GEO series
Oncofetal RNA-binding proteins IGF2BP suppress innate immune signaling pathways in leukemia stem cells [RNA-seq]
GSE311641
Homo sapiens (human)
RNA-seq (gene expression)
32 samples
Submitted 2026/07/30
Platform GPL24676
At a glance
RNA-seq (gene expression) · human · 32 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 myeloid leukemiaThis series is part of our curated briefing on it.
- Samples
- 32 samples: 12 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.
- Paper
- Oncofetal RNA-binding proteins of IGF2BP family suppress IRF-3 and NF-kB dependent transcription downstream of cytosolic RNA sensorsbioRxiv : the preprint server for biology · 2026
Summary (written by the submitters)
Activation of innate inflammatory signaling and tumor-specific antigen presentation in cancer cells provides a foundation for anti-cancer immunotherapies. Here, we show that Insulin-like Growth Factor 2 mRNA-Binding Proteins (IGF2BP1, IGF2BP2, and IGF2BP3), which are upregulated across various human malignancies, including acute myeloid leukemia (AML), suppress the activity of RNA-sensing pattern recognition receptors and downstream ISRE- and NF-κB-driven transcription.
Read the full summary ↓
IGF2BPs exert a strong inhibitory effect on RIG-I signaling. This suppression is most pronounced when all three paralogs are co-expressed, particularly in embryonic-like hematoendothelial and leukemia stem cells and is at least partly mediated through IGF2BP-dependent regulation of negative regulators of immune signaling. Genetic and pharmacological inhibition of IGF2BPs activates innate immune signaling and induces MHC class I gene expression in AML, highlighting a promising strategy for RIG-I- and TLR-based cancer immunotherapies.
Published in
Knox G, Agili-Shaban R, Morrissey A et al.
· bioRxiv : the preprint server for biology 2026
· PMID 42244769
· doi:10.64898/2026.05.22.726816
This dataset
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.
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 GSE311641_RAW.tar (it can run to tens of gigabytes).
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.
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 PRJNA1370069 and SRA study SRP649344. Searching any of these in the dataset finder brings you back here.
Study design
12 conditions, mostly in duplicate
Cytoplasmic RNA-Seq, CRISPR Control, ×4
Cytoplasmic RNA-Seq, IGF2BP3 Knockout, ×4
Nuclear RNA-Seq, CRISPR Control, ×4
Total RNA-Seq, CRISPR Control, ×4
Cytoplasmic RNA-Seq, IGF2BP1 Knockout, ×2
Cytoplasmic RNA-Seq, IGF2BP2 Knockout, ×2
Nuclear RNA-Seq, IGF2BP1 Knockout, ×2
Nuclear RNA-Seq, IGF2BP2 Knockout, ×2
+4 more
Supports a case/control comparison: 20 samples read as cases, 12 as controls.
How we read this: 12 replicated groups read from 32 sample titles; they account for 32 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
- GSM9328623 Cytoplasmic RNA-Seq, CRISPR Control, Replicate 1 Cytoplasmic RNA-Seq, CR…
- GSM9328624 Cytoplasmic RNA-Seq, CRISPR Control, Replicate 2 Cytoplasmic RNA-Seq, CR…
- GSM9328625 Cytoplasmic RNA-Seq, CRISPR Control, Replicate 3 Cytoplasmic RNA-Seq, CR…
- GSM9328626 Cytoplasmic RNA-Seq, CRISPR Control, Replicate 4 Cytoplasmic RNA-Seq, CR…
- GSM9328627 Cytoplasmic RNA-Seq, IGF2BP1 Knockout, Replicate 1 Cytoplasmic RNA-Seq, IG…
- GSM9328628 Cytoplasmic RNA-Seq, IGF2BP1 Knockout, Replicate 2 Cytoplasmic RNA-Seq, IG…
- GSM9328629 Cytoplasmic RNA-Seq, IGF2BP2 Knockout, Replicate 1 Cytoplasmic RNA-Seq, IG…
- GSM9328630 Cytoplasmic RNA-Seq, IGF2BP2 Knockout, Replicate 2 Cytoplasmic RNA-Seq, IG…
- GSM9328631 Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 1 Cytoplasmic RNA-Seq, IG…
- GSM9328632 Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 2 Cytoplasmic RNA-Seq, IG…
- GSM9328633 Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 3 Cytoplasmic RNA-Seq, IG…
- GSM9328634 Cytoplasmic RNA-Seq, IGF2BP3 Knockout, Replicate 4 Cytoplasmic RNA-Seq, IG…
- GSM9328635 Nuclear RNA-Seq, CRISPR Control, Replicate 1 Nuclear RNA-Seq, CRISPR…
- GSM9328636 Nuclear RNA-Seq, CRISPR Control, Replicate 2 Nuclear RNA-Seq, CRISPR…
- GSM9328637 Nuclear RNA-Seq, CRISPR Control, Replicate 3 Nuclear RNA-Seq, CRISPR…
- GSM9328638 Nuclear RNA-Seq, CRISPR Control, Replicate 4 Nuclear RNA-Seq, CRISPR…
- GSM9328639 Nuclear RNA-Seq, IGF2BP1 Knockout, Replicate 1 Nuclear RNA-Seq, IGF2BP…
- GSM9328640 Nuclear RNA-Seq, IGF2BP1 Knockout, Replicate 2 Nuclear RNA-Seq, IGF2BP…
- GSM9328641 Nuclear RNA-Seq, IGF2BP2 Knockout, Replicate 1 Nuclear RNA-Seq, IGF2BP…
- GSM9328642 Nuclear RNA-Seq, IGF2BP2 Knockout, Replicate 2 Nuclear RNA-Seq, IGF2BP…
- GSM9328643 Nuclear RNA-Seq, IGF2BP3 Knockout, Replicate 1 Nuclear RNA-Seq, IGF2BP…
- GSM9328644 Nuclear RNA-Seq, IGF2BP3 Knockout, Replicate 2 Nuclear RNA-Seq, IGF2BP…
- GSM9328645 Total RNA-Seq, CRISPR Control, Replicate 1 Total RNA-Seq, CRISPR C…
- GSM9328646 Total RNA-Seq, CRISPR Control, Replicate 2 Total RNA-Seq, CRISPR C…
- GSM9328647 Total RNA-Seq, CRISPR Control, Replicate 3 Total RNA-Seq, CRISPR C…
- GSM9328648 Total RNA-Seq, CRISPR Control, Replicate 4 Total RNA-Seq, CRISPR C…
- GSM9328649 Total RNA-Seq, IGF2BP1 Knockout, Replicate 1 Total RNA-Seq, IGF2BP1 …
- GSM9328650 Total RNA-Seq, IGF2BP1 Knockout, Replicate 2 Total RNA-Seq, IGF2BP1 …
- GSM9328651 Total RNA-Seq, IGF2BP2 Knockout, Replicate 1 Total RNA-Seq, IGF2BP2 …
- GSM9328652 Total RNA-Seq, IGF2BP2 Knockout, Replicate 2 Total RNA-Seq, IGF2BP2 …
- GSM9328653 Total RNA-Seq, IGF2BP3 Knockout, Replicate 1 Total RNA-Seq, IGF2BP3 …
- GSM9328654 Total RNA-Seq, IGF2BP3 Knockout, Replicate 2 Total RNA-Seq, IGF2BP3 …
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