缺氧和拟缺氧预处理后人骨髓间充质干细胞的基因表达谱分析——RNA 测序分析。

Gene Expression Profile of Human Mesenchymal Stromal Cells Exposed to Hypoxic and Pseudohypoxic Preconditioning-An Analysis by RNA Sequencing.

机构信息

Department of Immunology, Transplantology and Internal Diseases, Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland.

Department of Clinical Immunology, Medical University of Warsaw, Nowogrodzka 59, 02-006 Warsaw, Poland.

出版信息

Int J Mol Sci. 2021 Jul 29;22(15):8160. doi: 10.3390/ijms22158160.

DOI:10.3390/ijms22158160

PMID:34360925

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8348678/

Abstract

Mesenchymal stromal cell (MSC) therapy is making its way into clinical practice, accompanied by research into strategies improving their therapeutic potential. Preconditioning MSCs with hypoxia-inducible factors-α (HIFα) stabilizers is an alternative to hypoxic priming, but there remains insufficient data evaluating its transcriptomic effect. Herein, we determined the gene expression profile of 6 human bone marrow-derived MSCs preconditioned for 6 h in 2% O (hypoxia) or with 40 μM Vadadustat, compared to control cells and each other. RNA-Sequencing was performed using the Illumina platform, quality control with FastQC and adapter-trimming with BBDUK2. Transcripts were mapped to the Homo_sapiens. GRCh37 genome and converted to relative expression using Salmon. Differentially expressed genes (DEGs) were generated using DESeq2 while functional enrichment was performed in GSEA and g:Profiler. Comparison of hypoxia versus control resulted in 250 DEGs, Vadadustat versus control 1071, and Vadadustat versus hypoxia 1770. The terms enriched in both phenotypes referred mainly to metabolism, in Vadadustat additionally to vesicular transport, chromatin modifications and interaction with extracellular matrix. Compared with hypoxia, Vadadustat upregulated autophagic, phospholipid metabolism, and TLR cascade genes, downregulated those of cytoskeleton and GG-NER pathway and regulated 74 secretory factor genes. Our results provide valuable insight into the transcriptomic effects of these two methods of MSCs preconditioning.

摘要

间充质基质细胞（MSC）治疗正在进入临床实践，同时也在研究提高其治疗潜力的策略。用缺氧诱导因子-α（HIFα）稳定剂预处理 MSC 是缺氧预适应的替代方法，但仍缺乏足够的数据评估其转录组效应。在此，我们比较了 6 个人骨髓来源的 MSC 在 2%O2（缺氧）或 40μMVadadustat 预处理 6 小时与对照细胞的基因表达谱。使用 Illumina 平台进行 RNA 测序，使用 FastQC 进行质量控制，使用 BBDUK2 进行接头修剪。将转录物映射到 Homo_sapiens.GRCh37 基因组，并使用 Salmon 将其转换为相对表达量。使用 DESeq2 生成差异表达基因（DEG），并在 GSEA 和 g：Profiler 中进行功能富集。与对照相比，缺氧组有 250 个 DEG，Vadadustat 组有 1071 个 DEG，Vadadustat 组与缺氧组有 1770 个 DEG。这两种表型中富集的术语主要涉及代谢，Vadadustat 组还涉及囊泡运输、染色质修饰和与细胞外基质的相互作用。与缺氧相比，Vadadustat 上调了自噬、磷脂代谢和 TLR 级联基因，下调了细胞骨架和 GG-NER 途径的基因，并调节了 74 个分泌因子基因。我们的结果为这两种 MSC 预处理方法的转录组效应提供了有价值的见解。