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Mitochondrial transcription factor A (TFAM) represses the expression of interferon signaling genes in human lung epithelial cells

ABSTRACT: Mitochondrial transcription factor A (TFAM) is associated with a number of neurodegenerative diseases and also with asthma. TFAM deficiency-induced mitochondrial DNA stress primes the antiviral innate immune response in mouse embryonic fibroblasts. In this study, we overexpressed TFAM in human lung epithelial cells (A549), then obtained and analyzed the TFAM-regulated transcriptome by Illumina-sequencing technology. We found that TFAM overexpression down-regulated and up-regulated the expression 642 and 169 genes (DEGs), respectively. The TFAM-repressed genes were highly enriched in cytokine-mediated signaling pathway, type I interferon- and INFmediated signaling pathways, and viral response pathways. We also revealed that 2563 alternative splicing events in 1796 genes (ASG) were de-regulated upon TFAM overexpression. These TFAM-responding ASGs were strongly enriched in DNA repair, nerve growth factor receptor signaling pathway, and also transcription regulation. Further analysis revealed that the promoters of TFAM-repressed DEGs were enriched by DNA binding motifs of transcription factors whose alternative splicing regulated by TFAM. These findings suggested that TFAM regulates not only immune response gene expression in human lung epithelial cells, but also alternative splicing which may play a role in mediating transcriptional regulation. This TFAM-centered gene regulation network could be targeted in developing therapies against various diseases.

ORGANISM(S): Homo sapiens

PROVIDER: GSE162384 | GEO | 2021/12/15

REPOSITORIES: GEO

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Project description:Background: Angiogenesis is an essential step for tissue development and its dysregulation is associated with various diseases, including moyamoya disease. Among the regulators of angiogenesis, galectin-1 encoded by LGALS1, plays essential roles, but the underlying mechanisms need to be further expounded. In this study, we systematically investigated the potential targets of galectin-1 by silencing LGALS1 (siLGALS1) in human umbilical vein endothelial cells (HUVECs) and performing whole transcriptome sequencing (RNA-seq) experiments. We also integrated galectin-1-interacting RNA data to explore how galectin-1 regulates gene expression and alternative splicing. Results: By systematical analysis, we found siLGALS1 treatment significantly regulated 1451 differentially expressed genes (DEGs), including 604 up-regulated DEGs and 847 down-regulated DEGs. The down-regulated DEGs were significantly enriched in angiogenesis and inflammatory response pathways. The involved genes included CCL2, GJA5, CALCRL, ACKR3, HEY1, AQP1, CD34, ECM1, RAMP2, and SELP, which were also validated by RT-qPCR experiment. We also analyzed the dysregulated alternative splicing (AS) profile by siLGALS1, and found siLGALS1 had obvious bias for dysregulated AS types, preferring to promote exon skipping and intron retention, and inhibit cassette exon events. Interestingly, we found the regulated AS genes (RASGs) were enriched in focal adhesion and VEGF signaling pathway, which were highly related to angiogenesis. Finally, we found hundreds of RASGs were also bound by galectin-1 using the published iRIP-seq data of galectin-1, including RASGs from angiogenesis pathway. Conclusions: In summary, our results demonstrated that galectin-1 could regulate angiogenesis-related genes at transcriptional and post-transcriptional levels, which is associated its RNA binding ability in HUVECs. The discovery extends our understanding on the functions and molecular mechanisms of galectin-1 during the development of angiogenesis, which could be served as a therapeutic option in anti-angiogenic treatment in future.

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Mitochondrial transcription factor A (TFAM) represses the expression of interferon signaling genes in human lung epithelial cells

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