Mapping choroid plexus inflammation in alzheimer's disease with pixel-SEQV2 and immune repertoire-aware spatialtranscriptomics - the choroid plexus (CHP) is a specialized brain structure located…

Mapping choroid plexus inflammation in alzheimer's disease with pixel-SEQV2 and immune repertoire-aware spatialtranscriptomics - the choroid plexus (CHP) is a specialized brain structure located within the ventricles, composed of an epithelial layer facing the cerebrospinal fluid (CSF) and a highly vascularized stroma that together form the blood-CSF barrier (BCSFB). Transport across the CHP is tightly regulated by epithelial adherens and tight junctions. This epithelial layer is highly metabolically active, supporting blood-CSF exchange and producing neurotrophic factors such as bdnf. Unlike other brain regions, CHP capillaries are surrounded by a fenestrated epithelium that permits exchange with circulating components, including peripheral immune cells. Resident immune cells within the stroma, such as macrophages and dendritic cells, contribute to CNS immune surveillance. In alzheimer's disease (ad), the CHP helps clear AΒ from the CSF; however, exposure to AΒ aggregates induces transcriptional changes in the epithelium, including increased cytokine production. The consequences of these inflammatory changes for broader brain inflammation remain poorly understood. I hypothesize that chronic inflammatory signaling in ad drives epithelial cell-state transitions that reprogram the BCSFB, promoting the recruitment and persistence of immune cells and creating inflammatory niches that contribute to cognitive decline. To investigate this, I have analyzed CHP samples from the seattle alzheimer's disease (sea-ad) cohort using pixel-SEQV2 spatial transcriptomics. This analysis revealed localized expression of B-cell receptor genes, suggesting clonal expansion within the CHP, not previously documented in ad. In this proposal, I outline an integrated strategy combining bioinformatic analyses, expansion of the patient cohort, and validation through immunofluorescence and immunopixel-SEQ to characterize these immune populations more deeply. Extensive clinical data already exists for the sea-ad cohort, including cognitive measures from the adult changes in thought (act) study. Integrating spatial mrna sequencing with these clinical datasets will provide new insight into how inflammatory remodeling of the CHP contributes to cognitive impairment. Importantly, I have obtained samples from cognitively resilient patients (those with preserved cognition despite significant pathology) and pathology-resistant patients (those with minimal pathology despite advanced age). Comparing these groups with ad and control cases will elucidate how CHP inflammatory states relate to disease susceptibility and resilience. Finally, I will validate immune cell infiltration using immunofluorescence and apply immunopixel-SEQ to identify TCR and BCR sequences within the CHP. These analyses will reveal patterns of clonal expansion and, when extended to other brain regions, will determine whether immune cells originating in the CHP infiltrate the brain parenchyma. This work will advance understanding of how CHP barrier dysfunction and immune activation contribute to cognitive decline in ad.