table_1_Integrated Characterization of MicroRNA and mRNA Transcriptome in Papillary Thyroid Carcinoma.xlsx

The incidence rate of papillary thyroid carcinoma (PTC) has rapidly increased in the recent decades, and the microRNA (miRNA) is one of the potential biomarkers in this cancer. Despite good prognosis, certain features such as lymph node metastasis (LNM) and BRAF V600E mutation are associated with a poor outcome. More than 50% of PTC patients present with LNM and BRAF V600E is the most common mutation identified in this cancer. The molecular mechanisms underlying these features are yet to be elucidated. This study aims to elucidate miRNA–genes interaction networks in PTC with or without LNM and to determine the association of BRAF V600E mutation with miRNAs and genes expression profiles. Next generation sequencing was performed to characterize miRNA and gene expression profiles in 20 fresh frozen tumor and the normal adjacent tissues of PTC with LNM positive (PTC LNM-P) and PTC without LNM (PTC LNN). BRAF V600E was genotyped using Sanger sequencing. Bioinformatics integration and pathway analysis were performed to determine the regulatory networks involved. Based on network analysis, we then investigated the association between miRNA and gene biomarkers, and pathway enrichment analysis was performed to study the role of candidate biomarkers. We identified 138 and 43 significantly deregulated miRNAs (adjusted p value < 0.05; log2 fold change ≤ −1.0 or ≥1.0) in PTC LNM-P and PTC LNN compared to adjacent normal tissues, respectively. Ninety-six miRNAs had significant expression ratios of 3p-to-5p in PTC LNM-P as compared to PTC LNN. In addition, ribosomal RNA-reduced RNA sequencing analysis revealed 699 significantly deregulated genes in PTC LNM-P versus normal adjacent tissues, 1,362 genes in PTC LNN versus normal adjacent tissue, and 1,576 genes in PTC LNM-P versus PTC LNN. We provide the evidence of miRNA and gene interactions, which are involved in LNM of papillary thyroid cancer. These findings may lead to better understanding of carcinogenesis and metastasis processes. This study also complements the existing knowledge about deregulated miRNAs in papillary thyroid carcinoma development.

近数十年来，甲状腺乳头状癌（papillary thyroid carcinoma, PTC）的发病率快速攀升，微小RNA（microRNA, miRNA）是该类癌症的潜在生物标志物之一。尽管多数患者预后良好，但淋巴结转移（lymph node metastasis, LNM）及BRAF V600E突变等特征与不良预后相关。超过50%的PTC患者会出现淋巴结转移，而BRAF V600E是该癌症中最常见的突变类型，但其背后的分子机制尚未阐明。本研究旨在阐明伴/不伴淋巴结转移的PTC中miRNA-基因相互作用网络，并明确BRAF V600E突变与miRNA及基因表达谱的关联。本研究采用下一代测序技术，对20例伴淋巴结转移阳性PTC（PTC LNM-P）、20例不伴淋巴结转移PTC（PTC LNN）的新鲜冰冻肿瘤组织及配对癌旁正常组织的miRNA和基因表达谱进行表征。通过桑格测序对BRAF V600E进行基因分型。随后开展生物信息学整合分析与通路分析，以明确相关调控网络。基于网络分析结果，我们进一步探究了miRNA与基因生物标志物之间的关联，并通过通路富集分析解析候选生物标志物的功能。研究结果显示，相较于癌旁正常组织，PTC LNM-P组与PTC LNN组分别鉴定出138种和43种显著差异表达的miRNA（校正p值<0.05；log₂倍变化≤-1.0或≥1.0）。与PTC LNN组相比，PTC LNM-P组中有96种miRNA的3p与5p表达比值存在显著差异。此外，核糖体RNA去除RNA测序结果显示，相较于正常癌旁组织，PTC LNM-P组存在699个显著差异表达基因，PTC LNN组存在1362个显著差异表达基因，而PTC LNM-P组与PTC LNN组间则存在1576个显著差异表达基因。本研究明确了参与甲状腺乳头状癌淋巴结转移的miRNA与基因相互作用证据，这些发现有助于进一步理解癌变与转移过程，同时也补充了当前关于PTC发生过程中差异表达miRNA的相关认知。