Systems Biology of Tumor Progression and Drug-Resistance

COLUMBIA UNIVERSITY CENTER FOR:

CancerTarget Discovery and Development

CTD2 Network

The Road to Drug Development

CTD2 Network

Broad

CSHL

ColumbiaDanaFarber

UT South-western

ClinicalTrials

Hit compoundMechanism

of Action

Biomarkers:Response/Efficacy

How many tumor types are there?

(Epi-)Genetic Alterations

Subtype Signature

Cancer Genome Atlas Research Network. Comprehensive genomic characterization defines human glioblastoma genes and core pathways. Nature. 2008 Oct 23;455(7216):1061-8

Verhaak RG et al.; The Cancer Genome Atlas Research Network. Integrated Genomic Analysis Identifies Clinically Relevant Subtypes of Glioblastoma Characterized by Abnormalities in PDGFRA, IDH1, EGFR, and NF1. Cancer Cell. 2010 Jan 19;17(1):98-110

Changing the model

Cell Dynamics

Genetics

EpigeneticsHuman Cancer

LymphoidGlioblastoma

ProstateBreast

Ovarian…

CellRegulatory

Logic

ProteinProtein

ProteinMembrane

ProteinDNA

The Harsh Reality of Cancer Genetics

GBM (Epi)Genetic Alteration SpectrumG1 G2 G3 G4

G5 G6 G7 G8

G10 G11 G12

Patient X

MolecularPhenotype

E.g. GBM subtypes

G9

X

Y Z

W

V

MasterRegulatorModule(s)

DiseaseStratificationBiomarkers

Therapeutic Targets

…

= EGFR= PDGFRA= p16= p53= PTEN= MDM2= MDM4= MYC= NF1= ERBB2= RB1= CDK4

G1

G2

G3

G4

G5

G6

G7

G8

G9

G10

G11

G12

Glioblastoma: Carro MS et al. The transcriptional

network for mesenchymal transformation of brain tumours. Nature. 2010 Jan 21;463(7279):318-25.

Master Regulators: C/EBP + Stat3

Diffuse Large B Cell Lymphoma: Compagno M et al. Mutations of

multiple genes cause deregulation of NF-kappaB in diffuse large B-cell lymphoma. Nature. 2009 Jun 4;459(7247):717-21

Master Regulator: Nf-kB pathway

GC-Resistance in T-ALL: Real PJ et al. Gamma-secretase

inhibitors reverse glucocorticoid resistance in T cell acute lymphoblastic leukemia. Nat Med. 2009 Jan;15(1):50-8.

Master Regulator: NOTCH1 pathway

Identify and validate tumor-acquired Gene and Pathway Dependencies (Oncogene/Oncopathway addiction)

Identify their Small-Molecule Modulators

Characterize their associated Biomarkers of Response

Characterize their associated Biomarkers of Treatment Efficacy

Characterize the Mechanism of Action of their small-molecule modulators

Oncogene(s) Addiction

POST-TRANSLATIONAL INTERACTIONS

TRANSCRIPTIONAL INTERACTIONS

Zhao X et al. (2009) Dev Cell. 17(2):210-21.Mani KM et al. (2008) Mol Syst Biol. 4:169Palomero T et al., Proc Natl Acad Sci U S A 103, 18261 (Nov 28, 2006).Margolin AA et al., Nature Protocols; 1(2): 662-671 (2006)Margolin AA et al., BMC Bioinformatics 7 Suppl 1, S7 (2006).Basso K et al. (2005), Nat Genet.;37(4):382-90. (Apr. 2005)

Wang K, Saito M, et al. (2009) Nat Biotechnol. 27(9):829-39Zhao X et al. (2009) Dev Cell. 17(2):210-21.Wang K et al. (2009) Pac Symp Biocomput. 2009:264-75.Mani KM et al. (2008) Mol Syst Biol. 4:169Wang K et al. (2006) RECOMB

POST-TRANSCRIPTIONAL INTERACTIONS

Basso et al. Immunity. 2009 May;30(5):744-52Klein et al, Cancer Cell, 2010 Jan 19;17(1):28-40.

MASTER REGULATORS AND MECHANISM OF ACTION

Lefebvre C. et al (2010), Mol Syst. Biol, in pressCarro MS et al. (2010) Nature 2010 Jan 21;463(7279):318-25Mani K et al, (2008) Molecular Systems Biology, 4:169

Unsupervised clustering of 76 high grade tumors by expression of 108 genes that are positively or negatively associated with survival reveals 3 tumors classes (Proneural (PN), Mesenchymal (Mes) and Proliferative (Prolif).

Phillips et al., Cancer Cell, 2006

Malignant gliomas belonging to the mesenchymal sub-class express genes linked to the most aggressive properties of glioblastoma (migration, invasion and angiogenesis).

Mesenchymal Subtype of High-Grade Gliomas

MGES

PNGES

PROGES

Mes signature genesActivatorRepressor

Identification of a mesenchymal regulatory module

Biochemical Validation of ARACNe Inferred Targets of Stat3, C/EBPb, FosL2, and bHLH-B2

Master Regulators control >75% of the Mesenchymal Signature of High-Grade Glioma

Hierarchical Regulatory Module

C/EBPb and Stat3 modulate mesenchymal lineage in mouse neural stem cells and human glioma cells

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Vector Stat3C+C/EBPGFP GFP

CTGF CTGF

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shCtr shStat3 shC/EBPβ shStat3 + shC/EBPβFibronectin/DAPIFibronectin/DAPIFibronectin/DAPI Fibronectin/DAPI

Cola51/DAPICola51/DAPICola51/DAPI Cola51/DAPI

YKL40/DAPIYKL40/DAPIYKL40/DAPI YKL40/DAPI

Cola51/DAPICola51/DAPICola51/DAPI Cola51/DAPI

YKL40/DAPIYKL40/DAPIYKL40/DAPI YKL40/DAPI

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Control VectorStat3-C/EBPb-Stat3-/C/EBPb-

Human

MouseMouse immunohistochemistry

Significantly Altered

Not Altered

Pathway-Wide Association Study (PWAS)

Other (56)Poor Prognosis (Mesenchymal + Proliferative) (174)

MES signature

CEBPb/d

HMG20B, PTPRAInferred via MINDY and functional association of CNVs

Inferred via ARACNE and functional association of CNVs with change in mRNA levels

TEAD3, ZFP36L2

KLHL9

Inferred via functional association of CNVs with change in mRNA levels, increase in CEBPD regulon activity

Odd Ratio = 5.405, p-value = 1.12e-6

Mutation CHR OR p-value #samples

CEBPD (amp) 8 4.61 1e-4 36

PTPRA (amp) 20 4.78 0.032 10

HMG20B (amp)

19 2.83 0.042 16

KLHL9 (del) 9 4.70 0.018 32

Mutation CHR OR p-value

C/EBPd (amp) TF Master Regulator 8 4.61 0.004

PTPRA (amp) MINDy Modulator of C/EBP subunits (YP) 20 4.78 0.032

HMG20B (amp) MINDy Modulator of C/EBP subunits (TF) 19 2.83 0.042

KLHL9 (del) Ubiquitin Conjugating Ligase. Modulates TEAD3, which is a Transcriptional Activator of C/EBP subunits

9 4.70 0.018

Gene

Focal Amplification of C/EBPd locus

CEBPD EFCAB1 PXNDNL

Mesenchymal Non-Mesenchymal

CEBPD EFCAB1

Red: amplificationBlue: deletion

KLH

L9

MLL

T3

CDKN

2A

ELAV

L2

-log(

p) a

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n w

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ES

Position (MB)

RRA

GA

FAM

29A

AD

FP

DEN

ND

4C

RPS6

ASA

H3L

SLC2

4A2

MLL

T3

KIA

A17

97

PTPL

AD

2

IFN

B1

IFN

W1

IFN

A14

KLH

L9

IFN

A2

IFN

A8

IFN

E1

MTA

P

CDKN

2A

CDKN

2B

DM

RTA

1

ELA

VL2

Pro

ne

ura

lM

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CDKN2AKLHL9

The Network Address of a compound

DHFR

Both Mtx and PdxPdx Only

Mtx Only

Top 2028

Network-based Activity Signature for Methotrexate and Pralatrexate (both are DHFR inhibitors): NetMoA

CTD2: Cancer Target Discovery and Development Network

Systems Pharmacology at Columbia University

A Califano (PI), R. Dalla-Favera, A. Ferrando, A. Iavarone, B. Stockwell, J. Silva

Collaboration with the Broad Institute (S. Schreiber) Identification of Small-molecule inhibitors of Stat3 and C/EBP

Collaboration with UT Southwestern (M. White, J. Minna) Validation of synergistic oncopathway dependencies in tyrosine kinase signaling

networks, in Non Small Cell Lung Cancer

Collaboration with Dana Farber (B. Hahn, L. Chin, R. DePinho) and the Broad Institute (S. Schreiber) Identification and validation of oncopathway addiction in ovarian cancer

Collaboration with CSHL (S. Powers, S. Lowe) Prioritization of genetic aberrations as drivers of oncogenesis in ovarian cancer

from Genome Wide Association Studies

Network Collaborations

Parallel discovery pipeline Target(s) + small-molecule

modulators + biomarkers + MoA

Integrated, State-of-the-Art Technological Platforms RNAi + Systems Biology +

Chemistry + HT Screening + Functional Genomics

Direct Path to Translation

Large-Scale functional datasets in vitro and in vivo

Complete, network-validated data + model + reagent sharing

Investigator Network Excellence

CTD2 Conclusions

Linear discovery pipeline

Individual Technological Platform

Potential for Translation

Small Individual functional datasets

Partial data sharing

Investigator Excellence

CTD2 ModelTraditional Discovery