Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.

We present the results of a global study of dysregulated miRNAs in paired samples of normal mucosa and tumor from eight patients with colorectal cancer. Although there is existing data of miRNA contribution to colorectal tumorigenesis, these studies are typically small to medium scale studies of cel...

Descripción completa

Guardado en:

Detalles Bibliográficos
Autores principales:	Julian Hamfjord, Astrid M Stangeland, Timothy Hughes, Martina L Skrede, Kjell M Tveit, Tone Ikdahl, Elin H Kure
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/fe0f939751684591ad85fb3c5eb04b16
Etiquetas:	Agregar Etiqueta Sin Etiquetas, Sea el primero en etiquetar este registro!

id	oai:doaj.org-article:fe0f939751684591ad85fb3c5eb04b16
record_format	dspace
spelling	oai:doaj.org-article:fe0f939751684591ad85fb3c5eb04b162021-11-18T07:21:58ZDifferential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.1932-620310.1371/journal.pone.0034150https://doaj.org/article/fe0f939751684591ad85fb3c5eb04b162012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22529906/?tool=EBIhttps://doaj.org/toc/1932-6203We present the results of a global study of dysregulated miRNAs in paired samples of normal mucosa and tumor from eight patients with colorectal cancer. Although there is existing data of miRNA contribution to colorectal tumorigenesis, these studies are typically small to medium scale studies of cell lines or non-paired tumor samples. The present study is to our knowledge unique in two respects. Firstly, the normal and adjacent tumor tissue samples are paired, thus taking into account the baseline differences between individuals when testing for differential expression. Secondly, we use high-throughput sequencing, thus enabling a comprehensive survey of all miRNAs expressed in the tissues. We use Illumina sequencing technology to perform sequencing and two different tools to statistically test for differences in read counts per gene between samples: edgeR when using the pair information and DESeq when ignoring this information, i.e., treating tumor and normal samples as independent groups. We identify 37 miRNAs that are significantly dysregulated in both statistical approaches, 19 down-regulated and 18 up-regulated. Some of these miRNAs are previously published as potential regulators in colorectal adenocarcinomas such as miR-1, miR-96 and miR-145. Our comprehensive survey of differentially expressed miRNAs thus confirms some existing findings. We have also discovered 16 dysregulated miRNAs, which to our knowledge have not previously been associated with colorectal carcinogenesis: the following significantly down-regulated miR-490-3p, -628-3p/-5p, -1297, -3151, -3163, -3622a-5p, -3656 and the up-regulated miR-105, -549, -1269, -1827, -3144-3p, -3177, -3180-3p, -4326. Although the study is preliminary with only eight patients included, we believe the results add to the present knowledge on miRNA dysregulation in colorectal carcinogenesis. As such the results would serve as a robust training set for validation of potential biomarkers in a larger cohort study. Finally, we also present data supporting the hypothesis that there are differences in miRNA expression between adenocarcinomas and neuroendocrine tumors of the colon.Julian HamfjordAstrid M StangelandTimothy HughesMartina L SkredeKjell M TveitTone IkdahlElin H KurePublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 4, p e34150 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Julian Hamfjord Astrid M Stangeland Timothy Hughes Martina L Skrede Kjell M Tveit Tone Ikdahl Elin H Kure Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
description	We present the results of a global study of dysregulated miRNAs in paired samples of normal mucosa and tumor from eight patients with colorectal cancer. Although there is existing data of miRNA contribution to colorectal tumorigenesis, these studies are typically small to medium scale studies of cell lines or non-paired tumor samples. The present study is to our knowledge unique in two respects. Firstly, the normal and adjacent tumor tissue samples are paired, thus taking into account the baseline differences between individuals when testing for differential expression. Secondly, we use high-throughput sequencing, thus enabling a comprehensive survey of all miRNAs expressed in the tissues. We use Illumina sequencing technology to perform sequencing and two different tools to statistically test for differences in read counts per gene between samples: edgeR when using the pair information and DESeq when ignoring this information, i.e., treating tumor and normal samples as independent groups. We identify 37 miRNAs that are significantly dysregulated in both statistical approaches, 19 down-regulated and 18 up-regulated. Some of these miRNAs are previously published as potential regulators in colorectal adenocarcinomas such as miR-1, miR-96 and miR-145. Our comprehensive survey of differentially expressed miRNAs thus confirms some existing findings. We have also discovered 16 dysregulated miRNAs, which to our knowledge have not previously been associated with colorectal carcinogenesis: the following significantly down-regulated miR-490-3p, -628-3p/-5p, -1297, -3151, -3163, -3622a-5p, -3656 and the up-regulated miR-105, -549, -1269, -1827, -3144-3p, -3177, -3180-3p, -4326. Although the study is preliminary with only eight patients included, we believe the results add to the present knowledge on miRNA dysregulation in colorectal carcinogenesis. As such the results would serve as a robust training set for validation of potential biomarkers in a larger cohort study. Finally, we also present data supporting the hypothesis that there are differences in miRNA expression between adenocarcinomas and neuroendocrine tumors of the colon.
format	article
author	Julian Hamfjord Astrid M Stangeland Timothy Hughes Martina L Skrede Kjell M Tveit Tone Ikdahl Elin H Kure
author_facet	Julian Hamfjord Astrid M Stangeland Timothy Hughes Martina L Skrede Kjell M Tveit Tone Ikdahl Elin H Kure
author_sort	Julian Hamfjord
title	Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
title_short	Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
title_full	Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
title_fullStr	Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
title_full_unstemmed	Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
title_sort	differential expression of mirnas in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/fe0f939751684591ad85fb3c5eb04b16
work_keys_str_mv	AT julianhamfjord differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing AT astridmstangeland differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing AT timothyhughes differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing AT martinalskrede differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing AT kjellmtveit differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing AT toneikdahl differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing AT elinhkure differentialexpressionofmirnasincolorectalcancercomparisonofpairedtumortissueandadjacentnormalmucosausinghighthroughputsequencing
_version_	1718423575476568064

Differential expression of miRNAs in colorectal cancer: comparison of paired tumor tissue and adjacent normal mucosa using high-throughput sequencing.

Ejemplares similares