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Resolution of acinar dedifferentiation regulates tissue remodeling in pancreatic injury and cancer initiation.

GSE235809 Mus musculus (mouse) Single-cell RNA-seq 17 samples Submitted 2025/05/01 Platform GPL24247
At a glance

Single-cell RNA-seq · mouse · 17 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
Mus musculus (mouse)
Samples
17 samples: 3 × Pancreas, Day 2, Caeruelein treated, Sox4 conditional knock-out, Kras WT background, mouse vs 3 × Pancreas, Day 2, PBS treated, Sox4 wild-type, Kras WT background, mouse vs 3 × Pancreas, Day 21, Caeruelein treated, Sox4 conditional knock-out, Kras G12D background, mouse vs 3 × Pancreas, Day 21, PBS treated, Sox4 wild-type, Kras G12D background, mouseGroups 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
Resolution of Acinar Dedifferentiation Regulates Tissue Remodeling in Pancreatic Injury and Cancer InitiationGastroenterology · 2024
Summary (written by the submitters)
Background and Aims: Acinar to ductal metaplasia (ADM) is crucial in the development of pancreatic ductal adenocarcinoma (PDAC). However, our understanding of the induction and resolution of ADM remains limited. We conducted comparative transcriptome analyses to identify conserved mechanisms of ADM in mouse and human. Methods: We identified Sox4 among the top upregulated genes.
Read the full summary ↓
We validated the analysis by RNA in situ hybridization (ISH). We performed experiments in mice with acinar-specific deletion of Sox4 (Ptf1a: CreER; Rosa26-LSL-YFPLSL-YFP; Sox4fl/fl ) with and without an activating mutation in Kras (KrasLSL-G12D/+). Mice were given caerulein to induce pancreatitis. We performed phenotypic analysis by immunohistochemistry, tissue decellularization and single cell RNA sequencing. Results: We demonstrated that Sox4 is reactivated in ADM and PanINs. Contrary to findings in other tissues, Sox4 actually counteracts cellular dedifferentiation and helps maintain tissue homeostasis. Moreover, our investigations unveiled the indispensable role of Sox4 in the specification of mucin-producing cells and tuft-like cells from acinar cells. We identified Sox4-dependent non-cell-autonomous mechanisms regulating the stromal reaction during disease progression. Notably, Sox4-inferred targets are activated upon KRAS inactivation and tumor regression. Conclusions: Our results indicate that our transcriptome analysis can be used to investigate conserved mechanisms of tissue injury. We demonstrate that Sox4 acts as a switch to promote healing in pancreatic injury and cancer initiation and is activated upon Kras ablation and tumor regression in mice. By uncovering novel potential strategies to promote tissue homeostasis, our findings offer new avenues for preventing the development of PDAC.
Published in
Resolution of Acinar Dedifferentiation Regulates Tissue Remodeling in Pancreatic Injury and Cancer Initiation
Baldan J, Camacho-Roda J, Ballester M et al. · Gastroenterology 2024 · PMID 38729450 · doi:10.1053/j.gastro.2024.04.031
This dataset
Open GSE235809 in finder → Find more mouse 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 GSE235809_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 PRJNA987653 and SRA study SRP445848. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 38729450) ↗
Study design
3 × Pancreas, Day 2, Caeruelein treated, Sox4 conditional knock-out, Kras WT background, mouse vs 3 × Pancreas, Day 2, PBS treated, Sox4 wild-type, Kras WT background, mouse vs 3 × Pancreas, Day 21, Caeruelein treated, Sox4 conditional knock-out, Kras G12D background, mouse vs 3 × Pancreas, Day 21, PBS treated, Sox4 wild-type, Kras G12D background, mouse

Supports a between-group comparison across 12 samples.

How we read this: 4 replicated groups read from 17 sample titles; they account for 12 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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