[PPT] - promoters can help to find new drugs. (Practical guide to PowerPoint Presentation

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“Walking pathways” and how promoters can help to find new drugs.

(Practical guide to multi-omics and multi- scale data integration)

alexander.kel@genexplain.com

Alexander Kel

Biosoft.ru, Skolkovo Moscow Wolfenbüttel Novosibirsk

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Trovafloxacin - antibiotic

Withdrawn from market due to risk of idiosyncratic hepatotoxicity in 2001.

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Failure Affects National Economies: Medicines & Equitable Distribution

13 November 2012 Hensley 3

Combined treatment and productivity costs for US in 2007

Milken Institute 2008

Total: 1.3 T$

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R&D Pipeline



10 20 30 40 50 60 $10 $20 $30 $40 $50 $60 $70 $80 Global R&D Spending Drug approvals: NMEs/BLAs $ 0 1993 1994 1995 1996 1997 1998 1999 2000 2001 2002 2003 2004 2005 2006 2007 2008E

P/

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One of the main causes of high death rate for such diseases is the unsatisfactory quality of treatment, which in the first place is brought by low efficiency and insufficient safety of today’s drugs and therapies. About 50% of prescribed medicine doesn’t have any therapeutic effect at all. Moreover, 125 thousand deaths annually (in USA) are caused by the drugs’ side effects. It becomes more and more obvious that the main cause of this crisis is the insufficient understanding of deep biological mechanisms of initiation and flowing of pathological conditions and toxicity mechanisms used in drugs.

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13/11/2012

Drug discovery – the Gold Rush

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13/11/2012

Drug discovery – should become a technology

Disease

Patient

Therapy

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Systems approaches will transform the way drugs are developed … that will target multiple components of networks and pathways perturbed in diseases. They will enable medicine to become predictive, personalized, preventive and participatory

Systems medicine: the future of medical genomics and healthcare Charles Auffray1*, Zhu Chen2 and Leroy Hood3 Genome Med 2009, 1:2

Systems medicine

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We should find a key pathway of a disease, select a good target and inhibit it.

TRANSPATH

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Pathway mapping

Differentially expressed genes/proteins Mapping on pathways

Cause of disease ??

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TNF-a 117 differentially expressed genes

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Can we predict TNF pathway?

117 differentially expressed genes

?

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Canonical TNF pathway

TRANSPATH

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Lets do mapping the differentially expressed genes on canonical pathways.

Pathway name Hits Pathway_id Hit names Pathway size p-value M-CSF ---> c-Ets-2 2 CH000000060 ETS2; CSF1 5 3.07E-03 IFNalpha, IFNbeta, IFNgamma ---> Rap1 3 CH000000595 IFNGR1; TYK2; IFNGR2 19 4.34E-03 Epo ---Lyn---> STAT5A 2 CH000000524 STAT5A; LYN 6 4.56E-03 activin A ---> Smad3 2 CH000000680 INHBA; SMAD3 10 1.31E-02 IFN pathway 3 CH000000740 IFNGR1; TYK2; IFNGR2 29 1.44E-02 Sonic Hedgehog pathway 2 CH000001022 MTSS1; PTCH 19 4.48E-02 hypoxia pathways 2 CH000000987 CDKN1B; NRIP1 21 5.38E-02 EDAR pathway 2 CH000000759 NFKBIA; CYLD 27 8.40E-02 Epo pathway 2 CH000000741 STAT5A; LYN 32 1.12E-01 TGFbeta pathway 3 CH000000711 BMP2; INHBA; SMAD3 72 1.39E-01 IL-22 pathway 1 CH000000762 TYK2 9 1.51E-01 IL-10 pathway 1 CH000000761 TYK2 9 1.51E-01 VEGF-A pathway 2 CH000000723 NOS3; VEGFA 42 1.75E-01 TLR3 pathway 2 CH000000820 TANK; IKBKE 44 1.88E-01 IL-8 pathway 2 CH000000786 CXCL1; IL8 46 2.01E-01 TNF-alpha pathway 2 CH000000772 NFKBIA; OSIL 53 2.48E-01 p38 pathway 2 CH000000849 MAP2K3; DUSP8 55 2.61E-01

Not significant

Pathway name Hits Pathway_id Hit names Pathway size p-value M-CSF ---> c-Ets-2 2 CH000000060 ETS2; CSF1 5 3.07E-03 IFNalpha, IFNbeta, IFNgamma ---> Rap1 3 CH000000595 IFNGR1; TYK2; IFNGR2 19 4.34E-03 Epo ---Lyn---> STAT5A 2 CH000000524 STAT5A; LYN 6 4.56E-03 activin A ---> Smad3 2 CH000000680 INHBA; SMAD3 10 1.31E-02 IFN pathway 3 CH000000740 IFNGR1; TYK2; IFNGR2 29 1.44E-02 Sonic Hedgehog pathway 2 CH000001022 MTSS1; PTCH 19 4.48E-02 hypoxia pathways 2 CH000000987 CDKN1B; NRIP1 21 5.38E-02 EDAR pathway 2 CH000000759 NFKBIA; CYLD 27 8.40E-02 Epo pathway 2 CH000000741 STAT5A; LYN 32 1.12E-01 TGFbeta pathway 3 CH000000711 BMP2; INHBA; SMAD3 72 1.39E-01 IL-22 pathway 1 CH000000762 TYK2 9 1.51E-01 IL-10 pathway 1 CH000000761 TYK2 9 1.51E-01 VEGF-A pathway 2 CH000000723 NOS3; VEGFA 42 1.75E-01 TLR3 pathway 2 CH000000820 TANK; IKBKE 44 1.88E-01 IL-8 pathway 2 CH000000786 CXCL1; IL8 46 2.01E-01 TNF-alpha pathway 2 CH000000772 NFKBIA; OSIL 53 2.48E-01 p38 pathway 2 CH000000849 MAP2K3; DUSP8 55 2.61E-01

TNF pathway can not be found by direct maping on canonical pathways....

Not significant

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Human epidermoid carcinoma A431 cells treated by epidermal growth factor (EGF) EGF 320 differntially expressed proteins

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Pathway name #Hits in group Hit names Group size p-value Caspase network 6 K18; E1; Cytochrome C; Hsp10; Ku70; Cdc42 104 0.00201348 CHIP ---/ Pael-R 2 E1; Hsc70 12 0.01177937 p53 pathway 4 E1; L23; Cytochrome C; Ku70 79 0.02072214 beta-catenin ---/ KAI1 1 Reptin52 5 0.06701759 Aurora-A cell cycle regulation 2 Ubc5B; E1 34 0.07924485 JNK pathway 3 E1; 14-3-3zeta; Trx1 75 0.0813304 parkin associated pathways 2 E1; Hsc70 40 0.10447487 beta-catenin:E-cadherin complex phosphorylation and dissociation 1 alpha-catenin 9 0.11739049 stress-associated pathways 3 E1; 14-3-3zeta; Trx1 100 0.15476 hypoxia pathways 1 Trx1 24 0.2849595 TNF-alpha pathway 1 Trx1 36 0.39594524 EGF pathway 1 E1 103 0.57615756

Mapping differentially expressed proteins to canonical signal transduction pathways

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Why ?

Mapping on pathways does not work (even in such a simple cases)

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Pathways are far from being fully undersood.

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BIG gap of knowledge on interactions between TF and their target sites in DNA

TF2 TF3 TF1

TRANSPATH

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Search for new TF binding sites with PWMs (Match algorithm)

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p=M/N N n=k+s k M s

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Overrepresented TFs in TNF-alpha regulated promoters

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13/11/2012

Master regulator

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Search for the reason by the analysis of the ripples

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Can we predict TNF pathway?

117 differntially expressed genes

?

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13/11/2012

GeneXplain platform – drug target discovery pipeline

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TNF-alpha

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Human epidermoid carcinoma A431 cells treated by epidermal growth factor (EGF) EGF 320 differntially expressed proteins

?

Master regulator analysis

EGF was still not in the list !

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Pathways are far .....far....far from being fully undersood!

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Combinatorial regulation

„Fuzzy puzzle“

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TGAgTCA

AP-1

TGAGTCA

Human collagenase (-2013) *******

TGTGTAA ** ** *

Mouse IL-2 (-143)

TGTAATA ** *

Mouse IL-2 (-82) Consensus:

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Mouse c-fos promoter (Matrix search for TF binding sites)

1 <------------V$IK1_01(0.86) -----...V$CREBP1CJUN_01(0.85) 2 <-----------V$IK2_01(0.90) -----...V$CREB_01(0.96) 3 ----------->V$AP2_Q6(0.87) <-------------V$GKLF_01(0.87) 4-->V$ATF_01(0.89) <-------V$MZF1_01(0.99) ----...V$ELK1_01(0.87) 5 <-----------V$AP2_Q6(0.92) <------------V$SP1_Q6(0.88) 6>V$AP1FJ_Q2(0.89) <-------------V$GKLF_01(0.85) 7>V$AP1_Q2(0.87) <-------------V$GKLF_01(0.86) 8->V$CREB_Q2(0.86) <---------V$CETS1P54_01(0.90) 9->V$CREB_Q4(0.90) <---------V$NRF2_01(0.90) 10 <-------------V$GC_01(0.88) 11 ----------->V$CAAT_01(0.87) 12 <------------V$TCF11_01(0.87) 13 ----------->V$AP2_Q6(0.87) 14 <---------V$USF_Q6(0.93) 16 --------...V$ATF_01(0.94) 17 -------...V$AP1FJ_Q2(0.95) 20 -------...V$CREBP1_Q2(0.93) 21 -------...V$CREB_Q2(0.95) 23 ---...V$IK2_01(0.85) MMCFOS_1 GAGCGCCCGCAGAGGGCCTTGGGGCGCGCTTCCCCCCCCTTCCAGTTCCGCCCAGTGACG 420 1-->V$CREBP1CJUN_01(0.85) -------------->V$BARBIE_01(0.86) 2-->V$CREB_01(0.96) -------------->V$TATA_01(0.95) 3 ----------->V$CAAT_01(0.91) --------->V$AP4_Q5(0.95) 4----------->V$ELK1_01(0.87) --------------------->V$HEN1_01(0.87) 5 --------->V$AP4_Q5(0.88) <---...V$CMYB_01(0.93) 6 <---------V$CDPCR3HD_01(0.93) --...V$VMYB_02(0.89) 7 <--------------V$TATA_01(0.88) 8 --------------------->V$HEN1_02(0.87) 9 <---------------------V$HEN1_02(0.86) 10 <-----------------V$AP4_01(0.88) 11 ----------->V$LMO2COM_01(0.93) 12 <-----------V$LMO2COM_01(0.93) 13 <-----------V$MYOD_01(0.88) 17--->V$AP1FJ_Q2(0.95) <---------V$AP4_Q6(0.99) 20---->V$CREBP1_Q2(0.93) <---------V$MYOD_Q6(0.96) 21---->V$CREB_Q2(0.95) Transcription start 23-------->V$IK2_01(0.85) 24 <=========== E2F (0.80) MMCFOS_1 TAGGAAGTCCATCCATTCACAGCGCTTCTATAAAGGCGCCAGCTGAGGCGCCTACTACTC 480 1 <-----------------V$CMYB_01(0.91) -------...V$ER_Q6(0.86) 2 <-----------V$LMO2COM_01(0.90) <----...V$TCF11_01(0.87) 3 --------->V$MYOD_Q6(0.90) -------->V$STAT_01(0.93) 4 --------->V$VMYB_01(0.89) <--------V$STAT_01(0.89) 5--------------V$CMYB_01(0.93) -------->V$LMO2COM_02(0.93) 6------>V$VMYB_02(0.89) <-----------V$CAAT_01(0.85) 7 -------->V$VMYB_02(0.88) 8 -------------->V$EVI1_04(0.86) 9 ------------->V$GATA1_02(0.93) 12 <------------V$ZID_01(0.85) 13 <----------V$CP2_01(0.97) 14 ---------->V$GATA_C(0.92) 15 ----------------->V$CMYB_01(0.86) 16 --------->V$CREL_01(0.91) 24 <=========== E2F (0.82) MMCFOS_1 CAACCGCGACTGCAGCGAGCAACTGAGAAGACTGGATAGAGCCGGCGGTTCCGCGAACGA 540

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One of the TF binding sites in a composite elements can be rather weak. Weak DNA-protein interactions are stabilized by protein-protein interactions. AP-1 consensus

tgccacacaggtagactcttTTGAAAATAtgTGTAATAtgtaaaa catcgtgaca cccccatatt… …

. . . . . . .

96
79

ST

COMPEL:C00050 NF-ATp AP-1

Mouse Interleukin-2 gene promoter

TGAGTCA

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Composite Module (CM) Composite Modules (CM)

(Mark Ptashne, Alexander Gann Genes and Signals, 2002)

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w

...

Start of transcription

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Composite Modules (CM)

mk

We created a genetic algorithm to find site combinations

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MAX q q q cms

R r r r r K k m i k i k

k

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Composite Module Score (cms)

Composite Modules (CM)

K, the number of individual PWMs in the module, (k=1,K) Matrix cut-off values:

) (k

ff

cut

q



Relative impact values:

) (k

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Maximal number of best matches: mk R, the number of pairs of PWMs (r=1,R) Matrix cut-off values:

] [ , 1 r

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Relative impact values:

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Maximal and minimal distances:

] [ max r

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] [ min r

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Fitness function of the Genetic-Regression Algorithm (GRA)

k N T FP FN R F                     a ) 1 ( ) 1 ( ) 1 (

FN – false negatives FP – false positives T – T-test (difference between mean values) N – normal likeness k – number of free parameters R – linear regression cms

# promoters

FN FP N

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Weight: TF matrix 1.000000 0.840072 V$E2F_19 0.954483 0.737637 V$TATA_01 0.888064 0.939687 V$CREB_01 0.816179 0.941583 V$SP1_Q6 0.039746 0.839702 V$TAL1BETAE47_01



No of sequences 10 20 30 40

0,5

0,0 0,5 1,0 1,5 2,0 2,5 3,0 3,5 4,0

Background sequences Cell cycle-related promoters

ff

cut

q



Composite module in promoters of cell cycle-related genes

SLIDE 40 1 <------------V$IK1_01(0.86) -----...V$CREBP1CJUN_01(0.85) 2 <-----------V$IK2_01(0.90) -----...V$CREB_01(0.96) 3 ----------->V$AP2_Q6(0.87) <-------------V$GKLF_01(0.87) 4-->V$ATF_01(0.89) <-------V$MZF1_01(0.99) ----...V$ELK1_01(0.87) 5 <-----------V$AP2_Q6(0.92) <------------V$SP1_Q6(0.88) 6>V$AP1FJ_Q2(0.89) <-------------V$GKLF_01(0.85) 7>V$AP1_Q2(0.87) <-------------V$GKLF_01(0.86) 8->V$CREB_Q2(0.86) <---------V$CETS1P54_01(0.90) 9->V$CREB_Q4(0.90) <---------V$NRF2_01(0.90) 10 <-------------V$GC_01(0.88) 11 ----------->V$CAAT_01(0.87) 12 <------------V$TCF11_01(0.87) 13 ----------->V$AP2_Q6(0.87) 14 <---------V$USF_Q6(0.93) 16 --------...V$ATF_01(0.94) 17 -------...V$AP1FJ_Q2(0.95) 20 -------...V$CREBP1_Q2(0.93) 21 -------...V$CREB_Q2(0.95) 23 ---...V$IK2_01(0.85) MMCFOS_1 GAGCGCCCGCAGAGGGCCTTGGGGCGCGCTTCCCCCCCCTTCCAGTTCCGCCCAGTGACG 420 1-->V$CREBP1CJUN_01(0.85) -------------->V$BARBIE_01(0.86) 2-->V$CREB_01(0.96) -------------->V$TATA_01(0.95) 3 ----------->V$CAAT_01(0.91) --------->V$AP4_Q5(0.95) 4----------->V$ELK1_01(0.87) --------------------->V$HEN1_01(0.87) 5 --------->V$AP4_Q5(0.88) <---...V$CMYB_01(0.93) 6 <---------V$CDPCR3HD_01(0.93) --...V$VMYB_02(0.89) 7 <--------------V$TATA_01(0.88) 8 --------------------->V$HEN1_02(0.87) 9 <---------------------V$HEN1_02(0.86) 10 <-----------------V$AP4_01(0.88) 11 ----------->V$LMO2COM_01(0.93) 12 <-----------V$LMO2COM_01(0.93) 13 <-----------V$MYOD_01(0.88) 17--->V$AP1FJ_Q2(0.95) <---------V$AP4_Q6(0.99) 20---->V$CREBP1_Q2(0.93) <---------V$MYOD_Q6(0.96) 21---->V$CREB_Q2(0.95) Transcription start 23-------->V$IK2_01(0.85) 24 <----------- E2F (0.80) MMCFOS_1 TAGGAAGTCCATCCATTCACAGCGCTTCTATAAAGGCGCCAGCTGAGGCGCCTACTACTC 480 1 <-----------------V$CMYB_01(0.91) -------...V$ER_Q6(0.86) 2 <-----------V$LMO2COM_01(0.90) <----...V$TCF11_01(0.87) 3 --------->V$MYOD_Q6(0.90) -------->V$STAT_01(0.93) 4 --------->V$VMYB_01(0.89) <--------V$STAT_01(0.89) 5--------------V$CMYB_01(0.93) -------->V$LMO2COM_02(0.93) 6------>V$VMYB_02(0.89) <-----------V$CAAT_01(0.85) 7 -------->V$VMYB_02(0.88) 8 -------------->V$EVI1_04(0.86) 9 ------------->V$GATA1_02(0.93) 12 <------------V$ZID_01(0.85) 13 <----------V$CP2_01(0.97) 14 ---------->V$GATA_C(0.92) 15 ----------------->V$CMYB_01(0.86) 16 --------->V$CREL_01(0.91) 24 <----------- E2F (0.82) MMCFOS_1 CAACCGCGACTGCAGCGAGCAACTGAGAAGACTGGATAGAGCCGGCGGTTCCGCGAACGA 540 1----------->V$ER_Q6(0.86) 2--------V$TCF11_01(0.87) 3 --------->V$AP4_Q5(0.91) 4 --------->V$AP4_Q6(0.87) 5 ---------->V$AP1FJ_Q2(0.93) 6 ---------->V$AP1_Q2(0.90) 7 ---------->V$AP1_Q4(0.87) 8 <-----------V$IK2_01(0.94) MMCFOS_1 GCAGTGACCGCGCTCCCACCCAGCTCTGCTCTGCAGCTCC 580

Mouse c-fos promoter

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180
150
249

AP-1 NFAT HMG Y NFAT NFAT AP-1 STAT 6 NF-Y

114
88

AP-1 NFAT HMG Y

60

AP-1 NFAT TATA

28

c-MAF CE CE TSS +1

Mouse IL-4 promoter

Promoter structure: curret paradigm

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Promoter is a parking place

SLIDE 43 1 <------------V$IK1_01(0.86) -----...V$CREBP1CJUN_01(0.85) 2 <-----------V$IK2_01(0.90) -----...V$CREB_01(0.96) 3 ----------->V$AP2_Q6(0.87) <-------------V$GKLF_01(0.87) 4-->V$ATF_01(0.89) <-------V$MZF1_01(0.99) ----...V$ELK1_01(0.87) 5 <-----------V$AP2_Q6(0.92) <------------V$SP1_Q6(0.88) 6>V$AP1FJ_Q2(0.89) <-------------V$GKLF_01(0.85) 7>V$AP1_Q2(0.87) <-------------V$GKLF_01(0.86) 8->V$CREB_Q2(0.86) <---------V$CETS1P54_01(0.90) 9->V$CREB_Q4(0.90) <---------V$NRF2_01(0.90) 10 <-------------V$GC_01(0.88) 11 ----------->V$CAAT_01(0.87) 12 <------------V$TCF11_01(0.87) 13 ----------->V$AP2_Q6(0.87) 14 <---------V$USF_Q6(0.93) 16 --------...V$ATF_01(0.94) 17 -------...V$AP1FJ_Q2(0.95) 20 -------...V$CREBP1_Q2(0.93) 21 -------...V$CREB_Q2(0.95) 23 ---...V$IK2_01(0.85) MMCFOS_1 GAGCGCCCGCAGAGGGCCTTGGGGCGCGCTTCCCCCCCCTTCCAGTTCCGCCCAGTGACG 420 1-->V$CREBP1CJUN_01(0.85) -------------->V$BARBIE_01(0.86) 2-->V$CREB_01(0.96) -------------->V$TATA_01(0.95) 3 ----------->V$CAAT_01(0.91) --------->V$AP4_Q5(0.95) 4----------->V$ELK1_01(0.87) --------------------->V$HEN1_01(0.87) 5 --------->V$AP4_Q5(0.88) <---...V$CMYB_01(0.93) 6 <---------V$CDPCR3HD_01(0.93) --...V$VMYB_02(0.89) 7 <--------------V$TATA_01(0.88) 8 --------------------->V$HEN1_02(0.87) 9 <---------------------V$HEN1_02(0.86) 10 <-----------------V$AP4_01(0.88) 11 ----------->V$LMO2COM_01(0.93) 12 <-----------V$LMO2COM_01(0.93) 13 <-----------V$MYOD_01(0.88) 17--->V$AP1FJ_Q2(0.95) <---------V$AP4_Q6(0.99) 20---->V$CREBP1_Q2(0.93) <---------V$MYOD_Q6(0.96) 21---->V$CREB_Q2(0.95) Transcription start 23-------->V$IK2_01(0.85) 24 <----------- E2F (0.80) MMCFOS_1 TAGGAAGTCCATCCATTCACAGCGCTTCTATAAAGGCGCCAGCTGAGGCGCCTACTACTC 480 1 <-----------------V$CMYB_01(0.91) -------...V$ER_Q6(0.86) 2 <-----------V$LMO2COM_01(0.90) <----...V$TCF11_01(0.87) 3 --------->V$MYOD_Q6(0.90) -------->V$STAT_01(0.93) 4 --------->V$VMYB_01(0.89) <--------V$STAT_01(0.89) 5--------------V$CMYB_01(0.93) -------->V$LMO2COM_02(0.93) 6------>V$VMYB_02(0.89) <-----------V$CAAT_01(0.85) 7 -------->V$VMYB_02(0.88) 8 -------------->V$EVI1_04(0.86) 9 ------------->V$GATA1_02(0.93) 12 <------------V$ZID_01(0.85) 13 <----------V$CP2_01(0.97) 14 ---------->V$GATA_C(0.92) 15 ----------------->V$CMYB_01(0.86) 16 --------->V$CREL_01(0.91) 24 <----------- E2F (0.82) MMCFOS_1 CAACCGCGACTGCAGCGAGCAACTGAGAAGACTGGATAGAGCCGGCGGTTCCGCGAACGA 540 1----------->V$ER_Q6(0.86) 2--------V$TCF11_01(0.87) 3 --------->V$AP4_Q5(0.91) 4 --------->V$AP4_Q6(0.87) 5 ---------->V$AP1FJ_Q2(0.93) 6 ---------->V$AP1_Q2(0.90) 7 ---------->V$AP1_Q4(0.87) 8 <-----------V$IK2_01(0.94) MMCFOS_1 GCAGTGACCGCGCTCCCACCCAGCTCTGCTCTGCAGCTCC 580

Mouse c-fos promoter

Promoter structure: reality

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Parking in Italy

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ChIP-seq data: EPS-FLI1

Ewing sarcoma transcription factor – gene fusion

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Network plasticity

„Walking pathways“

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small tumor transgenic transgenic/normal

small tumor/normal

Hepatocellular transcriptome data of IgEGF-overexpressing mice

Epidermal Growth Factor induced Carcinogenicity

Philip Stegmaier1, Alexander Kel1, Edgar Wingender1,2, and Jürgen Borlak3

Tumoregenic switch ?

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EGF

Cell proliferation

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EGF Egf

Cell proliferation

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Calveolin-1 EGF Egf Cav1

Cell proliferation

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Calveolin-1 EGF IGF-2 IGFBP-6 Egf Cav1 Pparg Igfbp6 Igf2

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IGF-2 IGFBP-6 Pparg Igfbp6 Igf2

Cell proliferation

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DNA is an active component

f biochemical networks.

Network plasticity is a result

f epigenetic evolution

in the cells.

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Cancer is cracking the combinatorial regulatory code

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13/11/2012

Net2Drug

?

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F2 F4 F3 F1

p53

TSS

Enhanceosome binding aria

Repression of genes

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13/11/2012

Survival mechanisms of cancer cells upon RITA treatment and potential target proteins for a complementary compound PI3-kinase

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13/11/2012

Death of Cancer cells treated with 0.1 M RITA and PI3-kinase inhibitor LY294002

RITA

LY

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13/11/2012

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Systems Medicine

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13/11/2012

SAR/QSAR

… …

Identified

16 novel componds

ChemNavigator Library

24 million

compounds

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13/11/2012

Cyclin-dependent kinase 2 inhibitor Myc inhibitor

Tested 16 compounds in a panel of several cancer cell lines.

Showed growth suppression in 3 different breast cancer cell lines. The effect appears to be p53-independent (kills p53-null colon cancer cells) and it does not affect the growth of non-transformed mammary epithelial cells

Hypoxia inducible factor 1 alpha inhibitor Phosphatidylinositol 3-kinase beta inhibitor

Compound N15 Compound N6 Out of panel of 7 different cancer lines it killed only melanoma cells without any effects in other cell lines and on control non- transformed mammary epithelial cells. Found active: Found active: Targets Targets

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Phosphoproteome Proteome Transcriptome ChIP-chip ChIP-seq Metabolome

Multiple data sources can be integrated with the goal to find master regulatory nodes

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Bentele M, 2004 Neumann L, 2010

CD95L module and results of fitting its dynamics to experimental data

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Modules: clear specification of interfaces

input/output contacts

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Modular model of apoptosis

13 modules
286 species
684 reactions
719 parameters

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13/11/2012

From virtual cell to virtual human

www. .com www.biouml.org

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Build virtual human to find novel drugs

www. .com

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Trovafloxacin - antibiotic

Withdrawn from market due to risk of idiosyncratic hepatotoxicity in 2001.

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13/11/2012

Trovafloxacin (TVX)

TGF-beta1

We found TGF-beta1 as a master

regulator – a potential off-target of TVX

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13/11/2012

TGF-beta dependent positive feedback TGFbeta SMAD STATs

Inhibition of genes of innate immune response

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13/11/2012

TGF-beta dependent positive feedback TGFbeta SMAD STATs

Inhibition of genes of innate immune response

SMAD site

A G

STAT site

C T

Inhibition of genes of innate immune response

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From virtual human to virtual patients

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geneXplain Platform

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On the first step the workflow identified the differentially expressed genes in the resistant versus sensitive patients and identified transcription factors involved.

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Here is the list of transcription factors predicted to be involved

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Here are the predicted sites for these transcription factors.

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Master node

On the next step the workflow identified the mater nodes.

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Here it visualized the found mater nodes.

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Some of the master nodes have information in PASS about inhibitors or agonists

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PASS / PharmaExpert multi-target search

Searching in a library of known drugs for compounds with potential of multi-target activity against selected targets

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Found a drug– imiquimod, with potential of activity for three targets

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We predict that Imiquimod can be used as a second drug to overcome the resitance to methotrexate

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