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Effects of Oxaliplatin on Hematopoietic Pathways with Implications for Chronic Pain

GSE301439 Mus musculus (mouse) RNA-seq (gene expression) 20 samples Submitted 2025/12/31 Platform GPL24247Platform GPL34290
At a glance

RNA-seq (gene expression) · mouse · 20 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
Mus musculus (mouse)
Samples
20 samples: 5 × Kidney_ctrl vs 5 × Kidney_oxa vs 5 × BM_ctrl vs 5 × BM_oxaGroups 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
Lineage-Specific Disruption of Hematopoiesis by Oxaliplatin: Mechanisms of Erythropoietin Resistance and Immune SuppressionJournal of hematology and oncology research · 2026
Summary (written by the submitters)
Background: Oxaliplatin, a widely used chemotherapeutic agent, is associated with hematologic toxicities such as anemia, leukopenia, and thrombocytopenia. Despite their clinical relevance, the molecular mechanisms underlying lineage-specific bone marrow suppression remain poorly understood. Methods: We administered oxaliplatin to mice over eight weeks and performed bulk RNA-sequencing on bone marrow alongside peripheral blood analysis and cytokine profiling.
Read the full summary ↓
Transcriptomic data were analyzed to identify differentially expressed genes (DEGs) and enriched pathways, with a focus on hematopoietic and immune lineages. Results: Oxaliplatin induced broad transcriptional suppression of erythropoiesis and lymphopoiesis, with 3,690 DEGs identified (FDR<0.05, |FC|>1.5). Upregulation of Cdkn1a and downregulation of E2f2 suggest G1/S cell cycle arrest, correlating with repression of key erythroid maturation genes (e.g., Spta1, Slc4a1, Alas2) and hemoglobin subunits (Hba-a12, Hbb-bs/t). Despite a ~3000-fold increase in renal Epo expression, bone marrow Epor was reduced, indicating erythropoietin resistance. B and T cell markers were also significantly downregulated, signifying a collapse in adaptive immunity. Notably, neutrophils were largely spared. Cytokine analysis revealed a pro-inflammatory shift with elevated TNF-α and CCL2 and reduced TGF-β, potentially exacerbating hematopoietic dysfunction. The data also point to a neuro-immune axis in which oxaliplatin-induced inflammation in the bone marrow contributes to peripheral nerve sensitization as seen with upregulation of nociceptive signaling components such as Tacr1. Conclusions: Oxaliplatin induces a lineage-dependent suppression of hematopoiesis, driven by coordinated cell cycle arrest, metabolic stress, and disrupted cytokine signaling. These findings provide mechanistic insights into oxaliplatin’s hematologic toxicity linking bone marrow failure and neuropathic pain via interconnected inflammatory and metabolic pathways and may inform therapeutic strategies to mitigate myelosuppression and peripheral neuropathy in cancer patients.
Published in
Lineage-Specific Disruption of Hematopoiesis by Oxaliplatin: Mechanisms of Erythropoietin Resistance and Immune Suppression
Sudlow LC, Du J, Shahverdi K et al. · Journal of hematology and oncology research 2026 · PMID 41868970 · doi:10.14302/issn.2372-6601.jhor-25-5944
This dataset
Open GSE301439 in finder → Find more mouse RNA-seq datasets →
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 GSE301439_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 PRJNA1285180 and SRA study SRP597111. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41868970) ↗
Study design
5 × Kidney_ctrl vs 5 × Kidney_oxa vs 5 × BM_ctrl vs 5 × BM_oxa

Supports a between-group comparison across 20 samples.

How we read this: 4 replicated groups read from 20 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
Datasets on a similar topic

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