A cross-species spatial transcriptomic atlas of the human and non-human primate basal ganglia
Year: 2025
Type: preprint
Abstract: The basal ganglia are interconnected subcortical nuclei with complex topographical organization that orchestrate goal-directed behaviors and are implicated in neurodegenerative movement disorders. We generated a cellular-resolution, spatial transcriptomic atlas of the basal ganglia in human, rhesus macaque, and common marmoset, sampling over one million cells in each species. By integrating spatial data with a cross-species, consensus snRNA-seq cell type taxonomy, this atlas reveals conserved principles of molecular organization within and across structures. The cellular architecture is complex but highly stereotyped, with gene expression gradients superimposed onto discrete compartments. Extensive spatial sampling illuminates 3D gradients of molecular organization in the striatum and reveals cell type-specific core and shell compartments in the primate internal globus pallidus, which is conserved with mouse. This unified, cross-species spatial transcriptomic atlas will be a foundational resource for characterizing the molecular and functional organization of the basal ganglia and their roles in health and disease.
Authors: Madeleine N. Hewitt, Meghan A. Turner, Nelson Johansen, Delissa A. McMillen, Shu Dan, Mike DeBerardine, Augustin Ruiz, Mike Huang, Jacob Quon, Yuanyuan Fu, Inkar Kapen, Stuard Barta, Naomi Martin, Nasmil Valera Cuevas, Paul Olsen, Josh Nagra, Jazmin Campos, Marshall M. VanNess, Shea Ransford, Zoe Juneau, Sam Hastings, Lindsey Ching, Michael Kunst, Soumyadeep Basu, Thomas Höllt, Chang Li, Boudewijn Lelieveldt, Faraz Yazdani, Qiangge Zhang, Kirsten Levandowski, Guoping Feng, Burke Q. Rosen, Matthew F. Glasser, Takuya Hayashi, Aaron D. Garcia, Omar Kana, Zoe M. Maltzer, Luke Campagnola, Tim Jarsky, Lauren Kruse, Winrich Freiwald, C. Dirk Keene, David C. Van Essen, Jeanelle Ariza, Jack Waters, Fenna M. Krienen, Trygve E. Bakken, Rebecca D. Hodge, Lydia Ng, Hongkui Zeng, Ed S. Lein, Jennie L. Close, Brian Long, Stephanie C. Seeman
Institutions: Allen Institute for Brain Science, Princeton University, Leiden University Medical Center, Delft University of Technology, Rockefeller University, Broad Institute, McGovern Institute for Brain Research, Stanley Center for Psychiatric Research, Massachusetts Institute of Technology, Washington University in St. Louis, Kyoto University, RIKEN Center for Biosystems Dynamics Research, University of Washington, Harborview Medical Center
Subfield: Molecular Biology
Domain: Life Sciences
Open Access status: green
OpenAlex ID: W4416940919