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Alveolar type-II cells (ATII cells) are lung progenitor cells responsible for regeneration of alveolar epithelium during homeostatic turnover and in response to injury. Characterization of ATII cells will have a profound impact on our understanding and treatment of lung disease. The identification of novel ATII cell-surface proteins can be used for sorting and enrichment of these cells for further characterization. Here we combined a high-resolution mass spectrometry-based membrane proteomic approach using lungs of the SILAC mice with an Affymetrix microarray-based transcriptome analysis of ATII cells. We identified 16 proteins that are enriched in the membrane fraction of ATII cells and whose genes are highly expressed in these cells. Interestingly, we confirmed our data for two of these genes, integrin beta 2 and 6 (Itgb2 and Itgb6), by qRT-PCR expression analysis and Western blot analysis of protein extracts. Moreover, flow cytometry and immunohistochemistry in adult lung revealed that ITGB2 and ITGB6 are present in subpopulations of surfactant-associated-protein- C-positive cells, suggesting the existence of different types of ATII cells. Furthermore, analysis of the Itgb2-/- mice showed that Itgb2 is required for proper WNT signaling regulation in the lung. © 2013 American Chemical Society.

Morphological and metabolic adaptations of the human skeletal muscle to exercise are crucial to improve performance and prevent chronic diseases and metabolic disorders. In this study we investigated human skeletal muscle protein composition in endurance trained (ET) versus untrained individuals (UT) and its modulation by an acute bout of endurance exercise. Participants were recruited based on their VO 2 max and subjected to a bicycle exercise test. M. vastus lateralis biopsies were taken before and three hours after exercise. Muscle lysates were analyzed using off-gel LC-MS/MS. Relative protein abundances were compared between ET and UT at rest and after exercise. Comparing UT and ET, we identified 92 significantly changed proteins under resting conditions. Specifically, fiber-type-specific and proteins of the oxidative phosphorylation and tricarboxylic acid cycle were increased in ET. In response to acute exercise, 71 proteins in ET and 44 in UT were altered. Here, a decrease of proteins involved in energy metabolism accompanied with alterations of heat shock and proteasomal proteins could be observed. In summary, long-term endurance training increased the basal level of structural and mitochondrial proteins in skeletal muscle. In contrast, acute exercise resulted in a depletion of proteins related to substrate utilization, especially in trained athletes. Biological significance The investigation of the human skeletal muscle proteome in response to exercise may provide novel insights into the process of muscular plasticity. It is of importance in the development of exercise-based strategies in the prevention and therapy of many chronic inflammatory and degenerative diseases which are often accompanied by muscular deconditioning. Up to date, proteomic investigations of the human muscle proteome in adaptation to exercise are mainly focused on untrained individuals and often restricted to animal studies. In the present study we compare the protein composition in endurance trained athletes and untrained individuals in the resting muscle and its modulation in response to acute exercise. To our knowledge, we present the first comprehensive analysis of skeletal muscle proteome alterations in response to acute and long-term exercise intervention.

The zebrafish has become a widely used model organism employed for developmental studies, live cell imaging, and genetic screens. High-resolution transcriptional profiles of different developmental and adult stages of the fish and of its various organs were generated, which are readily accessible via the ZFIN database. In contrast, quantitative proteomic studies of zebrafish organs are still in their infancy. Here, we used the SILAC (stable isotope labeling by amino acids in cell culture) zebrafish as a "spike-in" reference to generate a protein atlas of nine organs including gills, brain, heart, muscle, liver, spleen, skin, swim bladder, and testis. Single-shot 4 h LC gradients coupled to a Quadrupole-Orbitrap (QExactive) instrument allowed identification of over 5000 proteins in less than 5 days, of which more than 70% were quantified in triplicate. Identified proteins were subjected to BLAST searches and Gene Ontology classification to improve annotation of zebrafish proteins and obtain insights into potential functions. Comparison to mouse tissue proteome data sets revealed differences and similarities in the protein composition of zebrafish versus mouse organs. We reason that the data set will be helpful for the proteomic characterization of zebrafish organs and identification of tissue-specific proteins that might serve as biomarkers. Our approach provides a complementary view into the biochemistry of zebrafish models and will assist large-scale protein quantification in zebrafish disease models.

Cardiomyocyte proteostasis is mediated by the ubiquitin/proteasome system (UPS) and autophagy/lysosome system and is fundamental for cardiac adaptation to both physiologic (e.g., exercise) and pathologic (e.g., pressure overload) stresses. Both the UPS and autophagy/lysosome system exhibit reduced efficiency as a consequence of aging, and dysfunction in these systems is associated with cardiomyopathies. The muscle-specific ubiquitin ligase atrogin-1 targets signaling proteins involved in cardiac hypertrophy for degradation. Here, using atrogin-1 KO mice in combination with in vivo pulsed stable isotope labeling of amino acids in cell culture proteomics and biochemical and cellular analyses, we identified charged multivesicular body protein 2B (CHMP2B), which is part of an endosomal sorting complex (ESCRT) required for autophagy, as a target of atrogin-1-mediated degradation. Mice lacking atrogin-1 failed to degrade CHMP2B, resulting in autophagy impairment, intracellular protein aggregate accumulation, unfolded protein response activation, and subsequent cardiomyocyte apoptosis, all of which increased progressively with age. Cellular proteostasis alterations resulted in cardiomyopathy characterized by myocardial remodeling with interstitial fibrosis, with reduced diastolic function and arrhythmias. CHMP2B downregulation in atrogin-1 KO mice restored autophagy and decreased proteotoxicity, thereby preventing cell death. These data indicate that atrogin-1 promotes cardiomyocyte health through mediating the interplay between UPS and autophagy/lysosome system and its alteration promotes development of cardiomyopathies.

Quantitative proteomics is an important tool to study biological processes, but so far it has been challenging to apply to zebrafish. Here, we describe a large scale quantitative analysis of the zebrafish proteome using a combination of stable isotope labeling and liquid chromatography-mass spectrometry (LC-MS). Proteins derived from the fully labeled fish were used as a standard to quantify changes during embryonic heart development. LC-MS-assisted analysis of the proteome of activated leukocyte cell adhesion molecule zebrafish morphants revealed a down-regulation of components of the network required for cell adhesion and maintenance of cell shape as well as secondary changes due to arrest of cellular differentiation. Quantitative proteomics in zebrafish using the stable isotope-labeling technique provides an unprecedented resource to study developmental processes in zebrafish.

Metabolic labeling of living organisms with stable isotopes has become a powerful tool for global protein quantitation. The SILAC (stable isotope labeling with amino acids in cell culture) approach is based on the incorporation of nonradioactive-labeled isotopic forms of amino acids into cellular proteins. The effective SILAC labeling of immortalized cells and single-cell organisms (e.g., yeast and bacteria) was recently extended to more complex organisms, including worms, flies, and even rodents. The administration of a (13)C6-lysine (heavy) containing diet for one mouse generation leads to a complete exchange of the natural (light) isotope (12)C6-lysine. SILAC-labeled organisms are mainly used as a heavy "spike-in" standard into nonlabeled counterparts, and the combination with high-performance mass spectrometers allows for global proteomic screening. Here we used the fully labeled SILAC mice to identify proteins based on SILAC pairs from isolated cardiomyocytes, and we analyzed β-parvin-deficient hearts. Our approach confirmed the absence β-parvin and revealed simultaneously a clear up regulation of α-parvin in heart tissue. In this protocol, we describe the generation of a SILAC mouse colony and show two approaches to perform a proteome-wide analysis of heart tissue. Thus, the SILAC mouse spike-in approach is a readily available procedure and allows for a straightforward systematic analysis of disease models and knockout mice.

Resampling algorithms provide an empirical, non-parametric approach to determine the statistical significance of annotations in different experimental settings. ResA(3) (Resampling Analysis of Arbitrary Annotations, short: ResA) is a novel tool to facilitate the analysis of enrichment and regulation of annotations deposited in various online resources such as KEGG, Gene Ontology and Pfam or any kind of classification. Results are presented in readily accessible navigable table views together with relevant information for statistical inference. The tool is able to analyze multiple types of annotations in a single run and includes a Gene Ontology annotation feature. We successfully tested ResA using a dataset obtained by measuring incorporation rates of stable isotopes into proteins in intact animals. ResA complements existing tools and will help to evaluate the increasing number of large-scale transcriptomics and proteomics datasets (resa.mpi-bn.mpg.de).

Purpose: Control of cardiomyocyte (CM) proteostasis operated by the ubiquitin/proteasome (UPS) and autophagy/lysosome systems is fundamental for heart adaptation to both physiologic and pathologic stresses. Reduced efficiency of either UPS or autophagy/lysosome system occurs during ageing and has been associated to cardiomyopathies. Atrogin-1 is a muscle specific ubiquitin ligase, targeting for degradation signalling proteins involved in cardiac hypertrophy. However, the role of Atrogin-1 in CM biology and its involvement in the molecular mechanism of cardiac dysfunction, are largely unexplored. Methods: We analyzed hearts from Atrogin-1 knock-out (KO) mice from 6 mo. onwards until death, and compared it to that of age- and sex-matched controls. Functional, immunofluorescence and electron microscopy analyses were performed. Markers of ER/SR stress and autophagy/lysosome systems were investigated by RTqPCR and WB. In vivo pulsed SILAC proteomics and bioinformatics, Co-IP, in vitro assays and in vivo viral silencing were performed to identify novel targets of Atrogin-1. Results: By using in vivo and in vitro assays we identified a novel target of Atrogin-1, the ESCRTIII protein CHMP2B, that plays a fundamental role in autophagy. Failure to degrade CHMP2B in Atrogin-1 KO mice caused autophagy impairment, accumulation of intracellular protein aggregates, activation of the unfolded protein response and subsequent CM apoptosis, all of which increased progressively during ageing. The alterations in cellular proteostasis resulted in cardiomyopathy with a restrictive pattern, characterized by myocardial remodelling with interstitial fibrosis, diastolic dysfunction (Edt, KO: 20.7±2.7 vs WT: 27.8±5.7, in msec), arrhythmias and secondary LA and ventricular remodelling, as well as CM hypertrophy (CM area, KO: 289.34±2.23 vs WT: 236.77±1.64, in μm2). Aged Atrogin-1 KO mice had reduced tolerance to treadmill exercise compared to controls, and shortened life span (KO: 17±1 vs WT: 24±1.2, in mo.). In vivo reduction of CHMP2B protein level in the KO mice restored normal autophagy and protected CMs from cell death resulting from CHMP2B proteotoxicity. Conclusions: Our data highlight the importance of regulated proteolysis in the heart and show that the loss of Atrogin-1 per se is sufficient to cause cardiac damage, which evolves into cardiomyopathy when protein quality control becomes less efficient, as occurring in aging. Such cardiomyopathy represents a novel model of proteotoxic myocardial remodelling and will be useful to determine the mechanism of impaired proteostasis to CM damage.

Skeletal muscle tissue contains slow as well as fast twitch muscle fibers that possess different metabolic and contractile properties. Although the distribution of individual proteins in fast and slow fibers has been investigated extensively, a comprehensive proteomic analysis, which is key for any systems biology approach to muscle tissues, is missing. Here, we compared the global protein levels and gene expression profiles of the predominantly slow soleus and fast extensor digitorum longus muscles using the principle of in vivo stable isotope labeling with amino acids based on a fully lysine-6 labeled SILAC-mouse. We identified 551 proteins with significant quantitative differences between slow soleus and fast extensor digitorum longus fibers out of >2000 quantified proteins, which greatly extends the repertoire of proteins differentially regulated between both muscle types. Most of the differentially regulated proteins mediate cellular contraction, ion homeostasis, glycolysis, and oxidation, which reflect the major functional differences between both muscle types. Comparison of proteomics and transcriptomics data uncovered the existence of fiber-type specific posttranscriptional regulatory mechanisms resulting in differential accumulation of Myosin-8 and α-protein kinase 3 proteins and mRNAs among others. Phosphoproteome analysis of soleus and extensor digitorum longus muscles identified 2573 phosphosites on 973 proteins including 1040 novel phosphosites. The in vivo stable isotope labeling with amino acids-mouse approach used in our study provides a comprehensive view into the protein networks that direct fiber-type specific functions and allows a detailed dissection of the molecular composition of slow and fast muscle tissues with unprecedented resolution.