Cargando…
Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates
BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as key players in a remarkably variety of biological processes and pathologic conditions, including cancer. Next-generation sequencing technologies and bioinformatics procedures predict the existence of tens of thousands of lncRNAs, from which...
Autores principales: | , , , |
---|---|
Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2017
|
Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385094/ https://www.ncbi.nlm.nih.gov/pubmed/28405244 http://dx.doi.org/10.1186/s13148-017-0334-6 |
_version_ | 1782520543950405632 |
---|---|
author | de Lena, Pelayo G. Paz-Gallardo, Abel Paramio, Jesús M. García-Escudero, Ramón |
author_facet | de Lena, Pelayo G. Paz-Gallardo, Abel Paramio, Jesús M. García-Escudero, Ramón |
author_sort | de Lena, Pelayo G. |
collection | PubMed |
description | BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as key players in a remarkably variety of biological processes and pathologic conditions, including cancer. Next-generation sequencing technologies and bioinformatics procedures predict the existence of tens of thousands of lncRNAs, from which we know the functions of only a handful of them, and very little is known in cancer types such as head and neck squamous cell carcinomas (HNSCCs). RESULTS: Here, we use RNAseq expression data from The Cancer Genome Atlas (TCGA) and various statistic and software tools in order to get insight about the lncRNome in HNSCC. Based on lncRNA expression across 426 samples, we discover five distinct tumor clusters that we compare with reported clusters based on various genomic/genetic features. Results demonstrate significant associations between lncRNA-based clustering and DNA methylation, TP53 mutation, and human papillomavirus infection. Using “guilt-by-association” procedures, we infer the possible biological functions of representative lncRNAs of each cluster. Furthermore, we found that lncRNA clustering is correlated with some important clinical and pathologic features, including patient survival after treatment, tumor grade, or sub-anatomical location. CONCLUSIONS: We present a landscape of lncRNAs in HNSCC and provide associations with important genotypic and phenotypic features that may help to understand the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13148-017-0334-6) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-5385094 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2017 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-53850942017-04-12 Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates de Lena, Pelayo G. Paz-Gallardo, Abel Paramio, Jesús M. García-Escudero, Ramón Clin Epigenetics Research BACKGROUND: Long non-coding RNAs (lncRNAs) have emerged as key players in a remarkably variety of biological processes and pathologic conditions, including cancer. Next-generation sequencing technologies and bioinformatics procedures predict the existence of tens of thousands of lncRNAs, from which we know the functions of only a handful of them, and very little is known in cancer types such as head and neck squamous cell carcinomas (HNSCCs). RESULTS: Here, we use RNAseq expression data from The Cancer Genome Atlas (TCGA) and various statistic and software tools in order to get insight about the lncRNome in HNSCC. Based on lncRNA expression across 426 samples, we discover five distinct tumor clusters that we compare with reported clusters based on various genomic/genetic features. Results demonstrate significant associations between lncRNA-based clustering and DNA methylation, TP53 mutation, and human papillomavirus infection. Using “guilt-by-association” procedures, we infer the possible biological functions of representative lncRNAs of each cluster. Furthermore, we found that lncRNA clustering is correlated with some important clinical and pathologic features, including patient survival after treatment, tumor grade, or sub-anatomical location. CONCLUSIONS: We present a landscape of lncRNAs in HNSCC and provide associations with important genotypic and phenotypic features that may help to understand the disease. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13148-017-0334-6) contains supplementary material, which is available to authorized users. BioMed Central 2017-04-08 /pmc/articles/PMC5385094/ /pubmed/28405244 http://dx.doi.org/10.1186/s13148-017-0334-6 Text en © The Author(s). 2017 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research de Lena, Pelayo G. Paz-Gallardo, Abel Paramio, Jesús M. García-Escudero, Ramón Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates |
title | Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates |
title_full | Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates |
title_fullStr | Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates |
title_full_unstemmed | Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates |
title_short | Clusterization in head and neck squamous carcinomas based on lncRNA expression: molecular and clinical correlates |
title_sort | clusterization in head and neck squamous carcinomas based on lncrna expression: molecular and clinical correlates |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5385094/ https://www.ncbi.nlm.nih.gov/pubmed/28405244 http://dx.doi.org/10.1186/s13148-017-0334-6 |
work_keys_str_mv | AT delenapelayog clusterizationinheadandnecksquamouscarcinomasbasedonlncrnaexpressionmolecularandclinicalcorrelates AT pazgallardoabel clusterizationinheadandnecksquamouscarcinomasbasedonlncrnaexpressionmolecularandclinicalcorrelates AT paramiojesusm clusterizationinheadandnecksquamouscarcinomasbasedonlncrnaexpressionmolecularandclinicalcorrelates AT garciaescuderoramon clusterizationinheadandnecksquamouscarcinomasbasedonlncrnaexpressionmolecularandclinicalcorrelates |