Copyright, Seiya Imoto, Human Genome Center, University of Tokyo, 2009

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Human umbilical vein endothelial cell (HUVEC)Fenofibrate: agonist of PPAR�, drug for hyperlipemia

Time-course data (triplicate)

CodeLink Human Uniset I 20K (20,469 probes)TM

Time-course data (triplicate)- HUVEC treated with 25�M fenofibrate- 0 (control), 2, 4, 6, 8 and 18 hours (6 time-points)

Knock-down data- 400 KD (by siRNA) arrays (in 2006 we use 270 KDs)400 KD (by siRNA) arrays (in 2006 we use 270 KDs)- Most knock-down genes are transcription factor

1192 id tifi d th f fib t l t d1192 genes are identified as the fenofibrate-related genes(The details are described in Imoto et al. (2006) PSB)

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E FCont siRNACont siRNA

By the microarray (D k

C DsiRNA for D

Cont siRNACont siRNA

AB

Cont siRNA

Cont siRNACont siRNA

Imoto, S., Tamada, Y., Araki, H., Yasuda, K., Print, C.G., D. Charnock-Jones, S., Sanders, D., Savoie, C.J., Tashiro, K., Kuhara, S., Miyano, S. (2006) Computational strategy for discovering druggable gene networks from genome-wide RNA expression profiles. Pacific Symposium on Biocomputing, 11, 559–571.

PPAR�

Network of 1192 fenofibrate-inducedgenes

Downstream pathway of PPAR�

Focus on lipid PPAR�metabolism genes

PPARaperoxisome proliferative activated receptor alpha Fatty acid synthesisactivated receptor, alphaFatty acid beta-oxidation Fatty acid synthesis

RARGretinoic acid receptor,

gamma

ITPR3inositol 1,4,5-triphosphate

receptor, type 3

EHHADHDCI Kassam et al.

enoyl-Coenzyme A, hydratase/3-hydroxyacyl

Coenzyme A dehydrogenase

DCIdodecenoyl-Coenzyme A

delta isomerase (2000) J. Biol. Chem.

SREBF1sterol regulatory element

binding transcription factor 1

IL4interleukin 4

binding transcription factor 1

LDLRHSD17B4Cholesterol metabolism

Knight et al. (2005) Biochemical. J.

LDLRlow density

lipoprotein receptor

HSD17B4hydroxysteroid (17-beta)

dehydrogenase 4 Fan et al. (1998) J. Endocrino. Bernal-Mizrachi et al. (2003) Nat. Med.

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HMGCR: Sankyo

LIPG

HMGCR: Sankyo

LSS: RocheLSS: Roche

AKR1C3 COX2

PPARa: Fenofibrate

Druggable: Nat. Rev. Drug Discov. 1:727-30, 2002

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GENE X Down stream of GENE X(pick up lipid metabolism genes)

C14orf1(ERG28)

ACAT2TCEA2

LSS

ACAT2

LSSPTGS1

IDI1HMGCS1

BMP4

PTGS2

HMGCR

FDFT1

DHCR24

FDFT1

ACAS2

•Cholesterol synthesis genes•Lipid metabolism genes

Copyright (C) Seiya Imoto, Human Genome Center, University of Tokyo

COX 2 inhibitors cause heart diseaseCOX-2 inhibitors cause heart diseaseand cerebral stroke!!

Various COX-2 inhibitors� Vioxx@Merck@� Celebrex@Pfizer� Bextra@Pfizer

Copyright (C) Seiya Imoto, Human Genome Center, University of Tokyo

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Araki, H., Tamada, Y., Imoto, S., Dunmore, B., Sanders, D., Humphrey, S., Nagasaki, M., Doi, A., Nakanishi, Y., Yasuda, K., Tomiyasu, Y., Tashiro, K., Print, C., Charnock-Jones, D. S., Kuhara, S., Miyano, S. (2009). Analysis of PPAR alpha-dependent and PPAR alphaindependent transcript regulation following fenofibrate treatment of human endothelial cells, Angiogenesis, in press.

Gene 1 Gene 2 Gene k

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Control Drug Control Drug Control DrugExp

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Dr g

Side Effect

Drug Drug Efficacy

D = {x1,...,xt ,...,xT } :Time Course Microarray Data

xt = (x1(t),...,xp(t)): Expression Data at Time t

Markov Property Between TimeMarkov Property Between Time

x1 x2 xTxT�1...

Gene Network: Bipartite Graph

p(x1,...,xt ,...,xT ) = p(x1) p(x2| x1) p(xT | xT�1)...

Gene Network: Bipartite Graph

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p(xt | xt�1) = �j p(xj(t) | paj(t �1), �j )

xj(t) = mj( paj(t �1)) + �j(t)

mj( paj(t�1)) = mj1(paj1(t�1)) + mj2 (paj2(t�1)) + ...

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Kim, Imoto, Miyano (2004) Biosystems, 75, 57-65.

gene 1 gene 2 gene k

A1 A2 A4

A2N1 = A1 N2 = A1 N4 = A3 A4U UNodeset

G1= (N1, E1) G2 = (N2, E2) G4 = (N4, E4)

Kim, Imoto, Miyano (2004) Biosystems, 75(1-3), 57–65. Tamada et al. (2009) Pac. Symp. Biocomput., 14, 251–263.

G G GG G1NG

2NG4NG

3NG5NG G G GG G

1NG2NG

4NG3NG

5NG

G G GG G1NG

2NG4NG

3NG5NG G G GG G

1NG2NG

4NG3NG

5NG

G G GG G1NG

2NG4NG

3NG5NG

Background

Fenofibrate is a synthetic ligand for PPARa. However there are reports that fenofibrate affects endothelial cellsHowever, there are reports that fenofibrate affects endothelial cellsin a PPARa-independent manner.

Aim and Method

Using siRNA for PPARa (not included in 400KDs),g ( ),we separate fenofibrate-regulated genes into PPARa-dependent or PPARa-independent

Thi iThis gene isPPARa-dependentlyregulated byregulated byfenofibrate

(1.7-fold & q < 0.05)( q )

(1.7-fold)

Fenofibrate Regulated GenesFenofibrate Regulated Genes

PPARa-dependently Regulated Genes by Fenofibrate

666 167 = 499666 – 167 = 499

499/666 ~ about 74.9 % PPARa-Independent

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GDF15 i hibit d th li l ll i ti d d t i t ll tidGDF15 inhibits endothelial cell migration and decreases matrix metallopeptidase2 (MMP2) activity produced by the HUVECs in a concentration-dependent manner. These effects are very similar to fenofibrate’s effects

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University of Tokyo University of AucklandUniversity of TokyoProf. Satoru MiyanoDr. Yoshinori Tamada

University of AucklandProf. Cristin Print

Dr. Masao Nagasaki

Kyushu University

University of CambridgeProf. D. Stephen Charnock-JonesDr Ben Dunmore

Prof. Satoru KuharaProf. Kousuke Tashiro

Dr. Ben DunmoreDr. Deborah SandersDr. Sally Humphreys

Cell Innovator Inc.Dr. Hiromitsu ArakiDr Atsushi DoiDr. Atsushi DoiDr. Kaori Yasuda

Yukiko NakanishiYuki TomiyasuYuki Tomiyasu