Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease(Dataset ID: STDS0000188)
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Summary:
Human middle temporal gyrus (MTG) is a vulnerable brain region in early Alzheimer’s disease (AD), but little is known about the molecular mechanisms underlying this regional vulnerability. Here we utilize the 10x Visium platform to define the spatial transcriptomic profile in both AD and control (CT) MTG. We identify unique marker genes for cortical layers and the white matter, and layer-specific differentially expressed genes (DEGs) in human AD compared to CT. Deconvolution of the Visium spots showcases the significant difference in particular cell types among cortical layers and the white matter. Gene co-expression analyses reveal eight gene modules, four of which have significantly altered co-expression patterns in the presence of AD pathology. The co-expression patterns of hub genes and enriched pathways in the presence of AD pathology indicate an important role of cell-cell-communications among microglia, oligodendrocytes, astrocytes, and neurons, which may contribute to the cellular and regional vulnerability in early AD. Using single-molecule fluorescent in situ hybridization, we validated the cell-type-specific expression of three novel DEGs (e.g., KIF5A, PAQR6, and SLC1A3) and eleven previously reported DEGs associated with AD pathology (i.e., amyloid beta plaques and intraneuronal neurofibrillary tangles or neuropil threads) at the single cell level. Our results may contribute to the understanding of the complex architecture and neuronal and glial response to AD pathology of this vulnerable brain region.Overall design:
Human MTG was cryosectioned at 10 µm and mounted on the Visium GE slide for Visium profiling. Spatial resovled transcriptomic (SRT) was performed using the 10x Genomics Visium Spatial Gene Expression Kit (Slide Kit, Part# 1000188. Reagent Kit, Par# 1000189) by following 10x Visium user guide (CG000239 Rev A).Technology:
10x Visium
Platform:
Illumina NovaSeq 6000
Species:
Homo sapiens(hg38)
Tissues:
Brain
Organ parts:
Postmortem brain
Submission date: 2022-12-07Update date: 2022-12-27
Sample number: 6Section number: 6
DOI: To be continue
Contributors
Wang, Cankun,Chen, Shuo,Chang, Yuzhou,Li, Liangping,Acosta, Diana,Li, Yang,Guo, Qi,Turkes, Emir,Morr
Accessions
GEO Series Accessions:
GSE220442
How to cite
- Cite database of STOmicsDB:[1] Xu, Zhicheng et al. "STOmicsDB: a comprehensive database for spatial transcriptomics data sharing, analysis and visualization." Nucleic acids research vol. 52,D1 (2024): D1053-D1061. doi: 10.1093/nar/gkad933'
- Cite visualization dataset:[2] Wang, Cankun,Chen, Shuo,Chang, Yuzhou,Li, Liangping,Acosta, Diana,Li, Yang,Guo, Qi,Turkes, Emir,Morr. Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer’s disease[DS/OL]. STOmicsDB, 2022[2022-12-07]. https://db.cngb.org/stomics/datasets/STDS0000188/. doi: xxxxxx#Format: {contributors}. {title}[DS/OL]. STOmicsDB, {the year of submission data}[{submission data}]. {dataset link}. doi: {doi ID}
- Cite original data article:Citation: Chen, Shuo et al. “Spatially resolved transcriptomics reveals genes associated with the vulnerability of middle temporal gyrus in Alzheimer's disease.” Acta neuropathologica communications vol. 10,1 188. 21 Dec. 2022, doi:10.1186/s40478-022-01494-6