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

Abstract

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.

A Cellular Taxonomy of the Adult Human Spinal Cord

“…Over-expression of mouse NEFL, human NEFM, human NEFH, or mouse PRPH in transgenic mice can each cause enlargement and swellings of motoneuron somas and subsequent axon degeneration 29–34 , providing a direct link between human motoneuron gene expression and cellular phenotype. Relatedly, these neurofilament genes are found in other large neurons in the brain and peripheral nervous system, suggesting that they may be part of a common signature that permits increased cell size 59, 65–68 .…”

“…Over-expression of mouse NEFL, human NEFM, human NEFH, or mouse PRPH in transgenic mice can each cause enlargement and swellings of motoneuron somas and subsequent axon degeneration (Beaulieu et al, 1999; Côté et al, 1993; Gama Sosa et al, 2003; Marszalek et al, 1996; Xu et al, 1993b; 1993a), linking human motoneuron gene expression and cellular phenotype. Relatedly, these neurofilament genes are found in other large neurons in the brain and peripheral nervous system, suggesting that they may be part of a common signature that permits increased cell size (Bakken et al, 2021a; Limone et al, 2021; M. Q. Nguyen et al, 2021; Tsang et al, 2000; Zeisel et al, 2018).…”

Update on genetics of amyotrophic lateral sclerosis

“…This was not the case for genes expressed in other nonneuronal CNS (central nervous system) cell types or non-CNS tissues including peripheral nervous system tissue and muscle. Limone et al [15] detected enriched expression of ALS/FTD genes specifically in corticospinal motor neurons. Saez-Atienzar et al [9] and Megat et al [16] also detected enrichment of ALS-related genes in inhibitory neurons and oligodendrocytes.…”

Pluripotent stem cell strategies for rebuilding the human brain

“…These protocols made scalability challenging so others have devised ways to further push immature myeloid progenitors toward microglia-like cells (MGLs) with defined medias containing M-CSF to generate myeloid cells coupled with CNS-enriched TGF-beta and CNS-specific, CSF1-receptor ligand IL34 to promote a brain-like specification of these myeloid progenitors. Generated MGLs show competence to phagocytose ( Muffat et al, 2016 ; Abud et al, 2017 ; Douvaras et al, 2017 ; Haenseler et al, 2017 ; Pandya et al, 2017 ; Limone et al, 2021 ; Dolan et al, 2022 ) respond to IFN-γ and LPS stimulation via secretion of pro-inflammatory cytokines ( Muffat et al, 2016 ; Abud et al, 2017 ), and migrate to sites of injury ( Muffat et al, 2016 ). When co-cultured with neurons, MGLs have also been observed to secrete anti-inflammatory and pro-remodeling cytokines ( Haenseler et al, 2017 ).…”

“…Microglia: diff. 20–28 Muffat et al, 2016 ; Abud et al, 2017 ; Douvaras et al, 2017 ; Haenseler et al, 2017 ; Pandya et al, 2017 ; Takata et al, 2017 ; Chen et al, 2021 ; Limone et al, 2021 ; Dolan et al, 2022 ; transpl. 29–30 Svoboda et al, 2019 ; Xu et al, 2020 .…”