Li Si Ying, Liu Shu Ting, Wang Chen Yi, Bai Yu Zuo, Yuan Zheng Wei, Tang Xiao Bing
Department of Pediatric Surgery, Shengjing Hospital of China Medical University, Shenyang, Liaoning Province, China.
The Key Laboratory of Health Ministry for Congenital Malformation, Shenyang, Liaoning Province, China.
Ann Med. 2025 Dec;57(1):2497111. doi: 10.1080/07853890.2025.2497111. Epub 2025 Apr 25.
Understanding the expression of non-coding RNA in the liver during embryonic development provides important insights into liver diseases. Therefore, we investigated circular RNA (circRNA) roles in human liver development, an unexplored research domain.
Using high-throughput sequencing and bioinformatics, we analysed foetal liver samples across developmental stages (7-20 weeks post-conception). Differentially expressed (DE) genes were identified and subjected to enrichment analysis using Gene Ontology (GO), Kyoto Encyclopaedia of Genes and Genomes (KEGG), and Disease Ontology (DO). Modular analysis was performed using the Search Tool for Retrieval of Interacting Genes (STRING), followed by construction of a protein-protein interaction (PPI) network using Cytoscape software. The key genes were screened using Molecular Complex Detection (MCODE). The mRNA levels of hub genes were validated using quantitative reverse transcription polymerase chain reaction (qRT-PCR).
There were 645 DE circRNAs and 5,145 DE mRNAs between human livers at the three growth stages (HB, EH, and LH). It was found that the activity of circRNAs was boosted remarkably in the hepatoblastic stage. Enrichment analysis found they mainly involved in nervous system regulation of liver function, embryonic organ development and digestive system development. In addition, DE circRNAs were primarily involved in the PI3K-AKT, MAPK and calcium pathways, potentially contributing to adult liver diseases. Notably, only hsa_circ_001471 and novel_circ_017382 were simultaneously identified at all stages and were persistently downregulated. A co-expression regulatory network involving these circRNAs was established. Three hub genes (LGR5, FOXL1 and RSPO3) were identified from the PPI network of 167 genes and may play key roles in human liver development. The RT-qPCR validation results were in agreement with the sequencing data.
Our findings provide the first insights into the roles and regulatory networks of circRNAs in human liver development, laying the groundwork for further investigations of molecular and signalling networks.
了解胚胎发育过程中肝脏中非编码RNA的表达情况有助于深入了解肝脏疾病。因此，我们对人类肝脏发育过程中环状RNA（circRNA）的作用进行了研究，这是一个尚未被探索的研究领域。
利用高通量测序和生物信息学技术，我们分析了不同发育阶段（受孕后7 - 20周）的胎儿肝脏样本。鉴定出差异表达（DE）基因，并使用基因本体论（GO）、京都基因与基因组百科全书（KEGG）和疾病本体论（DO）进行富集分析。使用检索相互作用基因的搜索工具（STRING）进行模块分析，随后使用Cytoscape软件构建蛋白质-蛋白质相互作用（PPI）网络。使用分子复合物检测（MCODE）筛选关键基因。使用定量逆转录聚合酶链反应（qRT-PCR）验证枢纽基因的mRNA水平。
在人类肝脏的三个生长阶段（HB、EH和LH）之间，有645个差异表达的circRNA和5145个差异表达的mRNA。研究发现，circRNA的活性在成肝细胞阶段显著增强。富集分析发现它们主要参与肝脏功能的神经系统调节、胚胎器官发育和消化系统发育。此外，差异表达的circRNA主要参与PI3K - AKT、MAPK和钙信号通路，可能与成人肝脏疾病有关。值得注意的是，只有hsa_circ_001471和novel_circ_017382在所有阶段均被同时鉴定出，且持续下调。建立了一个涉及这些circRNA的共表达调控网络。从167个基因的PPI网络中鉴定出三个枢纽基因（LGR5、FOXL1和RSPO3），它们可能在人类肝脏发育中起关键作用。RT - qPCR验证结果与测序数据一致。
我们的研究结果首次揭示了circRNA在人类肝脏发育中的作用和调控网络，为进一步研究分子和信号网络奠定了基础。
