Spatial Transcriptomics for Dissecting Cellular and Molecular Heterogeneity in the Aging and Diseased Brain

The brain is a spatially organized tissue where the molecular characteristics of each cell are closely linked to its anatomical location. However, conventional bulk and single-cell RNA sequencing lose this spatial context during the tissue separation process. Spatial transcriptomics (ST) overcomes these limitations by measuring gene expression while preserving the positional information of cells within intact tissues, making it a powerful approach for elucidating the cellular and molecular heterogeneity that defines brain structure and disease. This review summarizes the two main types of ST technology: next-generation sequencing (NGS)-based platforms (Visium, Stereo-Seq, Slide-Seq) and in situ platforms (MERFISH, seqFISH+, Xenium). NGS-based platforms provide unbiased whole-transcriptome profiling across extensive tissue regions, while in situ platforms offer subcellular resolution within individual cells. We aim to assist in platform selection by comparing the principles, advantages, and limitations of each platform. Next, we focus on how spatial sequencing (ST) has been utilized to analyze the spatial heterogeneity of aging and diseased brains, and examine region- and cell-type changes observed in brain aging, the lesion-related microenvironments of Alzheimer's and Parkinson's diseases, and the spatially isolated tumor cell states and immunosuppressive environments of glioblastoma. We also introduce the key brain ST data resources that underpin these studies. Collectively, ST is emerging as an essential tool for understanding the spatial logic of brain function and pathology, demonstrating increasingly greater potential in the field of precision medicine.