![Page 1: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/1.jpg)
Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray
PLoS ONE 9(9): e106314. doi:10.1371/journal.pone.0106314
![Page 2: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/2.jpg)
Yoshiki Murakami1, Toshihito Tanahashi2,3, Rina Okada4, Hidenori Toyoda5, Takashi Kumada5, Masaru Enomoto1, Akihiro Tamori1, Norifumi Kawada1, Y-h Taguchi6, Takeshi Azuma4
1 Department of Hepatology, Osaka City University Graduate School of Medicine, Osaka, Japan2 Department of Medical Pharmaceutics, Kobe Pharmaceutical University, Kobe, Japan, 3 Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan4 Division of Gastroenterology, Department of Internal Medicine, Kobe University Graduate School of Medicine, Kobe, Japan5 Department of Gastroenterology, Ogaki Municipal Hospital, Ogaki, Japan6 Department of Physics, Chuo University, Tokyo 112-8551, Japan
![Page 3: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/3.jpg)
Purpose: How can we measure microRNA expression using MiSeq + miRDeep2?
MiSeq: Desktop sequencerMiRDeep2: easy to use pipeline for miRNA-seq
We would like to measure miRNA expression as easy & precisely as possible ….
(without any complicated or sophisticated or advanced procedures)
How accurate are those outcomes?
![Page 4: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/4.jpg)
Materials:14 HCC (liver cancer) + 6 Normal tissue (same patients)
MiRNA-seq : 14 HCC + 6 Normal tissueMicroarray : 14 HCC
Questions:How coincident between miRNA-seq and microarray?
Can miRNA-seq diagnose HCC vs normal tissue?
Are novel miRNAs detected?
![Page 5: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/5.jpg)
How coincident between miRNA-seq and microarray?
log10(NGS)
log1
0(m
icro
arra
y)Corr. Coef. = 0.6059
![Page 6: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/6.jpg)
Microarray:Agilent microRNA GprocessedSignal + mean=0 + SD=1
miRDeep2:Bowtie + hg19 + miRBase 18 + default settings
Essentially, no normalization, but they are correlated very well.
![Page 7: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/7.jpg)
Te
ch
ni c
al re
plic
ate
s
An
oth
er p
atie
nt
![Page 8: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/8.jpg)
Independent of technical replicates / patients, miRNA-seq and microarray are well correlated without any sophisticated/complicated/advanced normalizations
![Page 9: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/9.jpg)
Next: Consistency of differential miRNA expression between miRNA-seq and microarray
log10(NGS)
log1
0(m
icro
arra
y)K-177 vs CU-087
Corr. Coef. = 0.5555
![Page 10: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/10.jpg)
Com
pari
sons
bet
wee
n te
chni
cal r
eplic
ates
An
oth
er p
atie
nt
![Page 11: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/11.jpg)
Independent of technical replicates / patients, miRNA-seq and microarray of differential expression were well correlated without any sophisticated/complicated/advanced normalizations
![Page 12: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/12.jpg)
Comparisons between technical replicates of miRNA-seq
0.986
0.984 0.986
![Page 13: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/13.jpg)
Comparisons between technical replicates of miRNA-seq of differential expression
0.913
0.929 0.907
0.926 0.852 0.865
0.834 0.925 0.843 0.899
0.853 0.830 0.843 0.925 0.896
0.918 0.841 0.856 0.922 0.818 0.850
0.830 0.919 0.842 0.845 0.922 0.847 0.899
0.836 0.815 0.914 0.844 0.818 0.922 0.921 0.899
![Page 14: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/14.jpg)
Independent of technical replicates / patients, reproducibilities of miRNA-seq of expression and differential expression were well without any sophisticated/complicated/advanced normalizations
MiRNA-seq expression/differential expression does not require any sophisticated/complicated/advanced normalizations, possibly because of the fact that limited number of miRNAs are generally expressive.
![Page 15: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/15.jpg)
Can miRNA-seq diagnose HCC ?
11 miRNAs were selected using PCA based unsupervised FE
miR-10a-5p, miR-122-5p, miR-146b-5p, miR-148a-3p, miR-192-5p, miR-22-3p, miR-26a-5p, and miR-27b-3p, miR-10b-5p, miR-143-3p, and miR-21-5p
True Tumor ControlPredicted Tumor 12 0 Control 2 6
![Page 16: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/16.jpg)
M features
N sample
Q
=+ noise
M' N✕matrix
Q N matrix✕
N(≪M)samples
M'(≪M)✕Q matrix
M features
M features embedded
PC1
PC1
M'
N(≪M)samples
![Page 17: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/17.jpg)
Individual miRNAs are not always expressed between tumor and control
Combinatorial expression is important !
![Page 18: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/18.jpg)
Discovery of Novel miRNAs
![Page 19: Comparison of Hepatocellular Carcinoma miRNA Expression Profiling as Evaluated by Next Generation Sequencing and Microarray](https://reader030.vdocuments.net/reader030/viewer/2022032421/55a735bf1a28abc4528b45b4/html5/thumbnails/19.jpg)
Conclusions
※Miseq+miRDeep2 detect miRNA expression and differential miRNA expression coincident with microarray
・Miseq+miRDeep2 give reproducible miRNA expression and differential miRNA expression
・miRNA expression measured by Miseq+miRDeep2 can diagnose between HCC and normal control
・Miseq+miRDeep2 can identify novel miRNAs