Dept. of Biological Sciences, BITS Pilani, K. K. Birla Goa Campus, Zuarinagar, Goa 403726, India.
Bioinformatics Institute, Agency for Science Technology and Research, 30 Biopolis Street, #07-01 Matrix, Singapore 1386713, Singapore.
Cytokine. 2020 Jan;125:154815. doi: 10.1016/j.cyto.2019.154815. Epub 2019 Aug 30.
TNF-α, a pro-inflammatory cytokine is one of the major contributors for metabolic syndromes including insulin resistance, obesity, type II diabetes etc. The role of alternative splicing, a post-transcriptional regulation of gene expression on the onset of these syndromes is poorly understood. However, the role of alternative splicing, which more than 95% of all exons in eukaryotic cells undergo in several other diseases including cancer and muscle dystrophy, has been elucidated. In this study we aim to investigate the role of alternative splicing in pathways leading to metabolic syndromes mediated by TNF-α.
A genome wide transcriptome analysis was carried out using Illumina platform. Results were validated using RT-PCR analysis. Various bioinformatics tools and databases (for example IPA, KEGG, STRING etc) were used for the pathway and interactome analysis.
Transcriptome wide analysis revealed that TNF-α treatment in vitro causes a significant change in expression of 228 genes at the level of alternative splicing. Regulation of some of these genes was validated in different cell lines. Pathway analysis showed at least 15% of the alternatively spliced genes fall under the contributory pathways leading to different metabolic syndromes, among which the maximally interconnected genes were transcription regulators.
These findings suggest that TNF-α.-mediated alternative splicing plays a crucial role in regulating various genes involved in pathways connected to metabolic syndromes.
TNF-α，一种促炎细胞因子，是导致代谢综合征的主要因素之一，包括胰岛素抵抗、肥胖症、2 型糖尿病等。替代剪接作为一种基因表达的转录后调控，对这些综合征的发生作用机制尚不清楚。然而，替代剪接在其他几种疾病中的作用已经阐明，包括癌症和肌肉营养不良等，超过 95%的真核细胞中的所有外显子都经历了替代剪接。在这项研究中，我们旨在研究 TNF-α 介导的代谢综合征相关途径中替代剪接的作用。
使用 Illumina 平台进行全基因组转录组分析。使用 RT-PCR 分析验证结果。使用各种生物信息学工具和数据库（例如 IPA、KEGG、STRING 等）进行通路和互作网络分析。
体外 TNF-α 处理的转录组广泛分析显示，替代剪接水平上有 228 个基因的表达发生了显著变化。这些基因中的一些在不同的细胞系中得到了验证。通路分析显示，至少有 15%的替代剪接基因属于导致不同代谢综合征的贡献途径，其中最大相互关联的基因是转录调节剂。
这些发现表明，TNF-α 介导的替代剪接在调节与代谢综合征相关途径中涉及的各种基因方面发挥着关键作用。
