Disease vs Normal Comparative Spatial Transcriptomics Service

This study investigates the molecular pathological mechanisms of Alzheimer's disease (AD), with specific emphasis on the spatial relationship between layer-specific gene expression alterations in the cerebral cortex and core AD pathological hallmarks—amyloid-beta (Aβ) plaques and neurofibrillary tangles (NFTs) formed by hyperphosphorylated tau protein. Leveraging the 10x Genomics Visium spatial transcriptomics platform, the research aims to characterize spatially resolved gene expression profiles associated with AD pathology, thereby addressing a critical limitation of conventional bulk or single-cell RNA-seq approaches that lack spatial context.

This study analyzed postmortem human brain tissues to map Alzheimer's disease (AD) pathology (Aβ plaques and phosphorylated tau) via immunohistochemistry, using adjacent non-pathological regions as controls. Spatial transcriptomics enabled systematic comparison of gene expression between AD and control tissues, including differential expression, functional enrichment, and layer-specific transcriptional profiling. Result robustness was confirmed by subsampling validation. Statistical analyses applied multiple testing correction to evaluate gene set overlaps and performed pathway-level assessments linked to specific pathological features, uncovering molecular mechanisms underlying AD progression.

The study identified several novel marker genes specific to different cortical layers. For instance, SPARC was identified as a marker for Layer I, and MBP for white matter. These markers were consistent across AD and control cases, highlighting stable layer architecture despite AD pathology (Figure 2).

Figure 2. Layer-specific genes define the anatomical architecture of the human MTG and the frontal cortex.

The deconvolution of single-nucleus RNA-seq data with Visium spatial data revealed that excitatory neurons predominated in layers II-VI, which are particularly vulnerable to AD. Interestingly, AD pathology did not significantly alter the distribution of other cell types, but microglia were significantly increased in white matter in AD cases (Figure 3).

Figure 3. Cell type deconvolution analysis of snRNA-seq data and Visium SRT data from human MTG.

The DEGs analysis revealed 1,008 upregulated genes in AD, many associated with synaptic transmission, axonogenesis, and immune responses (Figure 4). These genes were mapped to specific cortical layers, providing insights into regional vulnerability.

Figure 4. Differentially expressed genes (DEGs), Top-20 enriched pathways and layer-specific DEGs in AD vs CT human MTG.

WGCNA identified eight gene modules, with notable changes in co-expression patterns in the presence of AD pathology (Figure 5). For example, cell communication pathways between microglia, oligodendrocytes, and neurons were significantly altered, suggesting a role in AD's early pathogenesis.

Figure 5. AD-associated gene modules and their co-expression patterns within areas of AD pathology.

The study reveals crucial molecular changes in the MTG of AD patients, particularly the layer-specific expression of genes and alterations in cell-cell communication networks. These findings provide a deeper understanding of the regional vulnerability of the MTG in AD and may contribute to the development of targeted therapeutics. Furthermore, the use of spatial transcriptomics combined with single-cell analysis offers a powerful approach to studying complex neurodegenerative diseases like Alzheimer's.