Cell-type modeling in spatial transcriptomics data elucidates spatially variable colocalization and communication between cell-types in mouse brain.
IF: 11.091
Cited by: 12


Single-cell spatial transcriptomics (sc-ST) holds the promise to elucidate architectural aspects of complex tissues. Such analyses require modeling cell types in sc-ST datasets through their integration with single-cell RNA-seq datasets. However, this integration, is nontrivial since the two technologies differ widely in the number of profiled genes, and the datasets often do not share many marker genes for given cell types. We developed a neural network model, spatial transcriptomics cell-types assignment using neural networks (STANN), to overcome these challenges. Analysis of STANN's predicted cell types in mouse olfactory bulb (MOB) sc-ST data delineated MOB architecture beyond its morphological layer-based conventional description. We find that cell-type proportions remain consistent within individual morphological layers but vary significantly between layers. Notably, even within a layer, cellular colocalization patterns and intercellular communication mechanisms show high spatial variations. These observations imply a refinement of major cell types into subtypes characterized by spatially localized gene regulatory networks and receptor-ligand usage.


Spatial Transcriptomics
cellular colocalization
cellular composition
deep neural network
intercellular communication
mouse olfactory bulb
single-cell RNA-seq
spatial transcriptomics
tissue architecture

MeSH terms

Gene Regulatory Networks
Neural Networks, Computer
Single-Cell Analysis


Grisanti Canozo, Francisco Jose
Zuo, Zhen
Martin, James F
Samee, Md Abul Hassan

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