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Molecular taxonomy and spatial organization define neuronal subtypes in the mouse inferior colliculus.

Overview

Authors: Mengting Liu1,2,3, Qi Hu1,2, Wenhao Feng1,2, Qi Guo1,2, Tianyu Ma1,2, Xiang Li1,2, Qi Meng4, Shijia Xu1,2, Jueqi Li1,2, Tianhong Zhang1,2, Huaizhang Shi1,5
  1. First Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang 150001, China
  2. Department of Otorhinolaryngology Head and Neck Surgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
  3. Shanghai Key Laboratory of Gene Editing and Cell Therapy for Rare Diseases, Fudan University, Shanghai 200031, China
  4. Department of Science and Technology, Second Affiliated Hospital of Harbin Medical University, Harbin, China
  5. Department of Neurosurgery, First Affiliated Hospital of Harbin Medical University, Harbin, China
Institutions: Harbin Medical University (China); Fudan University (China); First Affiliated Hospital of Harbin Medical University (China); Second Affiliated Hospital of Harbin Medical University (China)
Journal: iScience, volume 29, issue 7, article 116484
Dates: received 1 February 2026; accepted 4 June 2026; published online 23 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1016/j.isci.2026.116484 · PMID 42389572 · PMCID PMC13320336 · OpenAlex W7165661464
Open access: gold, a free copy (OpenAlex)
Status: code on request
Categories: genetics / omics (modality), mouse (organism), cellular / molecular (subfield)
Methods: Statistics, Smoothing, state filtering, decompositions, Machine learning
Keywords: molecular neuroscience, cell biology, transcriptomics
Topic: Hearing, Cochlea, Tinnitus, Genetics (Sensory Systems, Neuroscience), according to OpenAlex
Funding: Key Research and Development Program of Heilongjiang (2023ZX06C07); Heilongjiang Provincial Postdoctoral Science Foundation (LBH-Z23220); National Natural Science Foundation of China (gect-2025-Q01, 82401346); Harbin Medical University (2024B08); National Key Research and Development Program of China (2023YFC2412105)
Citations: cited by 2 papers (Europe PMC); 63 references in the paper

Abstract

The inferior colliculus (IC) is a critical auditory midbrain hub that processes sound localization and multisensory behaviors. Using single-nucleus RNA sequencing, we identify 14 transcriptionally distinct neuronal subtypes in the adult mouse IC. In situ sequencing and spatial mapping confirm these organizational patterns. Excitatory subtypes show region-specific spatial enrichment across the central, dorsal, and external cortices, whereas inhibitory subtypes are more diffusely distributed. A somatostatin-expressing (Sst+) neuronal population is predominantly excitatory but exhibits regional heterogeneity, with a subset co-expressing Gad2. Sub-clustering resolves Sst+ neurons into five molecularly distinct subtypes. Complementary to the Allen Brain Cell Atlas, this work provides an IC-focused molecular and spatial resource for studying neuronal diversity and cell-type-specific circuit organization in the auditory midbrain.

Reproduced under the paper's license (CC BY), from the paper cited above.

Code

The paper says that its authors' code is available on request: it was not published with the paper, so there is nothing to verify.

The paper's code and data availability statement is in the Data section.

Tracing map

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Data

Datasets cited

Data and code availability

Data: The raw sequencing data reported in this paper have been deposited in the NCBI Sequence Read Archive under BioProject accession number PRJNA1395172. The data are publicly accessible at: https://trace.ncbi.nlm.nih.gov/Traces/?view=run_browser&acc=SRR36629270&display=data-access. All other data will be shared by the lead contact upon request.

Code: This paper does not report original code. All software used is described in the key resources table and STAR Methods.

Other items: Any additional information required to reanalyze the data reported in this paper is available from the lead contact upon request.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 11 authors, 3 keywords, 5 funders, 61 references.

Cite

This paper

Liu, M., Hu, Q., Feng, W., Guo, Q., Ma, T., Li, X., Meng, Q., Xu, S., Li, J., Zhang, T., & Shi, H. (2026). Molecular taxonomy and spatial organization define neuronal subtypes in the mouse inferior colliculus. iScience, 29(7), 116484. https://doi.org/10.1016/j.isci.2026.116484

BibTeX

@article{liu2026molecular,
author = {Liu, Mengting and Hu, Qi and Feng, Wenhao and Guo, Qi and Ma, Tianyu and Li, Xiang and Meng, Qi and Xu, Shijia and Li, Jueqi and Zhang, Tianhong and Shi, Huaizhang},
title = {{Molecular taxonomy and spatial organization define neuronal subtypes in the mouse inferior colliculus}},
journal = {iScience},
year = {2026},
month = jun,
volume = {29},
number = {7},
pages = {116484},
publisher = {Elsevier},
issn = {2589-0042},
doi = {10.1016/j.isci.2026.116484},
url = {https://doi.org/10.1016/j.isci.2026.116484},
pmid = {42389572},
pmcid = {PMC13320336}
}

RIS

TY - JOUR
AU - Liu, Mengting
AU - Hu, Qi
AU - Feng, Wenhao
AU - Guo, Qi
AU - Ma, Tianyu
AU - Li, Xiang
AU - Meng, Qi
AU - Xu, Shijia
AU - Li, Jueqi
AU - Zhang, Tianhong
AU - Shi, Huaizhang
TI - Molecular taxonomy and spatial organization define neuronal subtypes in the mouse inferior colliculus
T2 - iScience
J2 - iScience
PY - 2026
DA - 2026/06/23
VL - 29
IS - 7
SP - 116484
SN - 2589-0042
PB - Elsevier
DO - 10.1016/j.isci.2026.116484
UR - https://doi.org/10.1016/j.isci.2026.116484
LA - en
ER -

CSL-JSON

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