CRISPR/Cas9 generated PTCHD1 2489T>G stem cells recapitulate patient phenotype when undergoing neural induction

Abstract

Abstract An estimated 3.5–5.9% of the global population live with rare diseases, and approximately 80% of these diseases have a genetic cause. Rare genetic diseases can be difficult to diagnose, with patients experiencing diagnostic delays of 5–30 years. Next generation sequencing has improved clinical diagnostic rates to 33–48% however a novel potentially disease causative variant is often identified. These variants require validation of pathogenicity in specialist laboratories, resulting in a diagnostic delay that on average lasts five years. In the interim, the finding is classified as a genetic variant of uncertain significance (VUS) and the patient remains undiagnosed. A VUS (PTCHD1 c. 2489T > G) was identified in a child with autistic behaviour, global developmental delay and hypotonia. Loss of function mutations in PTCHD1 are associated with autism spectrum disorder and intellectual disability; however, the molecular function of PTCHD1, and its role in neurodevelopmental disease is unknown. Here, we apply CRISPR gene editing and induced pluripotent stem cell (iPSC) neural disease modelling to assess the patient VUS. During differentiation from iPSCs to neural progenitors, we detect subtle, but significant gene signatures in synaptic transmission and muscle contraction pathways. Our work supports the causal link between the genetic variant and the child’s phenotype. Additionally, this study informs on the potential role of PTCHD1 in other neurodevelopmental and neuromuscular disorders and demonstrates the value of combining laboratory and computational variant assessment.