Mining TCGA database for screening and identification of hub genes in kidney renal clear cell carcinoma microenvironment

2019 ◽  
Vol 121 (8-9) ◽  
pp. 3952-3960 ◽  
Author(s):  
Song Li ◽  
Weibo Xu
Keyword(s):  
Cell Carcinoma ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Renal Clear Cell Carcinoma ◽  
Hub Genes ◽  
Screening And Identification

scholarly journals Identification of Potential Biomarkers For The Prognosis, Diagnosis, And Targeted Therapy in Kidney Renal Clear Cell Carcinoma

2021 ◽  
Author(s):  
Fang Cheng ◽  
Qiang Li ◽  
Jinglin Wang ◽  
Yumei Wang ◽  
Zhendi Wang ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Signaling Pathway ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Expression Profiles ◽  
Prognostic Significance ◽  
Reduction Process ◽  
Renal Clear Cell Carcinoma ◽  
Biological Functions ◽  
Hub Genes

Abstract Background: Kidney renal clear cell carcinoma (KIRC) is the most common renal cell carcinoma types. This work aims to find potential diagnostic biomarkers and explore the biological functions related to the prognosis of KIRC. Method: First, Gene expression profiles of GSE15641, GSE72304, GSE71963, GSE53757, and GSE36895 from GEO database. Differentially expressed genes (DEGs) were identified by the limma package in R software. Next, gene ontology (GO) and Kyoto Encyclopedia of Gene and Genome (KEGG) pathway analysis were performed. Then protein-protein interaction (PPI) and hub genes were visualized by Cytoscape with STRING database. Then, we evaluate the predictive potential of hub genes expressions in KIRC with TCGA data. In addition, the relevant biological functions were identified using GSEA. Finally, we examined the differences of hub genes expression between multiple tumor tissues and normal tissues.Results: A total of 141 DEGs (including 99 upregulated and 42 downregulated genes) were identified. GO analysis indicated that DEGs were mainly involved in oxidation-reduction process and response to hypoxia. The KEGG analysis primarily related to PPAR signaling pathway, and HIF-1 signaling pathway. Moreover, the PPI analysis revealed 5 hub genes (AOX1, ALDH6A1, ABAT, HADH, and PCCA). The 5 hub genes were significantly correlated with KIRC progression and might have prognostic significance for KIPC patients. And low expression of the hub genes associated biological pathways were enriched in the NF-KB activation, focal adhesion, and JAK-STAT signaling pathway, respectively. Conclusion: Our study demonstrated that AOX1, ALDH6A1, ABAT, HADH, and PCCA can be used as prognostic biomarkers for KIRC.

Delayed Pancreatic Metastasis of Renal Clear Cell Carcinoma

2013 ◽  
Vol 13 (2) ◽  
pp. 79-80
Author(s):  
Zane Simtniece ◽  
Gatis Kirsakmens ◽  
Ilze Strumfa ◽  
Andrejs Vanags ◽  
Maris Pavars ◽  
...  
Keyword(s):  
Abdominal Pain ◽  
Surgical Treatment ◽  
Cell Carcinoma ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Primary Tumour ◽  
Renal Clear Cell Carcinoma ◽  
Pancreatic Metastasis ◽  
Distal Pancreatic Resection

Abstract Here, we report surgical treatment of a patient presenting with pancreatic metastasis (MTS) of renal clear cell carcinoma (RCC) 11 years after nephrectomy. RCC is one of few cancers that metastasise in pancreas. Jaundice, abdominal pain or gastrointestinal bleeding can develop; however, asymptomatic MTS can be discovered by follow-up after removal of the primary tumour. The patient, 67-year-old female was radiologically diagnosed with a clinically silent mass in the pancreatic body and underwent distal pancreatic resection. The postoperative period was smooth. Four months after the surgery, there were no signs of disease progression.

scholarly journals LncRNA CDKN2B-AS1 stabilized by IGF2BP3 drives the malignancy of renal clear cell carcinoma through epigenetically activating NUF2 transcription

2021 ◽  
Vol 12 (2) ◽  
Author(s):  
Xina Xie ◽  
Jiatian Lin ◽  
Xiaoqin Fan ◽  
Yuantang Zhong ◽  
Yequn Chen ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Survival Data ◽  
Kinase Inhibitor ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Binding Protein ◽  
Renal Clear Cell Carcinoma ◽  
Receiver Operating Curve ◽  
Migration And Invasion ◽  
Integrated Analysis

AbstractBecause of the lack of sensitivity to radiotherapy and chemotherapy, therapeutic options for renal clear cell carcinoma (KIRC) are scarce. Long noncoding RNAs (lncRNAs) play crucial roles in the progression of cancer. However, their functional roles and upstream mechanisms in KIRC remain largely unknown. Exploring the functions of potential essential lncRNAs may lead to the discovery of novel targets for the diagnosis and treatment of KIRC. Here, according to the integrated analysis of RNA sequencing and survival data in TCGA-KIRC datasets, cyclin-dependent kinase inhibitor 2B antisense lncRNA (CDKN2B-AS1) was discovered to be the most upregulated among the 14 lncRNAs that were significantly overexpressed in KIRC and related to shorter survival. Functionally, CDKN2B-AS1 depletion suppressed cell proliferation, migration, and invasion both in vitro and in vivo. Mechanistically, CDKN2B-AS1 exerted its oncogenic activity by recruiting the CREB-binding protein and SET and MYND domain-containing 3 epigenetic-modifying complex to the promoter region of Ndc80 kinetochore complex component (NUF2), where it epigenetically activated NUF2 transcription by augmenting local H3K27ac and H3K4me3 modifications. Moreover, we also showed that CDKN2B-AS1 interacted with and was stabilized by insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3), an oncofetal protein showing increased levels in KIRC. The Kaplan–Meier method and receiver operating curve analysis revealed that patients whose IGF2BP3, CDKN2B-AS1 and NUF2 are all elevated showed the shortest survival time, and the combined panel (containing IGF2BP3, CDKN2B-AS1, and NUF2) possessed the highest accuracy in discriminating high-risk from low-risk KIRC patients. Thus, we conclude that the stabilization of CDKN2B-AS1 by IGF2BP3 drives the malignancy of KIRC through epigenetically activating NUF2 transcription and that the IGF2BP3/CDKN2B-AS1/NUF2 axis may be an ideal prognostic and diagnostic biomarker and therapeutic target for KIRC.

scholarly journals Prognostic Impact of MITD1 and Associates With Immune Infiltration in Kidney Renal Clear Cell Carcinoma

2021 ◽  
Vol 20 ◽  
pp. 153303382110362
Author(s):  
Chujie Chen ◽  
Yiyu Sheng
Keyword(s):  
Cell Carcinoma ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Disease Free Survival ◽  
Renal Clear Cell Carcinoma ◽  
Functional Enrichment ◽  
Prognostic Impact ◽  
Clinical Value ◽  
Immune Infiltration ◽  
Potential Biomarker

Kidney renal clear cell carcinoma (KIRC) is one of the most malignant diseases with poor survival rate over the world. The tumor microenvironment (TME) is highly related to the oncogenesis, development, and prognosis of KIRC. Thus, making the identification of KIRC biomarkers and immune infiltrates critically important. Microtubule Interacting and Trafficking Domain containing 1(MITD1) was reported to participate in cytokinesis of cell division. In the present study, multiple bioinformatics tools and databases were applied to investigate the expression level and clinical value of MITD1 in KIRC. We found that the expression of MITD1 was significantly increased in KIRC tissues. Further, the KIRC patients with high MITD1 levels showed a worse overall survival (OS) rate and disease free survival (DFS) rate. Otherwise, we found a significant correlation MITD1 expression and the abundance of CD8+ T cells. Functional enrichment analyses revealed that immune response and cytokine-cytokine receptor are very critical signaling pathways which associated with MITD1 in KIRC. In conclusion, our findings indicated that MITD1 may be a potential biomarker and associated with immune infiltration in KIRC.

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