title: A disease module in the interactome explains disease heterogeneity, drug response and captures novel pathways and genes in asthma.
abstract: Recent advances in genetics have spurred rapid progress towards the systematic identification of genes involved in complex diseases. Still, the detailed understanding of the molecular and physiological mechanisms through which these genes affect disease phenotypes remains a major challenge. Here, we identify the asthma disease module, i.e. the local neighborhood of the interactome whose perturbation is associated with asthma, and validate it for functional and pathophysiological relevance, using both computational and experimental approaches. We find that the asthma disease module is enriched with modest GWAS P-values against the background of random variation, and with differentially expressed genes from normal and asthmatic fibroblast cells treated with an asthma-specific drug. The asthma module also contains immune response mechanisms that are shared with other immune-related disease modules. Further, using diverse omics (genomics, gene-expression, drug response) data, we identify the GAB1 signaling pathway as an important novel modulator in asthma. The wiring diagram of the uncovered asthma module suggests a relatively close link between GAB1 and glucocorticoids (GCs), which we experimentally validate, observing an increase in the level of GAB1 after GC treatment in BEAS-2B bronchial epithelial cells. The siRNA knockdown of GAB1 in the BEAS-2B cell line resulted in a decrease in the NFkB level, suggesting a novel regulatory path of the pro-inflammatory factor NFkB by GAB1 in asthma.
authors.affiliation: Center for Complex Networks Research, Department of Physics, Northeastern University, Boston, MA 02115, USA Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Amitabh
authors.initials: A
authors.lastname: Sharma
authors.affiliation: Center for Complex Networks Research, Department of Physics, Northeastern University, Boston, MA 02115, USA Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Theoretical Physics, Budapest University of Technology and Economics, H1111, Budapest, Hungary Center for Network Science, Central European University, Nador u. 9, 1051 Budapest, Hungary.
authors.forename: Jörg
authors.initials: J
authors.lastname: Menche
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: C Chris
authors.initials: CC
authors.lastname: Huang
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: Tatiana
authors.initials: T
authors.lastname: Ort
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Xiaobo
authors.initials: X
authors.lastname: Zhou
authors.affiliation: Center for Complex Networks Research, Department of Physics, Northeastern University, Boston, MA 02115, USA Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Maksim
authors.initials: M
authors.lastname: Kitsak
authors.affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Nidhi
authors.initials: N
authors.lastname: Sahni
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Derek
authors.initials: D
authors.lastname: Thibault
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Linh
authors.initials: L
authors.lastname: Voung
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Feng
authors.initials: F
authors.lastname: Guo
authors.affiliation: Center for Complex Networks Research, Department of Physics, Northeastern University, Boston, MA 02115, USA Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA.
authors.forename: Susan Dina
authors.initials: SD
authors.lastname: Ghiassian
authors.affiliation: Department of Cellular and Molecular Pharmacology, University of California 1700, 4th Street, Byers Hall 308D, San Francisco, CA 94158, USA.
authors.forename: Natali
authors.initials: N
authors.lastname: Gulbahce
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: Frédéric
authors.initials: F
authors.lastname: Baribaud
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Tocker
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: Radu
authors.initials: R
authors.lastname: Dobrin
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: Elliot
authors.initials: E
authors.lastname: Barnathan
authors.affiliation: Janssen Research & Development, Inc., 1400 McKean Road, Spring House, PA 19477, USA.
authors.forename: Hao
authors.initials: H
authors.lastname: Liu
authors.affiliation: Pulmonary Allergy and Critical Care Division, Department of Medicine, University of Pennsylvania, 125 South 31st Street, TRL Suite 1200, Philadelphia, PA 19104, USA.
authors.forename: Reynold A
authors.initials: RA
authors.lastname: Panettieri
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Kelan G
authors.initials: KG
authors.lastname: Tantisira
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Weiliang
authors.initials: W
authors.lastname: Qiu
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Benjamin A
authors.initials: BA
authors.lastname: Raby
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Edwin K
authors.initials: EK
authors.lastname: Silverman
authors.affiliation: Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Department of Genetics, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Marc
authors.initials: M
authors.lastname: Vidal
authors.affiliation: Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA.
authors.forename: Scott T
authors.initials: ST
authors.lastname: Weiss
authors.affiliation: Center for Complex Networks Research, Department of Physics, Northeastern University, Boston, MA 02115, USA Center for Cancer Systems Biology (CCSB) and Department of Cancer Biology, Dana-Farber Cancer Institute, Boston, MA 02215, USA Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA Department of Theoretical Physics, Budapest University of Technology and Economics, H1111, Budapest, Hungary Center for Network Science, Central European University, Nador u. 9, 1051 Budapest, Hungary barabasi@gmail.com.
authors.forename: Albert-László
authors.initials: AL
authors.lastname: Barabási
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000235:genetics / Q000378:metabolism; D018927:Anti-Asthmatic Agents / Q000494:pharmacology* / Q000627:therapeutic use; D001249:Asthma / Q000188:drug therapy / Q000235:genetics* / Q000378:metabolism; D001483:Base Sequence; D004305:Dose-Response Relationship, Drug; D015870:Gene Expression; D005786:Gene Expression Regulation; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D007249:Inflammation / Q000235:genetics / Q000378:metabolism; D008957:Models, Genetic; D016328:NF-kappa B / Q000235:genetics / Q000378:metabolism; D025941:Protein Interaction Mapping; D015398:Signal Transduction
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D018927:Anti-Asthmatic Agents; C098587:GAB1 protein, human; D016328:NF-kappa B