title: The species translation challenge-a systems biology perspective on human and rat bronchial epithelial cells.
abstract: The biological responses to external cues such as drugs, chemicals, viruses and hormones, is an essential question in biomedicine and in the field of toxicology, and cannot be easily studied in humans. Thus, biomedical research has continuously relied on animal models for studying the impact of these compounds and attempted to 'translate' the results to humans. In this context, the SBV IMPROVER (Systems Biology Verification for Industrial Methodology for PROcess VErification in Research) collaborative initiative, which uses crowd-sourcing techniques to address fundamental questions in systems biology, invited scientists to deploy their own computational methodologies to make predictions on species translatability. A multi-layer systems biology dataset was generated that was comprised of phosphoproteomics, transcriptomics and cytokine data derived from normal human (NHBE) and rat (NRBE) bronchial epithelial cells exposed in parallel to more than 50 different stimuli under identical conditions. The present manuscript describes in detail the experimental settings, generation, processing and quality control analysis of the multi-layer omics dataset accessible in public repositories for further intra- and inter-species translation studies.
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland ; These authors contributed equally to this work.
authors.forename: Carine
authors.initials: C
authors.lastname: Poussin
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland ; These authors contributed equally to this work.
authors.forename: Carole
authors.initials: C
authors.lastname: Mathis
authors.affiliation: ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos , 15343 Ag. Paraskevi, Attiki, Greece ; National Technical University of Athens, Heroon Polytechniou 9 , Zografou 15780, Greece ; These authors contributed equally to this work.
authors.forename: Leonidas G
authors.initials: LG
authors.lastname: Alexopoulos
authors.affiliation: ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos , 15343 Ag. Paraskevi, Attiki, Greece ; National Technical University of Athens, Heroon Polytechniou 9 , Zografou 15780, Greece.
authors.forename: Dimitris E
authors.initials: DE
authors.lastname: Messinis
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Rémi H J
authors.initials: RH
authors.lastname: Dulize
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Belcastro
authors.affiliation: ProtATonce Ltd, Scientific Park Lefkippos, Patriarchou Grigoriou & Neapoleos , 15343 Ag. Paraskevi, Attiki, Greece ; National Technical University of Athens, Heroon Polytechniou 9 , Zografou 15780, Greece.
authors.forename: Ioannis N
authors.initials: IN
authors.lastname: Melas
authors.affiliation: National Technical University of Athens, Heroon Polytechniou 9 , Zografou 15780, Greece.
authors.forename: Theodore
authors.initials: T
authors.lastname: Sakellaropoulos
authors.affiliation: IBM Computational Biology Center , Yorktown Heights, NY 10598, USA.
authors.forename: Kahn
authors.initials: K
authors.lastname: Rhrissorrakrai
authors.affiliation: IBM Computational Biology Center , Yorktown Heights, NY 10598, USA.
authors.forename: Erhan
authors.initials: E
authors.lastname: Bilal
authors.affiliation: IBM Computational Biology Center , Yorktown Heights, NY 10598, USA.
authors.forename: Pablo
authors.initials: P
authors.lastname: Meyer
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Marja
authors.initials: M
authors.lastname: Talikka
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Stéphanie
authors.initials: S
authors.lastname: Boué
authors.affiliation: IBM Computational Biology Center , Yorktown Heights, NY 10598, USA.
authors.forename: Raquel
authors.initials: R
authors.lastname: Norel
authors.affiliation: IBM Computational Biology Center , Yorktown Heights, NY 10598, USA.
authors.forename: John J
authors.initials: JJ
authors.lastname: Rice
authors.affiliation: IBM Computational Biology Center , Yorktown Heights, NY 10598, USA.
authors.forename: Gustavo
authors.initials: G
authors.lastname: Stolovitzky
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Nikolai V
authors.initials: NV
authors.lastname: Ivanov
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Manuel C
authors.initials: MC
authors.lastname: Peitsch
authors.affiliation: Philip Morris International R&D, Philip Morris Products S. A. , Quai Jeanrenaud 5, 2000 Neuchâtel, Switzerland.
authors.forename: Julia
authors.initials: J
authors.lastname: Hoeng
mesh_terms: D000818:Animals; D001980:Bronchi / Q000166:cytology / Q000378:metabolism*; D016207:Cytokines / Q000378:metabolism; D004847:Epithelial Cells / Q000378:metabolism*; D006801:Humans; D023421:Models, Animal; D040901:Proteomics; D051381:Rats; D049490:Systems Biology / Q000379:methods; D059467:Transcriptome; D057170:Translational Research, Biomedical
chemical_list: D016207:Cytokines