GEO series

Tyk2 controls immunosurveillance of colorectal cancer liver metastasis

GSE299638 Mus musculus (mouse) Single-cell RNA-seq 18 samples Submitted 2025/09/16 Platform GPL34328

At a glance

Single-cell RNA-seq · mouse · 18 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: 18 samples: 6 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: TYK2 Promotes Immunosurveillance of Colorectal Cancer Liver MetastasisCancer research · 2026

Summary (written by the submitters)

Colorectal cancer liver metastasis (CRLM) is a major clinical problem. However, little is known about immunosurveillance of CRLM. The Janus kinase Tyk2 is involved in several immune processes, but its role in CRLM is unclear. We have developed a murine colorectal cancer (CRC) organoid-based transplantation model to investigate the functions of Tyk2 in CRLM.

Read the full summary ↓

Organoids with mutations in Apc, Kras, and p53 were injected into the spleen or portal vein of host mice with Tyk2 deletion in different subsets of immune cells as well as into wild-type host mice treated with the Tyk2 inhibitor deucravacitinib. In addition, cancer cell-intrinsic effects on CRLM were investigated using organoids with CRISPR/Cas9-mediated deletion of Tyk2. Our data show that Tyk2 is a key factor controlling CRLM. We found that Tyk2 is not required in cancer cells, macrophages, NK cells, T cells, and Kupffer cells, but controls CRLM via a dendritic cell-dependent mechanism that relies on MHC-I-dependent cross presentation of antigens to CD8+ T cells. Analysis of a scRNA-seq dataset for primary CRC and CRLM revealed that Tyk2 is predominantly expressed in a specific dendritic cell population that is destined to present antigens in tumor-draining lymph nodes. Although our data cannot prove a role for Tyk2 in immune surveillance of CRLM in humans, they should be considered when treating patients with Tyk2 inhibitors.

Published in

TYK2 Promotes Immunosurveillance of Colorectal Cancer Liver Metastasis

Mödl B, Zwolanek D, Schwertner K et al. · Cancer research 2026 · PMID 40991399 · doi:10.1158/0008-5472.CAN-24-4224

This dataset

Open GSE299638 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 GSE299638_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 PRJNA1275817 and SRA study SRP591823. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 40991399) ↗

Study design

6 conditions, mostly in triplicate

WT tumor ×3 KO tumor ×3 WT tumorliver ×3 KO tumorliver ×3 WT liver ×3 KO liver ×3

Supports a case/control comparison: 6 samples read as cases, 3 as controls.

How we read this: 6 replicated groups read from 18 sample titles; they account for 18 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

GSM9042763 WT tumor rep1 WT tumor
GSM9042764 WT tumor rep2 WT tumor
GSM9042765 WT tumor rep3 WT tumor
GSM9042766 KO tumor rep1 KO tumor
GSM9042767 KO tumor rep2 KO tumor
GSM9042768 KO tumor rep3 KO tumor
GSM9042769 WT tumorliver rep1 WT tumorliver
GSM9042770 WT tumorliver rep2 WT tumorliver
GSM9042771 WT tumorliver rep3 WT tumorliver
GSM9042772 KO tumorliver rep1 KO tumorliver
GSM9042773 KO tumorliver rep2 KO tumorliver
GSM9042774 KO tumorliver rep3 KO tumorliver
GSM9042775 WT liver rep1 WT liver
GSM9042776 WT liver rep2 WT liver
GSM9042777 WT liver rep3 WT liver
GSM9042778 KO liver rep1 KO liver
GSM9042779 KO liver rep2 KO liver
GSM9042780 KO liver rep3 KO liver

Datasets on a similar topic

GSE266900 Cxcr3 promotes protection from colorectal cancer liver metastasis by driving NK infiltration and plasticity 18 samples shares colorectal, metastasis, liver
GSE286169 Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_InVitro] 35 samples shares colorectal, metastasis
GSE286166 Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_CRISPR] 34 samples shares colorectal, metastasis
GSE324743 Hepatocytes promote liver metastasis of pancreatic cancer by providing exogenous serine 24 samples shares metastasis, liver
GSE286167 Ceramides drive colorectal cancer metastasis through a revival stemness program [BulkRNAseq_HFD] 23 samples shares colorectal, metastasis
GSE287625 Mitochondrial Ca2+ controls pancreatic cancer growth and metastasis by regulating epithelial cell plasticity 18 samples shares metastasis, controls
GSE324997 Hepatocytes promote liver metastasis of pancreatic cancer by providing exogenous serine, 2. 16 samples shares metastasis, liver
GSE290752 Lineage Plasticity Driven by GATA6 Loss Fuels Colorectal Cancer Metastasis [RNA-seq_met] 15 samples shares colorectal, metastasis

Search all mouse RNA-seq datasets in GEO →

Share this dataset

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.