Multiple cellular pathways are now implicated in the etiology of ALS, but it remains unclear how dysfunction of these diverse processes can result in the same disease phenotype. Furthermore, the same genetic mutation can result in either ALS, FTD or both conditions, implying that specific disease modifiers exist. Studies using in vivo and in vitro models of FALS suggest that the intrinsic properties of MNs are crucial for degeneration and/or protection (Boillée et al., 2006a). Importantly, resistant MN subtypes appear to display diverse gene expression profiles from susceptible MNs. Microarray analysis and laser capture microdissection of MNs isolated from oculomotor/trochlear nuclei, the hypoglossal nucleus and the lateral column of the cervical spinal cord in SOD1G93A rats (Hedlund et al., 2010), or in human brain and spinal cords (Brockington et al., 2013), have revealed marked differences between these subpopulations. Importantly, many of the genes that were differentially expressed encode proteins that function in pathways implicated in ALS pathogenesis, such as ER function, calcium regulation, mitochondrial function, ubiquitination, apoptosis, nitrogen metabolism, transport and cellular growth. Interestingly, oculomotor neurons possess a specific and relatively conserved protein signature between humans and rodents, implying that this contributes to the relative resistance of these MNs in ALS/FTD (Hedlund et al., 2010; Comley et al., 2015). Several of these proteins are known to be protective against MN neurodegeneration, such as insulin-like growth factors (IGF) and their receptors (see section “Neuroprotective and Neurotoxic Factor Expression in MN Subpopulations” below). Similarly, other genes highly expressed in vulnerable MNs are implicated in their susceptibility to degeneration, such as semaphorin A3 (Sema A3) and matrix metalloproteinase 9 (MMP-9) (see section “Neuroprotective and Neurotoxic Factor Expression in MN Subpopulations” below). Recently, a comprehensive bioinformatics meta-analysis of ALS modifier genes was performed from 72 published studies (Yanagi et al., 2019). A total of 946 modifier genes were identified and of these, 43 genes were identified as modifiers in more than one ALS gene/model. These included TDP-43, SOD1, ATXN2 and MMP9. Intrinsic factors in MNs might therefore underlie their relative vulnerability or resistance to neurodegeneration in ALS. The two pioneering studies linking gene expression differences to MN vulnerability in ALS (Hedlund et al., 2010; Brockington et al., 2013) have led to several subsequent reports, where the role of specific genes were examined further (summarized in Table 7, and discussed further in the sections below). However, it is also possible that the differences in gene expression reflect the diverse embryological origins or milieu of resistant and susceptible MN groups, or simply the structural and functional differences between oculomotor units and motor units of other skeletal muscles. To date, no studies have extensively characterized the specific transcriptional profile of vulnerable vs. susceptible MNs in TDP-43, C9orf72 FUS or other models of ALS, similar to those performed in SOD1G93A mice and ALS patients (Hedlund et al., 2010; Brockington et al., 2013).