← BioTransfer GEO Dataset Finder
GEO series

TNF-α Deficiency Underlies NK Cell Dysfunction in Colorectal Cancer

GSE305244 Homo sapiens (human) RNA-seq (gene expression) 18 samples Submitted 2026/03/04 Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 18 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
Homo sapiens (human)
Topic
Colorectal cancerThis series is part of our curated briefing on it.
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
TNF-α deficiency underlies NK cell dysfunction in colorectal cancerOncoimmunology · 2026
Summary (written by the submitters)
Natural killer (NK) cells are central to innate antitumor immunity, yet their function is systemically compromised in colorectal cancer (CRC). We show that CRC patients exhibit early and pronounced alterations in peripheral blood NK cells, marked by a reduced frequency of total CD56⁺ cells, a shift toward CD56lowCD16⁺ subset, and impaired cytotoxic and cytokine responses.
Read the full summary ↓
Notably, plasma from CRC patients, particularly those with advanced disease, induces similar dysfunction in healthy donor (HD) NK cells, suppressing mTORC1 signaling and effector activity. Transcriptomic profiling of HD NK cells exposed to CRC plasma revealed downregulation of TNF-α signaling components, concordant with reduced systemic and intracellular TNF-α levels in patients. Additionally, CRC plasma suppressed the JAK-STAT pathway and upregulated SOCS family genes, further dampening NK cell responsiveness. Inhibition of TNF-α in HD NK cells recapitulated the CRC plasma–induced defects, while exogenous TNF-α partially restored NK cell function, including STAT5 and S6 phosphorylation. These findings uncover TNF-α signaling deficiency as a systemic mechanism of NK cell suppression in CRC, linking impaired metabolism to immune evasion. Targeting this axis may offer a novel strategy to reinvigorate NK cell–mediated antitumor immunity in CRC.
Published in
TNF-α deficiency underlies NK cell dysfunction in colorectal cancer
Ruggeri S, Pizzitola B, Laffranchi M et al. · Oncoimmunology 2026 · PMID 41742461 · doi:10.1080/2162402X.2026.2636311
This dataset
Open GSE305244 in finder → Find more human RNA-seq datasets → Colorectal cancer landscape →
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 GSE305244_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 PRJNA1304910 and SRA study SRP608375. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41742461) ↗
Study design
6 conditions, mostly in triplicate
HD_Plasma_Donor1 ×3 CRC_Plasma_Donor1 ×3 HD_Plasma_Donor2 ×3 CRC_Plasma_Donor2 ×3 HD_Plasma_Donor3 ×3 CRC_Plasma_Donor3 ×3

Supports a between-group comparison across 18 samples.

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
More Colorectal cancer datasets

Search all human 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.