miR-361-5p as a promising qRT-PCR internal control for tumor and normal breast tissues.

PloS One
Sogol GhanbariSeyed Javad Mowla

Abstract

One of the most widely used evaluation methods in miRNA experiments is qRT-PCR. However, selecting suitable internal controls (IC) is crucial for qRT-PCR experiments. Currently, there is no consensus on the ICs for miRNA qRT-PCR experiments in breast cancer. To this end, we tried to identify the most stable (the least expression alteration) and promising miRNAs in normal and tumor breast tissues by employing TCGA miRNA-Seq data and then experimentally validated them on fresh clinical samples. A multi-component scoring system was used which takes into account multiple expression stability criteria as well as correlation with clinical characteristics. Furthermore, we extended the scoring system for more than two biological sub-groups. TCGA BRCA samples were analyzed based on two grouping criteria: Tumor & Normal samples and Tumor subtypes. The top 10 most stable miRNAs were further investigated by differential expression and survival analysis. Then, we examined the expression level of the top scored miRNA (hsa-miR-361-5p) along with two commonly used ICs hsa-miR-16-5p and U48 on 34 pairs of Primary breast tumor and their adjacent normal tissues using qRT-PCR. According to our multi-component scoring system, hsa-miR-361-5p had the...Continue Reading

References

Jan 30, 2010·Methods : a Companion to Methods in Enzymology·Vladimir Benes, Mirco Castoldi
Feb 6, 2010·Annals of Surgery·Helen M HeneghanMichael J Kerin
Oct 5, 2010·Experimental & Molecular Medicine·Annika SchaeferKlaus Jung
Jan 17, 2012·Bioinformatics·Raivo KoldeJaak Vilo
Feb 16, 2012·Epigenomics·Nicoletta BianchiRoberto Gambari
May 9, 2012·Wiley Interdisciplinary Reviews. RNA·Pauline Chugh, Dirk P Dittmer
Sep 28, 2013·Nature Genetics·UNKNOWN Cancer Genome Atlas Research NetworkJoshua M Stuart
Feb 4, 2014·Genome Biology·Charity W LawGordon K Smyth
Sep 30, 2014·Biochemical and Biophysical Research Communications·Cheng ZhanQun Wang
Jan 22, 2015·Nucleic Acids Research·Matthew E RitchieGordon K Smyth
May 15, 2015·PloS One·Yijuan ZhangBingyun Sun
Dec 26, 2015·Nucleic Acids Research·Antonio ColapricoHoutan Noushmehr
Apr 15, 2016·Biomolecular Detection and Quantification·David SvecMikael Kubista
Aug 9, 2016·Journal of Thoracic Disease·Zhi-Gang CaoZhi-Min Shao
Nov 3, 2016·Breast Cancer Research and Treatment·András LánczkyBalázs Győrffy
Sep 15, 2018·OncoTargets and Therapy·Jing LiuShizhu Yu
Sep 23, 2018·International Journal of Molecular Sciences·Monika DrobnaMałgorzata Dawidowska
Sep 25, 2018·Journal of Cellular Physiology·Ting LiuJi Zhang
Jan 19, 2019·Trends in Biotechnology·Sean C TaylorJoshua Fenrich
Mar 19, 2019·Frontiers in Genetics·George S KrasnovAlexey A Dmitriev
Jul 15, 2020·Cancers·Alexis ForterreMasako Harada
Jul 28, 2020·Journal of Oncology·Zhiguang Yang, Zhaoyu Liu
Oct 29, 2020·Anticancer Research·Emmanuel N KontomanolisZacharias Fasoulakis

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Software Mentioned

limma
Normfinder
OligoAnalyzer
TCGAbiolinks package
miRBaseConverter
geNorm
METABRIC
RStudio environment
BestKeeper
ggplot2

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