Prideapplication/xmlftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_MS1Quant_Qclassic_LocalNorm_NoImp.xlsxftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_SF4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_SF3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_SF1.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_SF2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_EV4.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_EV3.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_EV2.rawftp://ftp.pride.ebi.ac.uk/pride/data/archive/2026/07/PXD053755/2022-46_EV1.rawprimaryOK200j.c.wolters@umcg.nlJustina Clarinda WoltersMass SpectrometryData-independent acquisitionChronic Obstructive Pulmonary DiseaseCopdPulmonary microvascular endothelial cellsBmp6https://www.ebi.ac.uk/pride/archive/projects/PXD053755Endothelial CellProteomics sample preparation Around 2.5 microgram total protein in the extracellular vesicles and 75 microgram total protein for the soluble factors was loaded on precast 4-12% Bis-Tris gels (Thermo Scientific). The samples were run shortly into the gel (approximately 5 min at 100V). The gel was stained with Biosafe Coomassie G-250 stain (Biorad) and after destaining with milliQ-H2O, the band containing all proteins was excised from gel. The gel band was sliced into small pieces, washed subsequently with 30% and 50% v/v acetonitrile in 100 mM ammonium bicarbonate (dissolved in milliQ-H2O), each incubated at RT for 30 min while mixing (500 rpm) and lastly with 100% acetonitrile for 5 min, before drying the gel pieces in an oven at 37 °C. The proteins were reduced with 30 μL 10 mM dithiothreitol (in 100 mM ammonium bicarbonate dissolved in milliQ-H2O, 30 min, 55 °C) and alkylated with 30 μL 55 mM iodoacetamide (in 100 mM ammonium bicarbonate dissolved in milliQ-H20, 30 min, in the dark at RT). The gel pieces were washed with 100% acetonitrile for 30 min while mixing (500 rpm) and dried in an oven at 37 °C) before overnight digestion with 30 μL trypsin (1:100, sequencing grade modified trypsin V5111, Promega) at 37 °C. The next day, the peptides were eluted from the gel pieces with 50 µL 75% v/v acetonitrile plus 5% v/v formic acid (incubation 20 min at RT, mixing 500 rpm). The eluted fractions were dried under vacuum and resuspended in 40 μL 0.1% v/v formic acid for the extracellular vesicles and 80 μL for the soluble factors. Discovery-based proteomics analyses Discovery mass spectrometric analyses were performed on a quadrupole orbitrap mass spectrometer equipped with a nano-electrospray ion source (Orbitrap Exploris 480, Thermo Scientific). Chromatographic separation of the peptides was performed by liquid chromatography (LC) on a Evosep system (Evosep One, Evosep) using a nano-LC column (EV1137 Performance column 15 cm x 150 µm, 1.5 µm, Evosep; buffer A: 0.1% v/v formic acid, dissolved in milliQ-H2O, buffer B: 0.1% v/v formic acid, dissolved in acetonitrile). Half of the extracellular vesicles digests and 2.5% of the soluble factor digests were injected in the LC-MS and the peptides were separated using the 30SPD workflow (Evosep). The mass spectrometer was operated in positive ion mode and data-independent acquisition mode (DIA) using isolation windows of 16 m/z with a precursor mass range of 400-1000, switching the FAIMS between CV-45V and -60V with three scheduled MS1 scans during each screening of the precursor mass range.PrideLC-MS raw data were processed with Spectronaut (version 16.0.220606) (Biognosys) using the standard settings of the directDIA workflow except that quantification was performed on MS1. For the quantification, the Q-value filtering was set to the classic setting with local normalization and no imputation.ProteomicsJustina Clarinda WoltersDepartment of Pediatrics, UMCG/RUG, Groningen, The NetherlandsPARTIALHomo Sapiens (human)40439543 van der Koog L, Wu X, Nugraha DF, Ravi A, Wolters JC, Verhamme FM, Horvatovich PL, Bracke KR, van der Does AM, Hiemstra PS, Johnson JR, Harmsen MC, Nagelkerke A, Gosens R. Pulmonary Microvascular Endothelial Cells Support Alveolar Epithelial Growth via Bone Morphogenetic Protein 6 Secretion. Am J Respir Cell Mol Biol. 2025 73(6):920-937 10.1165/rcmb.2024-0409ocj.c.wolters@umcg.nlUMCGNetherlandsChronic obstructive pulmonary disease (COPD) is characterized by progressive airflow limitation and emphysema development, associated with enhanced tissue destruction and defective repair. Supporting cells in the alveolar niche play a crucial role in guiding the activation of alveolar epithelial progenitor cells during repair. Despite their close anatomical proximity, understanding of the supportive role of the pulmonary microvascular endothelium in adult alveolar epithelial repair remains limited. We hypothesized that factors secreted by pulmonary endothelial cells support alveolar epithelial cell growth. Here, we report that human pulmonary microvasculature endothelial cells support murine and human alveolar organoid formation through paracrine signaling via the secretion of extracellular vesicles and soluble factors. Transcriptomic and proteomic analysis pinpointed human pulmonary microvasculature endothelial cell-derived BMP6 (bone morphogenetic protein 6) as a critical factor for alveolar organoid formation. BMP6 promoted alveolar epithelial cell growth, whereas function-blocking antibodies targeting BMP6 inhibited the beneficial effect of endothelial cells on murine alveolar organoid formation. Transcriptomic analysis revealed that BMP6 specifically enhances distal epithelial cell markers and increases Wnt signaling in epithelial progenitors. In contrast, BMP6 deficiency in mouse lungs was associated with reduced Wnt signaling and augmented oxidative stress signaling in murine lung tissue. Taken together, our findings highlight BMP6 as a key regulator of adult epithelial repair and suggest its potential as a therapeutic target for defective epithelial repair, particularly in individuals with early stages of COPD.Pulmonary Microvascular Endothelial Cells Support Alveolar Epithelial Growth via Bone Morphogenetic Protein 6 Secretion.van der Koog Luke L, Wu Xinhui X, Nugraha Dyan F DF, Ravi Abilash A, Wolters Justina C JC, Verhamme Fien M FM, Horvatovich Peter L PL, Bracke Ken R KR, van der Does Anne M AM, Hiemstra Pieter S PS, Johnson Jill R JR, Harmsen Martin C MC, Nagelkerke Anika A, Gosens Reinoud RfalsePulmonary microvascular endothelial cells support alveolar epithelial growth via bone morphogenetic protein 6 secretionChronic obstructive pulmonary disease (COPD) is characterized by progressive airflow limitation and emphysema development, associated with enhanced tissue destruction and defective repair. Supporting cells in the alveolar niche play a crucial role in guiding the activation of alveolar epithelial progenitor cells during repair. Despite their close anatomical proximity, understanding of the supportive role of the pulmonary microvascular endothelium in adult alveolar epithelial repair remains limited. We hypothesized that angiocrine factors secreted by pulmonary endothelial cells support alveolar epithelial cell growth. Here, we report that human pulmonary microvasculature endothelial cells (HPMECs) support murine and human alveolar organoid formation through paracrine signaling via the secretion of extracellular vesicles and soluble factors. Transcriptomic and proteomic analysis pinpointed HPMEC-derived bone morphogenetic protein 6 (BMP6) as a critical factor for alveolar organoid formation. BMP6 deficiency was associated with reduced Wnt signaling and augmented oxidative stress signaling in murine lung tissue. Furthermore, BMP6 promoted alveolar epithelial cell growth, whereas function-blocking antibodies targeting BMP6 inhibited the beneficial effect of endothelial cells on murine alveolar organoid formation. Taken together, our findings highlight BMP6 as a key regulator of adult epithelial repair and suggest its potential as a therapeutic target for lung repair, particularly in individuals with 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