A consensus spinal cord cell type atlas across mouse, macaque, and human
The spinal cord contains evolutionarily conserved cell types critical for motor function, sensory processing, and autonomic regulation, many of which are implicated in diverse neurological diseases and injuries. Yet the field lacks a comprehensive molecular characterization of cellular diversity in human, macaque, and mouse spinal cord. Here, we present a unified, cross-species cell type atlas based on the integration of single-nucleus gene expression, chromatin accessibility, and spatial transcriptomic data from segments within cervical, thoracic, lumbar, and sacral regions, including motor neurons (MNs) sampled across the entire rostro-caudal axis of the macaque spinal cord. Leveraging the spatial distributions of our molecularly defined cell types, we generated a cell type-guided anatomical map of spinal cord laminae and nuclei. We identified both conserved and species-specific cellular features, including gene expression patterns across distinct MN subtypes in the primate spinal cord. Cross-species cis-regulatory analysis and deep learning sequence models dissected the enhancer logic underlying viral targeting, uncovering conserved transcription factor grammar encoding cellular identity. Together, these results establish a unifying molecular and anatomical taxonomy of spinal cord cell types across species.
Authors
- Madeleine N. Hewitt (ORCID: https://orcid.org/0000-0002-4387-327X)
- Michael J. Leone (ORCID: https://orcid.org/0000-0002-0218-8612)
- Trangthanh Pham (ORCID: https://orcid.org/0000-0002-4738-5062)
- Nelson Johansen (ORCID: https://orcid.org/0000-0002-4436-969X)
- Emily Kussick (ORCID: https://orcid.org/0000-0001-7885-3116)
- Yuan Gao (ORCID: https://orcid.org/0000-0002-7644-2994)
- Ding Song-lin
- Ashwin A. Bhandiwad (ORCID: https://orcid.org/0000-0002-6963-1594)
- Olivia Gautier
- Stephanie C. Seeman (ORCID: https://orcid.org/0000-0003-3894-1992)
- Niklas Kempynck (ORCID: https://orcid.org/0000-0002-0104-4844)
- Jacob A. Blum (ORCID: https://orcid.org/0000-0002-7015-6815)
- Yuanyuan Fu (ORCID: https://orcid.org/0000-0001-5934-6573)
- Inkar Kapen (ORCID: https://orcid.org/0009-0007-0159-0590)
- Nasmil Valera Cuevas
- Trygve E. Bakken
- Ed S. Lein
- Nicholas Donadio
- Jeanelle Ariza
- Angela Ayala
- Liliana Cano-Gomez
- Cindy Huang
- Katie Fancher
- Anish Bhaswanth Chakka
- Rebecca D. Hodge
- Stuard Barta
- Kimberly A. Smith
- Trygve E. Bakken
Institutions
- Tallinn University of Technology (EE)
- University of Pittsburgh (US)
- University of Washington (US)
- VIB-KU Leuven Center for Cancer Biology (BE)
- Allen Institute (US)
- VIB-KU Leuven Center for Brain & Disease Research (BE)
- Protobios (Estonia) (EE)
- Carnegie Mellon University (US)
- The University of Texas Southwestern Medical Center (US)
- Stanford University (US)
- KU Leuven (BE)
Publication Details
- Journal
- bioRxiv (Cold Spring Harbor Laboratory)
- Published
- 2026-02-05
- DOI
- https://doi.org/10.64898/2026.02.04.703852
- Primary Topic
- Zebrafish Biomedical Research Applications
- Type
- article
- Field-Weighted Citation Impact
- 0.00