Next-generation sequencing-based miRNA expression analysis in Parp1-deficient embryonic stem cell-derived exosomes.
Next-generation sequencing-based miRNA expression analysis in Parp1-deficient embryonic stem cell-derived exosomes.
复制标题
Parp1 缺陷型胚胎干细胞衍生的外泌体中基于下一代测序的 miRNA 表达分析。
DOI：
10.1016/j.bbrc.2018.03.073
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发表时间：
2018
影响因子：
3.1
通讯作者：
Masutani Mitsuko
中科院分区：
文献类型：
--
作者：
Nozaki Tadashige;Sasaki Yuka;Fukuda Itsuko;Isumi Mayu;Nakamoto Keitaro;Onodera Takae;Masutani Mitsuko
多聚腺苷二磷酸核糖聚合酶家族成员1（Poly（ADP-ribose）polymerase family，member 1，Parp 1）通过翻译后蛋白质修饰在多个细胞信号转导通路中具有多效性和不同的功能。它有助于调节各种细胞过程，包括DNA损伤修复，细胞死亡和细胞分化，遗传或表观遗传。同时，Parp 1在细胞间信号传导中的功能仍有待确定。为了研究Parp 1在细胞间信号传导中的功能，我们研究了来自Parp 1缺陷（Parp 1 −/−）胚胎干（ES）细胞的外泌体中的microRNA（miRNA）调控。在Parp 1 +/+和Parp 1 −/−ES细胞来源的外泌体中，总RNA（包括小RNA，如miRNA、snRNA、snoRNA、tRNA、外显子RNA和内含子RNA）中miRNA的百分比分别为8.2%和3.5%。总体而言，329种不同的miRNA表现出≥2倍的变化（118种上调; 211种下调）。上调的miRNA靶向810个候选基因，下调的miRNA靶向716个候选基因。通路分析显示，上调的miRNAs与包括MAPK信号级联在内的5条通路显著相关（p< 0.05），表明这些通路中的靶基因在Parp 1 −/−ES细胞中受到抑制。在miRNA表达的定量分析中，miR 365 - 3 p、let-7a-5 p、miR 196 b-5 p、miR 203 - 3 p、miR 98 - 5 p和miR 146 a-5 p在Parp 1 −/−ES细胞来源的外泌体中增加≥ 2倍。基因本体富集分析显示，上调的miRNAs与生长和应激相关的细胞信号和细胞通讯有显著关系（p<0. 05），Parp 1缺陷导致ES细胞的细胞间通讯受到抑制，可能通过细胞间信号转导，提示Parp 1通过调控外泌体miRNAs发挥细胞外功能。
Poly (ADP-ribose) polymerase family, member 1 (Parp1) has pleiotropic and disparate functions in multiple cellular signaling pathways through post-translational protein modification. It contributes to the regulation of various cellular processes, including DNA damage repair, cell death, and cell differentiation, genetically or epigenetically. Meanwhile, the functions of Parp1 in intercellular signaling remain to be established. To examine the functions of Parp1 in intercellular signaling, we examined microRNA (miRNA) regulation in exosomes derived fromParp1-deficient (Parp1−/−) embryonic stem (ES) cells. The percentages of miRNAs among total RNAs, including small RNAs such as miRNAs, snRNAs, snoRNAs, tRNAs, exonic RNAs, and intronic RNAs, inParp1+/+andParp1−/−ES cell-derived exosomes were 8.2% and 3.5%, respectively. Overall, 329 distinct miRNAs exhibited ≥2-fold changes (118 upregulated; 211 downregulated). The upregulated miRNAs targeted 810 candidate genes, and the downregulated miRNAs targeted 716 candidate genes. Pathway analyses revealed that the upregulated miRNAs were significantly associated with five pathways including MAPK signaling cascades (p< 0.05), indicating that the target genes in these pathways were suppressed inParp1−/−ES cells. In quantitative analyses of miRNA expression,miR365-3p,let-7a-5p,miR196b-5p,miR203-3p,miR98-5p, andmiR146a-5pwere increased by ≥ 2-fold inParp1−/−ES cell-derived exosomes. Gene ontology enrichment analyses revealed that the upregulated miRNAs were significantly annotated for growth and stress-related cell signaling and cell communication (p< 0.05).Parp1deficiency in ES cells led to inhibition of cell–cell communication, possibly by intercellular signal transduction, suggesting that Parp1 functions extracellularly by regulating exosomal miRNAs.