Integrative genetic and single cell RNA sequencing analysis provides new clues to the amyotrophic lateral sclerosis neurodegeneration

Abstract

IntroductionThe gradual loss of motor neurons (MNs) in the brain and spinal cord is a hallmark of amyotrophic lateral sclerosis (ALS), but the mechanisms underlying neurodegeneration in ALS are still not fully understood.MethodsBased on 75 ALS-pathogenicity/susceptibility genes and large-scale single-cell transcriptomes of human/mouse brain/spinal cord/muscle tissues, we performed an expression enrichment analysis to identify cells involved in ALS pathogenesis. Subsequently, we created a strictness measure to estimate the dosage requirement of ALS-related genes in linked cell types.ResultsRemarkably, expression enrichment analysis showed that α- and γ-MNs, respectively, are associated with ALS-susceptibility genes and ALS-pathogenicity genes, revealing differences in biological processes between sporadic and familial ALS. In MNs, ALS-susceptibility genes exhibited high strictness, as well as the ALS-pathogenicity genes with known loss of function mechanism, indicating the main characteristic of ALS-susceptibility genes is dosage-sensitive and the loss of function mechanism of these genes may involve in sporadic ALS. In contrast, ALS-pathogenicity genes with gain of function mechanism exhibited low strictness. The significant difference of strictness between loss of function genes and gain of function genes provided a priori understanding for the pathogenesis of novel genes without an animal model. Besides MNs, we observed no statistical evidence for an association between muscle cells and ALS-related genes. This result may provide insight into the etiology that ALS is not within the domain of neuromuscular diseases. Moreover, we showed several cell types linked to other neurological diseases [i.e., spinocerebellar ataxia (SA), hereditary motor neuropathies (HMN)] and neuromuscular diseases [i.e. hereditary spastic paraplegia (SPG), spinal muscular atrophy (SMA)], including an association between Purkinje cells in brain and SA, an association between α-MNs in spinal cord and SA, an association between smooth muscle cells and SA, an association between oligodendrocyte and HMN, a suggestive association between γ-MNs and HMN, a suggestive association between mature skeletal muscle and HMN, an association between oligodendrocyte in brain and SPG, and no statistical evidence for an association between cell type and SMA.DiscussionThese cellular similarities and differences deepened our understanding of the heterogeneous cellular basis of ALS, SA, HMN, SPG, and SMA.

A broken network of susceptibility genes in the monocytes of Crohn’s disease patients

“…Strictness refers to the spectrum of expression fold change in normal cells. Our prior research demonstrated that amyotrophic lateral sclerosis susceptibility genes with a known mechanism of loss of function (LoF) exhibit high strictness and the gain-of-function genes exhibit low strictness ( 18 ). On this premise, we calculated the strictness of susceptibility genes in monocytes and demonstrated that susceptibility genes have significantly higher strictness than LoF-tolerant (LoFT) genes ( P = 5.52 × 10 −15 ) ( Fig 1C ) and all background genes ( P = 1.13 × 10 −5 ) ( Fig 1D ), indicating that they are dosage-sensitive.…”

“…In our previous study ( 18 ), the strictness measure was defined to estimate the dosage requirement for a given gene. Strictness was calculated by the SD of fold change: , in which S denotes strictness, C refers to fold change, i refers to the i th cell, and n refers to the total number of cells.…”

“…Benefited by single-cell RNA (scRNA)-sequencing technology ( 16 ), we can investigate the gene expression characteristics, disease-related cell types, and gene networks at the single-cell level. Our previous research ( 17 , 18 ) in this field indicated that there are specific cell types associated with genes and diseases. For instance, serotonin neurons in the brain express genes associated with anxiety disorders, whereas motor neurons in the spinal cord express genes associated with amyotrophic lateral sclerosis.…”

A genome-wide association study of neonatal metabolites

“…76 Cell type expression enrichment analysis was performed in large-scale single-cell transcriptome datasets of liver, 37,77 heart, 78 kidney, 79 and gut 80 via EWCE 81 method described in our previous study. 82,83 P -values were adjusted by the FDR method. Adjusted P -value at a threshold of < 0.05 was used to indicate the significant enrichment.…”

Current State and Future Directions in the Diagnosis of Amyotrophic Lateral Sclerosis

“…Currently, various in vitro cellular models with induced pluripotent stem cells (iPSCs) [166] and organoids [167] from donors with sporadic ALS show phenotypic differences in the pattern of neuronal organization and degeneration, protein aggregation, cell death, as well as in onset and progression [168]. The further development of these methods in combination with advanced omics technologies, such as single-cell sequencing and Deep Learning algorithms, will allow precise, accurate and reliable decoding of patient-specific cellular and genetic dysfunction, leading not only to an individual molecular diagnosis but a solid predictive model for applying personalized therapies [169,170].…”