bulk RNA-seq data analysis of primary human mesenchymal stem cells of Multiple Myeloma patients compared to control patients

Purpose: In this study we compared bone marrow-derived mesenchymal stem cells (MSC) of 6 Multiple Myeloma patients (MM-MSC) with MSC of 5 control donors with other (non) malignant diseases (CTR-MSC) to detect transciptomic alterations in RNA sequencing and to identify altered gene expression patterns. Methods: MSC were obtained from bone marrow, cultivated, analyzed by flow cytometry and underwent quality control using the 4200 TapeStation (Agilent, California, USA). Following the TrueSeq stranded protocol (Illumina, California, USA) we sequenced the RNA in a 100 bp paired-end run on the HiSeq 4000 (Illumina). Results: We detected 2174 significant DEGs (adjusted p<0.05) between MM-MSC and CTR-MSC, among which 967 were up-regulated in MM-MSC. 18 out of 50 MSigDB Hallmark gene sets were significantly enriched in MM-Act-MSC compared to CTR-MSC (FDR<0.05) including PI3K-AKT-mTOR signaling, as well as NOTCH, MYC and Inflammatory response. Conclusion: Our data provides a deeper insight into the molecular signature and function of MSC associated MM-cells and show that targeting PI3K-AKT-mTOR signaling in MSC may represent an additional therapeutic pathway in the treatment of MM-patients. Overall design: bulk-RNA sequencing data analysis of Multiple Myeloma MSC compared to control MSC

研究目的：本研究对比6名多发性骨髓瘤（Multiple Myeloma, MM）患者的骨髓来源间充质干细胞（bone marrow-derived mesenchymal stem cells, MSC，其中多发性骨髓瘤患者来源MSC记为MM-MSC）与5名罹患其他各类疾病（含非恶性与恶性病变）的对照供者的MSC（CTR-MSC），旨在通过RNA测序检测转录组学改变，并筛选差异基因表达模式。
研究方法：从骨髓中分离获取MSC，经体外扩增培养后通过流式细胞术完成鉴定分析，并采用美国加利福尼亚州安捷伦（Agilent）公司的4200 TapeStation进行质量控制。随后遵循Illumina公司的TrueSeq链特异性建库流程（TrueSeq stranded protocol），在Illumina HiSeq 4000平台上以100 bp双端测序模式完成RNA测序。
研究结果：在MM-MSC与CTR-MSC之间共检测到2174个显著差异表达基因（differentially expressed genes, DEGs，校正P值<0.05），其中967个在MM-MSC中呈上调表达。与CTR-MSC相比，MM-Act-MSC中显著富集了50个MSigDB经典特征基因集（MSigDB Hallmark gene sets）中的18个（错误发现率false discovery rate, FDR<0.05），涵盖PI3K-AKT-mTOR信号通路、NOTCH通路、MYC通路以及炎症反应通路。
研究结论：本研究数据深入解析了多发性骨髓瘤相关MSC的分子特征与功能，并证实靶向MSC中的PI3K-AKT-mTOR信号通路，可作为多发性骨髓瘤患者治疗的潜在备选治疗途径。
整体实验设计：多发性骨髓瘤患者来源MSC与对照MSC的批量RNA（bulk-RNA）测序数据分析。