×2 Control_P65 ×2 Control_RelB ×2 Control_NFkB2 ×2

Supports a between-group comparison across 16 samples.

How we read this: 8 replicated groups read from 16 sample titles; they account for 16 of them. These groups are guessed from the sample names, not taken from the paper, so check them against the sample list below before relying on them.

Samples in this study

GSM7110052 DAB2IP KD_Input_Rep1 DAB2IP KD_Input
GSM7110053 DAB2IP KD_P65_Rep1 DAB2IP KD_P65
GSM7110054 DAB2IP KD_RelB_Rep1 DAB2IP KD_RelB
GSM7110055 DAB2IP KD_NFkB2_Rep1 DAB2IP KD_NFkB2
GSM7110056 DAB2IP KD_Input_Rep2 DAB2IP KD_Input
GSM7110057 DAB2IP KD_P65_Rep2 DAB2IP KD_P65
GSM7110058 DAB2IP KD_RelB_Rep2 DAB2IP KD_RelB
GSM7110059 DAB2IP KD_NFkB2_Rep2 DAB2IP KD_NFkB2
GSM7110060 Control_Input_Rep1 Control_Input
GSM7110061 Control_P65_Rep1 Control_P65
GSM7110062 Control_RelB_Rep1 Control_RelB
GSM7110063 Control_NFkB2_Rep1 Control_NFkB2
GSM7110064 Control_Input_Rep2 Control_Input
GSM7110065 Control_P65_Rep2 Control_P65
GSM7110066 Control_RelB_Rep2 Control_RelB
GSM7110067 Control_NFkB2_Rep2 Control_NFkB2

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GSE227877 DAB2IP Loss in Luminal A Breast Cancer Leads to NF-kB- Associated Aggressive Oncogenic Phenotypes 22 samples shares dab2ip, aggressive, phenotypes, oncogenic, luminal, breast, leads, nf-kb
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GSE281736 Single-cell RNA Sequencing Reveals the Heterogeneity in Differentiation Trajectory and Tumor Microenvironment Leading to More Aggressive Phenotypes of Papillary Thyroid Cancer in Children and Young Adult Patients 12 samples shares aggressive, phenotypes
GSE230466 Aberrant non-canonical NF-κB signalling reprograms the epigenome landscape to drive oncogenic transcriptomes in multiple myeloma [ChIP-seq] 61 samples shares oncogenic
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