title: Pathway reporter genes define molecular phenotypes of human cells.
abstract: BACKGROUND
  The phenotype of a living cell is determined by its pattern of active signaling networks, giving rise to a "molecular phenotype" associated with differential gene expression. Digital amplicon based RNA quantification by sequencing is a useful technology for molecular phenotyping as a novel tool to characterize the state of biological systems.
  
  
  RESULTS
  We show here that the activity of signaling networks can be assessed based on a set of established key regulators and expression targets rather than the entire transcriptome. We compiled a panel of 917 human pathway reporter genes, representing 154 human signaling and metabolic networks for integrated knowledge- and data-driven understanding of biological processes. The reporter genes are significantly enriched for regulators and effectors covering a wide range of biological processes, and faithfully capture gene-level and pathway-level changes. We apply the approach to iPSC derived cardiomyocytes and primary human hepatocytes to describe changes in molecular phenotype during development or drug response. The reporter genes deliver an accurate pathway-centric view of the biological system under study, and identify known and novel modulation of signaling networks consistent with literature or experimental data.
  
  
  CONCLUSIONS
  A panel of 917 pathway reporter genes is sufficient to describe changes in the molecular phenotype defined by 154 signaling cascades in various human cell types. AmpliSeq-RNA based digital transcript imaging enables simultaneous monitoring of the entire pathway reporter gene panel in up to 150 samples. We propose molecular phenotyping as a useful approach to understand diseases and drug action at the network level.
authors.affiliation: Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland.
authors.forename: Jitao David
authors.initials: JD
authors.lastname: Zhang
authors.affiliation: Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland.
authors.forename: Erich
authors.initials: E
authors.lastname: Küng
authors.affiliation: Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland.
authors.forename: Franziska
authors.initials: F
authors.lastname: Boess
authors.affiliation: Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland.
authors.forename: Ulrich
authors.initials: U
authors.lastname: Certa
authors.affiliation: Pharmaceutical Research and Early Development, Pharmaceutical Sciences, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, 4070, Basel, Switzerland. martin.ebeling@roche.com.
authors.forename: Martin
authors.initials: M
authors.lastname: Ebeling
mesh_terms: D000465:Algorithms; D000894:Anti-Inflammatory Agents, Non-Steroidal / Q000633:toxicity; D002454:Cell Differentiation; D004008:Diclofenac / Q000633:toxicity; D017930:Genes, Reporter / Q000235:genetics*; D022781:Hepatocytes / Q000166:cytology / Q000187:drug effects / Q000378:metabolism; D006801:Humans; D057026:Induced Pluripotent Stem Cells / Q000166:cytology / Q000378:metabolism; D053858:Metabolic Networks and Pathways / Q000235:genetics*; D032383:Myocytes, Cardiac / Q000166:cytology / Q000378:metabolism; D010641:Phenotype; D025341:Principal Component Analysis; D015398:Signal Transduction / Q000235:genetics*
chemical_list: D000894:Anti-Inflammatory Agents, Non-Steroidal; D004008:Diclofenac