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Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues

Formalin-fixed paraffin embedded (FFPE) tissues are a valuable resource for biomarker discovery in order to understand the etiology of different cancers and many other diseases. Proteins are the biomarkers of interest with respect to FFPE tissues as RNA degradation is the major challenge in these ti...

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Autores principales: Tripathi, Manish K., Zacheaus, Chidi, Doxtater, Kyle, Keramatnia, Fatemeh, Gao, Cuilan, Yallapu, Murali M., Jaggi, Meena, Chauhan, Subhash C.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162476/
https://www.ncbi.nlm.nih.gov/pubmed/30189670
http://dx.doi.org/10.3390/ncrna4030020
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author Tripathi, Manish K.
Zacheaus, Chidi
Doxtater, Kyle
Keramatnia, Fatemeh
Gao, Cuilan
Yallapu, Murali M.
Jaggi, Meena
Chauhan, Subhash C.
author_facet Tripathi, Manish K.
Zacheaus, Chidi
Doxtater, Kyle
Keramatnia, Fatemeh
Gao, Cuilan
Yallapu, Murali M.
Jaggi, Meena
Chauhan, Subhash C.
author_sort Tripathi, Manish K.
collection PubMed
description Formalin-fixed paraffin embedded (FFPE) tissues are a valuable resource for biomarker discovery in order to understand the etiology of different cancers and many other diseases. Proteins are the biomarkers of interest with respect to FFPE tissues as RNA degradation is the major challenge in these tissue samples. Recently, non-protein coding transcripts, long non-coding RNAs (lncRNAs), have gained significant attention due to their important biological actions and potential involvement in cancer. RNA sequencing (RNA-seq) or quantitative reverse transcription-polymerase chain reaction (qRT-PCR) are the only validated methods to evaluate and study lncRNA expression and neither of them provides visual representation as immunohistochemistry (IHC) provides for proteins. We have standardized and are reporting a sensitive Z probe based in situ hybridization method to visually identify and quantify lncRNA in FFPE tissues. This assay is highly sensitive and identifies transcripts visible within different cell types and tumors. We have detected a scarcely expressed tumor suppressor lncRNA NRON (non-coding repressor of nuclear factor of activated T-cells (NFAT)), a moderately expressed oncogenic lncRNA UCA1 (urothelial cancer associated 1), and a highly studied and expressed lncRNA MALAT1 (metastasis associated lung adenocarcinoma transcript 1) in different cancers. High MALAT1 staining was found in colorectal, breast and pancreatic cancer. Additionally, we have observed an increase in MALAT1 expression in different stages of colorectal cancer.
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spelling pubmed-61624762018-10-09 Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues Tripathi, Manish K. Zacheaus, Chidi Doxtater, Kyle Keramatnia, Fatemeh Gao, Cuilan Yallapu, Murali M. Jaggi, Meena Chauhan, Subhash C. Noncoding RNA Article Formalin-fixed paraffin embedded (FFPE) tissues are a valuable resource for biomarker discovery in order to understand the etiology of different cancers and many other diseases. Proteins are the biomarkers of interest with respect to FFPE tissues as RNA degradation is the major challenge in these tissue samples. Recently, non-protein coding transcripts, long non-coding RNAs (lncRNAs), have gained significant attention due to their important biological actions and potential involvement in cancer. RNA sequencing (RNA-seq) or quantitative reverse transcription-polymerase chain reaction (qRT-PCR) are the only validated methods to evaluate and study lncRNA expression and neither of them provides visual representation as immunohistochemistry (IHC) provides for proteins. We have standardized and are reporting a sensitive Z probe based in situ hybridization method to visually identify and quantify lncRNA in FFPE tissues. This assay is highly sensitive and identifies transcripts visible within different cell types and tumors. We have detected a scarcely expressed tumor suppressor lncRNA NRON (non-coding repressor of nuclear factor of activated T-cells (NFAT)), a moderately expressed oncogenic lncRNA UCA1 (urothelial cancer associated 1), and a highly studied and expressed lncRNA MALAT1 (metastasis associated lung adenocarcinoma transcript 1) in different cancers. High MALAT1 staining was found in colorectal, breast and pancreatic cancer. Additionally, we have observed an increase in MALAT1 expression in different stages of colorectal cancer. MDPI 2018-09-05 /pmc/articles/PMC6162476/ /pubmed/30189670 http://dx.doi.org/10.3390/ncrna4030020 Text en © 2018 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Tripathi, Manish K.
Zacheaus, Chidi
Doxtater, Kyle
Keramatnia, Fatemeh
Gao, Cuilan
Yallapu, Murali M.
Jaggi, Meena
Chauhan, Subhash C.
Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
title Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
title_full Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
title_fullStr Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
title_full_unstemmed Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
title_short Z Probe, An Efficient Tool for Characterizing Long Non-Coding RNA in FFPE Tissues
title_sort z probe, an efficient tool for characterizing long non-coding rna in ffpe tissues
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6162476/
https://www.ncbi.nlm.nih.gov/pubmed/30189670
http://dx.doi.org/10.3390/ncrna4030020
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