Dysregulated RNA G-quadruplex binding proteins reveal shifted stress responses in Alzheimer's Disease

Single-cell sequencing has reshaped the research paradigm of Alzheimers Disease (AD) by revealing the heterogeneous transcriptional states of brain cells. Large single-cell cohort datasets, such as ROSMAP and SEA-AD, provide valuable atlases but primarily focus on RNA expression and chromatin accessibility, often overlooking the roles of RNA secondary structures. Although RNA G-quadruplexes (rG4s) are increasingly recognized as regulators of neurodegeneration, their interacting RNA-binding proteins (RBPs) remain poorly understood. We analyzed multiple independent scRNA-seq datasets to investigate rG4-associated biological functions across AD-relevant cell types and transcriptional states. We discovered that rG4-binding RBPs (RG4BPs) directly regulate essential glial cell functions, which are frequently impaired in AD. At the transcriptional state level, distinct sets of dysregulated RG4BPs correspond to the impaired state-specific biological features of astrocytes and microglia during AD progression, including a shift from an acute protective state to a chronic stress-associated state. This progressive state transition is accompanied by glial exhaustion and accumulated rG4s, which ultimately compromise glial support functions. We report several RG4BPs that are known regulators, including CIRBP, HSP90AA1, VIM, and PICALM, whose altered expression is associated with either pathological activation or severe functional impairment. These dysregulated RG4BPs provide a lens to examine the mechanism of rG4 accumulation in AD and position RG4BPs as novel targets for understanding and potentially intervening in AD progression.