Multiomic profiling reveals aberrant immunomodulatory signature in β-propeller protein-associated neurodegeneration patient iPSC-derived microglia

Microglia are the primary immune cells of the central nervous system and play a crucial role in maintaining brain homeostasis. In common neurodegenerative diseases such as Alzheimer's disease and Parkinson's disease (PD), early and sustained microglial activation has been shown to precede neuronal loss, with elevated levels of microglia-derived inflammatory mediators detected in affected brain regions. In contrast, little is known about the role of microglia in rare neurodegenerative disorders. One such disorder is β-propeller protein-associated neurodegeneration (BPAN), a common subtype of neurodegeneration with brain iron accumulation (NBIA). BPAN shares pathological features with PD, including iron accumulation and selective loss of dopaminergic neurons in the substantia nigra, and is caused by mutations in the WD repeat domain 45 ( WDR45 ) gene encoding an autophagy protein also called WIPI4. However, the pathological role of mutant WDR45 in BPAN and the possible contribution of microglia remain unresolved. We generated the first BPAN patient microglia model system using induced pluripotent stem cells (iPSCs) to identify immune-related alterations and immunomodulatory signaling changes in a disease-relevant context. Integrated transcriptomic and proteomic profiling of iPSC-derived microglia from BPAN patients revealed a consistent shift from a homeostatic to a reactive, disease-associated state. Transcriptomic analysis showed disruption of core microglial pathways, including immune activation, stress response, and autophagy, consistent with a chronic pro-inflammatory phenotype. Complementary secretome analysis identified impaired lysosomal function and increased antigen presentation pathways, further supporting persistent microglial activation. Together this suggests that dysfunctional microglial states may contribute to BPAN pathogenesis. Our findings lay the groundwork for advancing immunomodulatory research in BPAN and may open new avenues for therapeutic development targeting microglial dysfunction.