GEO series

Cancer-intrinsic Cxcl5 orchestrates global metabolic reprogramming of three dimensional cancers by upregulating Hif1α and Myc expression

GSE269318 Mus musculus (mouse) RNA-seq (gene expression) 31 samples Submitted 2025/07/30 Platform GPL24247

At a glance

RNA-seq (gene expression) · mouse · 31 samples

What it is: RNA-seq (gene expression)Gene activity measured by sequencing. The summary does not mention single-cell work, so this is most likely bulk: one average per sample, the usual starting point for comparing groups.
Organism: Mus musculus (mouse)
Samples: 31 samples: 11 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: Cancer-intrinsic Cxcl5 orchestrates a global metabolic reprogramming for resistance to oxidative cell death in 3DCell death and differentiation · 2025

Summary (written by the submitters)

The tumor microenvironment (TME) of pancreatic cancer is characterized by deposition of extracellular matrix (ECM). In 3D TME comprising cellular and non-cellular components, physical and chemical restriction induce oxygen and nutrients shortage in tumor site. Therefore, it is inevitable for cancer cells to manipulate the biological processes and metabolism for survival.

Read the full summary ↓

However, it has not been fully explored the metablic phenotype coupling to the components existed in 3D and how the cancer cells exploit the metabolic reprogramming. In this study, we establisehd in vitro 3D tumor spheroid-in-Matrigel culture system recapitulating the 3D TME. We discovered the significant upregulation of Cxcl5 expression in murine pancreatic cancer cell line Panc02 by 3D culture with M1 macrophage conditioned media treatment. The loss of Cxcl5 in 3D Panc02 cells showed dramatical reduction of cancer growth. Importantly, the Cxcl5-deficient 3D cancer cells showed global alteration in metabolism. Additionally, Cxcl5 loss failed to control oxidative stress and in turn, increased ferroptotic cell death. Overexpression of Hif1α and Myc in Cxcl5-deficient cancer cells rescued the impaired metabolic processes, ferroptotic cell death, and cancer growth.

Published in

Cancer-intrinsic Cxcl5 orchestrates a global metabolic reprogramming for resistance to oxidative cell death in 3D

Seo R, de Guzman ACV, Park S et al. · Cell death and differentiation 2025 · PMID 40050422 · doi:10.1038/s41418-025-01466-y

This dataset

Open GSE269318 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 GSE269318_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: For RNA-seq the counts are usually a table among the supplementary files (look for 'counts', 'expression', 'FPKM' or 'TPM' in the file name). The series matrix of a sequencing study is sometimes nearly empty.

Also filed as BioProject PRJNA1121207 and SRA study SRP512391. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40050422) ↗

Study design

11 conditions, mostly in triplicate

Panc02 spheroid, ctrl ×3 Panc02 spheroid, M0 ×3 Panc02 spheroid, M1 ×3 2D WT ×3 2D KO ×3 3D WT ×3 3D KO ×3 3DHif1a ×3 +3 more

Supports a between-group comparison across 31 samples.

How we read this: 11 replicated groups read from 31 sample titles; they account for 31 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

GSM8312992 Panc02 spheroid, ctrl_rep1 Panc02 spheroid, ctrl
GSM8312993 Panc02 spheroid, ctrl_rep2 Panc02 spheroid, ctrl
GSM8312994 Panc02 spheroid, ctrl_rep3 Panc02 spheroid, ctrl
GSM8312995 Panc02 spheroid, M0_rep1 Panc02 spheroid, M0
GSM8312996 Panc02 spheroid, M0_rep2 Panc02 spheroid, M0
GSM8312997 Panc02 spheroid, M0_rep3 Panc02 spheroid, M0
GSM8312998 Panc02 spheroid, M1_rep1 Panc02 spheroid, M1
GSM8312999 Panc02 spheroid, M1_rep2 Panc02 spheroid, M1
GSM8313000 Panc02 spheroid, M1_rep3 Panc02 spheroid, M1
GSM8313001 2D WT_rep1 2D WT
GSM8313002 2D WT_rep2 2D WT
GSM8313003 2D WT_rep3 2D WT
GSM8313004 2D KO_rep1 2D KO
GSM8313005 2D KO_rep2 2D KO
GSM8313006 2D KO_rep3 2D KO
GSM8313007 3D WT_rep1 3D WT
GSM8313008 3D WT_rep2 3D WT
GSM8313009 3D WT_rep3 3D WT
GSM8313010 3D KO_rep1 3D KO
GSM8313011 3D KO_rep2 3D KO
GSM8313012 3D KO_rep3 3D KO
GSM8313013 2-3DWT_rep1 2-3DWT
GSM8313014 2-3DWT_rep2 2-3DWT
GSM8313015 2-3DKO_rep1 2-3DKO
GSM8313016 2-3DKO_rep2 2-3DKO
GSM8313017 3DHif1a_rep1 3DHif1a
GSM8313018 3DHif1a_rep2 3DHif1a
GSM8313019 3DHif1a_rep3 3DHif1a
GSM8313020 3DMyc_rep1 3DMyc
GSM8313021 3DMyc_rep2 3DMyc
GSM8313022 3DMyc_rep3 3DMyc

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Metadata from NCBI GEO, cached and refreshed periodically — the NCBI page above is authoritative. Downloads link straight to NCBI/ENA; nothing is proxied through BioTransfer.