Identification and validation of a novel ferroptosis-related 11-lncRNA prognostic signature related to immune infiltration and drug sensitivity in ccRCC
Authors: Hu Xing , Liu Yujie , Hu Liang , Liang Xuemei , Zhang Zhihong 
Published: April 2022

Abstract
Background. Abnormal expressions of long noncoding RNAs (lncRNAs) are very common in clear cell renal cell carcinoma (ccRCC), and some of these have been reported to be highly correlated with the prognosis of ccRCC patients. This study aimed to evaluate and test the role of the lncRNA signature associated with ferroptosis as a prognostic tool for ccRCC and to evaluate their predictive value for immune infiltration and chemotherapeutic drug sensitivity. Methods. LncRNA expression profiles were downloaded from The Cancer Genome Atlas (TCGA) database. Differentially expressed lncRNAs (DELs) between ccRCC tumor tissues and normal tissues were analyzed using the R package limma. We further applied single sample gene set enrichment analysis (ssGSEA) to generate ferroptosis activity scores for ccRCC patients. The correlation between lncRNA and ferroptosis score was analyzed using R packages plyr, tidyr and dplyr. A ferroptosis-related lncRNAs signature was constructed with univariate and multivariate cox regression analyses in the training cohort, and its prognostic value was further tested in the validation cohort. To further explore the relationship between ferroptosis-related lncRNAs signature and tumor immune infiltration, we performed ImmuCellAI and spearman correlation analysis. Chemotherapy drug sensitivity was predicted by R package pRRophetic. Finally, construction and validation of the ceRNA network based on the ferroptosis-related 11-lncRNA signature. Results. The results of Kaplan-Meier survival analysis indicated that the patients with higher ferroptosis ssGSEA scores had a shorter survival period than those with lower ferroptosis ssGSEA scores. By overlapping the 153 DELs and 260 ferroptosis-related lncRNAs, we obtained 16 up-regulated lncRNAs positively correlated with ferroptosis and 16 down-regulated lncRNAs negatively correlated ferroptosis. A 11 ferroptosis-related prognostic DELs signature was established by cox proportional hazards regression model combined with Kaplan-Meier survival analysis and could predict the overall survival of ccRCC. ImmuCellAI and spearman correlation analysis showed that ferroptosis-related lncRNAs signature were closely associated with immune infiltration in ccRCC. Further research found that 3 risk lncRNAs (LINC01871, PRKAR1B-AS1 and CYTOR) were the key ferroptosis-related lncRNAs in the regulation of tumor immune infiltration. High-risk patients were found to be more sensitive to several chemotherapeutic agents, including methotrexate, paclitaxel, cisplatin, and doxorubicin. Meanwhile, we identified 3 lncRNAs, 15 miRNAs and 15 mRNAs to construct a lncRNA-miRNA-mRNA ceRNA network. Lastly, qRT-PCR validated the differential expression of 3 lncRNAs. Conclusion. A novel prognostic signature, which was established according to ferroptosis-related 11-lncRNA through genome-wide expression spectrum, could effectively identify samples with poor prognosis, enhanced immune infiltration and different sensitivities to chemotherapeutic drugs.