The Neuronal Primary Cilium is a Key Regulator of Homeostatic Plasticity

The capacity of neurons to maintain stable activity levels through homeostatic plasticity is essential for proper brain function. Primary cilia, which are non-motile, antenna-like organelles projecting from the surface of most vertebrate cells, serve as key hubs for signal transduction, playing crucial roles in tissue development and cellular homeostasis. In this study, we identify a previously unrecognised role for primary cilia in mediating neuronal homeostatic plasticity using human induced pluripotent stem cell-derived neurons. We show that neuronal cilia exhibit dynamic, bidirectional changes in volume in response to alterations in network activity: elongating during chronic activity suppression and shortening after increased activity. To assess the functional relevance of this ciliary plasticity, we modelled ciliary dysfunction in neurons carrying homozygous loss-of-function mutations in genes associated with neuronal ciliopathies, including NPHP1 and CEP290. Mutations affecting ciliary function either increased ciliary length or led to ciliary loss, and these mutant neurons exhibited severe impairments in homeostatic regulation across multiple domains—morphological, functional, and transcriptional. Specifically, NPHP1 and CEP290 deficient neurons failed to adapt synaptic strength, intrinsic excitability, and ciliary morphology in response to prolonged activity suppression. They also displayed dysregulated baseline network activity, and exhibited blunted gene expression changes. Together, these findings establish the primary cilium as a critical regulator of homeostatic plasticity in human neurons and provide a new framework through which to examine neurodevelopmental and neuropsychiatric disorders linked to ciliary dysfunction. Overall design: Neurons derived from human iPSCs were grown together with rat astrocytes in culture plates. Three replicates were prepared for each condition: control (WT iPSC-neurons), NPHP1?/? iPSC-neurons, and CEP290?/? iPSC-neurons. For each genotype, cells were treated either with vehicle or with TTX for 24 hours (three replicates per condition). For quality checks, additional cells from the same batches were grown on microelectrode arrays and coverslips for imaging. After treatment, cells were collected, and RNA was isolated. RNA quality was high (RIN 9.4–9.8). Libraries were prepared using a standard RNA-seq kit and sequenced with paired-end reads on an Illumina NovaSeq 6000 platform.