Chen Ruoran, Gao Wei, Liang Linlang, Yu Hao, Song Wei
Department of Endocrinology, General Hospital of Northern Theater Command, Shenyang, 110016, China.
Heliyon. 2024 May 25;10(11):e31970. doi: 10.1016/j.heliyon.2024.e31970. eCollection 2024 Jun 15.
An mRNA expression-based stemness index (mRNAsi) has been developed to characterize cancer stemness. However, the predictive value of mRNAsi-based signature in therapeutic resistance and immunotherapy in thyroid cancer (THCA) remains unclarified. This study evaluated and validated the role of mRNAsi in drug sensitivity, its relationship between mRNAsi and THCA clinical features and immunity based on bioinformatics.
Based on transcriptome data of THCA patients from the Tumor Genome Atlas Project (TCGA) database, and expression data of multifunctional stem cell samples from the Progenitor Cell Biology Consortium (PCBC) databases, mRNAsi was calculated by the " one class logistic regression (OCLR)" method, Molecular subtypes of TCGA-THCA samples were identified with mRNAsi-related genes using ConsensusClusterPlus method. The gene mutation, clinical characteristics, immune characteristics, TIDE and drug sensitivity were compared among molecular subtypes. A prognostic model was designed with Lasso cox method. Modulation of malignant phenotype of THCA cell lines by model characterization genes is validated by CCK-8, flow cytometry. DNA methylation disorder in promoter region was analyzed between risk groups. The model was validated for survival in the internal Test dataset, while TCGA pan-cancer and immunotherapy datasets were further employed to validate the performance of this model.
We obtained a total of 78 stem cell samples, each containing the expression profile of 8087 mRNA genes. Based on mRNAsi, THCA was divided into 3 subtypes. Subtype C2 had the poorest prognosis and highest immune score, while subtype C3 had the best prognosis, lowest mRANsi and highest TIDE score. Patients in subtype C2 showed higher sensitivity to Cisplatin, Erlotinib, Paclitaxel, and Lapatinib. The prognostic signature was generated using 5 mRNAsi-related genes, which could predict prognosis for THCA. qRT-PCR results showed that the expression of 5 genes were various in Hth7 and KTC-1 cells, and inhibition CELSR3 expression increased percentage of apoptosis in Hth7 and KTC-1 cells. mRNAsi related DNA methylation sites were mainly enriched in tumor related pathways. Good performance of this model was validated in Test dataset, pan-cancer and immunotherapy datasets.
This study identified three subtypes for classification and developed a prognostic model with mRNAsi-related genes, which provided great potential for prognosis and immunotherapy prediction.
基于mRNA表达的干性指数（mRNAsi）已被开发用于表征癌症干性。然而，基于mRNAsi的特征在甲状腺癌（THCA）治疗耐药性和免疫治疗中的预测价值仍不明确。本研究基于生物信息学评估并验证了mRNAsi在药物敏感性中的作用、mRNAsi与THCA临床特征及免疫之间的关系。
基于肿瘤基因组图谱计划（TCGA）数据库中THCA患者的转录组数据以及祖细胞生物学联盟（PCBC）数据库中多功能干细胞样本的表达数据，采用“单类逻辑回归（OCLR）”方法计算mRNAsi。使用ConsensusClusterPlus方法通过与mRNAsi相关的基因鉴定TCGA-THCA样本的分子亚型。比较分子亚型之间的基因突变、临床特征、免疫特征、TIDE和药物敏感性。采用Lasso cox方法设计预后模型。通过CCK-8、流式细胞术验证模型特征基因对THCA细胞系恶性表型的调节作用。分析风险组之间启动子区域的DNA甲基化紊乱情况。在内部测试数据集中验证该模型的生存情况，同时进一步利用TCGA泛癌和免疫治疗数据集验证该模型的性能。
我们共获得78个干细胞样本，每个样本包含8087个mRNA基因的表达谱。基于mRNAsi，将THCA分为3个亚型。C2亚型预后最差，免疫评分最高，而C3亚型预后最好，mRNAsi最低，TIDE评分最高。C2亚型患者对顺铂、厄洛替尼、紫杉醇和拉帕替尼表现出更高的敏感性。使用5个与mRNAsi相关的基因生成预后特征，可预测THCA的预后。qRT-PCR结果显示，5个基因在Hth7和KTC-1细胞中的表达各不相同，抑制CELSR3表达可增加Hth7和KTC-1细胞的凋亡百分比。与mRNAsi相关的DNA甲基化位点主要富集在肿瘤相关途径中。该模型在测试数据集、泛癌和免疫治疗数据集中均验证了良好的性能。
本研究确定了三个用于分类的亚型，并开发了一个与mRNAsi相关基因的预后模型，为预后和免疫治疗预测提供了巨大潜力。
