scholarly journals Abnormal methylation status of FBXW10 and SMPD3, and associations with clinical characteristics in clear cell renal cell carcinoma

2015 ◽  
Vol 10 (5) ◽  
pp. 3073-3080 ◽  
Author(s):  
JINYOU WANG ◽  
JIAN LI ◽  
JUN GU ◽  
JIAN YU ◽  
SHICHENG GUO ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clinical Characteristics ◽  
Clear Cell ◽  
Methylation Status ◽  
Cell Renal Cell Carcinoma

scholarly journals Identification of Prognostic Metabolism-Related Genes in Clear Cell Renal Cell Carcinoma

2021 ◽  
Vol 2021 ◽  
pp. 1-13
Author(s):  
Yusa Chen ◽  
Yumei Liang ◽  
Ying Chen ◽  
Shaxi Ouyang ◽  
Kanghan Liu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Random Forest ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Renal Cell ◽  
Multivariate Regression ◽  
Clinical Characteristics ◽  
Clear Cell ◽  
Cell Renal Cell Carcinoma ◽  
Immune Infiltration

Background. Clear cell renal cell carcinoma (ccRCC) is a cancer with abnormal metabolism. The purpose of this study was to investigate the effect of metabolism-related genes on the prognosis of ccRCC patients. Methods. The data of ccRCC patients were downloaded from the TCGA and the GEO databases and clustered using the nonnegative matrix factorization method. The limma software package was used to analyze differences in gene expression. A random forest model was used to screen for important genes. A novel Riskscore model was established using multivariate regression. The model was evaluated based on the metabolic pathway, immune infiltration, immune checkpoint, and clinical characteristics. Results. According to metabolism-related genes, kidney clear cell carcinoma (KIRC) datasets downloaded from TCGA were clustered into two groups and showed significant differences in prognosis and immune infiltration. There were 667 differentially expressed genes between the two clusters, of which 408 were screened by univariate analysis. Finally, 12 differentially expressed genes (MDK, SLC1A1, SGCB, C4orf3, MALAT1, PILRB, IGHG1, FZD1, IFITM1, MUC20, KRT80, and SALL1) were filtered out using the random forest model. The model of Riskscore was obtained by multiplying the expression levels of these 12 genes with the corresponding coefficients of the multivariate regression. We found that the Riskscore correlated with the expression of these 12 genes; the high Riskscore matched the low survival rate verified in the verification set. The analysis found that the Riskscore model was associated with most of the metabolic processes, immune infiltration of cells such as plasma cells, immune checkpoints such as PD-1, and clinical characteristics such as M stage. Conclusion. We established a new Riskscore model for the prognosis of ccRCC based on metabolism. The genes in the model provided several novel targets for the study of ccRCC.

Epigenetic inactivation of HOXA5 and MSH2 gene in clear cell renal cell carcinoma.

2012 ◽  
Vol 30 (5_suppl) ◽  
pp. 424-424
Author(s):  
Seung-Kwon Choi ◽  
Joong Geun Lee ◽  
Koo Han Yoo
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Survival Curve ◽  
Methylation Status ◽  
Clinicopathological Parameters ◽  
Cell Renal Cell Carcinoma ◽  
Value Differences ◽  
Normal Tissues

424 Background: The high-throughput method using microarray is easy and fast way to analyze the methylation status of hundreds of preselected genes and to screen them for signatures in methylation. The aim of our study is to detect hypermethylated genes and to analyze the association between methylation status and clinicopathological parameters of clear cell renal cell carcinoma. Methods: The genetic substrate included 62 cancer tissues and 62 matched adjacent normal kidney tissues. We adapted the GoldenGate genotyping assay to determine the methylation state of 1505 specific CpG sites in 807 genes. Results: We identified two genes (HOXA5 and MSH2) with β-value differences of more than 0.3 between cancer and normal tissues. High methylation group in HOXA5 had high Fuhrman’s nuclear grade (P=0.041). Other data in HOXA5 and MSH2 were not significant with methylation status (P>0.05). Survival curve of high methylation group in HOXA5 was slightly lower than that of low methylation group. However, the statistical significances of overall survival in HOXA5 and MSH2 were low (P>0.05). Conclusions: We report the hypermethylation of two genes in clear cell renal cell carcinoma. The data we obtained could provide the basis for a diagnostic test pathological assessment, or prognosis in clear cell renal cell carcinoma.

DNA methylation status defines clinicopathological parameters including survival for patients with clear cell renal cell carcinoma (ccRCC)

Tumor Biology ◽  
2016 ◽  
Vol 37 (8) ◽  
pp. 10219-10228 ◽  
Author(s):  
Emma Andersson Evelönn ◽  
Sofie Degerman ◽  
Linda Köhn ◽  
Mattias Landfors ◽  
Börje Ljungberg ◽  
...  
Keyword(s):  
Dna Methylation ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Methylation Status ◽  
Clinicopathological Parameters ◽  
Cell Renal Cell Carcinoma

scholarly journals Analyzing and validating the prognostic value and immune microenvironment of clear cell renal cell carcinoma

2021 ◽  
Author(s):  
Jingwei Ke ◽  
Jie Chen ◽  
Xin Liu
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clinical Characteristics ◽  
Cox Regression ◽  
Clear Cell ◽  
Gene Set Enrichment Analysis ◽  
Hub Genes ◽  
Cell Renal Cell Carcinoma ◽  
Significant Difference

Abstract Background: There is still controversy regarding immunotherapy biomarkers. Therefore, we aimed to identify prognostic biomarkers related to immunotherapy for clear cell renal cell carcinoma (ccRCC).Methods: Fragments Per Kilobase Million (FPKM) data and clinical characteristics for ccRCC patients from The Cancer Genome Atlas (TCGA) database were downloaded. Unsupervised consensus clustering analysis was performed to divide patients into different immune subgroups according to their single-sample gene set enrichment analysis (ssGSEA) scores. Then, we validated the differences in immune cell infiltration, prognosis, clinical characteristics and expression levels of HLA and immune checkpoint genes between different immune subgroups. Weighted gene coexpression network analysis (WGCNA) was used to identify the significant modules and hub genes that were related to the immune subgroups. A nomogram was established to predict the overall survival (OS) outcomes after independent prognostic factors were identified by least absolute shrinkage and selection operator (LASSO) regression and multivariate Cox regression analyses.Results: Five clusters (immune subgroups) were identified. There was no significant difference in age, sex or N stage. And there were significant differences in race, T stage, M stage, grade, prognosis and tumor microenvironment. HLA gene families and CTLA4 showed significant differences between the five clusters, while PD1 and PDL1 did not. The red module was significant, and 14 hub genes were obtained. In addition, the nomogram containing LAG3 and GZMK accurately predicted OS outcomes of ccRCC patients.Conclusion: LAG3 and GZMK are strongly related to immunity and may provide suggestions for ccRCC immunotherapy.

scholarly journals Genetic and epigenetic alterations of VHL gene in clear cell renal cell carcinoma

2019 ◽  
Vol 24 ◽  
pp. 221-226
Author(s):  
K. V. Onyshchenko ◽  
V. M. Grygorenko ◽  
L. V. Pereta ◽  
Yu. R. Serbai ◽  
T. V. Voitsitskyi ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Loss Of Heterozygosity ◽  
Renal Cell ◽  
Clear Cell ◽  
Malignant Tumors ◽  
Polymorphic Information Content ◽  
Methylation Status ◽  
Cell Renal Cell Carcinoma ◽  
Vhl Gene

Aim. Renal cell carcinomas (RCC) – cancerous neoplasms of the genitourinary system representing about 3% of human malignant tumors. For malignancy degree indexing and tumor typing, shape of cell nucleus is widely used. However, genetic changes, in particular inactivation of von Hippel-Lindau (VHL) gene can serve as indicators of RCC progression. Thus, the purpose of our study was establishing the methylation status and loss of heterozygosity of the VHL gene as a potential and applicable clinical marker of kidney tumors. Methods. Determination of allelic imbalance in VHL gene expression was performed by PCR of STR-markers with subsequent fragments separation in 8% PAAG and by capillary gel electrophoresis of fluorescent-labeled PCR fragments. Methyl-specific PCR was used for epigenetic variability of VHL gene promoter. To detect statistically significant differences between tumor specimens and adjacent kidney tissues, Fisher's exact test and Mann-Whitney U-criterion were applied. Results. In 57% of the tumor samples for the marker D3S1038 and 48% for the D3S1317 loss of heterozygosity of the VHL gene was detected. Polymorphic information content for these loci was 84% for D3S1038 and 90% for D3S1317. The VHL promoter hypermethylation was 77%. Conclusions. The obtained results indicate that VHL gene can be reviewed as a candidate for not only diagnostic, but also prognostic application in RCC cancer. Keywords: clear cell renal cell carcinoma, epigenetic changes, methylation, loss of heterozygosity, VHL.

638: Macroscopic Tumor Necrosis is a Prognostic Indicator for Non-Metastatic Clear Cell Renal Cell Carcinoma

2007 ◽  
Vol 177 (4S) ◽  
pp. 214-214
Author(s):  
Sung Kyu Hong ◽  
Byung Kyu Han ◽  
In Ho Chang ◽  
June Hyun Han ◽  
Ji Hyung Yu ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Tumor Necrosis ◽  
Clear Cell ◽  
Prognostic Indicator ◽  
Cell Renal Cell Carcinoma ◽  
Macroscopic Tumor

Rare localization of renal cell carcinoma metastases in the paranasal sinuses and breast: a case report

2019 ◽  
Vol 22 (6) ◽  
pp. 13-22
Author(s):  
E. V. Kryaneva ◽  
N. A. Rubtsova ◽  
A. V. Levshakova ◽  
A. I. Khalimon ◽  
A. V. Leontyev ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Paranasal Sinuses ◽  
Renal Cell ◽  
Clinical Case ◽  
Clear Cell ◽  
Malignant Tumors ◽  
Metastatic Potential ◽  
Cell Renal Cell Carcinoma ◽  
Metastatic Lesions

This article presents a clinical case demonsratinga high metastatic potential of clear cell renal cell carcinoma combined with atypical metastases to breast and paranasal sinuses. The prevalence of metastatic lesions to the breast and paranasal sinuses in various malignant tumors depending on their morphological forms is analyzed. The authors present an analysis of data published for the last 30 years. The optimal diagnostic algorithms to detect the progression of renal cell carcinoma and to evaluate the effectiveness of the treatment are considered.

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