title: Regulators of calcium homeostasis identified by inference of kinetic model parameters from live single cells perturbed by siRNA.
abstract: Assigning molecular functions and revealing dynamic connections between large numbers of partially characterized proteins in regulatory networks are challenges in systems biology. We showed that functions of signaling proteins can be discovered with a differential equations model of the underlying signaling process to extract specific molecular parameter values from single-cell, time-course measurements. By analyzing the effects of 250 small interfering RNAs on Ca(2+) signals in single cells over time, we identified parameters that were specifically altered in the Ca(2+) regulatory system. Analysis of the screen confirmed known functions of the Ca(2+) sensors STIM1 (stromal interaction molecule 1) and calmodulin and of Ca(2+) channels and pumps localized in the endoplasmic reticulum (ER) or plasma membrane. Furthermore, we showed that the Alzheimer's disease-linked protein presenilin-2 and the channel protein ORAI2 prevented overload of ER Ca(2+) and that feedback from Ca(2+) to phosphatidylinositol 4-kinase and PLCδ (phospholipase Cδ) may regulate the abundance of the plasma membrane lipid PI(4,5)P2 (phosphatidylinositol 4,5-bisphosphate) to control Ca(2+) extrusion. Thus, functions of signaling proteins and dynamic regulatory connections can be identified by extracting molecular parameter values from single-cell, time-course data.
authors.affiliation: Department of Chemical and Systems Biology, Stanford University, Stanford, CA 94305, USA. sbandara@alumni.stanford.edu
authors.forename: Samuel
authors.initials: S
authors.lastname: Bandara
authors.forename: Seth
authors.initials: S
authors.lastname: Malmersjö
authors.forename: Tobias
authors.initials: T
authors.lastname: Meyer
mesh_terms: D002118:Calcium / Q000378:metabolism*; D020013:Calcium Signaling / Q000502:physiology*; D002462:Cell Membrane / Q000235:genetics / Q000378:metabolism; D004721:Endoplasmic Reticulum / Q000235:genetics / Q000378:metabolism; D006367:HeLa Cells; D006706:Homeostasis / Q000502:physiology*; D006801:Humans; D008565:Membrane Proteins / Q000235:genetics / Q000378:metabolism; D008954:Models, Biological; D009363:Neoplasm Proteins / Q000235:genetics / Q000378:metabolism; D000071741:ORAI2 Protein; D018129:Phosphatidylinositol Phosphates / Q000235:genetics / Q000378:metabolism; D054803:Phospholipase C delta / Q000235:genetics / Q000378:metabolism; D053766:Presenilin-2 / Q000235:genetics / Q000378:metabolism; D034741:RNA, Small Interfering / Q000235:genetics / Q000378:metabolism*; D000071737:Stromal Interaction Molecule 1
chemical_list: D008565:Membrane Proteins; D009363:Neoplasm Proteins; D000071741:ORAI2 Protein; C514506:ORAI2 protein, human; D018129:Phosphatidylinositol Phosphates; D053766:Presenilin-2; D034741:RNA, Small Interfering; C103530:STIM1 protein, human; D000071737:Stromal Interaction Molecule 1; C060980:phosphatidylinositol 3,4-diphosphate; D054803:Phospholipase C delta; D002118:Calcium