Identification of key genes and miRNA-mRNA regulatory networks associated with bone marrow immune microenvironment regulations in multiple myeloma by integrative bioinformatics analysis

The deregulation of microRNAs (miRNAs) and genes in the bone marrow microenvironment have been involved with the pathogenesis of multiple myeloma (MM). However, the exploration of miRNA-mRNA regulatory networks in MM remains lacking. We used GSE125363, GSE125361, GSE47552, GSE2658, GSE136324, GSE16558, and GSE13591 datasets for this bioinformatics study. We identified 156 downregulated and 13 upregulated differentially expressed miRNAs (DEmiRs) in MM. The DEmiRs are associated with the enrichment of pathways mainly involved with cancers, cellular signaling, and immune regulations. We identified 112 hub genes associated with five significant clusters in MM. Moreover, we identified 9 upregulated hub genes (such as <i>IGF1, RPS28, UBA52, CDKN1A,</i> and <i>CDKN2A</i>) and 52 downregulated hub genes (such as <i>TP53, PCNA, BRCA1, CCNB1,</i> and <i>MSH2</i>) in MM that is targeted by DEmiRs. The expression of DEmiRs targeted two hub genes (<i>CDKN2A</i> and <i>TP53</i>) are correlated with the survival prognosis of MM patients. Furthermore, the expression level of <i>CDKN2A</i> is correlated with immune signatures, including CD4+ Regulatory T cells, T cell exhaustion, MHC Class I, immune checkpoint genes, macrophages, neutrophils, and TH2 cells in the TME of MM. Finally, we revealed the consistently deregulated expression level of key gene <i>CDKN2A</i> and its co-regulatory DEmiRs, including hsa-mir-192, hsa-mir-10b, hsa-mir-492, and hsa-mir-24 in the independent cohorts of MM. Identifying key genes and miRNA-mRNA regulatory networks may provide new molecular insights into the tumor immune microenvironment in MM.

骨髓微环境中微小RNA（miRNAs）与基因的表达失调，与多发性骨髓瘤（MM）的发病机制密切相关。然而，目前针对多发性骨髓瘤中miRNA-mRNA调控网络的探索仍存在显著缺口。本生物信息学研究纳入GSE125363、GSE125361、GSE47552、GSE2658、GSE136324、GSE16558及GSE13591共7组数据集进行分析。我们在多发性骨髓瘤样本中鉴定出156个下调、13个上调的差异表达微小RNA（DEmiRs）。这些DEmiRs富集的通路主要涵盖癌症发生、细胞信号转导与免疫调控等方向。随后，我们鉴定出与多发性骨髓瘤中5个显著聚类相关的112个枢纽基因。此外，我们筛选出9个受DEmiRs靶向的上调枢纽基因（如<i>IGF1</i>、<i>RPS28</i>、<i>UBA52</i>、<i>CDKN1A</i>及<i>CDKN2A</i>），以及52个受DEmiRs靶向的下调枢纽基因（如<i>TP53</i>、<i>PCNA</i>、<i>BRCA1</i>、<i>CCNB1</i>及<i>MSH2</i>）。DEmiRs所靶向的<i>CDKN2A</i>与<i>TP53</i>这两个枢纽基因的表达水平，与多发性骨髓瘤患者的生存预后显著相关。进一步分析显示，<i>CDKN2A</i>的表达水平与多发性骨髓瘤肿瘤微环境（Tumor Microenvironment, TME）中的多种免疫特征密切相关，包括CD4+调节性T细胞、T细胞耗竭、MHC I类分子、免疫检查点基因、巨噬细胞、中性粒细胞及TH2细胞。最终，我们在独立的多发性骨髓瘤队列中验证了关键基因<i>CDKN2A</i>及其共调控DEmiRs（包括hsa-mir-192、hsa-mir-10b、hsa-mir-492及hsa-mir-24）的表达失调模式具有一致性。本研究鉴定的关键基因及miRNA-mRNA调控网络，可为多发性骨髓瘤的肿瘤免疫微环境研究提供全新的分子视角。