In the human brain, the dorsal anterior cingulate cortex (dACC) plays a key role in the reward pathway, which is connected to drug addiction, substance abuse, and some psychiatric disorders. Specific cell types in the dACC are associated with these disorders, but the breakdown of cell populations and their relative positions are unknown. Uniquely, the dACC has agranular laminar structure due to a lack of layer IV, which relates to distinct biological functions. We generated a human dACC spatial transcriptomic map by integrating 10x Genomics Visium Spatial Gene Expression data from ten neurotypical donors and combining this map with corresponding 10x Genomics Chromium Single Cell Gene Expression data. We utilized nonnegative matrix factorization (NMF) to discover various gene programs, which shed light on von Economo neurons (VENs) in Layer V of the dACC.To better understand the molecular landscape of this region, we compared it with the dorsolateral prefrontal cortex (dlPFC) region in the same ten donors. The brain’s structure and function are closely connected, so our precise pairing of gene expression to spatial information sheds light on how dysregulation in the dACC relates to psychiatric disorders.
from sddb import Catalog
cohort = Catalog().collection("geo-gse296789")
cohort.members # the 21 datasets as a table
print(cohort.licenses()) # check the terms before you download
sdatas = cohort.to_dict() # {uid: SpatialData}, cached locally
# or keep the .zarr files in a folder of your choice:
# sdatas = cohort.to_dict(dest="data/")Needs pip install lamindb and network access to the Lamin database, which is limited during the alpha. If it fails, use the Client tab.
import lamindb as ln
db = ln.DB("scverse/spatialdata-db")
coll = db.Collection.get(key="geo-gse296789")
coll.ordered_artifacts.to_dataframe() # the 21 members, ordered
# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse296789 --dest data/Licenses: 21 NCBI GEO policy
@article{Shah_2026,
title = {Spatio-molecular gene expression reflects dorsal anterior cingulate cortex structure and function in the human brain},
volume = {45},
ISSN = {2211-1247},
url = {http://dx.doi.org/10.1016/j.celrep.2026.117500},
DOI = {10.1016/j.celrep.2026.117500},
number = {6},
journal = {Cell Reports},
publisher = {Elsevier BV},
author = {Shah, Kinnary and Totty, Michael S. and Bach, Svitlana V. and Valentine, Madeline R. and Chandra, Atharv and AlGrain, Haya A. and Divecha, Heena R. and Miller, Ryan A. and Siewe, Felix Rene M. and Kwon, Sang Ho and Del Rosario Alvia, Ishbel and Ramnauth, Anthony D. and Tippani, Madhavi and Tyagi, Sanjana and Kleinman, Joel E. and Collado-Torres, Leonardo and Han, Shizhong and Hyde, Thomas M. and Page, Stephanie C. and Maynard, Kristen R. and Hicks, Stephanie C. and Martinowich, Keri},
year = {2026},
month = June,
pages = {117500}
}