Expression Profiles and Clinical Significance of MicroRNAs in Papillary Renal Cell Carcinoma

Ge, Yu‐Zheng; Xu, Luwei; Xu, Zheng; Wu, Rongqian; Hui, Xin; Zhu, Meng; Lu, Tian-Ze; Geng, Liguo; Liu, Hao; Zhou, Changcheng; Peng, Yu; Zhao, Yu; Hu, Zhikai; Zhao, Yan; Zhou, Lin; Wu, Jianping; Li, Wencheng; Zhu, Jun; Jia, Ru

doi:10.1097/md.0000000000000767

Cited by 23 publications

(12 citation statements)

References 44 publications

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“…miRNAs show aberrant expression profiles in various cancers, and dysregulation of miRNAs may alter the neoplastic progression and prognosis of human malignancies. 19 , 20 As the previous studies described, miRNA expression data were open access in the TCGA data portal, and analyzing the TCGA data has already become an important approach to investigate the association between miRNA expression patterns and pathologic characteristics and survival in various cancer types, including lung cancer, 12 hepatocellular carcinoma, 21 renal cell carcinoma, 22 and bladder cancer. 23 For LUAD patients, Li et al 12 identified an eight-miRNA signature for predicting the OS by mining the TCGA data before.…”

Section: Discussionmentioning

confidence: 99%

“…Furthermore, cases with OS <1 month were removed, which may affect the results of survival analysis. Ge et al 22 divided cases into two groups (follow-up time >30 days and <30 days) in the previous study and found that the survival-related miRNAs differed according to whether these cases with OS <1 month were included. Thus, given the differences in the approaches for the selection of cases and miRNAs, the authors identified differentially expressed miRNAs between LUAD and adjacent normal tissues with the TCGA dataset following the strict exclusion criteria and explored the cancer-specific miRNAs for predicting the development and survival in patients with LUAD.…”

Section: Discussionmentioning

confidence: 99%

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MicroRNA expression profiles predict progression and clinical outcome in lung adenocarcinoma

Kang

et al. 2016

OTT

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Lung cancer is one of the leading causes of cancer death worldwide. Accumulating evidence has indicated that microRNAs (miRNAs) can be proposed as promising diagnostic and prognostic markers for various cancers. The current study analyzed the miRNA expression profiles of 418 lung adenocarcinoma (LUAD) cases obtained from The Cancer Genome Atlas dataset, with the aim to investigate the relationship of miRNAs with progression and prognosis of LUAD. A total of 185 miRNAs were found to be differentially expressed between LUAD tumor tissues and adjacent normal tissues. Among them, 13, 10, 0, and 10 miRNAs were discovered to be associated with pathologic T, N, M, and Stage, respectively. Interestingly, mir-200 family (mir-200a, mir-200b, and mir-429) was shown to play a critical role in the progression of LUAD. In the multivariate Cox regression analysis, mir-1468 (P=0.009), mir-212 (P=0.026), mir-3653 (P=0.012), and mir-31 (P=0.002) were significantly correlated with recurrence-free survival. With regard to overall survival, mir-551b (P=0.011), mir-3653 (P=0.016), and mir-31 (P=0.001) were proven as independent prognostic markers. In summary, this study identified the cancer-specific miRNAs that may predict the progression and prognosis of LUAD.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

MicroRNA expression profiles predict progression and clinical outcome in lung adenocarcinoma

Kang

et al. 2016

OTT

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“…Hsa-miR-3074 has been associated with papillary renal cell carcinoma [108], but no publication is available about its role in BC.…”

Section: Discussionmentioning

confidence: 99%

How interacting pathways are regulated by miRNAs in breast cancer subtypes

Cava

Colaprico²,

Bertoli

et al. 2016

BMC Bioinformatics

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BackgroundAn important challenge in cancer biology is to understand the complex aspects of the disease. It is increasingly evident that genes are not isolated from each other and the comprehension of how different genes are related to each other could explain biological mechanisms causing diseases. Biological pathways are important tools to reveal gene interaction and reduce the large number of genes to be studied by partitioning it into smaller paths. Furthermore, recent scientific evidence has proven that a combination of pathways, instead than a single element of the pathway or a single pathway, could be responsible for pathological changes in a cell.ResultsIn this paper we develop a new method that can reveal miRNAs able to regulate, in a coordinated way, networks of gene pathways. We applied the method to subtypes of breast cancer. The basic idea is the identification of pathways significantly enriched with differentially expressed genes among the different breast cancer subtypes and normal tissue. Looking at the pairs of pathways that were found to be functionally related, we created a network of dependent pathways and we focused on identifying miRNAs that could act as miRNA drivers in a coordinated regulation process.ConclusionsOur approach enables miRNAs identification that could have an important role in the development of breast cancer.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1196-1) contains supplementary material, which is available to authorized users.

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“…The miRNA target prediction was conducted using three computational algorithms including TargetScan (version 7.1; http://www.targetscan.org ) 33 , miRDB ( http://www.mirdb.org/ ) 34 , and the Good mirSVR score collection within miRanda ( http://www.microrna.org ) 35 . The genes predicted by at least two independent tools were uploaded to the Database for Annotation, Visualization and Integrated Discovery (DAVID) program (version 6.8; https://david.ncifcrf.gov/ ) 36 , 37 for further annotation analyses including Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, as we previously reported 21 .…”

Section: Methodsmentioning

confidence: 99%

A BAP1 Mutation-specific MicroRNA Signature Predicts Clinical Outcomes in Clear Cell Renal Cell Carcinoma Patients with Wild-type BAP1

Zhou

et al. 2017

J. Cancer

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Background: Clear cell renal cell carcinoma (ccRCC) is the most prevalent histologic subtype of kidney cancers in adults, which could be divided into two distinct subgroups according to the BRCA1 associated protein-1 (BAP1) mutation status. In the current study, we comprehensively analyzed the genome-wide microRNA (miRNA) expression profiles in ccRCC, with the aim to identify the differentially expressed miRNAs between BAP1 mutant and wild-type tumors, and generate a BAP1 mutation-specific miRNA signature for ccRCC patients with wild-type BAP1.Methods: The BAP1 mutation status and miRNA profiles in BAP1 mutant and wild-type tumors were analyzed. Subsequently, the association of the differentially expressed miRNAs with patient survival was examined, and a BAP1 mutation-specific miRNA signature was generated and examined with Kaplan-Meier survival, univariate and multivariate Cox regression analyses. Finally, the bioinformatics methods were adopted for the target prediction of selected miRNAs and functional annotation analyses.Results: A total of 350 treatment-naïve primary ccRCC patients were selected from The Cancer Genome Atlas project, among which 35 (10.0%) subjects carried mutant BAP1 and had a shorter overall survival (OS) time. Furthermore, 33 miRNAs were found to be differentially expressed between BAP1 mutant and wild-type tumors, among which 11 (miR-149, miR-29b-2, miR-182, miR-183, miR-21, miR-365-2, miR-671, miR-365-1, miR-10b, miR-139, and miR-181a-2) were significantly associated with OS in ccRCC patients with wild-type BAP1. Finally, a BAP1 mutation-specific miRNA signature consisting of 11 miRNAs was generated and validated as an independent prognostic parameter.Conclusions: In summary, our study identified a total of 33 miRNAs differentially expressed between BAP1 mutant and wild-type tumors, and generated a BAP1 mutation-specific miRNA signature including eleven miRNAs, which could serve as a novel prognostic biomarker for ccRCC patients with wild-type BAP1.

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Expression Profiles and Clinical Significance of MicroRNAs in Papillary Renal Cell Carcinoma

Abstract: Supplemental Digital Content is available in the text

Cited by 23 publications

References 44 publications

MicroRNA expression profiles predict progression and clinical outcome in lung adenocarcinoma

MicroRNA expression profiles predict progression and clinical outcome in lung adenocarcinoma

How interacting pathways are regulated by miRNAs in breast cancer subtypes

A BAP1 Mutation-specific MicroRNA Signature Predicts Clinical Outcomes in Clear Cell Renal Cell Carcinoma Patients with Wild-type BAP1

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