scholarly journals Genome-wide Analysis of the Alternative Splicing Profiles Revealed Novel Prognostic Index for Kidney Renal Cell Clear Cell Carcinoma

2020 ◽  
Vol 11 (6) ◽  
pp. 1542-1554
Author(s):  
Li Gao ◽  
Rong-quan He ◽  
Zhi-guang Huang ◽  
Yi-wu Dang ◽  
Yong-yao Gu ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Prognostic Index ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Integrative Genome-wide Analysis of the Determinants of RNA Splicing in Kidney Renal Clear Cell Carcinoma

2014 ◽  
Author(s):  
Kjong-Van Lehmann ◽  
Andre Kahles ◽  
Cyriac Kandoth ◽  
William Lee ◽  
Nikolaus Schultz ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Cell Carcinoma ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Renal Clear Cell Carcinoma ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
A Genome ◽  
Alternative Splicing Events ◽  
Splicing Patterns

We present a genome-wide analysis of splicing patterns of 282 kidney renal clear cell carcinoma patients in which we integrate data from whole-exome sequencing of tumor and normal samples, RNA-seq and copy number variation. We proposed a scoring mechanism to compare splicing pat- terns in tumor samples to normal samples in order to rank and detect tumor-specific isoforms that have a potential for new biomarkers. We identified a subset of genes that show introns only observable in tumor but not in normal samples, ENCODE and GEUVADIS samples. In order to improve our understanding of the underlying genetic mechanisms of splicing variation we performed a large-scale association analysis to find links between somatic or germline variants with alternative splicing events. We identified 915 cis- and trans-splicing quantitative trait loci (sQTL) associated with changes in splicing patterns. Some of these sQTL have previously been associated with being susceptibility loci for cancer and other diseases. Our analysis also allowed us to identify the function of several COSMIC variants showing significant association with changes in alternative splicing. This demonstrates the potential significance of variants affecting alternative splicing events and yields insights into the mechanisms related to an array of disease phenotypes.

scholarly journals INTEGRATIVE GENOME-WIDE ANALYSIS OF THE DETERMINANTS OF RNA SPLICING IN KIDNEY RENAL CLEAR CELL CARCINOMA

2014 ◽  
Author(s):  
KJONG-VAN LEHMANN ◽  
ANDRÉ KAHLES ◽  
CYRIAC KANDOTH ◽  
WILLIAM LEE ◽  
NIKOLAUS SCHULTZ ◽  
...  
Keyword(s):  
Cell Carcinoma ◽  
Rna Splicing ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Renal Clear Cell Carcinoma ◽  
Genome Wide Analysis ◽  
Genome Wide

scholarly journals Genome-Wide Analysis of Differentially Expressed Genes and Splicing Isoforms in Clear Cell Renal Cell Carcinoma

PLoS ONE ◽  
2013 ◽  
Vol 8 (10) ◽  
pp. e78452 ◽  
Author(s):  
Alessio Valletti ◽  
Margherita Gigante ◽  
Orazio Palumbo ◽  
Massimo Carella ◽  
Chiara Divella ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Differentially Expressed Genes ◽  
Renal Cell ◽  
Clear Cell ◽  
Differentially Expressed ◽  
Cell Renal Cell Carcinoma ◽  
Genome Wide Analysis ◽  
Genome Wide ◽  
Splicing Isoforms

Sarcomatoid Renal Cell Carcinoma of Papillary Origin

2000 ◽  
Vol 124 (12) ◽  
pp. 1830-1832 ◽  
Author(s):  
Ronald J. Cohen ◽  
John E. McNeal ◽  
Marleen Susman ◽  
Loryn N. Sellner ◽  
Barry J. Iacopetta ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Conclusive Evidence ◽  
Clear Cell Tumor ◽  
Multiple Copies ◽  
Sarcomatoid Renal Cell Carcinoma ◽  
Trisomy 7

Abstract Sarcomatoid renal cell carcinoma (SRCC) is an aggressive tumor variant thought to arise predominantly from dedifferentiation of clear cell carcinoma. A few reports of SRCC associated with non–clear cell tumors led to the presumption that SRCC may arise from any renal cell carcinoma, although direct evidence of this is lacking. Cytogenetic studies on 3 previously documented SRCCs associated with papillary renal cancers showed either 3p deletions or absence of trisomy 7, 17 in the sarcomatoid tumors, suggesting origin from a coexistent clear cell tumor. The present case represents the first conclusive evidence of direct progression of non–clear cell carcinoma to SRCC with both tumor components containing multiple copies of chromosomes 7 and 17. Many genetic anomalies, including p53 mutations, frequently recognized in SRCC were not recognized in this case, highlighting the importance of cytogenetic evaluation of all SRCC. The patient is well and without evidence of tumor progression 1 year after surgery, and the sinister outlook of SRCC in association with clear cell carcinoma may not apply in SRCC of non–clear cell origin.

scholarly journals Unusual presentation of renal cell carcinoma: A rare case report

2018 ◽  
Vol 10 (02) ◽  
pp. 241-244 ◽  
Author(s):  
Manjari Kishore ◽  
Devender Singh Chauhan ◽  
Shruti Dogra
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Upper Lip ◽  
Rare Case Report ◽  
Aggressive Tumor ◽  
Oral Tumors ◽  
Metastatic Rcc

AbstractCutaneous and intraoral metastasis from any malignancy is not common. Cutaneous spread is usually noted in 5%–10% of high-grade malignancies, as in carcinoma breast, lung, colon, ovary, and malignant melanoma. Only 4.6% cases of cutaneous spread are from renal cell carcinoma (RCC). Intraoral spread from RCC is much rarer with an incidence of approximately 1% of all malignant oral tumors, noted sometimes in tongue, palate, buccal mucosa, gingiva, and lips. RCC is a highly aggressive tumor which requires early diagnosis for increasing the chance of cure. In our case, a 54-year-old male presented with swelling over upper lip, scalp, and retromolar area, which on histopathology and immunohistochemistry revealed clear cell carcinoma compatible with metastatic RCC.

scholarly journals LRRC19—A Bridge between Selenium Adjuvant Therapy and Renal Clear Cell Carcinoma: A Study Based on Datamining

Genes ◽  
2020 ◽  
Vol 11 (4) ◽  
pp. 440
Author(s):  
Yitong Zhang ◽  
Jiaxing Wang ◽  
Xiqing Liu
Keyword(s):  
Gene Expression ◽  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Independent Risk Factor ◽  
Clear Cell ◽  
Clear Cell Carcinoma ◽  
Renal Clear Cell Carcinoma ◽  
Cell Renal Cell Carcinoma ◽  
Low Expression

Kidney renal clear cell carcinoma (KIRC) is the most common and fatal subtype of renal cancer. Antagonistic associations between selenium and cancer have been reported in previous studies. Selenium compounds, as anti-cancer agents, have been reported and approved for clinical trials. The main active form of selenium in selenoproteins is selenocysteine (Sec). The process of Sec biosynthesis and incorporation into selenoproteins plays a significant role in biological processes, including anti-carcinogenesis. However, a comprehensive selenoprotein mRNA analysis in KIRC remains absent. In the present study, we examined all 25 selenoproteins and identified key selenoproteins, glutathione peroxidase 3 (GPX3) and type 1 iodothyronine deiodinase (DIO1), with the associated prognostic biomarker leucine-rich repeat containing 19 (LRRC19) in clear cell renal cell carcinoma cases from The Cancer Genome Atlas (TCGA) database. We performed validations for the key gene expression levels by two individual clear cell renal cell carcinoma cohorts, GSE781 and GSE6344, datasets from the Gene Expression Omnibus (GEO) database. Multivariate survival analysis demonstrated that low expression of LRRC19 was an independent risk factor for OS. Gene set enrichment analysis (GSEA) identified tyrosine metabolism, metabolic pathways, peroxisome, and fatty acid degradation as differentially enriched with the high LRRC19 expression in KIRC cases, which are involved in selenium therapy of clear cell renal cell carcinoma. In conclusion, low expression of LRRC19 was identified as an independent risk factor, which will advance our understanding concerning the selenium adjuvant therapy of clear cell renal cell carcinoma.

Association of genome-wide copy number alterations with metastasis of clear cell renal cell carcinoma.

2015 ◽  
Vol 33 (7_suppl) ◽  
pp. 428-428
Author(s):  
Banumathy Gowrishankar ◽  
Venkata Jaganmohan Thodima ◽  
Ana M. Molina ◽  
Charles Ma ◽  
Asha Guttapalli ◽  
...  
Keyword(s):  
Renal Cell Carcinoma ◽  
Cell Carcinoma ◽  
Renal Cell ◽  
Copy Number ◽  
Clear Cell ◽  
Rank Statistic ◽  
Copy Number Alterations ◽  
Cell Renal Cell Carcinoma ◽  
Metastatic Lesions ◽  
Genome Wide

428 Background: About one-third of patients with clear cell renal cell carcinoma (ccRCC) exhibit metastasis at the time of diagnosis and show poor prognosis. The genetic and epigenetic alterations associated with metastasis in ccRCC have variably been studied, and their role in the metastatic process is unclear. The goals of the current study were to identify genomic copy number alterations (CNAs) associated with ccRCC metastasis and examine their clinical utility. Methods: In this IRB-approved study, genome-wide copy number profiling was performed on DNA from 144 ccRCC (81 primary and 63 metastatic lesions). Differential CNAs between primary and metastatic lesions and between different metastatic sites were identified using Fisher’s exact test. Associations between CNAs and overall survival (OS) were tested using the log rank statistic and Kaplan-Meier method. Genomic profiling data of 437 and 240 primary ccRCC (TCGA and PMID: 23797736, respecitively) were used for verification. Results: Between primary and metastatic lesions, 25 CNAs were significantly different (p<0.05). Of the 11 more frequent in metastatic lesions, nine retained significance when comparing stage IV and stage I TCGA ccRCC. For 368 TCGA locally-invasive tumors (stages I, II, and III), three CNAs (loss of 9p24.3-p13.3, 9p12-q11, and 9q21.12-q21.33) were associated with inferior survival (p=0.002). In the second dataset of 214 locally-invasive lesions, loss of 18q11.2-q23 correlated with shorter OS (p=0.025). Across metastatic lesions, nine CNAs were found to be significantly enriched in lung lesions and three in bone. In a subset of 127 ccRCC with known metastatic status at 5 years after diagnosis, two of these CNAs (gain of 7q36.1-36.3 in lung and loss of 22q13.2 in bone) were significantly enriched in the corresponding primary specimens. Conclusions: This study identified CNAs associated with ccRCC metastasis and common sites of metastasis that have the potential to serve as biomarkers to assist in better risk stratification of patients with this disease. Integrated analyses of genes mapping to the loci of genomic imbalance would further our understanding of the biology of metastasis in renal cancer.

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