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 somatic motor neurons (MNs), which innervate skeletal muscles. However, certain MN groups including ocular MNs that regulate eye movement are relatively resilient to ALS. To reveal mechanisms of differential susceptibility, we investigate the transcriptional dynamics of two vulnerable and two resilient MN populations in SOD1G93A ALS mice. Analysis of differentially expressed genes (DEGs) shows that each neuron type displays a largely unique spatial and temporal response to disease. Baseline gene expression of resilient MNs is clearly divergent from vulnerable MNs and their response to mutant SOD1 is minor, with regulation of few genes, some with known neuroprotective properties, including e.g. Ucn, Cck and Postn. EASE, fGSEA and ANUBIX enrichment analysis demonstrate that vulnerable MN groups share pathway activation, including regulation of neuronal death, inflammatory response, ERK and MAPK cascades, cell adhesion and synaptic signaling. These pathways are largely driven by 11 upregulated genes, including Atf3, Nupr1, Cd44, Gadd45a, Ngfr, Ccl2, Ccl7, Gal, Timp1, Serpinb1a and Chl1, and indicate that cell death occurs through similar mechanisms across vulnerable MNs albeit with distinct timing. Machine learning using DEGs upregulated in our SOD1G93A spinal MNs predict disease in human stem cell-derived MNs harboring the SOD1E100G mutation, and show that dysregulation of VGF, INA, PENK and NTS are strong disease-predictors across SOD1 mutations and species. Meta-analysis across SOD1 transcriptome datasets identifies a shared vulnerability code of 32 genes including e.g Atf3, Nupr1, Vgf, Ina, Sprr1a, Fgf21, C1qb, Gap43, Adcyap1, and Mt1. In conclusion our study reveals cell-type-specific gene expression and dynamic disease-induced regulation that may act to preserve neurons and can be used to predict disease.