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Differential KEAP1/NRF2-mediated signaling widens the therapeutic window of redox-targeting drugs in SCLC therapy [seq]

GSE279100 Homo sapiens (human) RNA-seq (gene expression) 50 samples Submitted 2024/11/11 Platform GPL24247Platform GPL24676
At a glance

RNA-seq (gene expression) · human · 50 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
Small cell lung cancerThis series is part of our curated briefing on it.
Samples
50 samples: 10 conditions, mostly with about 5 replicates eachGroups 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)
Small cell lung cancer (SCLC) patients experience rapid disease progression despite frequently achieving a complete response to first-line therapy. Maintenance treatments, aiming at controlling residual tumor cells, generally fail due to cross-resistance, inability to target tumor vulnerabilities, or dose-limiting side effects. Here, we show that SCLC cells, like their cell-of-origin, pulmonary neuroendocrine cells (PNECs), exhibit notably low activity in pathways protecting against reactive oxygen species (ROS).
Read the full summary ↓
When exposed to a novel thioredoxin reductase 1 (TXNRD1) inhibitor, these cells quickly exhaust their ROS-scavenging capacity, independent of their molecular subtype and the resistance status against first-line therapy. Importantly, SCLC cells, in contrast to non-cancerous cells, cannot adapt to drug-induced ROS stress because they repress ROS defense enzymes through multiple layers of epigenetic and transcriptional mechanisms. By exploiting this differential ability to manage oxidative stress, we demonstrate that the therapeutic dose of TXNRD1 inhibitors can be safely increased in vivo through pharmacological activation of the NRF2 stress response pathway using Bardoxolon-Methyl (CDDO-Me), leading to improved tumor control without added toxicity to healthy tissues. These findings underscore the therapeutic potential of TXNRD1 inhibitors in cancers like SCLC, which are marked by reduced ROS-scavenging capacity and strong suppression of adaptive resistance mechanisms.
This dataset
Open GSE279100 in finder → Find more RNA-seq datasets → Small cell lung 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 GSE279100_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 PRJNA1170853 and SRA study SRP537355. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗
Study design
10 conditions, mostly with about 5 replicates each
Tumor vehicle biol ×5 Tumor CDDO biol ×5 Heart vehicle biol ×5 Heart CDDO biol ×5 Kidney vehicle biol ×5 Kidney CDDO biol ×5 Liver vehicle biol ×5 Liver CDDO biol ×5 +2 more

Supports a case/control comparison: 5 samples read as cases, 20 as controls.

How we read this: 10 replicated groups read from 50 sample titles; they account for 50 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

+ 10 more — browse all 50 samples with per-sample file links →

More Small cell lung cancer datasets

Search all RNA-seq datasets in GEO →

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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.