Stem cell index-based RiskScore model for predicting prognosis in thyroid cancer and experimental verification

Abstract

ObjectiveAn 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. MethodsBased 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. ResultsWe 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. ConclusionThis study identified three subtypes for classification and developed a prognostic model with mRNAsi-related genes, which provided great potential for prognosis and immunotherapy prediction.