Introduction:
Age-related macular degeneration (AMD) is a complex neurodegenerative disease and the leading cause of blindness in developed countries [1]. In this study, spatial transcriptomics was used to study the degenerating mouse retina at two levels: 1) transcriptional changes and 2) differential alternative cleavage and polyadenylation (APA).
Methods:
To model facets of AMD pathologies, mice were exposed to photo-oxidative damage (PD) using high-intensity light (100Klux) for 1, 3, and 5 days. We used the 10X Genomics Visium Spatial Gene Expression technology to profile gene expression changes in the mouse retina. The retinal clusters were annotated based on cell type-specific gene expression, and differential expression was compared across conditions. To gain further insights, we comprehensively mapped APA sites in the retina and compared their differential usage.
Results:
We observe spatial distribution of pathways involved in cell death and immune responses. Specifically, we observed an upregulation of neuronal apoptotic processes, immune effector processes and cytokine production terms in the superior retina. Further, we identified a key superior region with highly significant upregulation of vascular terms at 5 days of PD, despite no visible changes in retinal morphology.
Our APA analysis discovered a novel seesaw regulatory pattern that demonstrates differential APA usage in the inferior and superior retina at different PD stages. Furthermore, we observed that changes in 3’UTR length are closely correlated with biological changes during PD among different retinal clusters.
Conclusion:
We have developed the first-ever spatial database that allows people to visualize and analyse key aspects of retinal degeneration. This work demonstrates the power of spatial transcriptomics as a technique for elucidating molecular changes in retinal degenerations, especially in regards to novel vascular associated pathways. This work is relevant to neurodegenerative diseases (including AMD and diabetic retinopathy) where inflammation and vascular changes are key drivers of disease pathogenesis.