Cargando…

Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs

Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men and eighth leading cause of death in women in the United States in 2017. In our study, we sought to identify sncRNAs in various stages of development of HCC. We obtained publicly available small RNA-seq data derived fr...

Descripción completa

Detalles Bibliográficos
Autores principales: Koduru, Srinivas V., Leberfinger, Ashley N., Kawasawa, Yuka I., Mahajan, Milind, Gusani, Niraj J., Sanyal, Arun J., Ravnic, Dino J.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964116/
https://www.ncbi.nlm.nih.gov/pubmed/29789629
http://dx.doi.org/10.1038/s41598-018-26360-1
_version_ 1783325117977198592
author Koduru, Srinivas V.
Leberfinger, Ashley N.
Kawasawa, Yuka I.
Mahajan, Milind
Gusani, Niraj J.
Sanyal, Arun J.
Ravnic, Dino J.
author_facet Koduru, Srinivas V.
Leberfinger, Ashley N.
Kawasawa, Yuka I.
Mahajan, Milind
Gusani, Niraj J.
Sanyal, Arun J.
Ravnic, Dino J.
author_sort Koduru, Srinivas V.
collection PubMed
description Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men and eighth leading cause of death in women in the United States in 2017. In our study, we sought to identify sncRNAs in various stages of development of HCC. We obtained publicly available small RNA-seq data derived from patients with cirrhosis (n = 14), low-grade dysplastic nodules (LGDN, n = 9), high grade dysplastic nodules (HGDN, n = 6), early hepatocellular carcinoma (eHCC, n = 6), and advanced hepatocellular carcinoma (HCC, n = 20), along with healthy liver tissue samples (n = 9). All samples were analyzed for various types of non-coding RNAs using PartekFlow software. We remapped small RNA-seq to miRBase to obtain differential expressions of miRNAs and found 87 in cirrhosis, 106 in LGDN, 59 in HGDN, 80 in eHCC, and 133 in HCC. Pathway analysis of miRNAs obtained from diseased samples compared to normal samples showed signaling pathways in the microRNA dependent EMT, CD44, and others. Additionally, we analyzed the data sets for piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. We validated the in silico data using human HCC samples with NanoString miRNA global expression. Our results suggest that publically available data is a valuable resource for sncRNA identification in HCC progression (FDR set to <0.05 for all samples) and that a data mining approach is useful for biomarker development.
format Online
Article
Text
id pubmed-5964116
institution National Center for Biotechnology Information
language English
publishDate 2018
publisher Nature Publishing Group UK
record_format MEDLINE/PubMed
spelling pubmed-59641162018-05-24 Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs Koduru, Srinivas V. Leberfinger, Ashley N. Kawasawa, Yuka I. Mahajan, Milind Gusani, Niraj J. Sanyal, Arun J. Ravnic, Dino J. Sci Rep Article Hepatocellular carcinoma (HCC) was the fifth leading cause of cancer death in men and eighth leading cause of death in women in the United States in 2017. In our study, we sought to identify sncRNAs in various stages of development of HCC. We obtained publicly available small RNA-seq data derived from patients with cirrhosis (n = 14), low-grade dysplastic nodules (LGDN, n = 9), high grade dysplastic nodules (HGDN, n = 6), early hepatocellular carcinoma (eHCC, n = 6), and advanced hepatocellular carcinoma (HCC, n = 20), along with healthy liver tissue samples (n = 9). All samples were analyzed for various types of non-coding RNAs using PartekFlow software. We remapped small RNA-seq to miRBase to obtain differential expressions of miRNAs and found 87 in cirrhosis, 106 in LGDN, 59 in HGDN, 80 in eHCC, and 133 in HCC. Pathway analysis of miRNAs obtained from diseased samples compared to normal samples showed signaling pathways in the microRNA dependent EMT, CD44, and others. Additionally, we analyzed the data sets for piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs. We validated the in silico data using human HCC samples with NanoString miRNA global expression. Our results suggest that publically available data is a valuable resource for sncRNA identification in HCC progression (FDR set to <0.05 for all samples) and that a data mining approach is useful for biomarker development. Nature Publishing Group UK 2018-05-22 /pmc/articles/PMC5964116/ /pubmed/29789629 http://dx.doi.org/10.1038/s41598-018-26360-1 Text en © The Author(s) 2018 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as 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 images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.
spellingShingle Article
Koduru, Srinivas V.
Leberfinger, Ashley N.
Kawasawa, Yuka I.
Mahajan, Milind
Gusani, Niraj J.
Sanyal, Arun J.
Ravnic, Dino J.
Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
title Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
title_full Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
title_fullStr Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
title_full_unstemmed Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
title_short Non-coding RNAs in Various Stages of Liver Disease Leading to Hepatocellular Carcinoma: Differential Expression of miRNAs, piRNAs, lncRNAs, circRNAs, and sno/mt-RNAs
title_sort non-coding rnas in various stages of liver disease leading to hepatocellular carcinoma: differential expression of mirnas, pirnas, lncrnas, circrnas, and sno/mt-rnas
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5964116/
https://www.ncbi.nlm.nih.gov/pubmed/29789629
http://dx.doi.org/10.1038/s41598-018-26360-1
work_keys_str_mv AT kodurusrinivasv noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas
AT leberfingerashleyn noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas
AT kawasawayukai noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas
AT mahajanmilind noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas
AT gusaninirajj noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas
AT sanyalarunj noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas
AT ravnicdinoj noncodingrnasinvariousstagesofliverdiseaseleadingtohepatocellularcarcinomadifferentialexpressionofmirnaspirnaslncrnascircrnasandsnomtrnas