scholarly journals Integrated analysis on the N6‐methyladenosine‐related long noncoding RNAs prognostic signature, immune checkpoints, and immune cell infiltration in clear cell renal cell carcinoma

2021 ◽  
Author(s):  
Yuqin Qiu ◽  
Xiaogang Wang ◽  
Zhenjia Fan ◽  
Shanhui Zhan ◽  
Xin Jiang ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Renal Cell ◽  
Immune Cell ◽  
Clear Cell ◽  
Noncoding Rnas ◽  
Immune Checkpoints ◽  
Integrated Analysis ◽  
Immune Cell Infiltration ◽  
Prognostic Signature ◽  
Cell Renal Cell Carcinoma

scholarly journals The Correlation Between Novel Survival-related Alternative Splicing Signature and Prognostic Prediction and Immune Microenvironment in Clear Cell Renal Cell Carcinoma

2021 ◽  
Author(s):  
Wengang Jian ◽  
Gang Wang ◽  
Yipeng Yu ◽  
Licheng Cai ◽  
Yongchun Yu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Immune Cell ◽  
Risk Model ◽  
Clear Cell ◽  
Cell Infiltration ◽  
Immune Checkpoints ◽  
Splicing Factors ◽  
Immune Cell Infiltration ◽  
Immune Microenvironment ◽  
Cell Renal Cell Carcinoma

Abstract BackgroundAlthough extensive researches related alternative splicing (AS) as the prognostic markers of patients in cancers, which remains unknown in clear cell renal cell carcinoma (ccRCC), especially in immunotherapy. Therefore, a novel survival-associated AS signature was established to predict prognosis of patients and explored its correlation with immune cell infiltration or immune checkpoint expression to explain the phenomenon of resistance to immunotherapy in ccRCC.Methodsccording to AS data, clinical information and gene expression data in ccRCC, overall survival-related AS events was identified and further the AS-related prognostic risk model established by LASSO regression and multi-Cox regression analysis was evaluated by Kaplan-Meier survival analysis, the ROC curves and a nomogram model. Then we clarified the biological processes and pathways by GSEA, and further measured the immune cell infiltration by ESTIMATE, CIBERSORT and ssGSEA. Finally we analysed the clinical features and immune features of different parental genes, and quested the splicing factors regulating riskScore-related AS events by Spearman correlation analysis.ResultsWe obtained the most significant 5 AS events, including C4orf19|69001|AT, UACA|31438|AP, FAM120C|89237|AT, TRIM16L|39629|AP and SEC31A|100881|ES, to establish the prognostic risk model, and further illustrated the stability and importance of the riskScore prognostic signatures. Then we found that in high risk group, most of the top 10 GO enrichments and the KEGG pathway were closely related to the immunity, and the higher immune cell infiltration, and higher expression of classic immune checkpoints such as PD1 and CTLA4. In addition, 6 different parental genes were obtained, including C4orf19, ARHGAP24 DNASE1L3, P4HA1, SLC39A14 and TAF1D. These 6 genes could not be the independent prognostic signatures, but the expression of these genes was closely related to immune cells infiltration and the expression of immune checkpoints. Finally, we got aberrant 52 splicing factors regulating riskScore-related AS events.ConclusionOur study discovered that overall survival-related AS events mediated by aberrant splicing factors can be constructed a prognostic risk model to predict prognosis of patiens and utilized to index the situation of immune cell infiltration and immune checkpoint expression that impact tumor immune microenvironment in ccRCC.

scholarly journals PD49-08 CORRELATING IMMUNE CELL INFILTRATION PATTERNS WITH RECURRENT SOMATIC MUTATIONS IN CLEAR CELL RENAL CELL CARCINOMA

2021 ◽  
Vol 206 (Supplement 3) ◽  
Author(s):  
Nicholas Chakiryan ◽  
Ali Hajiran ◽  
Youngchul Kim ◽  
Jad Chahoud ◽  
Philippe Spiess ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Somatic Mutations ◽  
Immune Cell ◽  
Clear Cell ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Cell Renal Cell Carcinoma

scholarly journals Integrated Analysis to Identify a Redox-Related Prognostic Signature for Clear Cell Renal Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-35
Author(s):  
Yue Wu ◽  
Xian Wei ◽  
Huan Feng ◽  
Bintao Hu ◽  
Bo Liu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Molecular Mechanisms ◽  
Clear Cell ◽  
Risk Group ◽  
External Validation ◽  
Integrated Analysis ◽  
Prognostic Signature ◽  
Cell Renal Cell Carcinoma

The imbalance of the redox system has been shown to be closely related to the occurrence and progression of many cancers. However, the biological function and clinical significance of redox-related genes (RRGs) in clear cell renal cell carcinoma (ccRCC) are unclear. In our current study, we downloaded transcriptome data from The Cancer Genome Atlas (TCGA) database of ccRCC patients and identified the differential expression of RRGs in tumor and normal kidney tissues. Then, we identified a total of 344 differentially expressed RRGs, including 234 upregulated and 110 downregulated RRGs. Fourteen prognosis-related RRGs (ADAM8, CGN, EIF4EBP1, FOXM1, G6PC, HAMP, HTR2C, ITIH4, LTB4R, MMP3, PLG, PRKCG, SAA1, and VWF) were selected out, and a prognosis-related signature was constructed based on these RRGs. Survival analysis showed that overall survival was lower in the high-risk group than in the low-risk group. The area under the receiver operating characteristic curve of the risk score signature was 0.728 at three years and 0.759 at five years in the TCGA cohort and 0.804 at three years and 0.829 at five years in the E-MTAB-1980 cohort, showing good predictive performance. In addition, we explored the regulatory relationships of these RRGs with upstream miRNA, their biological functions and molecular mechanisms, and their relationship with immune cell infiltration. We also established a nomogram based on these prognostic RRGs and performed internal and external validation in the TCGA and E-MTAB-1980 cohorts, respectively, showing an accurate prediction of ccRCC prognosis. Moreover, a stratified analysis showed a significant correlation between the prognostic signature and ccRCC progression.

scholarly journals Association of CXCL13 and Immune Cell Infiltration Signature in Clear Cell Renal Cell Carcinoma

2020 ◽  
Vol 17 (11) ◽  
pp. 1610-1624 ◽  
Author(s):  
Fangdong Jiao ◽  
Hao Sun ◽  
Qingya Yang ◽  
Hui Sun ◽  
Zehua Wang ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Immune Cell ◽  
Clear Cell ◽  
Cell Infiltration ◽  
Immune Cell Infiltration ◽  
Cell Renal Cell Carcinoma
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