New study maps molecular organization of critical brain region

By Emma Vinokour | November 12, 2026
Adjacent post-mortem tissue sections of the human striatum stained with cresyl violet (left) and processed with Slide-tags (right). In the Slide-tags map, each of the 92,100 dots is one cell, placed at its original position, with genome-wide gene expression measured in every cell. Colors mark the six molecular zones identified in the study; gray marks the surrounding white matter. Image credit: Andrew Kraft.
Adjacent post-mortem tissue sections of the human striatum stained with cresyl violet (left) and processed with Slide-tags (right). In the Slide-tags map, each of the 92,100 dots is one cell, placed at its original position, with genome-wide gene expression measured in every cell. Colors mark the six molecular zones identified in the study; gray marks the surrounding white matter. Image credit: Andrew Kraft, MD, PhD.

Andrew Kraft, MD, PhD

In a new study from Mass General Brigham and the Broad Institute of MIT and Harvard, researchers have mapped the molecular organization of the striatum, a deep brain region involved in movement, motivation and learning. The work was led by Andrew Kraft, MD, PhD, and supervised by Evan Macosko, MD, PhD.

Evan Macosko, MD, PhD

The team used Slide-tags, a spatial transcriptomics technique that measures genome-wide gene expression in individual cells while recording where each cell sits in the tissue. The resulting atlas of more than 1 million spatially mapped nuclei from 19 human donors shows that the striatum is organized into six distinct zones, each defined by its own pattern of gene expression. The researchers found corresponding zones in macaques and mice, indicating that this organization is conserved across species.

To ask what the zones mean for brain function, the team turned to brain-wide maps of neural connections in mice. They found that each zone receives input from a distinct set of brain regions, suggesting each zone anchors a separate brain-wide circuit. Furthermore, the gene expression signatures that define each zone erode with age, and this may be a previously unrecognized mechanism of brain aging.

The study is part of a collection of publications from the BRAIN Initiative Cell Atlas Network (BICAN), a large-scale collaborative effort to map all of the cell types in the basal ganglia across species and generate resource atlases available for public use. Research reported in the publication package was funded by the National Institutes of Health’s Brain Research Through Advancing Innovative Neurotechnologies® Initiative, or The BRAIN Initiative®. Kraft was supported by a Transformative Scholar Award from the Mass General Brigham Neuroscience Institute.

 

Published in a special issue of Cell on Nov. 12, 2026 | Read the paper: “Mesoscale molecular architecture of the striatum across cell types and adult aging”

Summary reviewed by: Andrew Kraft, MD, PhD, co-lead author

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