Methylome analysis of human bone marrow MSCs reveals extensive age and culture induced changes at distal regulatory elements

Human mesenchymal stem cells (MSCs) need expansion prior to use as cell-based therapies in immunological and tissue repair applications. Aging and expansion of MSCs induce epigenetic changes that can impact therapeutic outcomes. By applying sequencing-based methods, we reveal that the breadth of DNA methylation dynamics associated with aging and expansion are greater than previously reported. Methylation changes are enriched at known distal transcription factor binding sites such as enhancer elements instead of CpG-rich regions and are associated with changes in gene expression. From this, we constructed hypo- and hypermethylation specific regulatory networks, including a sub-network of MSC master regulators and their predicted target genes, and identified putatively disrupted signaling pathways. Our genome-wide analyses provide a broader overview of age and expansion induced DNA methylation changes, and a better understanding of the extent to which these changes alter gene expression and functionality of human bone marrow MSCs.

人类间充质干细胞（human mesenchymal stem cells, MSCs）在应用于免疫相关及组织修复领域的细胞治疗前，需先进行扩增培养。间充质干细胞的衰老与扩增过程会诱导表观遗传改变，进而可能对治疗效果产生影响。本研究借助基于测序的技术方法，揭示出与衰老及扩增相关的DNA甲基化动态变化范围远超此前报道。甲基化改变显著富集于已知的远端转录因子结合位点（如增强子元件）而非CpG富集区域，且与基因表达变化存在关联。基于上述发现，我们构建了低甲基化与高甲基化特异性调控网络，其中包含间充质干细胞核心调控因子及其预测靶基因的子网络，并鉴定出可能受到扰动的信号通路。本项全基因组分析全面概述了衰老与扩增诱导的DNA甲基化改变，加深了我们对这类改变如何影响人类骨髓间充质干细胞基因表达与功能的认知程度。