GEO series
Integrated computational analysis identifies therapeutic targets with dual action in cancer cells and T cells
GSE261915
Mus musculus; Homo sapiens
Expression profiling by high throughput sequencing
21 samples
Submitted 2024/12/25
Platform GPL24676Platform GPL24247
Summary
Many cancer drugs that target cancer cell pathways have detrimental effects on the immune system. We developed a computational platform for the identification of therapeutic targets with beneficial effects in both cancer and immune cells. ICRAFT (https://icraft.pku-genomics.org/) enables integrated analysis of immune-related CRISPR screen datasets, scRNA-Seq data, and pre-treatment RNA-Seq data from clinical trials. This platform enabled the discovery of a substantial number of targets with dual action in cancer cells and T cells. Among these, TNFAIP3, a ubiquitin-editing enzyme also known as A20, emerged as a leading target. Inactivating TNFAIP3 in cancer cells sensitizes them to immune attacks by activating the NF-κB pathway, while targeting it in T cells significantly enhances their antitumor efficacy.
Published in
Luo C, Zhang R, Guo R et al.
· Immunity 2025
· PMID 40023158
· doi:10.1016/j.immuni.2025.02.007
This dataset
Download
Direct links to NCBI, no account and no request form: the whole study as GSE261915_RAW.tar, processed values as the series matrix, the supplementary file directory, and per-sample supplementary files for any of the 21 samples. Raw sequencing reads are also available from ENA.
Also filed as BioProject PRJNA1089567 and SRA study SRP496423. Searching any of these in the dataset finder brings you back here.
Study design
7 conditions, mostly in triplicate
A549 cancer cell, sgTNFAIP3-1, ×3
A549 cancer cell, sgTNFAIP3-2, ×3
A549 cancer cell, sgCtrl, ×3
OT-1 cell, untreated, sgCtrl, ×3
OT-1 cell, sgCtrl, co-culture with cancer cel… ×3
OT-1 cell, sgTnfaip3-1, co-culture with cance… ×3
OT-1 cell, sgTnfaip3-2, co-culture with cance… ×3
Supports a between-group comparison across 21 samples.
7 replicated groups read from 21 sample titles; they account for 21 of them. Check it against the sample list below before relying on it.
Samples in this study
0 selected
- GSM8154084 A549 cancer cell, sgTNFAIP3-1, rep1
- GSM8154085 A549 cancer cell, sgTNFAIP3-1, rep2
- GSM8154086 A549 cancer cell, sgTNFAIP3-1, rep3
- GSM8154087 A549 cancer cell, sgTNFAIP3-2, rep1
- GSM8154088 A549 cancer cell, sgTNFAIP3-2, rep2
- GSM8154089 A549 cancer cell, sgTNFAIP3-2, rep3
- GSM8154090 A549 cancer cell, sgCtrl, rep1
- GSM8154091 A549 cancer cell, sgCtrl, rep2
- GSM8154092 A549 cancer cell, sgCtrl, rep3
- GSM8154096 OT-1 cell, untreated, sgCtrl, rep1
- GSM8154101 OT-1 cell, untreated, sgCtrl, rep2
- GSM8154107 OT-1 cell, untreated, sgCtrl, rep3
- GSM8154108 OT-1 cell, sgCtrl, co-culture with cancer cell, rep1
- GSM8154109 OT-1 cell, sgCtrl, co-culture with cancer cell, rep2
- GSM8154110 OT-1 cell, sgCtrl, co-culture with cancer cell, rep3
- GSM8154111 OT-1 cell, sgTnfaip3-1, co-culture with cancer cell, rep1
- GSM8154112 OT-1 cell, sgTnfaip3-1, co-culture with cancer cell, rep2
- GSM8154113 OT-1 cell, sgTnfaip3-1, co-culture with cancer cell, rep3
- GSM8154114 OT-1 cell, sgTnfaip3-2, co-culture with cancer cell, rep1
- GSM8154115 OT-1 cell, sgTnfaip3-2, co-culture with cancer cell, rep2
- GSM8154116 OT-1 cell, sgTnfaip3-2, co-culture with cancer cell, rep3
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