Collections / Aging-Related Cellular and Molecular Changes Reveal a Role for Bglap3+ Neurons in MEC Spatial Cognition

Aging-Related Cellular and Molecular Changes Reveal a Role for Bglap3+ Neurons in MEC Spatial Cognition

Aging-related cognitive decline, including impairments in spatial orientation and memory, has been linked to dysfunction within the hippocampus and medial entorhinal cortex (MEC). However, the cellular and molecular alterations underlying MEC aging remain poorly understood. Here we show that old mice exhibit a reduced proportion of grid cells and decreased spatial stability. Transcriptomic profiling of the MEC using 10x Genomics Visium technology reveals 1664 differentially expressed genes between young and old mice. Among these, Bglap3 is identified as a marker gene for a subpopulation of Layer III neurons that showed an age-associated reduction in cell number. Chemogenetic silencing of Bglap3+ neurons in young mice impairs spatial tuning of MEC neurons. Together, these findings elucidate cellular and molecular mechanisms contributing to age-related MEC dysfunction and suggest that the loss of Bglap3+ neurons may underlie spatial coding deficits in aging.

Datasets14
Size~883 MB
AssayVisium
Samplemouse · entorhinal cortex
KindOther
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www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE347650 ↗
Download the whole collection
Python · sddb client 
from sddb import Catalog

cohort = Catalog().collection("geo-gse347650")
cohort.members        # the 14 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/")
Install (Python 3.12+) Docs →
Python · lamindb

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-gse347650")
coll.ordered_artifacts.to_dataframe()   # the 14 members, ordered

# download every member .zarr to the local cache:
paths = [a.cache() for a in coll.ordered_artifacts.all()]
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Shell 
# sddb client: download every member .zarr into data/
sddb-cli download --collection geo-gse347650 --dest data/
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Licenses: 14 NCBI GEO policy

Member datasets · 14
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058084
mouse entorhinal cortex 67.9 MB 2,940 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size67.9 MB
Spots2,940
silver H&E NCBI GEO policy Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058086
mouse entorhinal cortex 51.3 MB 2,920 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size51.3 MB
Spots2,920
silver H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058088
mouse entorhinal cortex 60.9 MB 3,114 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size60.9 MB
Spots3,114
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058085
mouse entorhinal cortex 52.5 MB 3,064 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size52.5 MB
Spots3,064
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058082
mouse entorhinal cortex 71.7 MB 3,504 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size71.7 MB
Spots3,504
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058090
mouse entorhinal cortex 62.0 MB 3,433 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size62.0 MB
Spots3,433
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058087
mouse entorhinal cortex 55.6 MB 3,038 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size55.6 MB
Spots3,038
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058083
mouse entorhinal cortex 67.1 MB 3,232 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size67.1 MB
Spots3,232
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058095
mouse entorhinal cortex 66.8 MB 2,936 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size66.8 MB
Spots2,936
silver H&E NCBI GEO policy Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058096
mouse entorhinal cortex 65.6 MB 2,678 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size65.6 MB
Spots2,678
silver H&E NCBI GEO policy
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058093
mouse entorhinal cortex 70.6 MB 3,363 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size70.6 MB
Spots3,363
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058092
mouse entorhinal cortex 61.1 MB 3,037 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size61.1 MB
Spots3,037
silver H&E NCBI GEO policy Open in Vitessce
Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058081
mouse entorhinal cortex 57.3 MB 3,447 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size57.3 MB
Spots3,447
silver H&E NCBI GEO policy Open in Vitessce
Visium
Mouse entorhinal cortex
GSM10058094
mouse entorhinal cortex 72.4 MB 3,139 spots silver H&E NCBI GEO policy
TechnologyVisium
Organismmouse
Tissueentorhinal cortex
Size72.4 MB
Spots3,139
silver H&E NCBI GEO policy

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