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Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers

BACKGROUND: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional...

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Autores principales: Brunner, Alayne L, Beck, Andrew H, Edris, Badreddin, Sweeney, Robert T, Zhu, Shirley X, Li, Rui, Montgomery, Kelli, Varma, Sushama, Gilks, Thea, Guo, Xiangqian, Foley, Joseph W, Witten, Daniela M, Giacomini, Craig P, Flynn, Ryan A, Pollack, Jonathan R, Tibshirani, Robert, Chang, Howard Y, van de Rijn, Matt, West, Robert B
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2012
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053743/
https://www.ncbi.nlm.nih.gov/pubmed/22929540
http://dx.doi.org/10.1186/gb-2012-13-8-r75
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author Brunner, Alayne L
Beck, Andrew H
Edris, Badreddin
Sweeney, Robert T
Zhu, Shirley X
Li, Rui
Montgomery, Kelli
Varma, Sushama
Gilks, Thea
Guo, Xiangqian
Foley, Joseph W
Witten, Daniela M
Giacomini, Craig P
Flynn, Ryan A
Pollack, Jonathan R
Tibshirani, Robert
Chang, Howard Y
van de Rijn, Matt
West, Robert B
author_facet Brunner, Alayne L
Beck, Andrew H
Edris, Badreddin
Sweeney, Robert T
Zhu, Shirley X
Li, Rui
Montgomery, Kelli
Varma, Sushama
Gilks, Thea
Guo, Xiangqian
Foley, Joseph W
Witten, Daniela M
Giacomini, Craig P
Flynn, Ryan A
Pollack, Jonathan R
Tibshirani, Robert
Chang, Howard Y
van de Rijn, Matt
West, Robert B
author_sort Brunner, Alayne L
collection PubMed
description BACKGROUND: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. RESULTS: We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. CONCLUSIONS: This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research.
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spelling pubmed-40537432014-06-13 Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers Brunner, Alayne L Beck, Andrew H Edris, Badreddin Sweeney, Robert T Zhu, Shirley X Li, Rui Montgomery, Kelli Varma, Sushama Gilks, Thea Guo, Xiangqian Foley, Joseph W Witten, Daniela M Giacomini, Craig P Flynn, Ryan A Pollack, Jonathan R Tibshirani, Robert Chang, Howard Y van de Rijn, Matt West, Robert B Genome Biol Research BACKGROUND: Molecular characterization of tumors has been critical for identifying important genes in cancer biology and for improving tumor classification and diagnosis. Long non-coding RNAs, as a new, relatively unstudied class of transcripts, provide a rich opportunity to identify both functional drivers and cancer-type-specific biomarkers. However, despite the potential importance of long non-coding RNAs to the cancer field, no comprehensive survey of long non-coding RNA expression across various cancers has been reported. RESULTS: We performed a sequencing-based transcriptional survey of both known long non-coding RNAs and novel intergenic transcripts across a panel of 64 archival tumor samples comprising 17 diagnostic subtypes of adenocarcinomas, squamous cell carcinomas and sarcomas. We identified hundreds of transcripts from among the known 1,065 long non-coding RNAs surveyed that showed variability in transcript levels between the tumor types and are therefore potential biomarker candidates. We discovered 1,071 novel intergenic transcribed regions and demonstrate that these show similar patterns of variability between tumor types. We found that many of these differentially expressed cancer transcripts are also expressed in normal tissues. One such novel transcript specifically expressed in breast tissue was further evaluated using RNA in situ hybridization on a panel of breast tumors. It was shown to correlate with low tumor grade and estrogen receptor expression, thereby representing a potentially important new breast cancer biomarker. CONCLUSIONS: This study provides the first large survey of long non-coding RNA expression within a panel of solid cancers and also identifies a number of novel transcribed regions differentially expressed across distinct cancer types that represent candidate biomarkers for future research. BioMed Central 2012 2012-08-28 /pmc/articles/PMC4053743/ /pubmed/22929540 http://dx.doi.org/10.1186/gb-2012-13-8-r75 Text en Copyright © 2012 Brunner et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Brunner, Alayne L
Beck, Andrew H
Edris, Badreddin
Sweeney, Robert T
Zhu, Shirley X
Li, Rui
Montgomery, Kelli
Varma, Sushama
Gilks, Thea
Guo, Xiangqian
Foley, Joseph W
Witten, Daniela M
Giacomini, Craig P
Flynn, Ryan A
Pollack, Jonathan R
Tibshirani, Robert
Chang, Howard Y
van de Rijn, Matt
West, Robert B
Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
title Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
title_full Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
title_fullStr Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
title_full_unstemmed Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
title_short Transcriptional profiling of long non-coding RNAs and novel transcribed regions across a diverse panel of archived human cancers
title_sort transcriptional profiling of long non-coding rnas and novel transcribed regions across a diverse panel of archived human cancers
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4053743/
https://www.ncbi.nlm.nih.gov/pubmed/22929540
http://dx.doi.org/10.1186/gb-2012-13-8-r75
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