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

Abstract

Muller cells are the most abundant glial cell type in the human and mouse retina, playing a crucial role in maintaining retinal homeostasis. However, many aspects of Muller cell function remain poorly characterized. In this study, we reanalyzed a single-cell RNA-seq (scRNA-seq) dataset from Aire-/- mice, focusing on Muller cells and T cells. We identified nine distinct Muller cell subgroups and five T cell subgroups, with activated Muller cells comprising the majority of the Muller cells in the inflamed retina. Using SCassist, an AI-based workflow assistant for single-cell analysis, we created a comparison matrix to quantify pathway involvement in each Muller cell subset. This approach unveils the functional dynamics of Muller cells during retinal inflammation. Activated Muller cells primarily exhibit enhanced inflammatory activity and adopt a macrophage or dendritic-cell-like phenotype, in the presence or absence of increased neuronal activity. These changes are primarily driven by Interferon Regulatory Factors (IRFs), acting alone or in concert with Neuronal Differentiation 1 (NEUROD1). We further inferred the interactions between Muller cells and T cells and found that activated Muller cells do not appear to exhibit extra chemoattraction to Th1 cells compared to other Muller cell subsets, but they do show such effects on the Th1-like regulatory T cells (Tregs). Activated Muller cells display nearly exclusive expression of immune checkpoint molecules, primarily targeting Th1 cells. These findings may uncover a previously unrecognized role for activated Muller cells in attenuating Th1 cell activity.