Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease

In the last ten years, single-cell technologies have advanced significantly, becoming widely used laboratory methods capable of analyzing the gene expression of thousands of cells simultaneously. These advancements have been particularly valuable in studying the central nervous system (CNS) due to its complex cellular composition. Single-cell RNA sequencing techniques now offer high accuracy in quantifying gene expression, allowing researchers to explore subtle differences between cell types and states. However, this method involves dissociating tissue samples, resulting in the loss of intercellular relationships. To overcome this limitation, spatial transcriptomic methods have emerged, preserving spatial information and enabling gene expression analysis within the context of tissue structure. In this article, we explore how single-cell and spatial transcriptomics have contributed to understanding the underlying mechanisms of brain disorders, focusing on selective neuronal vulnerability, neuroimmune dysfunction, and cell-type-specific treatment response.