Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection

Objectives The role of long non-coding RNA (lncRNA) expression in human head and neck squamous cell carcinoma (HNSCC) is still poorly understood. In this study, we aimed at establishing the onco-lncRNAome profiling of HNSCC and to identify lncRNAs correlating with prognosis and patient survival. M...

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Detalles Bibliográficos
Autores principales: Nohata, Nijiro, Abba, Martín Carlos, Gutkind, J. Silvio
Formato: Articulo
Lenguaje:Inglés
Publicado: 2016
Materias:
Ciencias Médicas
Long non-coding RNA
RNA-sequencing
head and neck squamous cell carcinoma (HNSCC)
human papilloma virus (HPV)
TP53
TCGA
Acceso en línea:http://sedici.unlp.edu.ar/handle/10915/128359
Aporte de:
SEDICI (UNLP) de Universidad Nacional de La Plata
id I19-R120-10915-128359
record_format dspace
institution Universidad Nacional de La Plata
institution_str I-19
repository_str R-120
collection SEDICI (UNLP)
language Inglés
topic Ciencias Médicas
Long non-coding RNA
RNA-sequencing
head and neck squamous cell carcinoma (HNSCC)
human papilloma virus (HPV)
TP53
TCGA
spellingShingle Ciencias Médicas
Long non-coding RNA
RNA-sequencing
head and neck squamous cell carcinoma (HNSCC)
human papilloma virus (HPV)
TP53
TCGA
Nohata, Nijiro
Abba, Martín Carlos
Gutkind, J. Silvio
Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection
topic_facet Ciencias Médicas
Long non-coding RNA
RNA-sequencing
head and neck squamous cell carcinoma (HNSCC)
human papilloma virus (HPV)
TP53
TCGA
description Objectives The role of long non-coding RNA (lncRNA) expression in human head and neck squamous cell carcinoma (HNSCC) is still poorly understood. In this study, we aimed at establishing the onco-lncRNAome profiling of HNSCC and to identify lncRNAs correlating with prognosis and patient survival. Materials and methods The Atlas of Noncoding RNAs in Cancer (TANRIC) database was employed to retrieve the lncRNA expression information generated from The Cancer Genome Atlas (TCGA) HNSCC RNA-sequencing data. RNA-sequencing data from HNSCC cell lines were also considered for this study. Bioinformatics approaches, such as differential gene expression analysis, survival analysis, principal component analysis, and Co-LncRNA enrichment analysis were performed. Results Using TCGA HNSCC RNA-sequencing data from 426 HNSCC and 42 adjacent normal tissues, we found 728 lncRNA transcripts significantly and differentially expressed in HNSCC. Among the 728 lncRNAs, 55 lncRNAs were significantly associated with poor prognosis, such as overall survival and/or disease-free survival. Next, we found 140 lncRNA transcripts significantly and differentially expressed between Human Papilloma Virus (HPV) positive tumors and HPV negative tumors. Thirty lncRNA transcripts were differentially expressed between TP53 mutated and TP53 wild type tumors. Co-LncRNA analysis suggested that protein-coding genes that are co-expressed with these deregulated lncRNAs might be involved in cancer associated molecular events. With consideration of differential expression of lncRNAs in a HNSCC cell lines panel (n = 22), we found several lncRNAs that may represent potential targets for diagnosis, therapy and prevention of HNSCC. Conclusion LncRNAs profiling could provide novel insights into the potential mechanisms of HNSCC oncogenesis.
format Articulo
Articulo
author Nohata, Nijiro
Abba, Martín Carlos
Gutkind, J. Silvio
author_facet Nohata, Nijiro
Abba, Martín Carlos
Gutkind, J. Silvio
author_sort Nohata, Nijiro
title Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection
title_short Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection
title_full Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection
title_fullStr Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection
title_full_unstemmed Unraveling the oral cancer lncRNAome: Identification of novel lncRNAs associated with malignant progression and HPV infection
title_sort unraveling the oral cancer lncrnaome: identification of novel lncrnas associated with malignant progression and hpv infection
publishDate 2016
url http://sedici.unlp.edu.ar/handle/10915/128359
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bdutipo_str Repositorios
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