Poster abstracts

Poster number 3 submitted by Shaokun Li

TBC1D16 alternative polyadenylation emerges as a candidate disease effector in pontocerebellar hypoplasia type 10 caused by CLP1 R140H mutation

Shaokun Li (Department of Neurosciences, Case Western Reserve University), He Li (Department of Genetics and Genome Sciences, Case Western Reserve University), Ashleigh Schaffer (Department of Molecular and Medical Genetics, Oregon Health & Science University)

Abstract:
Pontocerebellar hypoplasia type 10 (PCH10) is a monogenic neurodevelopmental disorder caused by the homozygous R140H mutation in CLP1, an RNA-processing factor involved in RNA 3′-end formation. How this mutation alters RNA processing during neuronal development remains unclear. Our previous studies showed developmental-stage dependence of CLP1 perturbation: CLP1 or CLP1R140H induction causes substantial transcriptomic changes in motor neuron progenitors (MNPs), whereas later-stage motor neurons are less responsive.
To identify early RNA-processing events in this vulnerable stage, we profiled alternative polyadenylation in two human MNP systems. 3′ RNA sequencing of isogenic CLP1+/+, CLP1R/+, and CLP1R/R MNPs defined APA changes in the PCH10 disease model. In parallel, nascent 3′ RNA sequencing at 1, 3, 6, and 24 hours after acute CLP1 or CLP1R140H induction resolved the kinetics of CLP1-responsive APA.
Integration of these datasets highlighted TBC1D16 as a robust CLP1-responsive target. Increased distal 3′-UTR polyadenylation-site usage was detectable within 1 hour and persisted across the time course. Both CLP1 and CLP1R140H promoted distal PAS usage, with CLP1R140H producing a stronger response. Importantly, the homozygous PCH10 model (CLP1R/R) showed the same directional shift. TBC1D16 regulates Rab-dependent receptor trafficking, suggesting a potential link between altered RNA 3′-end processing and developmental signaling.
Together, these findings identify TBC1D16 APA as a rapid CLP1-responsive event enhanced by CLP1R140H and present in the PCH10 disease model, nominating TBC1D16 as a candidate downstream effector of CLP1R140H pathogenesis.

Keywords: Alternative polyadenylation, CLP1, Neurodevelopmental disease