Heterozygous knockout of Synaptotagmin13 phenocopies ALS features and TP53 activation in human motor neurons

Spinal motor neurons (MNs) represent a highly vulnerable cellular population, which is affected in fatal neurodegenerative diseases such as amyotrophic lateral sclerosis (ALS) and spinal muscular atrophy (SMA). Despite the advances in our understanding of the genetic causes of these pathologies, the molecular determinants of MN vulnerability are still largely unknown. In this work, we aimed at clarifying the specific contribution of a member of the protein family synaptotagmins to MNs sufferance. We indeed combined multi-omics and deep learning strategies with human iPSC-derived MN to highlight Synaptotagmin 13 (SYT13) as a candidate gene contributing to MN vulnerability when its levels are detrimentally reduced. By using CRISPR-Cas9 technology, we investigated whether the heterozygous loss of SYT13 might be sufficient to trigger a neurodegenerative phenotype resembling those observed in ALS and SMA. SYT13+/- hiPSC-derived MNs displayed a progressive manifestation of typical neurodegenerative hallmarks such as loss of synaptic contacts and accumulation of aberrant aggregates. By comparing the transcriptome of SYT13-deficient cells to SYT13+/+ ones, we found a significant impairment in biological mechanisms involved in motoneuron specification and spinal cord differentiation. In addition, we identified a striking correlation of the Syt13+/- transcriptome with an ALS signature generated using RNAseq data from human MNs and post mortem spinal cord samples. This significant overlap converged toward a shared expression of pro-apoptotic and pro-inflammatory genes, which are controlled by the transcription factor TP53. Our data show for the first time that the heterozygous loss of a single member of the synaptotagmins family, SYT13, is sufficient to trigger a series of abnormal alterations leading to cellular sufferance in human MNs, thus revealing novel insights into the selective vulnerability of this cell population. Overall design: SYT13 WT and SYT13+/- hiPSCs were differentiated for 5 weeks into spinal motor neurons using a small molecules-based protocol (PMCID: PMC8261490) We then performed RNAseq analysis of SYT13 WT and SYT13+/- motor neurons