Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling

Mario Deng; Jasmine J. Blondeau; Doris Schmidt; Sven Perner; Stefan C. Müller; Jörg Ellinger

doi:10.1016/j.gdata.2015.06.016

Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling

Mario Deng, Jasmine J. Blondeau, Doris Schmidt, Sven Perner, Stefan C. Müller, Jörg Ellinger^*

^*Corresponding author for this work

Institute of Pathology

University of Bonn

31 Citations (Scopus)

Abstract

Clear cell renal cell carcinoma (ccRCC) is a common human malignancy. Despite numerous efforts, there is still no reliable biomarker or combination of biomarkers available for daily practice. Our study was designed to explore the expression profile of messenger RNA (mRNA) and long non-coding RNA (lncRNA) transcripts in ccRCC in order to identify potential diagnostic biomarkers for patients with ccRCC. Total RNA from corresponding normal and malignant tissue of 15 patients with ccRCC was isolated. Expression profiling was performed using a custom Agilent gene expression microarray which allowed the analysis of 34,144 mRNA and 32,183 lncRNA transcripts. We observed that a subset of mRNA (n = 1064; 3.1%) and lncRNA (n = 1308; 4.1%) transcripts are dysregulated (fold change > 2) in ccRCC tissue. The relative higher number of differentially expressed lncRNAs indicates that lncRNA profiling may be better suited for diagnostic purposes; a number of so far unknown RNAs with potential diagnostic interest in ccRCC are identified by our gene expression profiling study. The data are deposited in the Gene Expression Omnibus (GSE61763).

Original language	English
Journal	Genomics Data
Volume	5
Pages (from-to)	173-175
Number of pages	3
ISSN	2213-5960
DOIs	https://doi.org/10.1016/j.gdata.2015.06.016
Publication status	Published - 01.09.2015

Funding

The tissue samples were collected within the framework of the Center for Integrated Oncology CIO Köln Bonn; the CIO is supported by the German Cancer Aid . This work was supported by a grant of the Rudolf Becker Foundation to Sven Perner.

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

SDG 3 Good Health and Well-being

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10.1016/j.gdata.2015.06.016

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title = "Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling",

abstract = "Clear cell renal cell carcinoma (ccRCC) is a common human malignancy. Despite numerous efforts, there is still no reliable biomarker or combination of biomarkers available for daily practice. Our study was designed to explore the expression profile of messenger RNA (mRNA) and long non-coding RNA (lncRNA) transcripts in ccRCC in order to identify potential diagnostic biomarkers for patients with ccRCC. Total RNA from corresponding normal and malignant tissue of 15 patients with ccRCC was isolated. Expression profiling was performed using a custom Agilent gene expression microarray which allowed the analysis of 34,144 mRNA and 32,183 lncRNA transcripts. We observed that a subset of mRNA (n = 1064; 3.1\%) and lncRNA (n = 1308; 4.1\%) transcripts are dysregulated (fold change > 2) in ccRCC tissue. The relative higher number of differentially expressed lncRNAs indicates that lncRNA profiling may be better suited for diagnostic purposes; a number of so far unknown RNAs with potential diagnostic interest in ccRCC are identified by our gene expression profiling study. The data are deposited in the Gene Expression Omnibus (GSE61763).",

author = "Mario Deng and Blondeau, \{Jasmine J.\} and Doris Schmidt and Sven Perner and M{\"u}ller, \{Stefan C.\} and J{\"o}rg Ellinger",

note = "Funding Information: The tissue samples were collected within the framework of the Center for Integrated Oncology CIO K{\"o}ln Bonn; the CIO is supported by the German Cancer Aid . This work was supported by a grant of the Rudolf Becker Foundation to Sven Perner. Publisher Copyright: {\textcopyright} 2015 The Authors. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.",

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doi = "10.1016/j.gdata.2015.06.016",

language = "English",

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AU - Deng, Mario

AU - Blondeau, Jasmine J.

AU - Schmidt, Doris

AU - Perner, Sven

AU - Müller, Stefan C.

AU - Ellinger, Jörg

N1 - Funding Information: The tissue samples were collected within the framework of the Center for Integrated Oncology CIO Köln Bonn; the CIO is supported by the German Cancer Aid . This work was supported by a grant of the Rudolf Becker Foundation to Sven Perner. Publisher Copyright: © 2015 The Authors. Copyright: Copyright 2018 Elsevier B.V., All rights reserved.

PY - 2015/9/1

Y1 - 2015/9/1

N2 - Clear cell renal cell carcinoma (ccRCC) is a common human malignancy. Despite numerous efforts, there is still no reliable biomarker or combination of biomarkers available for daily practice. Our study was designed to explore the expression profile of messenger RNA (mRNA) and long non-coding RNA (lncRNA) transcripts in ccRCC in order to identify potential diagnostic biomarkers for patients with ccRCC. Total RNA from corresponding normal and malignant tissue of 15 patients with ccRCC was isolated. Expression profiling was performed using a custom Agilent gene expression microarray which allowed the analysis of 34,144 mRNA and 32,183 lncRNA transcripts. We observed that a subset of mRNA (n = 1064; 3.1%) and lncRNA (n = 1308; 4.1%) transcripts are dysregulated (fold change > 2) in ccRCC tissue. The relative higher number of differentially expressed lncRNAs indicates that lncRNA profiling may be better suited for diagnostic purposes; a number of so far unknown RNAs with potential diagnostic interest in ccRCC are identified by our gene expression profiling study. The data are deposited in the Gene Expression Omnibus (GSE61763).

AB - Clear cell renal cell carcinoma (ccRCC) is a common human malignancy. Despite numerous efforts, there is still no reliable biomarker or combination of biomarkers available for daily practice. Our study was designed to explore the expression profile of messenger RNA (mRNA) and long non-coding RNA (lncRNA) transcripts in ccRCC in order to identify potential diagnostic biomarkers for patients with ccRCC. Total RNA from corresponding normal and malignant tissue of 15 patients with ccRCC was isolated. Expression profiling was performed using a custom Agilent gene expression microarray which allowed the analysis of 34,144 mRNA and 32,183 lncRNA transcripts. We observed that a subset of mRNA (n = 1064; 3.1%) and lncRNA (n = 1308; 4.1%) transcripts are dysregulated (fold change > 2) in ccRCC tissue. The relative higher number of differentially expressed lncRNAs indicates that lncRNA profiling may be better suited for diagnostic purposes; a number of so far unknown RNAs with potential diagnostic interest in ccRCC are identified by our gene expression profiling study. The data are deposited in the Gene Expression Omnibus (GSE61763).

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DO - 10.1016/j.gdata.2015.06.016

M3 - Journal articles

AN - SCOPUS:84931269201

SN - 2213-5960

VL - 5

SP - 173

EP - 175

JO - Genomics Data

JF - Genomics Data

ER -

Identification of novel differentially expressed lncRNA and mRNA transcripts in clear cell renal cell carcinoma by expression profiling

Abstract

Funding

UN SDGs

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