Bone marrow-derived and dental pulp-derived human mesenchymal stem cell RNA-Seq

Lineage commitment and tumorigenesis specify adult stem cells from different tissues or organs. To gain insight into the mechanism of this programming, phenotypic, functional and transcriptome analyses were performed in mesenchymal stem cells derived from human dental pulp (DPSCs) and bone marrow (BMSCs). DPSCs and BMSCs had similar morphologies and flow cytometric profiles, and were capable of tri-lineage differentiation into osteoblast, adipocyte and chondocyte. However, compared with BMSCs, DPSCs increased in osteogenic potential, decreased in adipogenic potential, and formed dentin-pulp-like complexes in vivo. Genome-wide RNA-seq and differential expression analysis revealed that signalings such as, phosphatase and tensin homolog (PTEN)/PI3K/AKT pathway, and cancer-related pathway were different in both cells. Differential PTEN expression, higher in DPSCs than BMSCs, was responsible for the lineage commitment and tumorigenesis differences in both cells. Besides, BMSCs decreased in PTEN DNA methylation compared to DPSCs, which was mediated by increased DNA (cytosine-5) methyltransferase 3B (DNMT3B) expression. Furthermore, histone methyltransferase G9a mediated repressive epigenetic mark H3K9Me2 was selectively enriched in BMSCs. Moreover, DPSCs were more resistant to oncogenic transformation than BMSCs. To link lineage commitment with tumorigenesis, we demonstrated that DPSCs were more resistant to oncogenic transformation than BMSCs and PTEN deficiency increased the sensitivity of DPSCs for tumorigenic transformation. The results help understanding the roles of the epigenetic factors in lineage commitment and tumorigenesis and also for therapeutic uses of adult stem cells.

谱系定型与肿瘤发生是区分不同组织或器官来源成体干细胞的核心特征。为深入解析这一细胞命运编程的调控机制，本研究对人牙髓来源的间充质干细胞（dental pulp stem cells, DPSCs）与骨髓来源的间充质干细胞（bone marrow mesenchymal stem cells, BMSCs）开展了表型、功能及转录组分析。DPSCs与BMSCs具有相似的形态学特征与流式细胞术表型，均具备三系分化潜能，可分化为成骨细胞、脂肪细胞与软骨细胞。但相较BMSCs，DPSCs的成骨分化潜能更强，成脂分化潜能更弱，且可在体内形成牙髓牙本质样复合体。全基因组RNA测序与差异表达分析结果显示，两类细胞中存在多条信号通路的表达差异，包括张力蛋白同源物（phosphatase and tensin homolog, PTEN）/PI3K/AKT通路以及癌症相关通路。DPSCs中PTEN的表达水平显著高于BMSCs，这种差异表达是导致两类细胞在谱系定型与肿瘤发生特征上出现差异的关键原因。此外，相较于DPSCs，BMSCs中PTEN基因的DNA甲基化水平更低，这一现象由DNA（胞嘧啶-5）甲基转移酶3B（DNA (cytosine-5) methyltransferase 3B, DNMT3B）的表达上调所介导。同时，组蛋白甲基转移酶G9a介导的抑制性表观遗传标记H3K9Me2在BMSCs中选择性富集。进一步实验表明，DPSCs对致癌转化的抵抗能力强于BMSCs。为建立谱系定型与肿瘤发生之间的功能关联，本研究证实：DPSCs的致癌转化抵抗能力优于BMSCs，且PTEN缺失会增强DPSCs的致瘤转化敏感性。本研究结果不仅有助于阐明表观遗传因子在谱系定型与肿瘤发生过程中的调控作用，同时可为成体干细胞的临床治疗应用提供理论参考。