title: Targeted Proteomics-Driven Computational Modeling of Macrophage S1P Chemosensing.
abstract: Osteoclasts are monocyte-derived multinuclear cells that directly attach to and resorb bone. Sphingosine-1-phosphate (S1P)(1) regulates bone resorption by functioning as both a chemoattractant and chemorepellent of osteoclast precursors through two G-protein coupled receptors that antagonize each other in an S1P-concentration-dependent manner. To quantitatively explore the behavior of this chemosensing pathway, we applied targeted proteomics, transcriptomics, and rule-based pathway modeling using the Simmune toolset. RAW264.7 cells (a mouse monocyte/macrophage cell line) were used as model osteoclast precursors, RNA-seq was used to identify expressed target proteins, and selected reaction monitoring (SRM) mass spectrometry using internal peptide standards was used to perform absolute abundance measurements of pathway proteins. The resulting transcript and protein abundance values were strongly correlated. Measured protein abundance values, used as simulation input parameters, led to in silico pathway behavior matching in vitro measurements. Moreover, once model parameters were established, even simulated responses toward stimuli that were not used for parameterization were consistent with experimental findings. These findings demonstrate the feasibility and value of combining targeted mass spectrometry with pathway modeling for advancing biological insight.
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Nathan P
authors.initials: NP
authors.lastname: Manes
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Bastian R
authors.initials: BR
authors.lastname: Angermann
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Marijke
authors.initials: M
authors.lastname: Koppenol-Raab
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Eunkyung
authors.initials: E
authors.lastname: An
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Virginie H
authors.initials: VH
authors.lastname: Sjoelund
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Jing
authors.initials: J
authors.lastname: Sun
authors.affiliation: §Immunology Frontier Research Center, Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871, Japan.
authors.forename: Masaru
authors.initials: M
authors.lastname: Ishii
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Ronald N
authors.initials: RN
authors.lastname: Germain
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421;
authors.forename: Martin
authors.initials: M
authors.lastname: Meier-Schellersheim
authors.affiliation: From the ‡Laboratory of Systems Biology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, 9000 Rockville Pike, Bethesda, Maryland, 20892-0421; nitalazarau@niaid.nih.gov.
authors.forename: Aleksandra
authors.initials: A
authors.lastname: Nita-Lazar
mesh_terms: D000818:Animals; D002460:Cell Line; D002633:Chemotaxis / Q000502:physiology*; D008246:Lysophospholipids / Q000378:metabolism*; D008264:Macrophages / Q000378:metabolism* / Q000502:physiology; D051379:Mice; D040901:Proteomics; D017423:Sequence Analysis, RNA; D015398:Signal Transduction; D013110:Sphingosine / Q000031:analogs & derivatives* / Q000378:metabolism
chemical_list: D008246:Lysophospholipids; C060506:sphingosine 1-phosphate; D013110:Sphingosine