Comprehensive analysis of ceRNA networks to determine genes related to prognosis, overall survival, and immune infiltration in clear cell renal carcinoma

Abstract Background Clear cell renal cell carcinoma is susceptible to ferroptosis, and immunotherapy is recently recommended as a priority for the initial treatment of metastatic clear cell renal carcinoma. Increased ferroptosis and immune activation can synergistically reinforce each other in killing cancer cells. NCOA4 depletion can eliminate iron accumulation and thus weaken ferroptosis. Here, we aim to identify and validate the association between NCOA4 expression, clinicopathologic characteristics, and overall survival in ccRCC by using The Cancer Genome Atlas and Gene Expression Omnibus databases. We further analyze the interacted proteins of NCOA4 and infiltrated immune cells via TIMER and GEPIA databases. Methods NCOA4 expression in clear cell renal carcinoma (ccRCC) tissues and normal adjacent tissues in The Cancer Genome Atlas (TCGA) data were primarily screened, and further validated in another independent cohort from the gene expression omnibus (GEO) database and human protein atlas. The relationships of NCOA4 expression and clinicopathologic parameters and overall survival (OS) were assessed using multivariate methods and Kaplan-Meier survival curves. And the proteins network with which NCOA4 interacted were also built using the online STRING website. Meanwhile, we use TIMER and GEPIA databases to investigate the relationships between NCOA4 expression and infiltrated immune cells and their corresponding gene marker sets. Results Contrast to normal tissue, NCOA4 expression was lower in ccRCC tumor tissue(p < 0.05). Lower NCOA4 expression was closely associated with high-grade malignancy and advanced TNM stage. Univariate and multivariate analysis indicated the overall survival of ccRCC cases with low NCOA4 level is shorter than those of patients with high NCOA4 expression (p < 0.05). FTL and FTH1 were the important proteins interacting with NCOA4. ccRCC with NCOA4 deficiency presented the paucity of infiltrated immune cells and their matching marker sets, including CD8+ T cells. Conclusion Deficient NCOA4 expression was related to disease progression and poor prognosis, as well as impaired infiltration of immune cells in ccRCC.

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A Molecular Model for Predicting Overall Survival in Patients with Metastatic Clear Cell Renal Carcinoma: Results from CALGB 90206 (Alliance)

EBioMedicine ◽

10.1016/j.ebiom.2015.09.012 ◽

2015 ◽

Vol 2 (11) ◽

pp. 1814-1820 ◽

Cited By ~ 4

Author(s):

Hyung L. Kim ◽

Susan Halabi ◽

Ping Li ◽

Greg Mayhew ◽

Jeff Simko ◽

...

Keyword(s):

Overall Survival ◽

Renal Carcinoma ◽

Clear Cell ◽

Molecular Model ◽

Clear Cell Renal Carcinoma ◽

Cell Renal Carcinoma

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Comprehensive analysis of WGS and RNA-seq data to identify genetic variations in a patient with clear cell renal carcinoma

Molecular Genetics and Metabolism ◽

10.1016/s1096-7192(21)00160-8 ◽

2021 ◽

Vol 132 ◽

pp. S51

Author(s):

Sandhya Kiran Pemmasani ◽

Neelima Chitturi ◽

Anuradha Acharya

Keyword(s):

Renal Carcinoma ◽

Clear Cell ◽

Genetic Variations ◽

Comprehensive Analysis ◽

Rna Seq ◽

Clear Cell Renal Carcinoma ◽

Cell Renal Carcinoma

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MP44-01 A PROGNOSTIC MODEL FOR OVERALL SURVIVAL IN PATIENTS WITH METASTATIC CLEAR CELL RENAL CARCINOMA: RESULTS FROM CALGB 90206 (ALLIANCE)

The Journal of Urology ◽

10.1016/j.juro.2015.02.1543 ◽

2015 ◽

Vol 193 (4S) ◽

Cited By ~ 1

Author(s):

Hyung Kim ◽

Susan Halabi ◽

Ping Li ◽

Greg Mayhew ◽

Jeff Simko ◽

...

Keyword(s):

Overall Survival ◽

Prognostic Model ◽

Renal Carcinoma ◽

Clear Cell ◽

Clear Cell Renal Carcinoma ◽

Cell Renal Carcinoma

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PANK1 is a Prognostic Biomarker Associated with Immune Infiltration of Clear Cell Renal Carcinoma

10.21203/rs.3.rs-957747/v1 ◽

2021 ◽

Author(s):

Baishun Ma ◽

Pu Wang

Keyword(s):

Roc Curve ◽

Renal Carcinoma ◽

Clear Cell ◽

Prognostic Biomarker ◽

Gene Set Enrichment Analysis ◽

Coagulation Cascade ◽

Clear Cell Renal Carcinoma ◽

Immune Infiltration ◽

Cell Renal Carcinoma ◽

The Relationship

Abstract Background: PANK1 is expressed in some cancer types, but its role in clear cell renal carcinoma (ccRCC) is unclear. We aimed to demonstrate the relationship between PANK1 and ccRCC based on a cancer genomic atlas (TCGA) database.Methods: The Kruskal-Wallis test, Wilcoxon signed rank test and logistic regression were used to analyze the relationship between the clinical pathological characteristics of ccRCC and the expression of PANK1. The ROC curve was used to describe the prognostic value of PANK1 using area under curve (AUC) scores. Kaplan-Meier method and Cox regression analysis were used to evaluate the factors affecting the prognosis of ccRCC. Gene set enrichment analysis (GSEA) and immuno-infiltration analysis were performed to identify a significantly related function of PANK1.Results: PANK1 expression in renal clear cell carcinoma was different from that in stage N (P=1.3E-03),sex (P=5.1E-07),stage M(P=8.3E-04),residual tumor(P<0.001),T stage(T1 vsT4(P=6.5E-03),T1vsT3(P=6.9E-06)), histological grade (G1vsG4(P=3.6E-0.5),G2vsG4(P=2.1E-10),G3vsG4(P=1.7E-05)),pathologic stage(STAGE 1vs.STAGE4(P=1.4E-05),STAGE1vs.STAGE3(P=7.1E-05)). The ROC curve suggest that PANK1 has significant diagnostic and prognostic capabilities (AUC =0.898). Low expression of PANK1 predicted poor overall survival (OS) (P<0.001), while that of PANK1 (HR:0.398; 95% CI:0.248-0.639； P<0.001) is OS-independent predictor in patients with ccRCC. GSEA and immune infiltration analysis showed that the expression of PANK1 is related to extracellular matrix receptor pathway, signaling pathway related to hypertrophic cardiomyopathy, cytokine-cytokine receptor interaction pathway, as well as complement and coagulation cascade pathway.Conclusion: PANK1 expression is significantly associated with poor survival and immune infiltration of ccRCC, which may be a promising prognostic biomarker for ccRCC.

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