GEO series

TNF-mediated cell death: an actionable target for immunotherapy in T-ALL [2]

GSE266346 Homo sapiens (human) RNA-seq (gene expression) 38 samples Submitted 2026/05/31 Platform GPL18573

At a glance

RNA-seq (gene expression) · human · 38 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: Acute lymphoblastic leukemiaThis series is part of our curated briefing on it.
Samples: 38 samples: 10 conditions, mostly in duplicateGroups 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.

Summary (written by the submitters)

T-cell acute lymphoblastic leukemia (T-ALL) accounts for one of the most aggressive hematological tumors and remains associated with poor prognosis and dismal outcomes, notably for relapsed and refractory patients. Unlike leukemias of myeloid or B-cell origin, T-ALL has not benefited from the major advances in immune and cell-based therapies.

Read the full summary ↓

Hence, an unmet medical need persists for underserved T-ALL patients who fail to durably respond to conventional treatments. Herein, we report the robust antileukemic efficacy of ATG, a polyclonal cocktail of IgG enriched in human thymocyte antigens, in vivo. The treatment of a large series of preclinical models of T-ALL revealed a genuine cytotoxic mechanism of ATG mediated by TNF signaling. Critically, we revealed that ATG resistance may occur via the induction of negative regulators of TNF-induced cell death, and can be circumvented by SMAC mimetic birinapant ex vivo and in vivo. These promising results were validated in an important series of prospective primary R/R T-ALL samples. This study provides a strong rationale for clinically relevant ATG-based immunotherapy in combination with birinapant to better treat T-ALL patients.

This dataset

Open GSE266346 in finder → Find more human RNA-seq datasets → Acute lymphoblastic leukemia 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 GSE266346_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 PRJNA1106809 and SRA study SRP505184. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗

Study design

10 conditions, mostly in duplicate

UPNT380, CT, ×2 UPNT380, Thymo, ×2 UPNT420, CT, ×2 UPNT420, Thymo, ×2 RPMI, HO, ×2 RPMI, H1, CT, ×2 RPMI, H1, Thymo, ×2 ALL-SIL, H0, ×2 +20 more

Supports a between-group comparison across 20 samples.

How we read this: 10 replicated groups read from 38 sample titles; they account for 20 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

GSM8245405 UPNT1077, CT
GSM8245406 UPNT1077, Thymo
GSM8245407 UPNT525, CT
GSM8245408 UPNT525, Thymo
GSM8245409 Jurkat, CT
GSM8245410 Jurkat, Thymo
GSM8245411 UPNT474, CT
GSM8245412 UPNT474, Thymo
GSM8245413 UPNT380, CT, run1 UPNT380, CT,
GSM8245414 UPNT380, Thymo, run1 UPNT380, Thymo,
GSM8245415 UPNT420, CT, run1 UPNT420, CT,
GSM8245416 UPNT420, Thymo, run1 UPNT420, Thymo,
GSM8245417 UPNT534, CT
GSM8245418 UPNT534, Thymo
GSM8245419 UPNT1095, CT
GSM8245420 UPNT1095, Thymo
GSM8245421 RPMI, HO, rep2 RPMI, HO,
GSM8245422 RPMI, HO, rep1 RPMI, HO,
GSM8245423 RPMI, H1, CT, rep2 RPMI, H1, CT,
GSM8245424 RPMI, H1, CT, rep1 RPMI, H1, CT,
GSM8245425 RPMI, H1, Thymo, rep2 RPMI, H1, Thymo,
GSM8245426 RPMI, H1, Thymo, rep1 RPMI, H1, Thymo,
GSM8245427 ALL-SIL, H0, rep2 ALL-SIL, H0,
GSM8245428 ALL-SIL, H0, rep1 ALL-SIL, H0,
GSM8245429 ALL-SIL, H1, CT, rep2 ALL-SIL, H1, CT,
GSM8245430 ALL-SIL, H1, CT, rep1 ALL-SIL, H1, CT,
GSM8245431 ALL-SIL, H1, Thymo, rep2 ALL-SIL, H1, Thymo,
GSM8245432 ALL-SIL, H1, Thymo, rep1 ALL-SIL, H1, Thymo,
GSM8245433 UPNT380, CT, run3 UPNT380, CT,
GSM8245434 UPNT380, Thymo, run3 UPNT380, Thymo,
GSM8245435 UPNT1137, CT
GSM8245436 UPNT1137, Thymo
GSM8245437 UPNT420, CT, run3 UPNT420, CT,
GSM8245438 UPNT420, Thymo, run3 UPNT420, Thymo,
GSM8245439 UPNT802, CT
GSM8245440 UPNT802, Thymo
GSM8245441 UPNT1012, CT
GSM8245442 UPNT1012, Thymo

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GSE266348 TNF-mediated cell death: an actionable target for immunotherapy in T-ALL 50 samples shares t-all, immunotherapy, tnf-mediated, actionable, target, death

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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.