AI-Driven Analysis Unveils Functional Dynamics of Müller Cells in Retinal Autoimmune Inflammation.

Müllercell is the most common type of glial cell in the human and mouse retina, playing a crucial role in maintaining retinal homeostasis. In addition to providing structural support to the retina, Müllercells can also supply trophic substances to retinal neurons, remove metabolic waste, mitigate oxidative stress, and promote synaptic activities. However, many roles of Müllercells remain largely unknown, particularly for those in the inflamed retina. In this article, we reanalyzed a single cell RNA-seq (scRNA-seq) dataset from Aire-/- mice, which exhibits autoimmune retinal inflammation, specifically focusing on Müllercells and T cells, identifying nine distinct Müllercell subgroups along with five T cell subgroups. Among them, three subgroups of Müllercells are activated Müllercells, representing over 60% Müllercells in the inflamed retina. Using SCassist - an Artificial Intelligence (AI) based workflow assistant for single-cell analysis, we constructed a comparison matrix to quantify the involvement of pathways characterizing the functions of each Müllercell subpopulation. The activated Müllercells primarily present a macrophage-like phenotype with or without augmentation of the known Müllercell functions. Trajectory analysis further identified two paths, validating the presence of these two phenotypes, governed by Neurod1 and Irf family transcription factors (TFs). We further inferred the interactions between Müllercells and T cells and observed that activated Müllercells do not exhibit extra chemoattraction to Th1 cells compared to other Müllercells but display nearly exclusive expression of immune checkpoint molecules, primarily targeting Th1 cells. Our findings open new avenues for understanding the specialized mechanisms of retinal pathogenic autoimmunity and identifying candidates to explore potential inhibitory pathways in the inflamed retina.