Application of spatial transcriptome technologies to neurological diseases

Abstract

Spatial transcriptome technology acquires gene expression profiles while retaining spatial location information, it displays the gene expression properties of cells in situ. Through the investigation of cell heterogeneity, microenvironment, function, and cellular interactions, spatial transcriptome technology can deeply explore the pathogenic mechanisms of cell-type-specific responses and spatial localization in neurological diseases. The present article overviews spatial transcriptome technologies based on microdissection, in situ hybridization, in situ sequencing, in situ capture, and live cell labeling. Each technology is described along with its methods, detection throughput, spatial resolution, benefits, and drawbacks. Furthermore, their applications in neurodegenerative disease, neuropsychiatric illness, stroke and epilepsy are outlined. This information can be used to understand disease mechanisms, pick therapeutic targets, and establish biomarkers.

Molecular Genetics of Acquired Temporal Lobe Epilepsy

“…Research focusing more deeply on cell type-specific functions in the hippocampus indicates a strong context dependence for many molecular pathways ( Table 1 ). Novel technologies of spatial transcriptome analyses could paint a detailed picture of expression patterns across epileptogenesis [ 173 ]. The regulation of transcription via transcription factors or non-coding RNAs may offer more specific targeting of specific cells at specific points during differentiation after trauma [ 174 ].…”

Translational strategies and systems biology insights for blood-brain barrier opening and delivery in brain tumors and Alzheimer’s disease

“…Spatial transcriptomic and proteomics platforms can provide molecular profiling of the BBB in primary and metastatic brain tumors [ 60 ] and neurodegenerative diseases [ 61 ]. Further computational modeling for region-specific cell-cell-communication and signaling pathway prediction [ 62 ] would facilitate the identification of potential targetable strategies for opening or stabilizing the BBB for drug delivery.…”

Post-stroke cognitive impairment: exploring molecular mechanisms and omics biomarkers for early identification and intervention

“…Metabolomics helps identify neurological biomarkers ( Zhang et al, 2013 ) by linking metabolic activity to genetic and environmental variables ( Fiehn, 2002 ).Similarly, microbiomics helps analyze the interactions between microbial communities and the human body, offering insights into neurological dysfunctions ( Layeghifard et al, 2017 ; Sorboni et al, 2022 ). Genomics and transcriptomics, studying genetic variants and gene expression patterns respectively, have identified key molecular alterations associated with stroke and its cognitive aftermath ( Lockhart and Winzeler, 2000 ; Tan et al, 2021 ; Li W. et al, 2022 ; Tsimberidou et al, 2022 ; Ya et al, 2023 ). Lastly, proteomics, by mapping protein interactions and functions, supports the diagnosis and development of targeted therapies for neurological disorder ( Rohlff, 2001 ; Sancesario and Bernardini, 2018 ).…”