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Integrative genome-wide analysis of PBMCs confirmed SOD1-specific functionality of ATF3 in ALS blood

ABSTRACT: Amyotrophic Lateral Sclerosis (ALS) is characterized by a progressive loss of upper and lower motor neurons, leading to progressive weakness and atrophy of limb, bulbar and respiratory muscles. Since genetics alone fails to explain the etiology of ALS, the investigation of the epigenome might provide novel insights in disease mechanisms. Among all the different histone modifications the repressive trimethylation of lysine 27 on histone H3 (H3K27me3) is of particular interest in the context of ALS for several reasons. In this study, we interrogate the epigenetic landscape in peripheral blood mononuclear cells (PBMCs) of fALS patient with either chromosome 9 open reading frame 72 (C9orf72) or superoxide dismutase 1 (SOD1) mutation and aimed to identify key epigenetic footprints of the disease. To this end, we used an integrative approach that combines chromatin immunoprecipitation targeting H3K27me3 (ChIP-Seq) with the matching gene expression data to gain new insights into the impact of chromatin remodeling on ALS-related molecular mechanisms. In particular, multiple lines of evidence in this work indicated that one of the hub molecules that modulates changes in PBMC transcriptome in SOD1-positive ALS cases is ATF3. We also reported a potential suppression of SNAP25, with ATF3 involved as well, in SOD1-positive ALS blood.

ORGANISM(S): Homo sapiens

PROVIDER: GSE223834 | GEO | 2023/07/01

REPOSITORIES: GEO

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Project description:We established iPSCs from healthy donors, SOD1-ALS and TDP43-ALS patients. Using our differentiation protocol originally developed by Reinhardt et al.,2013, we diferentiated these iPSCs toward spinal motor neurons (MNs) and reproduce ALS pathology in a dish. To extend our understanding of finding different molecular mechanisms and pathways related to SOD1- and TDP43 mutations in ALS disease, we have performed a comprehensive gene expression profiling study using RNA-Seq of the iPSC-derived MN models from control individuals and carefully compared with those from SOD1-ALS and TDP43-ALS patients. To generate novel hypotheses of putative underlying molecular mechanisms in ALS, we used human induced pluripotent stem cell (hiPSCs)-derived motor neurons (MNs) from SOD1- and TARDBP (TDP-43 protein)-mutant-ALS patients and healthy controls to perform high-throughput RNA-sequencing (RNA-Seq). An integrated bioinformatics approach was employed to identify differentially expressed genes (DEGs) and key pathways underlying these familial forms of the disease (fALS). In TDP43-ALS, we found dysregulation of transcripts encoding components of the transcriptional machinery and transcripts involved in splicing regulation were particularly affected. In contrast, less is known about the role of SOD1 in RNA metabolism in motor neurons. Here we found that many transcripts relevant for mitochondrial function were specifically altered in SOD1-ALS, indicating transcriptional signatures and expression patterns can vary significantly depending on the causal gene that is mutated. Surprisingly, however, we identified a clear downregulation of genes involved in protein translation in SOD1-ALS suggesting that ALS-causing SOD1 mutations shift cellular RNA abundance profiles to cause neural dysfunction. Altogether, we provided here an extensive profiling of mRNA expression in two ALS models at the cellular level, corroborating the major role of RNA metabolism and protein translation as a common pathomechanism in ALS

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Integrative genome-wide analysis of PBMCs confirmed SOD1-specific functionality of ATF3 in ALS blood

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