Investigating and correcting a rare pathogenic mutation in GDF11
Single nucleotide variants (SNVs) and small insertions or deletions (indels) underlie most rare monogenic disorders, yet therapeutic strategies to precisely correct these mutations remain limited. Prime Editing enables repair of such pathogenic variants without introducing double-stranded breaks. Here, we applied CRISPR Prime Editing to model and correct a de novo GDF11 nonsense mutation (Tyr336*) identified in a participant from the Undiagnosed Diseases Network (UDN) with growth delay and multisystem abnormalities. Using HEK293T cells, we generated heterozygous GDF11 Tyr336* clones, which exhibited reduced GDF11 protein levels due to post-translational degradation likely mediated by ER- and Golgi-associated quality control pathways.  These cells displayed marked Golgi abnormalities, including an increased number of compact, irregularly shaped Golgi structures, findings consistent with Golgi fragmentation and stress. Transcriptomic profiling of HET cells revealed broad dysregulation of gene networks, including downregulation of metabolic and Golgi-linked biosynthetic genes, and upregulation of cell-adhesion and extracellular matrix genes. These transcriptional shifts paralleled the participant's developmental, neural, and cardiovascular phenotypes. To correct the mutation, we tested multiple bespoke Prime Editing strategies and identified PE7, in combination with a pegRNA designed by Pridict, as the most effective ribonucleoprotein complex for rescue. Editing efficiency was further enhanced by introducing an additional silent PAM-disrupting mutation, likely preventing both Cas9 re-binding and mismatch repair. Together, these findings support a haploinsufficiency mechanism for the GDF11 Tyr336* allele and establish a generalizable framework for disease modeling and allele-specific correction of pathogenic variants in human cells. Overall design: This study used CRISPR prime editing in HEK293T cells to generate a heterozygous line carrying the GDF11 Tyr336* allele on two of the three chromosomes, and we compared its transcriptomic profile to that of wild-type HEK293T cells