Modeling the cell cycle regulation by the RB/E2F pathway Laurence Calzone Service de Bioinformatique U900 Inserm / Ecoles de Mines / Institut Curie Collaborative work with two groups led by: François Radvanyi (UMR 144) Emmanuel Barillot (U900/ Ec. Des Mines/ Institut Curie)

– JSM 2008 – Laurence Calzone The role of bioinformatics and systems biology The main purpose is to understand the behavior of a complex system as a whole, as opposed to the behavior of its individual components. More specifically, the goal is: -provide a consensus picture of the cell functioning -integrate information from many experiments and publications -help confirm or infirm hypotheses: check that the mechanism is correct -propose experiments to experimentalists Ideally, the systems biology approach is iterative: 1.Build the molecular map and the corresponding mathematical model from experimental data; 2.Test experimentally theories, phenotypes or hypotheses predicted by the model; 3.Modify/Refine the model according to the biological results; 4.etc.

– JSM 2008 – Laurence Calzone DNA mRNA polypeptide A B C E F D network physiology substrate protein activity product(s)

– JSM 2008 – Laurence Calzone Motivation to work on cancer Cellular processes are based on complex networks of interacting genes and proteins Cancer is a pathology of the processes that govern differentiation, proliferation, apoptosis, that is a disregulation of these networks. The general questions we would like to answer are: How can we describe pathways and model them? What are the pathways involved in a pathology? How to use the pathways to improve predictions? What are the effects of a perturbation on a pathway? etc. The more specific questions we are interested in are: Why are some genes amplified in tumor cells; why and how can genomic alterations lead to cancers; etc. What are the pathways or actors involved in the activation of a protein? Which phenotypes can be predicted from certain perturbations?

– JSM 2008 – Laurence Calzone RB in tumor progression RB (Retinoblastoma) is a cell proliferation regulator: RB is a tumor suppressor that controls cell cycle progression (G0/G1 and G1/S transitions). The importance of the RB pathway is known in cancer:  RB is targeted and inactivated by viral oncoproteins (E7)  RB pathway is inactivated in most tumoral cells in different ways: - RB gene mutation - Deregulation of the kinases that control its activity Mitogenic Signal CDK4/6 RB RB-P E7 E2F Progression of Cell Cycle CKI (p16) Cyc D

– JSM 2008 – Laurence Calzone Step 1: Build a consensus protein-protein interaction map of RB/E2F network 78 proteins, 169 genes, 208 species, 166 reactions, more than 350 publications…

– JSM 2008 – Laurence Calzone Step 2: Make the map usable 1. From the complete network, build a modular view G0 Early G1Late G1SG2M

– JSM 2008 – Laurence Calzone Module RB (no information lost)

– JSM 2008 – Laurence Calzone Step 2: Make the map usable 2. Apply the map to real transcriptome and CGH data: example of bladder cancer (55 bladder tumor + 5 normal samples) - Definition of modules’ activity in invasive and non-invasive cancers:  Invasive cancers: « proliferation » modules are active and « inhibitors of proliferation » are inactive Other analysis of the data:  Classification of these samples according to their activity reveals the type of alterations that make tumors more invasive than others. upregulated downregulated normal sample level Invasive cancers

– JSM 2008 – Laurence Calzone Perspectives - Apply this method to other cancers (Ewing, retinoblastoma, etc.) - Model the pathway (discrete and numerical) in order to answer specific questions - Other project on modeling apoptosis (in collaboration with experimentalists)

– JSM 2008 – Laurence Calzone Webpage : Interactive map

– JSM 2008 – Laurence Calzone Loredana Martignetti SITCON project miRNA and sequence analysis

– JSM 2008 – Laurence Calzone