Transcriptional modulation unique to vulnerable motor neurons predicts ALS across species and SOD1 mutations

Amyotrophic lateral sclerosis (ALS) is characterized by the progressive loss of motor neurons that innervate skeletal muscles. However, certain motor neuron groups including ocular motor neurons, are relatively resilient. To reveal key drivers of resilience versus vulnerability in ALS, we investigate the transcriptional dynamics of four distinct motor neuron populations in SOD1G93A ALS mice using LCM-seq and single molecule fluorescent in situ hybridization. We find that resilient ocular motor neurons regulate few genes in response to disease. Instead, they exhibit high baseline gene expression of neuroprotective factors including En1 , Pvalb, Cd63 and Gal, some of which vulnerable motor neurons upregulate during disease. Vulnerable motor neuron groups upregulate both detrimental and regenerative responses to ALS and share pathway activation, indicating that breakdown occurs through similar mechanisms across vulnerable neurons, albeit with distinct timing. Meta-analysis across four rodent mutant SOD1 motor neuron transcriptome datasets identify a shared vulnerability code of 39 genes including e.g Atf4 , Nupr1 , Ddit3 and Penk, involved in apoptosis, as well as a proregenerative and anti-apoptotic signature consisting of Atf3 , Vgf , Ina , Sprr1a, Fgf21, Gap43, Adcyap1, and Mt1 . Machine learning using genes upregulated in SOD1G93A spinal motor neuron predicts disease in human stem cell-derived SOD1E100G motor neurons, and shows that dysregulation of VGF , INA, PENK and NTS are strong disease-predictors across species and SOD1 mutations. Our study reveals motor neuron population-specific gene expression and temporal disease-induced regulation that together provide a basis to explain ALS selective vulnerability and resilience and that can be used to predict disease.