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 MN vulnerability, we investigate the transcriptional dynamics of two vulnerable and two resilient MN populations in SOD1G93A ALS mice. Differential gene expression analysis shows that each neuron type displays a largely unique spatial and temporal response to ALS. Resilient MNs regulate few genes in response to disease, but show clear divergence in baseline gene expression compared to vulnerable MNs, which in combination may hold the key to their resilience. EASE, fGSEA and ANUBIX enrichment analysis demonstrate that vulnerable MN groups share pathway activation, including regulation of neuronal death, ERK and MAPK cascades, inflammatory response and synaptic signaling. These pathways are largely driven by 11 upregulated genes, including Atf3, Cd44, Gadd45a, Ngfr, Ccl2, Ccl7, Gal, Timp1, Nupr1 and indicate that cell death occurs through similar mechanisms across vulnerable MNs albeit with distinct timing. Random Forest machine learning-based approach 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, PENK, INA and NTS are strong disease-predictors across SOD1 mutations and species. A shared transcriptional vulnerability was also assessed through a meta-analysis across mouse SOD1 transcriptome datasets. In conclusion our study reveals vulnerability-specific gene regulation that may act to preserve neurons and can be used to predict disease.