title: Computational model for autophagic vesicle dynamics in single cells.
abstract: Macroautophagy (autophagy) is a cellular recycling program essential for homeostasis and survival during cytotoxic stress. This process, which has an emerging role in disease etiology and treatment, is executed in four stages through the coordinated action of more than 30 proteins. An effective strategy for studying complicated cellular processes, such as autophagy, involves the construction and analysis of mathematical or computational models. When developed and refined from experimental knowledge, these models can be used to interrogate signaling pathways, formulate novel hypotheses about systems, and make predictions about cell signaling changes induced by specific interventions. Here, we present the development of a computational model describing autophagic vesicle dynamics in a mammalian system. We used time-resolved, live-cell microscopy to measure the synthesis and turnover of autophagic vesicles in single cells. The stochastically simulated model was consistent with data acquired during conditions of both basal and chemically-induced autophagy. The model was tested by genetic modulation of autophagic machinery and found to accurately predict vesicle dynamics observed experimentally. Furthermore, the model generated an unforeseen prediction about vesicle size that is consistent with both published findings and our experimental observations. Taken together, this model is accurate and useful and can serve as the foundation for future efforts aimed at quantitative characterization of autophagy.
authors.affiliation: Laboratory of Systems Biology, Van Andel Research Institute, Grand Rapids, MI, USA.
authors.forename: Katie R
authors.initials: KR
authors.lastname: Martin
authors.forename: Dipak
authors.initials: D
authors.lastname: Barua
authors.forename: Audra L
authors.initials: AL
authors.lastname: Kauffman
authors.forename: Laura M
authors.initials: LM
authors.lastname: Westrate
authors.forename: Richard G
authors.initials: RG
authors.lastname: Posner
authors.forename: William S
authors.initials: WS
authors.lastname: Hlavacek
authors.forename: Jeffrey P
authors.initials: JP
authors.lastname: Mackeigan
mesh_terms: D001343:Autophagy / Q000187:drug effects / Q000235:genetics / Q000502:physiology*; D000071183:Autophagy-Related Proteins; D002460:Cell Line; D003198:Computer Simulation; D022162:Cytoplasmic Vesicles / Q000187:drug effects / Q000502:physiology; D049452:Green Fluorescent Proteins / Q000378:metabolism; D006801:Humans; D018942:Macrolides / Q000494:pharmacology; D008565:Membrane Proteins / Q000037:antagonists & inhibitors / Q000235:genetics; D008869:Microtubule-Associated Proteins / Q000378:metabolism; D008954:Models, Biological; D009025:Morpholines / Q000494:pharmacology; D011993:Recombinant Fusion Proteins / Q000378:metabolism; D020123:Sirolimus / Q000494:pharmacology; D058570:TOR Serine-Threonine Kinases / Q000037:antagonists & inhibitors; D033921:Vesicular Transport Proteins
chemical_list: C574794:ATG9A protein, human; D000071183:Autophagy-Related Proteins; C477012:MAP1LC3A protein, human; D018942:Macrolides; D008565:Membrane Proteins; D008869:Microtubule-Associated Proteins; D009025:Morpholines; D011993:Recombinant Fusion Proteins; D033921:Vesicular Transport Proteins; C485184:enhanced green fluorescent protein; D049452:Green Fluorescent Proteins; C040929:bafilomycin A1; C546624:(5-(2,4-bis((3S)-3-methylmorpholin-4-yl)pyrido(2,3-d)pyrimidin-7-yl)-2-methoxyphenyl)methanol; C546842:MTOR protein, human; D058570:TOR Serine-Threonine Kinases; D020123:Sirolimus