Discovery of the Transcriptional and Post-Transcriptional Changes During Retinal Degeneration

Abstract

Spatial transcriptomics, awarded Nature's Method of the Year 2020, has enabled high-resolution investigation of gene expression in intact tissues. Despite its rapid adoption in various biological fields, the spatial and molecular underpinnings of retinal degeneration, particularly age-related macular degeneration (AMD), remain incompletely understood.

This thesis applies spatial transcriptomics to study the cellular and regional mechanisms of retinal degeneration across five projects in six chapters. The first project constructs a high-resolution spatial atlas of the healthy mouse eye. The second investigates transcriptional responses to photo-oxidative damage (PD). The third explores alternative polyadenylation (APA) as a post-transcriptional regulator. Later chapters extend spatial transcriptomic techniques to the mouse intestine and brain.

Project 1 (Chapter II): Spatial Atlas of the Mouse Eye This chapter presents the first comprehensive spatial transcriptomic atlas of the healthy mouse eye using Stereo-seq and Visium. It maps key compartments - retina, cornea, lens, iris, and sclera - and introduces Eyelocator, a tool linking single-cell transcriptomes to spatial coordinates. Findings include molecular layer definitions in the retina, evidence of regenerative signatures in the cornea, and transcriptional gradients in the lens.

Project 2 (Chapter III): Spatial Transcriptomics in Retinal Degeneration Using a PD model, this project identifies a superior retinal hotspot with heightened expression of inflammatory and angiogenic genes. Spatial profiling reveals region-specific immune responses, with VEGF and novel pathways (pleiotrophin, midkine) implicated in vascular remodeling. This study provides new targets for therapy and advances our spatial understanding of retinal disease.

Project 3 (Chapter IV): Spatial APA in Degeneration This study characterizes spatial APA changes using a custom bioinformatics pipeline. It reveals a superior-inferior "APA seesaw" with reciprocal 3'UTR changes across retinal zones. APA remodeling affects genes involved in visual signaling, autophagy, and immune modulation. Photoreceptors exhibit light-responsive APA patterns, suggesting a role for APA in retinal stress regulation.

Together, these findings advance our spatial understanding of transcriptional and post-transcriptional regulation in retinal degeneration and identify APA as a potential therapeutic target. Show more