SIGBIO28

1. Inference of target gene regulation via m iRNAs
during cell senescence by MiRaGE S erver
Y-h. Taguchi
Departm ent of Physics
Chuo University

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

3. 1. What is cell senescence?
T cell division cannot continue forever
he
for incubated cell lines. It m ust stop after
several rounds of proliferation.
⇓
T is called “cell senescence”, which is
his
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?
m iRNA is a kind of non-coding RNA.
m iRNAs are believed to suppress target gene
expression by degradation of m RNAs.
Im portant features:
・T ypically, there are hundreds kinds of m iRNAs found for
each species (c.a., ≧1000 for hum an).
・ Each m iRNA targets m ore than hundreds of genes.
・ m iRNA m ainly contributes to cell type change
(e.g., cancer, defferentiation, diseases)
・Infulence to target gene expression by m iRNA is subtle
(〜10%) and contexts dependent.
・In spite of that,
m iRNA critically contributes to the related processes

5. 3. Previous works (wet)
Several researches suggest the contribution of miRNAs
to cell senescence.
Upregulation of m iRNAs during cell senescence
m iR-34a,m iR-486-5p,m iR-494,m iR-210...
Downregulation of m iRNAs during cell senescence
m iR-15a/b,m iR-20a,m iR-92,m iR-16b....
Induction of cell senescence by suppression of
m iRNA 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(!) m iRNAs and the downregulation of 131(!!)
m iRNAs during cell senescence by deep sequencing.
T reason why lim ited num ber of m iRNAs revealed
he
significant expression change during cell senescence seem s
to be due to less sensitivity of microarray analysis.
Is it truly critical the down/upregulation of such large
num ber of m iRNAs for cell senescence?

7. 4. MiRaGE Method
In order to select “Critical ” m iRNAs during
cell senescence, regulation of target genes
by m iRNAs is inferred by MiRaGE S erver.
For details, see
SIGBIO-25-5: S earch of m iRNAs critical for m edulloblastom a
form ation using MiRaGE m ethod
○Y-h. Taguchi(Chuo Univ.) ， Jun Yasuda(T ohoku Univ.)
SIGBIO-25-30:Gene expression regulation during
differentiation from m urine ES cells due to m icroRNA

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

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

10. Intersection between N top-ranked significant m iRNAs
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 m iRNAs upregulaed
(target genes are downreglated)
NMRC : Norm alied m iRNA Read Counts P<0.05 FC>1.0
SCORE : m iRDeeps score
P-value : downregulation of target genes
FC : Fold Change : senescent/young

14. Candidates of m iRNAs upregulaed
(target genes are downreglated) continued
NMRC : Norm alied m iRNA Read Counts P<0.05 FC>1.0
SCORE : m iRDeeps score
P-value : downregulation of targe genes
FC : Fold Change : senescent/young

15. 6. Summary & Conclusion
1. Selection of m iRNAs com m only
up/downregulated during cell senescence
2. Reciprocal relationship between target gene
regulation and m iRNA expression change
3. Reduction of num ber of critical candidate
m iRNAs during cell senescence
(down: 131 ⇒１０, up: 141 ⇒ 32)