ICIC2012

1. Inference of target gene regulation via
miRNAs during cell senescence by MiRaGE
Server
Y-h. Taguchi
Department of Physics
Chuo University

2. 1. What is cell senescence?
2. What is miRNA?
3. Previous works (wet)
4. MiRaGE Method
5. Correlation between target gene regulation
by miRNA and miRNA expression change
during cell senescence
6. Summary & Conclusion

3. 1. What is cell senescence?
The cell division cannot continue forever
for incubated cell lines. It must stop after
several rounds of proliferation.
⇓
This is called “cell senescence”, which is
believed to be related to aging.
aging
Thus, cell senescence is caused by the
interruption of cell divisions, typically
by cell cycle arrests.

4. 2. What is miRNA?
miRNA is a kind of non-coding RNA.
miRNAs are believed to suppress target gene
expression by degradation of mRNAs.
Important features:
・ Typically, there are hundreds kinds of miRNAs found
for each species (c.a., ≧1000 for human).
・ Each miRNA targets more than hundreds of genes.
・ miRNA mainly contributes to cell type change
(e.g., cancer, defferentiation, diseases)
・Infulence to target gene expression by miRNA is subtle
(〜10%) and contexts dependent.
・In spite of that,
miRNA critically contributes to the related processes
(e.g., induction of cell cycle arrest)

5. 3. Previous works (wet)
Several researches suggest the contribution of miRNAs
to cell senescence.
Upregulation of miRNAs during cell senescence
miR-34a,miR-486-5p,miR-494,miR-210...
Downregulation of miRNAs during cell senescence
miR-15a/b,miR-20a,miR-92,miR-16b....
Induction of cell senescence by suppression of
miRNA downregulated during cell senescence.

6. It is likely true that miRNAs contribute to cell senescence.
However, which one?
Dhahbi et al (2011) recently reported the upregulaton of
141(!) miRNAs and the downregulation of 131(!!)
miRNAs during cell senescence by deep sequencing.
The reason why limited number of miRNAs revealed
significant expression change during cell senescence
seems to be due to less sensitivity of microarray analysis.
Is it truly critical the down/upregulation of such large
number of miRNAs for cell senescence?

7. 4. MiRaGE Method
In order to select “Critical ” miRNAs during
cell senescence, regulation of target genes
by miRNAs is inferred by MiRaGE Server.
For details, see
Y-h. Taguchi and J. Yasuda (2010) Inference of Gene
Expression Regulation via microRNA Transfection,
ICIC2010
Y-h. Taguchi and J. Yasuda (2012) MiRaGE: Inference of
Gene Expression Regulation via MicroRNA Transfection II
ICIC2011

8. MiRaGE :
MiRNA Ranking by Gene Expression
considered
miRNA
target
miRNA gene
VS
target
gene significantly
up/downregulated?
gene (t test, Wilcoxon test, KS
test)

9. 5. Correlation between target gene regulation
by miRNA and miRNA expression change
during cell senescence
A) Confirmation of independence of cell line
Two Cell Lines:
IMR90 : young (PD 30) vs senescent (PD 48)
vs
MRC5 : young (PDL 28) vs senescent (PDL 63)
mRNA expression change
(during cell senescence)
MiRaGE ⇓ Server
P-values attributed to each miRNA

10. Intersection between N top-ranked significant miRNAs
based upon P-values (t test) IMR90 vs MRC5
100%
down 10
% of com m on m iRNAs
regulation
binomial: -log
random
P=0.05 30%
0
N 500 1500 N 500 1500
10
P10
100%
4 random
up 20%
regulation P=0.05
Thus, the results are cell line
independent (possibly robust)

11. B) Confirm ation of reciprocal relationship between m iRNA
expression change and P­value (upregulation of target genes)
IMR90,NGS
Correlation Coefficient
# of m iRNAs
700 0.35
100 0.05
quality score quality score
-log
2 m iRDeep2:
P=0.05 genom e alignm ent
10
1 01 10 2 10 4 program for m iRNA-seq
P
Threshold
quality score Value
(m iRDeep2)

12. Candidates of m iRNAs downregulaed
(target genes are upreglated)
NMRC : Norm alied m iRNA Read Counts P<0.05 RFC>1.0
SCORE : m iRDeeps score
P-value : upregulation of target genes
RFC : Reciprocal Fold Change : young/senescent

13. Candidates of miRNAs upregulaed
(target genes are downreglated)
NMRC : Normalied miRNA Read Counts P<0.05 FC>1.0
SCORE : miRDeeps score
P-value : downregulation of target genes
FC : Fold Change : senescent/young

14. Candidates of miRNAs upregulaed
(target genes are downreglated) continued
NMRC : Normalied miRNA Read P<0.05 FC>1.0
Counts
SCORE : miRDeeps score
P-value : downregulation of targe genes

15. 6. Summary & Conclusion
1. Selection of miRNAs commonly
up/downregulated during cell senescence
2. Reciprocal relationship between target gene
regulation and miRNA expression change
3. Reduction of number of critical candidate
miRNAs during cell senescence
(down: 131 ⇒１０, up: 141 ⇒ 32)

16. Full paper published in
Aging and Disease, (2012) No.4 in press
(Epub 7 Jun 2012, online)
MiRaGE Package will be included in
Bioconductior 2.11
(planed to be released in this Autumn)
MiRaGE Server
http://www.granular.com/MiRaGE/