title: Proteome annotations and identifications of the human pulmonary fibroblast.
abstract: We hereby report on a three year project initiative undertaken by our research team encompassing large-scale protein expression profiling and annotations of human primary lung fibroblast cells. An overview is given of proteomic studies of the fibroblast target cell involved in several diseases such as asthma, idiopatic pulmonary disease, and COPD. It has been the objective within our research team to map and identify the protein expressions occurring in both activated-, as well as resting cell states. The JGGL database www.2DDB.org has been built around these data, allowing advanced hypothesis building using the interactive query bioinformatic tools developed. Gene ontology has been applied to these annotations, classifying and correlating protein expressions to function. The localization as well as the biological processes involved for the annotations are being presented including an annotation-, and sequence-identification strategy, resulting in close to 2000 protein identities. Both gel based, high resolution 2D-gels, and liquid-phase separation (three-dimensional HPLC), as well as the combination of gel- and LC-based approaches (1D-gels and nano-capillary LC, reversed-phase) were utilized. Protein sequencing and structure identities were acquired by a combination of MALDI-, and electrospray-mass spectrometry techniques. Phenotypical and morphological characterizations were also made for this human disease target cell in both stimulated- and resting-cell states. The use of functional assays that demonstrate the key regulating role of growth factors and cytokine stimuli such as PDGF, TGF-beta, and EGF and the effect of ECM molecules such as Biglycan, are also presented and discussed.
authors.affiliation: Cell & Molecular Biology, C13, BMC, 221 84 Lund, Sweden.
authors.forename: Johan
authors.initials: J
authors.lastname: Malmström
authors.forename: Kristoffer
authors.initials: K
authors.lastname: Larsen
authors.forename: Lars
authors.initials: L
authors.lastname: Malmström
authors.forename: Ellen
authors.initials: E
authors.lastname: Tufvesson
authors.forename: Ken
authors.initials: K
authors.lastname: Parker
authors.forename: Jason
authors.initials: J
authors.lastname: Marchese
authors.forename: Brian
authors.initials: B
authors.lastname: Williamson
authors.forename: Steve
authors.initials: S
authors.lastname: Hattan
authors.forename: Dale
authors.initials: D
authors.lastname: Patterson
authors.forename: Steve
authors.initials: S
authors.lastname: Martin
authors.forename: Armin
authors.initials: A
authors.lastname: Graber
authors.forename: H Peter
authors.initials: HP
authors.lastname: Juhasz
authors.forename: Gunilla
authors.initials: G
authors.lastname: Westergren-Thorsson
authors.forename: György
authors.initials: G
authors.lastname: Marko-Varga
mesh_terms: D000595:Amino Acid Sequence; D002467:Cell Nucleus / Q000378:metabolism*; D030562:Databases, Protein; D015180:Electrophoresis, Gel, Two-Dimensional; D005347:Fibroblasts / Q000378:metabolism*; D005786:Gene Expression Regulation / Q000187:drug effects; D006801:Humans; D008168:Lung / Q000378:metabolism*; D008171:Lung Diseases / Q000378:metabolism; D008969:Molecular Sequence Data; D020543:Proteome; D029424:Pulmonary Disease, Chronic Obstructive / Q000378:metabolism; D019032:Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization; D016212:Transforming Growth Factor beta / Q000494:pharmacology
chemical_list: D020543:Proteome; D016212:Transforming Growth Factor beta