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A pathway from the anterior cingulate cortex to the lateral habenula controls chronic pain induced depression in male mice

GSE308643 Mus musculus (mouse) RNA-seq (gene expression) 22 samples Submitted 2026/06/03 Platform GPL30172
At a glance

RNA-seq (gene expression) · mouse · 22 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
22 samples: 8 × IP Sham (Immunoprecipitated RNA fraction from the Sham control group) vs 8 × IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) vs 3 × IP (Immunoprecipitated RNA fraction), naive mice vs 3 × Input (Input RNA fraction), naive miceGroups 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
A pathway from the anterior cingulate cortex to the lateral habenula controls chronic pain-induced depression in male miceNeuropsychopharmacology : official publication of the American College of Neuropsychopharmacology · 2026
Summary (written by the submitters)
Chronic pain induces long-lasting changes in the anterior cingulate cortex (ACC) activity that contribute to the development of comorbid mood disorders. However, how such alterations propagate throughout the ACC connectome remains to be elucidated. Here, we aimed to study the role of the ACC neurons projecting to the lateral habenula (LHb) (ACC-->LHb) in chronic pain induced depression (CPID).
Read the full summary ↓
CPID was induced using sciatic nerve cuffing in male C57BL/6J mice. Anxiodepressive-like behaviors were evaluated using a battery of behavioral tests. Fiber photometry was used to study the Ca2+ dynamics in the ACC, LHb and AC-->LHb neurons. We combined viral Translating Ribosome Affinity Purification (vTRAP) and RNA sequencing to study the molecular alterations in the ACC-->LHb neurons. Finally, we used an optogenetic approach to study the functional role of this pathway in CPID. Our results confirmed a functional connectivity between the ACC and LHb and demonstrated that this connection plays a critical role in emotional processing. Activation of ACCLHb neurons elicited Ca2+ responses in the LHb and induced anxiodepressive-like behaviors in naive mice. Cell-type specific transcriptomic analysis revealed that CPID altered the expression of genes involved in neuronal excitability such as genes related to sphingolipid metabolism, glycophospholipids and Ca2+ channels in ACCLHb neurons. Interestingly, inhibition of this hyperactivity alleviated chronic pain- but not stress-induced anxiodepressive-like behaviors, demonstrating that the ACCLHb pathway selectively contributed to pain-induced emotional dysregulation. These results reveal that hyperactivity of the neuronal pathway linking the ACC to the LHb is essential for CPID in male mice.
Published in
A pathway from the anterior cingulate cortex to the lateral habenula controls chronic pain-induced depression in male mice
Journée SH, Mathis VP, Waegaert R et al. · Neuropsychopharmacology : official publication of the American College of Neuropsychopharmacology 2026 · PMID 41559454 · doi:10.1038/s41386-026-02346-w
This dataset
Open GSE308643 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 GSE308643_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 PRJNA1331779 and SRA study SRP622559. Searching any of these in the dataset finder brings you back here.

NCBI GEO page ↗ Paper (PMID 41559454) ↗
Study design
8 × IP Sham (Immunoprecipitated RNA fraction from the Sham control group) vs 8 × IP Cuff (Immunoprecipitated RNA fraction from the Cuff group) vs 3 × IP (Immunoprecipitated RNA fraction), naive mice vs 3 × Input (Input RNA fraction), naive mice

Supports a between-group comparison across 22 samples.

How we read this: 4 replicated groups read from 22 sample titles; they account for 22 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
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