Laser-capture microdissection (LCM) allows the visualization and isolation of morphologically distinct subpopulations of cells from heterogeneous tissue specimens. In combination with formalin-fixed and paraffin-embedded (FFPE) tissue it provides a powerful tool for retrospective and clinically relevant studies of tissue proteins in a healthy and diseased context. We first optimized the protocol for efficient LCM analysis of FFPE tissue specimens. The use of SDS containing extraction buffer in combination with the single-pot solid-phase-enhanced sample preparation (SP3) digest method gave the best results regarding protein yield and protein/peptide identifications. Microdissected FFPE human substantia nigra tissue samples (∼3,000 cells) were then analyzed, using tandem mass tag (TMT) labeling and LC-MS/MS, resulting in the quantification of >5,600 protein groups. Nigral proteins were classified and analyzed by abundance, showing an enrichment of extracellular exosome and neuron-specific gene ontology (GO) terms among the higher abundance proteins. Comparison of microdissected samples with intact tissue sections, using a label-free shotgun approach, revealed an enrichment of neuronal cell type markers, such as tyrosine hydroxylase and alpha-synuclein, as well as proteins annotated with neuron-specific GO terms. Overall, this study provides a detailed protocol for laser-capture proteomics using FFPE tissue and demonstrates the efficiency of LCM analysis of distinct cell subpopulations for proteomic analysis using low sample amounts.

Animal models are important to mimic certain pathways or biological aspects of human pathologies including acute and chronic pulmonary diseases. We developed a novel and flexible mouse model of acute epithelial lung injury based on adeno-associated virus (AAV) variant 6.2 mediated expression of the human diphtheria toxin receptor (DTR). Following intratracheal administration of diphtheria toxin (DT), a cell-specific death of bronchial and alveolar epithelial cells can be observed. In contrast to other lung injury models, the here described mouse model provides the possibility of targeted injury using specific tropisms of AAV vectors or cell type specific promotors to drive the human DTR expression. Also, generation of cell specific mouse lines is not required. Detailed characterization of the AAV-DTR/DT mouse model including titration of viral genome (vg) load and administered DT amount revealed increasing cell numbers in bronchoalveolar lavage (BAL; macrophages, neutrophils, and unspecified cells) and elevation of degenerated cells and infiltrated leukocytes in lung tissue, dependent of vg load and DT dose. Cytokine levels in BAL fluid showed different patterns with higher vg load, e.g. IFNγ, TNFα, and IP10 increasing and IL-5 and IL-6 decreasing, while lung function was not affected. Additionally, laser-capture microdissection (LCM)-based proteomics of bronchial epithelium and alveolar tissue revealed upregulated immune and inflammatory response in all regions and extracellular matrix deposition in infiltrated alveoli. Overall, our novel AAV-DTR/DT model allows investigation of repair mechanisms following epithelial injury and resembles specific mechanistic aspects of acute and chronic pulmonary diseases.

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Background & aim: Recurring epithelial injury and aberrant repair are considered as a major driver of idiopathic pulmonary fibrosis (IPF) leading to chronic inflammation, fibroblast activation and ultimately to scarring and stiffening of the lung. As decline of lung function is the first reported symptom by IPF patients and occurs once fibrosis is firmly established, animal models are required to study early disease-driving mechanisms. Methods: We developed a novel and flexible mouse model of acute epithelial injury based on adeno-associated virus (AAV) variant 6.2 mediated expression of the human diphtheria toxin receptor (DTR). Following intratracheal administration of diphtheria toxin (DT), a cell-specific death of bronchial epithelial and alveolar epithelial type II cells can be observed. Results: Detailed characterization of the AAV-DTR/DT mouse model revealed increasing cell numbers in bronchoalveolar lavage (BAL; macrophages, neutrophils, and atypical cells) and elevation of apoptotic cells and infiltrated leukocytes in lung tissue, which were dependent of viral genome load and DT dose. Cytokine levels in BAL fluid showed different patterns dependent of viral genome load with IFNγ, TNFα, and IP-10 increasing and IL-5 and IL-6 decreasing, while lung function was not affected. Additionally, laser-capture microdissection-based proteomics of bronchial and alveolar epithelium showed upregulated immune and inflammatory response in all epithelial cell regions and extracellular matrix deposition in infiltrated alveoli, while proteins involved in pulmonary surfactant synthesis, alveolar fluid clearance and alveolar-capillary barrier were downregulated in the parenchyma. Conclusion: Our novel AAV-DTR/DT model resembles specific aspects of pulmonary diseases like IPF and acute respiratory distress syndrome.