Systems Biology for TB Gary Schoolnik James Galagan

Systems Approach to TB Metabolic Network Model Regulatory Network Model Combine genomic technology with computational methods to model TB metabolic and regulatory networks

An International Collaboration Gary Schoolnik (Stanford) RT-PCR Greg Dolganov Audrey Southwick Stefan Kaufmann (Max Planck) in vivo Sample Core Metabolomics Anca Dorhoi James Galagan (Broad, BU) ChIP-Seq Bioinf/Modeling Brian Weiner Matt Petersen Jeremy Zucker David Sherman (SBRI) in vitro sample Core Microarray Tige Rustad Kyle Minch Branch Moody (BWH) Lipidomics Lindsay Sweet Chris Becker (PPD) Proteomics Glycomics

Comprehensive Profiling for TB Chip-Seq SBRI/BU Transcriptomics SBRI/Stanford/ MPIIB Proteomics PPD Glycomics PPD Lipidomics BWH Metabolomics Metabolon in vitro Cultures SBRI Macrophage Cultures MPIIB Computational Regulatory and Metabolic Network Modeling Broad/BU

An In vitro Oxygen Limitation Model Progression Into and Out Of Non-Replicating Persistence Early/Late Time Points Monitor Adaptation To A New State Aerated Culture

in vitro Sampling 1 - Fermentor w/Tyloxapol Bioflo 110 Fermentor Vessel and Control Unit Established In SBRI BL3 Lab Hypoxic Culture Condition Generated

in vitro Sampling 2 – Small Batch Culture

Early Stages of M. tuberculosis—Macrophage Interaction Depicting Cell Entry Using The Same Ex vivo Macrophage Infection Model Employed By TBSysBio Mtb-Infected J774 Macrophage Cells A Model Of Intra-phagosomal Adaptation

Systems Approach to TB Metabolic Network Model Regulatory Network Model Combine genomic technology with computational methods to model TB metabolic and regulatory networks

Gene Regulatory Networks TF ChIP-Seq Expression Data/CLR TF Binding Site Prediction Literature Curation Comparative Genomics

Regulon Motif Discover Genes Regulated by the same TF Assume a shared promotor TF binding sites

kstR – Lipid/Cholesterol Regulator KstR Binding Motif

MTB Complex Comparative Analysis Environmental Mycobacteria Corynebactera Rhodococcus Streptomyces

Rv3515ckstR Conservation of Majority of KstR Sites Conserved kstR Binding Sites

Degrade organic compounds in soil and convert to lipid storage Degradation of polycyclic aromatic hydrocarbons (PAHs) in soil. Human smegma: neutral fats, fatty acids, sterols. Remediation of polycyclic aromatic hydrocarbon (PAH) in soil Relatives in Low Places

Origins of Lipid Metabolism Russell (2007) Pathogens Soil

Evolution of Fatty Acid Degradation Genes Size of circle = # Fad Genes Orthologs

KstR Far2 Far1 Conserved Circuitry for Lipid Metabolism? Free Fatty Acids Cholesterol qPCR Data – Greg Dolganov Lipid Metabolism Genes

Comparative Network Analysis Chip-Seq KstR, Far1, Far2

Eflux – Combining Expression with FBA Genome-Wide Metabolic Reconstruction Algorithmically Interpret Expression Data in a Metabolic Flux Context Expression Data Colijn et al. (2009) PLoS Comput Biol Poster: Jeremy Zucker

Genome Scale Model Merged Raman et al. (2005) and McFadden (2008) models and extended Jeremy Zucker

Acknowledgements TB Regulatory Network Matt Petersen Brian Weiner Abby McGuire David Sherman Tige Rustad Greg Dolganov GenomeView Browser Thomas Abeel TB SysBio Team Greg Dolganov David Sherman Tige Rustad Kyle Minch Louiza Dudin Stefan Kauffman Anca Dorhoi Branch Moody Lindsay Sweet Chris Becker Brian Weiner Jeremy Zucker Aaron Brandes Michael Koehrsen Audrey Southwick NIAID Valentina Di Francesco Karen Lacourciere Maria Giovanni