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Lipidomic Signatures and Associated Transcriptomic Profiles of Clear Cell Renal Cell Carcinoma.

ABSTRACT: Renal cell carcinoma (RCC) is the most common histological type of adult kidney cancer. In this study, we obtained lipidomic profiles of clear cell RCC (ccRCC), a major RCC subtype, by performing a lipidomic analysis of specimens of cancerous tissue and the surrounding normal renal cortex obtained from the same patients (N?=?49). We also compared the lipidomic profiles with the lipogenic transcriptome of specimens of cancerous tissue and the surrounding normal renal cortex for an additional set of patient samples (N?=?95). Overall, we detected 326 lipids, including phospholipids, sphingolipids, neutral lipids, and eicosanoids. The levels of more than 70% of the detected lipids were significantly different (P?

SUBMITTER: Saito K

PROVIDER: S-EPMC4928052 | biostudies-literature | 2016 Jun

REPOSITORIES: biostudies-literature

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Lipidomic Signatures and Associated Transcriptomic Profiles of Clear Cell Renal Cell Carcinoma.

Saito Kosuke K Arai Eri E Maekawa Keiko K Ishikawa Masaki M Fujimoto Hiroyuki H Taguchi Ryo R Matsumoto Kenji K Kanai Yae Y Saito Yoshiro Y

Scientific reports 20160630

Renal cell carcinoma (RCC) is the most common histological type of adult kidney cancer. In this study, we obtained lipidomic profiles of clear cell RCC (ccRCC), a major RCC subtype, by performing a lipidomic analysis of specimens of cancerous tissue and the surrounding normal renal cortex obtained from the same patients (N = 49). We also compared the lipidomic profiles with the lipogenic transcriptome of specimens of cancerous tissue and the surrounding normal renal cortex for an additional set ...[more]

PMID: 27357243

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Project description:BackgroundClear cell renal cell carcinoma (ccRCC) represents the most invasive and common adult kidney neoplasm. Mounting evidence suggests that microRNAs (miRNAs) are important regulators of gene expression. But their function in tumourigenesis in this tumour type remains elusive. With the development of high throughput technologies such as microarrays and NGS, aberrant miRNA expression has been widely observed in ccRCC. Systematic and integrative analysis of multiple microRNA expression datasets may reveal potential mechanisms by which microRNAs contribute to ccRCC pathogenesis.MethodsWe collected 5 public microRNA expression datasets in ccRCC versus non-matching normal renal tissues from GEO database and published literatures. We analyzed these data sets with an integrated bioinformatics framework to identify expression signatures. The framework incorporates a novel statistic method for abnormal gene expression detection and an in-house developed predictor to assess the regulatory activity of microRNAs. We then mapped target genes of DE-miRNAs to different databases, such as GO, KEGG, GeneGo etc, for functional enrichment analysis.ResultsUsing this framework we identified a consistent panel of eleven deregulated miRNAs shared by five independent datasets that can distinguish normal kidney tissues from ccRCC. After comparison with 3 RNA-seq based microRNA profiling studies, we found that our data correlated well with the results of next generation sequencing. We also discovered 14 novel molecular pathways that are likely to play a role in the tumourigenesis of ccRCC.ConclusionsThe integrative framework described in this paper greatly improves the inter-dataset consistency of microRNA expression signatures. Consensus expression profile should be identified at pathway or network level to address the heterogeneity of cancer. The DE-miRNA signature and novel pathways identified herein could provide potential biomarkers for ccRCC that await further validation.

Dataset Information

Lipidomic Signatures and Associated Transcriptomic Profiles of Clear Cell Renal Cell Carcinoma.

Publications

Lipidomic Signatures and Associated Transcriptomic Profiles of Clear Cell Renal Cell Carcinoma.

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