NETSseq Reveals Inflammatory and Aging Mechanisms in Distinct Cell Types Driving Cerebellar Decline in Ataxia Telangiectasia

The cellular and molecular changes driving the neurological abnormalities associated with the loss or functional deficiency of the ataxia–telangiectasia mutated (ATM) protein are not well understood. In this study, we applied our proprietary Nuclear Enriched Transcript Sort sequencing (NETSseq) platform to investigate changes in cell type composition and gene expression patterns in human cerebellar post-mortem tissue from ataxia–telangiectasia (A-T) donors and non-neurodegenerative disease control donors. Compared to single-cell technologies, NETSseq provided a more robust detection of lowly expressed and differentially expressed genes. Our differential gene expression analysis revealed high specificity to individual cell types. For instance, granule neurons exhibited dysregulation in neurotransmitter signaling and apoptotic pathways, potentially underlying the impaired motor coordination observed in A-T. Both astrocytes and microglia in A-T donors exhibited signs of accelerated aging, with astrocytes displaying upregulation of neurotoxic signatures and a downregulation of genes related to synaptic function, while microglia showed activation of pathways involved in the DNA damage response. This comprehensive analysis revealed significant changes in cell type composition and gene expression in the A-T cerebellum, shedding light on the cell type-specific mechanisms underlying neurodegeneration and motor dysfunction in A-T.