title: Identifying ultrasensitive HGF dose-response functions in a 3D mammalian system for synthetic morphogenesis.
abstract: Nonlinear responses to signals are widespread natural phenomena that affect various cellular processes. Nonlinearity can be a desirable characteristic for engineering living organisms because it can lead to more switch-like responses, similar to those underlying the wiring in electronics. Steeper functions are described as ultrasensitive, and can be applied in synthetic biology by using various techniques including receptor decoys, multiple co-operative binding sites, and sequential positive feedbacks. Here, we explore the inherent non-linearity of a biological signaling system to identify functions that can potentially be exploited using cell genome engineering. For this, we performed genome-wide transcription profiling to identify genes with ultrasensitive response functions to Hepatocyte Growth Factor (HGF). We identified 3,527 genes that react to increasing concentrations of HGF, in Madin-Darby canine kidney (MDCK) cells, grown as cysts in 3D collagen cell culture. By fitting a generic Hill function to the dose-responses of these genes we obtained a measure of the ultrasensitivity of HGF-responsive genes, identifying a subset with higher apparent Hill coefficients (e.g. MMP1, TIMP1, SNORD75, SNORD86 and ERRFI1). The regulatory regions of these genes are potential candidates for future engineering of synthetic mammalian gene circuits requiring nonlinear responses to HGF signalling.
authors.affiliation: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.|EMBL/CRG Systems Biology Research Unit, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain.|Universitat Pompeu Fabra (UPF), Barcelona, Spain.
authors.forename: Vivek Raj
authors.initials: VR
authors.lastname: Senthivel
authors.affiliation: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
authors.forename: Marc
authors.initials: M
authors.lastname: Sturrock
authors.affiliation: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.|Department of Biochemistry and Cambridge Systems Biology Centre, University of Cambridge, Cambridge CB2 1GA, UK.
authors.forename: Gabriel
authors.initials: G
authors.lastname: Piedrafita
authors.affiliation: Department of Life Sciences, Imperial College London, London SW7 2AZ, United Kingdom.
authors.forename: Mark
authors.initials: M
authors.lastname: Isalan
mesh_terms: D000818:Animals; D018929:Cell Culture Techniques; D016000:Cluster Analysis; D030541:Databases, Genetic; D004285:Dogs; D017228:Hepatocyte Growth Factor / Q000494:pharmacology*; D061985:Madin Darby Canine Kidney Cells; D020781:Matrix Metalloproteinase 1 / Q000235:genetics / Q000378:metabolism; D009024:Morphogenesis / Q000187:drug effects*; D025341:Principal Component Analysis; D012313:RNA / Q000737:chemistry / Q000302:isolation & purification / Q000378:metabolism; D017423:Sequence Analysis, RNA; D059467:Transcriptome / Q000187:drug effects
chemical_list: D012313:RNA; D017228:Hepatocyte Growth Factor; D020781:Matrix Metalloproteinase 1