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Genomic characterization of clear cell renal cell carcinoma using targeted gene sequencing.

ABSTRACT: Kidney cancer is one of the most lethal cancer types worldwide. The most common subtype of kidney cancer is clear cell renal cell carcinoma (ccRCC), and the somatic mutations of ccRCC have been identified through the development of large databases. The present study aimed to validate the status of the associated gene mutations in a Taiwanese cohort. Targeted sequencing was used to validate the mutation status of genes related to ccRCC in Taiwanese patients who had nephrectomy for kidney cancer. The top eight mutated genes in the Catalogue Of Somatic Mutations In Cancer (COSMIC) were selected. These genes were VHL, protein polybromo-1 (PBRM1), histone-lysine N-methyltransferase SETD2, BRCA1-associated protein-1 (BAP1), lysine-specific demethylase 5C (KDM5C), TP53, MTOR and PTEN. The association between the gene mutation status of VHL, PBRM1, SETD2 and BAP1 was validated with clinicopathological parameters as well as overall survival time. Tumor cells from 96 patients with ccRCC were target sequenced. The order of mutation rate of the eight aforementioned genes was similar to that reported within COSMIC. The present Taiwanese cohort exhibited lower PBRM1 and BAP1 mutation rates compared with average, with increased mutation rates for SETD2 and KDM5C. BAP1 mutation was associated with the tumor and cancerous stage. None of these four genes were positively associated with the overall survival of patients. The PBRM1 and SETD2 mutations were mutually exclusive to BAP1 mutation. Overall, the present study provided data confirming gene alteration in Taiwanese patients with ccRCC and showed some differences when compared with Western countries. Further comprehensive genomic and epigenomic studies, as well as downstream validation, are necessary to evaluate the impact of these differences.

SUBMITTER: Lin PH

PROVIDER: S-EPMC7802514 | biostudies-literature | 2021 Feb

REPOSITORIES: biostudies-literature

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Genomic characterization of clear cell renal cell carcinoma using targeted gene sequencing.

Lin Po-Hung PH Huang Chao-Yuan CY Yu Kai-Jie KJ Kan Hung-Cheng HC Liu Chung-Yi CY Chuang Cheng-Keng CK Lu Yu-Chuan YC Chang Ying-Hsu YH Shao I-Hung IH Pang See-Tong ST

Oncology letters 20210104 2

Kidney cancer is one of the most lethal cancer types worldwide. The most common subtype of kidney cancer is clear cell renal cell carcinoma (ccRCC), and the somatic mutations of ccRCC have been identified through the development of large databases. The present study aimed to validate the status of the associated gene mutations in a Taiwanese cohort. Targeted sequencing was used to validate the mutation status of genes related to ccRCC in Taiwanese patients who had nephrectomy for kidney cancer. ...[more]

PMID: 33456545

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Project description:BackgroundThe high drug resistance and metabolic reprogramming of clear cell renal cell carcinoma (ccRCC) are considered responsible for poor prognosis. In-depth research at multiple levels is urgently warranted to illustrate the lipid composition, distribution, and metabolic pathways of clinical ccRCC specimens.MethodsIn this project, a leading-edge targeted quantitative lipidomic study was conducted using 10 pairs of cancerous and adjacent normal tissues obtained from ccRCC patients. Accurate lipid quantification was performed according to a linear equation calculated using internal standards. Qualitative and quantitative analyses of lipids were performed with multiple reaction monitoring analysis based on ultra-performance liquid chromatography (UPLC) and mass spectrometry (MS). Additionally, a multivariate statistical analysis was performed using data obtained on lipids.ResultsA total of 28 lipid classes were identified. Among them, the most abundant were triacylglycerol (TG), diacylglycerol (DG), phosphatidylcholine (PC), and phosphatidylethanolamine (PE). Cholesteryl ester (CE) was the lipid exhibiting the most considerable difference between normal samples and tumor samples. Lipid content, chain length, and chain unsaturation of acylcarnitine (CAR), CE, and DG were found to be significantly increased. Based on screening for variable importance in projection scores ≥1, as well as fold change limits between 0.5 and 2, 160 differentially expressed lipids were identified. CE was found to be the most significantly upregulated lipid, while TG was observed to be the most significantly downregulated lipid.ConclusionBased on the absolute quantitative analysis of lipids in ccRCC specimens, it was observed that the content and change trends varied in different lipid classes. Upregulation of CAR, CE, and DG was observed, and analysis of changes in the distribution helped clarify the causes of lipid accumulation in ccRCC and possible carcinogenic molecular mechanisms. The results and methods described herein provide a comprehensive analysis of ccRCC lipid metabolism and lay a theoretical foundation for cancer treatment.

Dataset Information

Genomic characterization of clear cell renal cell carcinoma using targeted gene sequencing.

Publications

Genomic characterization of clear cell renal cell carcinoma using targeted gene sequencing.

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