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Cell-Type-Specific Transcriptome of CD4+, CD8+ T cells and CD14+ monocytes in multiple sclerosis

ABSTRACT: Multiple sclerosis (MS) is an autoimmune disease of the central nervous system in which both genetic and environmental factors are thought to be involved. Genome-wide association studies revealed more than 200 risk loci, most of which harbor genes primarily expressed in immune cells. However, whether genetic differences are translated into cell-specific gene expression profiles and to what extent these are altered in MS are not well understood. To assess cell-type-specific gene expression in a large cohort of MS patients, we sequenced the whole transcriptome of sorted T cells (CD4+ and CD8+) and CD14+ monocytes from treatment-naive MS patients (n=122) and healthy subjects (n=22). Next, we performed a comprehensive analysis of the RNA sequencing dataset and identified 612 differentially expressed genes (DEGs) in CD14+ monocytes, 464 in CD4+ T cells, and 93 in CD8+ T cells. Notably, about one third (36.6%) of DEGs were non-coding RNAs, the majority of which (88.2%) were down-regulated in MS. We identified large co-expressed gene modules and cis-eQTLs with key MS genes in each cell subset. Importantly, we discovered dysregulation of NAE1, a subunit of NEDD8 activating enzyme (NAE), in CD4+ T cells which activates the neddylation pathway. Finally, we demonstrated that NAE inhibition using Pevonedistat (MLN4924) dampened disease severity in murine experimental autoimmune encephalomyelitis (EAE). Our findings provide novel insights into MS-associated gene regulation unraveling neddylation as a crucial pathway in MS pathogenesis with implications for the development of tailored disease-modifying agents.

ORGANISM(S): Homo sapiens

PROVIDER: GSE137143 | GEO | 2020/12/31

REPOSITORIES: GEO

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Project description:The heart undergoes significant structural, metabolic, gene expression and functional alterations during the perinatal to postnatal transition. While recent studies have identified multiple epigenetic and transcriptional regulators of cardiac maturation, post-transcriptional mechanisms regulating this process remain poorly understood. Neddylation is a post-translational modification that conjugates a small ubiquitin-like protein, NEDD8, to protein substrates via an E1-E2-E3 enzymatic cascade. The goal of this study was to define the role of neddylation in perinatal cardiac development and cardiac maturation. Neddylation was inhibited in adult mouse hearts by cardiac-specific deletion of NAE1 gene, a regulatory subunit of NEDD8 E1 enzyme, or in neonatal cardiomyocytes (CMs) with a pharmacological neddylation inhibitor, MLN4924. The impact on cardiac transcriptome, metabolism, maturation and function was assessed. Mosaic deletion of NAE1 in ~40% neonatal CMs disrupted aspects of maturation, including transverse-tubule formation, cellular hypertrophy and fetal/adult isoform switching, whereas deletion of NAE1 in over 80% CMs led to rapid development of cardiomyopathy and heart failure. Transcriptome analysis demonstrated an association of metabolic derangement with immature cardiomyocyte signature. Biochemical, ultrastructural and metabolomics analyses confirmed downregulation of fatty acid and oxidative phosphorylation genes, deficits in fatty acid utilization, mitochondrial dysfunction, and significantly altered metabolic profiles in NAE1-deficient hearts or MLN4924-treated neonatal CMs. Mechanistically, we found that HIF1α, a transcription factor known to promote glycolysis and suppress oxidative metabolism, is a putative NEDD8 target. Inhibition of neddylation resulted in HIF1α accumulation and activation, which contributed to diminished fatty acid utilization. Taken together, we conclude that neddylation plays a crucial role in CM maturation and postnatal cardiac development through sustaining the glycolytic to oxidative metabolic switch in perinatal hearts.

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Cell-Type-Specific Transcriptome of CD4+, CD8+ T cells and CD14+ monocytes in multiple sclerosis

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