Cuproptosis-related lncRNAs predict prognosis and immune response of thyroid carcinoma

Frontiers in Genetics

Genetics

Pei Sheng¹  Yinli Shi¹  Kai Chen¹  Wenting Li²  Bo Li²  Hongguang Zhou²  Mianhua Wu²  Ming Guo³ 

[1] The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China;The First Clinical Medical College, Nanjing University of Chinese Medicine, Nanjing, China;Jiangsu Collaborative Innovation Center of Traditional Chinese Medicine Prevention and Treatment of Tumor, Nanjing University of Chinese Medicine, Nanjing, China;Zhongda Hospital Southeast University, Southeast University, Nanjing, China;

关键词: cuproptosis-related;    lncRNA;    thyroid carcinoma;    immune response;    machine learning;   

DOI  :  10.3389/fgene.2023.1100909

 received in 2022-11-17, accepted in 2023-06-26,  发布年份 2023

来源: Frontiers

【 摘 要 】

Objective: To estimate the survival and prognosis of patients with thyroid carcinoma (THCA) based on the Long non-coding RNA (lncRNA) traits linked to cuproptosis and to investigate the connection between the immunological spectrum of THCA and medication sensitivity.Methods: RNA-Seq data and clinical information for THCA were obtained from the Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases. We built a risk prognosis model by identifying and excluding lncRNAs associated with cuproptosis using Cox regression and LASSO methods. Both possible biological and immune infiltration functions were investigated using Principal Component Analysis (PCA), Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), and immunoassays. The sensitivity of the immune response to possible THCA medicines was assessed using ratings for tumor immune dysfunction and exclusion (TIDE) and tumor mutational burden (TMB).Results: Seven cuproptosis-related lncRNAs were used to construct our prognostic prediction model: AC108704.1, DIO3OS, AL157388.1, AL138767.3, STARD13-AS, AC008532.1, and PLBD1-AS1. Using data from TCGA’s training, testing, and all groups, Kaplan-Meier and ROC curves demonstrated this feature’s adequate predictive validity. Different clinical characteristics have varying effects on cuproptosis-related lncRNA risk models. Further analysis of immune cell infiltration and single sample Gene Set Enrichment Analysis (ssGSEA) supported the possibility that cuproptosis-associated lncRNAs and THCA tumor immunity were closely connected. Significantly, individuals with THCA showed a considerable decline in survival owing to the superposition effect of patients in the high-risk category and high TMB. Additionally, the low-risk group had a higher TIDE score compared with the high-risk group, indicating that these patients had suboptimal immune checkpoint blocking responses. To ensure the accuracy and reliability of our results, we further verified them using several GEO databases.Conclusion: The clinical and risk aspects of cuproptosis-related lncRNAs may aid in determining the prognosis of patients with THCA and improving therapeutic choices.

【 授权许可】

Unknown   
Copyright © 2023 Shi, Sheng, Guo, Chen, Zhou, Wu, Li and Li.