Single-nucleus sequencing reveals enriched expression of genetic risk factors sensitises Motor Neurons to degeneration in ALS

Amyotrophic Lateral Sclerosis (ALS) is a fatal neurodegenerative disorder characterised by a progressive loss of motor function. While it is known that the eponymous spinal sclerosis observed upon autopsy is the result of Cortico-Spinal Motor Neuron (CSMN) degeneration, it remains unclear why this neuronal subtype is selectively affected. To understand the unique molecular properties that sensitise deep-layer CSMNs to ALS, we performed RNA sequencing of 79,169 single nuclei from the frontal cortex of patients and controls. In unaffected individuals, we found that expression of ALS risk genes was most significantly enriched only in THY1+ presumptive CSMNs and not in other cortical cell types. In patients, these genetic risk factors, as well as additional genes involved in protein homeostasis and stress responses, were significantly induced in THY1+ CSMNs and a wider collection of deep layer neurons, but not in neurons with more superficial identities. Examination of oligodendroglial and microglial nuclei also revealed patient-specific gene expression changes We show microglial alterations can in part be explained by interactions with degenerating neurons. Overall, our findings suggest the selective vulnerability of CSMNs is due to a “first over the line” mechanism by which their intrinsic molecular properties sensitise them to genetic and mechanistic contributors to degeneration. ### Competing Interest Statement The authors have declared no competing interest.