RNA sequencing of LPS treated mouse bone marrow stromal cells

Background: Lipopolysaccharide (LPS) is a gram-negative bacterial antigen that triggers a series of cellular responses. LPS pre-conditioning was previously shown to improve the therapeutic efficacy of bone marrow stromal cells/bone-marrow derived mesenchymal stem cells (BMSCs) for repairing ischemic, injured tissue. Results: In this study, we systematically evaluated the effects of LPS treatment on genome-wide splicing pattern changes in mouse BMSCs by comparing transcriptome sequencing data from control vs. LPS-treated samples, revealing 197 exons whose BMSC splicing patterns were altered by LPS. Functional analysis of these alternatively spliced genes demonstrated significant enrichment of phosphoproteins, zinc finger proteins, and proteins undergoing acetylation. Additional bioinformatics analysis strongly suggest that LPS-induced alternatively spliced exons could have major effects on protein functions by disrupting key protein functional domains, protein-protein interactions, and post-translational modifications. Conclusion: Although it is still to be determined whether such proteome modifications improve BMSC therapeutic efficacy, our comprehensive splicing characterizations provide greater understanding of the intracellular mechanisms that underlie the therapeutic potential of BMSCs. Overall design: 6 samples (3 untreated wild type samples, 3 LPS treated wild type samples)

背景：脂多糖（Lipopolysaccharide，LPS）是革兰氏阴性菌抗原，可触发一系列细胞应答反应。既往研究表明，脂多糖预处理可提升骨髓基质细胞/骨髓来源间充质干细胞（bone-marrow derived mesenchymal stem cells，BMSCs）修复缺血损伤组织的治疗功效。
结果：本研究通过对比对照组与脂多糖处理组的转录组测序数据，系统评估了脂多糖处理对小鼠BMSCs全基因组剪接模式变化的影响，共鉴定出197个经脂多糖处理后剪接模式发生改变的BMSCs外显子。对上述可变剪接基因进行功能富集分析发现，其显著富集于磷蛋白、锌指蛋白及乙酰化修饰蛋白相关功能类别。进一步的生物信息学分析显示，脂多糖诱导的可变剪接外显子可通过破坏关键蛋白质功能结构域、蛋白质-蛋白质相互作用及翻译后修饰，对蛋白质功能产生重大影响。
结论：尽管目前仍需进一步明确此类蛋白质组修饰是否可提升BMSCs的治疗功效，本研究通过全面的剪接特征分析，加深了对BMSCs治疗潜能背后细胞内机制的理解。
整体实验设计：本研究共设置6个样本，包括3份未处理的野生型样本与3份脂多糖处理的野生型样本。