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Regulation of pancreatic cancer migration by signal convergence in the epigenome [RNA-Seq]

GSE278112 Homo sapiens (human) Single-cell RNA-seq 36 samples Submitted 2025/06/26 Platform GPL30173
At a glance

Single-cell RNA-seq · human · 36 samples

What it is
Single-cell RNA-seqGene activity measured in thousands of individual cells, so cell types can be told apart. Read from the summary: GEO's own type field only says 'expression profiling by sequencing', so confirm it in the paper.
Organism
Homo sapiens (human)
Samples
36 samples: 12 conditions, mostly in triplicateGroups 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
Therapeutic targeting of FOSL1 and RELA-dependent transcriptional mechanisms to suppress pancreatic cancer metastasisCell death & disease · 2025
Summary (written by the submitters)
Pancreatic ductal adenocarcinoma (PDAC) is frequently diagnosed at an advanced, metastatic stage. PDAC treatment is challenging due to high tumor cell plasticity, tumor heterogeneity, and a dense tumor microenvironment (TME), all of which strongly influence tumor metastasis. While mutations in the KRAS gene characterize PDAC, inflammatory signaling from the TME accelerates tumor progression, metastasis, and therapy resistance.
Read the full summary ↓
While individual roles of oncogenic and inflammatory signaling in promoting PDAC progression have been studied extensively, the epigenetic and transcriptional mechanisms by which they function combinatorially in metastasis remain unclear. Our study elucidates how inflammatory TNFα and oncogenic MAPK signaling pathways converge to control PDAC cell migration through activation of NF-κB and AP1 transcription factors, respectively. Combining single-cell RNA sequencing (scRNAseq) analyses, multiplex immunofluorescence staining, in vitro, and in vivo studies, we unveil that the simultaneous activation of these pathways with TNFα and EGF induces the expression of specific genes associated with cell motility and migration. We show that combinatorial induced genes are co-bound by FOSL1 and RELA. Remarkably, inhibition of NF-κB transcriptional activity using glucocorticoid receptor (GR) mixed agonists significantly reduces RNA polymerase II across the target genes and inhibits cell migration. These findings highlight the potential of GR agonists, commonly utilized to alleviate chemotherapy side effects, in mitigating PDAC tumor migration. Our study offers promising avenues for developing mechanism-based therapeutic strategies in PDAC management.
Published in
Therapeutic targeting of FOSL1 and RELA-dependent transcriptional mechanisms to suppress pancreatic cancer metastasis
Aggrey-Fynn JE, Manjunath M, Rajput A et al. · Cell death & disease 2025 · PMID 40634284 · doi:10.1038/s41419-025-07810-x
This dataset
Open GSE278112 in finder → Find more human RNA-seq 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 GSE278112_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: Single-cell studies usually ship their counts as 10x files (matrix.mtx, barcodes.tsv, features.tsv), an .h5 file, or an .rds / .h5ad object that Seurat or Scanpy can open. Look for those among the supplementary files.

Also filed as BioProject PRJNA1158478 and SRA study SRP531386. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40634284) ↗
Study design
12 conditions, mostly in triplicate
AsPC1_30min_Vehicle ×3 AsPC1_30min_EGF ×3 AsPC1_30min_TNFa ×3 AsPC1_30min_TNFaEGF ×3 AsPC1_48hr_Vehicle ×3 AsPC1_48hr_EGF ×3 AsPC1_48hr_TNFa ×3 AsPC1_48hr_TNFaEGF ×3 +4 more

Supports a between-group comparison across 36 samples.

How we read this: 12 replicated groups read from 36 sample titles; they account for 36 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
Datasets on a similar topic

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