{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T16:27:28Z","timestamp":1787934448286,"version":"build-2784847793"},"reference-count":85,"publisher":"Elsevier BV","issue":"2","license":[{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/tdm\/userlicense\/1.0\/"},{"start":{"date-parts":[[2024,2,1]],"date-time":"2024-02-01T00:00:00Z","timestamp":1706745600000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/www.elsevier.com\/legal\/tdmrep-license"},{"start":{"date-parts":[[2024,1,3]],"date-time":"2024-01-03T00:00:00Z","timestamp":1704240000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["cell.com","elsevier.com","sciencedirect.com"],"crossmark-restriction":true},"short-container-title":["Cell Reports"],"published-print":{"date-parts":[[2024,2]]},"DOI":"10.1016\/j.celrep.2024.113689","type":"journal-article","created":{"date-parts":[[2024,1,21]],"date-time":"2024-01-21T08:47:26Z","timestamp":1705826846000},"page":"113689","update-policy":"https:\/\/doi.org\/10.1016\/elsevier_cm_policy","source":"Crossref","is-referenced-by-count":23,"title":["Deep spatial proteomics reveals region-specific features of severe COVID-19-related pulmonary injury"],"prefix":"10.1016","volume":"43","author":[{"given":"Yiheng","family":"Mao","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ying","family":"Chen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuan","family":"Li","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Longda","family":"Ma","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qi","family":"Wang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"An","family":"He","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Xi","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Tianyi","family":"Dong","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Weina","family":"Gao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yanfen","family":"Xu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liang","family":"Ren","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Qian","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peng","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ben","family":"Hu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yiwu","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ruijun","family":"Tian","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-8089-163X","authenticated-orcid":false,"given":"Zheng-Li","family":"Shi","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"78","reference":[{"key":"10.1016\/j.celrep.2024.113689_bib1","doi-asserted-by":"crossref","first-page":"270","DOI":"10.1038\/s41586-020-2012-7","article-title":"A pneumonia outbreak associated with a new coronavirus of probable bat origin","volume":"579","author":"Zhou","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib2","doi-asserted-by":"crossref","first-page":"1708","DOI":"10.1056\/NEJMoa2002032","article-title":"Clinical Characteristics of Coronavirus Disease 2019 in China","volume":"382","author":"Guan","year":"2020","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib3","doi-asserted-by":"crossref","first-page":"141","DOI":"10.1038\/s41579-020-00459-7","article-title":"Characteristics of SARS-CoV-2 and COVID-19","volume":"19","author":"Hu","year":"2021","journal-title":"Nat. Rev. Microbiol."},{"key":"10.1016\/j.celrep.2024.113689_bib4","doi-asserted-by":"crossref","first-page":"320","DOI":"10.1016\/S0140-6736(20)31305-2","article-title":"Histopathology and ultrastructural findings of fatal COVID-19 infections in Washington State: a case series","volume":"396","author":"Bradley","year":"2020","journal-title":"Lancet"},{"key":"10.1016\/j.celrep.2024.113689_bib5","doi-asserted-by":"crossref","first-page":"95","DOI":"10.1016\/S2213-2600(21)00408-2","article-title":"Post-mortem lung tissue: the fossil record of the pathophysiology and immunopathology of severe COVID-19","volume":"10","author":"Milross","year":"2022","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib6","doi-asserted-by":"crossref","first-page":"1868","DOI":"10.1093\/nsr\/nwaa247","article-title":"Pathological changes in the lungs and lymphatic organs of 12 COVID-19 autopsy cases","volume":"7","author":"Liu","year":"2020","journal-title":"Natl. Sci. Rev."},{"key":"10.1016\/j.celrep.2024.113689_bib7","doi-asserted-by":"crossref","first-page":"836","DOI":"10.1038\/s41422-021-00523-8","article-title":"A cohort autopsy study defines COVID-19 systemic pathogenesis","volume":"31","author":"Yao","year":"2021","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2024.113689_bib8","doi-asserted-by":"crossref","first-page":"107","DOI":"10.1038\/s41586-021-03570-8","article-title":"COVID-19 tissue atlases reveal SARS-CoV-2 pathology and cellular targets","volume":"595","author":"Delorey","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib9","doi-asserted-by":"crossref","first-page":"114","DOI":"10.1038\/s41586-021-03569-1","article-title":"A molecular single-cell lung atlas of lethal COVID-19","volume":"595","author":"Melms","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib10","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.1038\/s41556-021-00796-6","article-title":"A single-cell transcriptomic landscape of the lungs of patients with COVID-19","volume":"23","author":"Wang","year":"2021","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.celrep.2024.113689_bib11","doi-asserted-by":"crossref","first-page":"775","DOI":"10.1016\/j.cell.2021.01.004","article-title":"Multi-organ proteomic landscape of COVID-19 autopsies","volume":"184","author":"Nie","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib12","doi-asserted-by":"crossref","first-page":"240","DOI":"10.1038\/s41392-020-00355-9","article-title":"Pathological features of COVID-19-associated lung injury: a preliminary proteomics report based on clinical samples","volume":"5","author":"Leng","year":"2020","journal-title":"Signal Transduct. Targeted Ther."},{"key":"10.1016\/j.celrep.2024.113689_bib13","doi-asserted-by":"crossref","first-page":"nwab143","DOI":"10.1093\/nsr\/nwab143","article-title":"Post-mortem tissue proteomics reveals the pathogenesis of multi-organ injuries of COVID-19","volume":"8","author":"Qiu","year":"2021","journal-title":"Natl. Sci. Rev."},{"key":"10.1016\/j.celrep.2024.113689_bib14","doi-asserted-by":"crossref","DOI":"10.1016\/j.celrep.2022.110955","article-title":"Spatial region-resolved proteome map reveals mechanism of COVID-19-associated heart injury","volume":"39","author":"Leng","year":"2022","journal-title":"Cell Rep."},{"key":"10.1016\/j.celrep.2024.113689_bib15","doi-asserted-by":"crossref","first-page":"5879","DOI":"10.1021\/acs.analchem.8b00596","article-title":"Spatial-Resolution Cell Type Proteome Profiling of Cancer Tissue by Fully Integrated Proteomics Technology","volume":"90","author":"Xu","year":"2018","journal-title":"Anal. Chem."},{"key":"10.1016\/j.celrep.2024.113689_bib16","doi-asserted-by":"crossref","first-page":"140","DOI":"10.1016\/j.aca.2020.06.049","article-title":"Spatial proteome profiling by immunohistochemistry-based laser capture microdissection and data-independent acquisition proteomics","volume":"1127","author":"Huang","year":"2020","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.celrep.2024.113689_bib17","doi-asserted-by":"crossref","DOI":"10.1016\/j.aca.2022.339615","article-title":"Fritted tip capillary column with negligible dead volume facilitated ultrasensitive and deep proteomics","volume":"1201","author":"Yang","year":"2022","journal-title":"Anal. Chim. Acta"},{"key":"10.1016\/j.celrep.2024.113689_bib18","doi-asserted-by":"crossref","first-page":"1229","DOI":"10.1038\/s41592-020-00998-0","article-title":"diaPASEF: parallel accumulation-serial fragmentation combined with data-independent acquisition","volume":"17","author":"Meier","year":"2020","journal-title":"Nat. Methods"},{"key":"10.1016\/j.celrep.2024.113689_bib19","doi-asserted-by":"crossref","first-page":"564","DOI":"10.1038\/s41586-021-03475-6","article-title":"The spatial landscape of lung pathology during COVID-19 progression","volume":"593","author":"Rendeiro","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib20","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1038\/s41556-020-0561-5","article-title":"A transitional stem cell state in the lung","volume":"22","author":"Verheyden","year":"2020","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.celrep.2024.113689_bib21","doi-asserted-by":"crossref","first-page":"934","DOI":"10.1038\/s41556-020-0542-8","article-title":"Persistence of a regeneration-associated, transitional alveolar epithelial cell state in pulmonary fibrosis","volume":"22","author":"Kobayashi","year":"2020","journal-title":"Nat. Cell Biol."},{"key":"10.1016\/j.celrep.2024.113689_bib22","doi-asserted-by":"crossref","first-page":"3559","DOI":"10.1038\/s41467-020-17358-3","article-title":"Alveolar regeneration through a Krt8+ transitional stem cell state that persists in human lung fibrosis","volume":"11","author":"Strunz","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib23","doi-asserted-by":"crossref","first-page":"366","DOI":"10.1016\/j.stem.2020.06.020","article-title":"Inflammatory Signals Induce AT2 Cell-Derived Damage-Associated Transient Progenitors that Mediate Alveolar Regeneration","volume":"27","author":"Choi","year":"2020","journal-title":"Cell Stem Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib24","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1016\/j.ccr.2013.04.002","article-title":"NKX2-1\/TTF-1: an enigmatic oncogene that functions as a double-edged sword for cancer cell survival and progression","volume":"23","author":"Yamaguchi","year":"2013","journal-title":"Cancer Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib25","doi-asserted-by":"crossref","first-page":"342","DOI":"10.1002\/jmv.27339","article-title":"Palmitoylation of SARS-CoV-2\u00a0S protein is critical for S-mediated syncytia formation and virus entry","volume":"94","author":"Li","year":"2022","journal-title":"J.\u00a0Med. Virol."},{"key":"10.1016\/j.celrep.2024.113689_bib26","doi-asserted-by":"crossref","first-page":"5204","DOI":"10.1038\/s41467-022-32957-y","article-title":"Suppression of ACE2 SUMOylation protects against SARS-CoV-2 infection through TOLLIP-mediated selective autophagy","volume":"13","author":"Jin","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib27","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1038\/s42255-021-00508-2","article-title":"GP73 is a glucogenic hormone contributing to SARS-CoV-2-induced hyperglycemia","volume":"4","author":"Wan","year":"2022","journal-title":"Nat. Metab."},{"key":"10.1016\/j.celrep.2024.113689_bib28","doi-asserted-by":"crossref","first-page":"126","DOI":"10.1038\/s41422-020-00460-y","article-title":"AXL is a candidate receptor for SARS-CoV-2 that promotes infection of pulmonary and bronchial epithelial cells","volume":"31","author":"Wang","year":"2021","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2024.113689_bib29","doi-asserted-by":"crossref","first-page":"730","DOI":"10.1038\/d41573-021-00158-9","article-title":"PIKfyve: a lipid kinase target for COVID-19, cancer and neurodegenerative disorders","volume":"20","author":"Huang","year":"2021","journal-title":"Nat. Rev. Drug Discov."},{"key":"10.1016\/j.celrep.2024.113689_bib30","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1038\/s41392-021-00508-4","article-title":"Multi-platform omics analysis reveals molecular signature for COVID-19 pathogenesis, prognosis and drug target discovery","volume":"6","author":"Li","year":"2021","journal-title":"Signal Transduct. Targeted Ther."},{"key":"10.1016\/j.celrep.2024.113689_bib31","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1089\/ars.2020.8111","article-title":"Is Low Alveolar Type II Cell SOD3 in the Lungs of Elderly Linked to the Observed Severity of COVID-19? Antioxid","volume":"33","author":"Abouhashem","year":"2020","journal-title":"Redox Signal"},{"key":"10.1016\/j.celrep.2024.113689_bib32","doi-asserted-by":"crossref","first-page":"619","DOI":"10.1038\/s41586-020-2922-4","article-title":"A molecular cell atlas of the human lung from single-cell RNA sequencing","volume":"587","author":"Travaglini","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib33","doi-asserted-by":"crossref","first-page":"970","DOI":"10.1038\/s41587-020-0602-4","article-title":"COVID-19 severity correlates with airway epithelium-immune cell interactions identified by single-cell analysis","volume":"38","author":"Chua","year":"2020","journal-title":"Nat. Biotechnol."},{"key":"10.1016\/j.celrep.2024.113689_bib34","doi-asserted-by":"crossref","first-page":"791","DOI":"10.1038\/s41467-023-36333-2","article-title":"Distinct tissue niches direct lung immunopathology via CCL18 and CCL21 in severe COVID-19","volume":"14","author":"Mothes","year":"2023","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib35","doi-asserted-by":"crossref","first-page":"293","DOI":"10.1038\/s41586-021-03237-4","article-title":"Loss of furin cleavage site attenuates SARS-CoV-2 pathogenesis","volume":"591","author":"Johnson","year":"2021","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib36","doi-asserted-by":"crossref","first-page":"2314","DOI":"10.1002\/jmv.25997","article-title":"Consider TLR5 for new therapeutic development against COVID-19","volume":"92","author":"Chakraborty","year":"2020","journal-title":"J.\u00a0Med. Virol."},{"key":"10.1016\/j.celrep.2024.113689_bib37","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1016\/j.cell.2020.05.032","article-title":"Proteomic and Metabolomic Characterization of COVID-19 Patient Sera","volume":"182","author":"Shen","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib38","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1038\/s41392-022-01118-4","article-title":"APOE interacts with ACE2 inhibiting SARS-CoV-2 cellular entry and inflammation in COVID-19 patients","volume":"7","author":"Zhang","year":"2022","journal-title":"Signal Transduct. Targeted Ther."},{"key":"10.1016\/j.celrep.2024.113689_bib39","doi-asserted-by":"crossref","first-page":"120","DOI":"10.1056\/NEJMoa2015432","article-title":"Pulmonary Vascular Endothelialitis, Thrombosis, and Angiogenesis in Covid-19","volume":"383","author":"Ackermann","year":"2020","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib40","doi-asserted-by":"crossref","first-page":"639","DOI":"10.1038\/s41577-022-00762-9","article-title":"Understanding COVID-19-associated coagulopathy","volume":"22","author":"Conway","year":"2022","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.celrep.2024.113689_bib41","doi-asserted-by":"crossref","first-page":"23763","DOI":"10.1002\/anie.202011015","article-title":"Structural Characterization of N-Linked Glycans in the Receptor Binding Domain of the SARS-CoV-2 Spike Protein and their Interactions with Human Lectins","volume":"59","author":"Lenza","year":"2020","journal-title":"Angew. Chem., Int. Ed. Engl."},{"key":"10.1016\/j.celrep.2024.113689_bib42","article-title":"IFI44 is an immune evasion biomarker for SARS-CoV-2 and Staphylococcus aureus infection in patients with RA","volume":"13","author":"Zheng","year":"2022","journal-title":"Front. Immunol."},{"key":"10.1016\/j.celrep.2024.113689_bib43","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1038\/s41590-020-00832-x","article-title":"Macrophage expression and prognostic significance of the long pentraxin PTX3 in COVID-19","volume":"22","author":"Brunetta","year":"2021","journal-title":"Nat. Immunol."},{"key":"10.1016\/j.celrep.2024.113689_bib44","doi-asserted-by":"crossref","DOI":"10.1172\/jci.insight.151777","article-title":"A dynamic mucin mRNA signature associates with COVID-19 disease presentation and severity","volume":"6","author":"Smet","year":"2021","journal-title":"JCI insight"},{"key":"10.1016\/j.celrep.2024.113689_bib45","doi-asserted-by":"crossref","first-page":"1523","DOI":"10.1038\/s41467-019-09234-6","article-title":"Metascape provides a biologist-oriented resource for the analysis of systems-level datasets","volume":"10","author":"Zhou","year":"2019","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib46","doi-asserted-by":"crossref","first-page":"463","DOI":"10.1038\/s41586-020-2588-y","article-title":"Longitudinal analyses reveal immunological misfiring in severe COVID-19","volume":"584","author":"Lucas","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib82","doi-asserted-by":"crossref","first-page":"1484","DOI":"10.1038\/s41596-020-0292-x","article-title":"CellPhoneDB: inferring cell-cell communication from combined expression of multi-subunit ligand-receptor complexes","volume":"15","author":"Efremova","year":"2020","journal-title":"Nat. Protoc."},{"key":"10.1016\/j.celrep.2024.113689_bib47","doi-asserted-by":"crossref","first-page":"E383","DOI":"10.1148\/radiol.2021211396","article-title":"CT of Post-Acute Lung Complications of COVID-19","volume":"301","author":"Solomon","year":"2021","journal-title":"Radiology"},{"key":"10.1016\/j.celrep.2024.113689_bib48","doi-asserted-by":"crossref","first-page":"6243","DOI":"10.1016\/j.cell.2021.11.033","article-title":"SARS-CoV-2 infection triggers profibrotic macrophage responses and lung fibrosis","volume":"184","author":"Wendisch","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib49","doi-asserted-by":"crossref","DOI":"10.1126\/sciadv.aau7426","article-title":"VSIG4 mediates transcriptional inhibition of Nlrp3 and Il-1beta in macrophages","volume":"5","author":"Huang","year":"2019","journal-title":"Sci. Adv."},{"key":"10.1016\/j.celrep.2024.113689_bib50","doi-asserted-by":"crossref","first-page":"958","DOI":"10.1056\/NEJMra2005230","article-title":"Spectrum of Fibrotic Lung Diseases","volume":"383","author":"Wijsenbeek","year":"2020","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib51","doi-asserted-by":"crossref","first-page":"807","DOI":"10.1016\/S2213-2600(20)30225-3","article-title":"Pulmonary fibrosis and COVID-19: the potential role for antifibrotic therapy","volume":"8","author":"George","year":"2020","journal-title":"Lancet Respir. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib52","doi-asserted-by":"crossref","DOI":"10.1073\/pnas.2217199120","article-title":"Innate immune cell activation causes lung fibrosis in a humanized model of long COVID","volume":"120","author":"Cui","year":"2023","journal-title":"Proc. Natl. Acad. Sci. USA"},{"key":"10.1016\/j.celrep.2024.113689_bib53","doi-asserted-by":"crossref","first-page":"1920","DOI":"10.1038\/s41467-020-15647-5","article-title":"Collagen-producing lung cell atlas identifies multiple subsets with distinct localization and relevance to fibrosis","volume":"11","author":"Tsukui","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib54","doi-asserted-by":"crossref","first-page":"4012","DOI":"10.1038\/s41467-022-31659-9","article-title":"Spatially resolved proteomic map shows that extracellular matrix regulates epidermal growth","volume":"13","author":"Li","year":"2022","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib55","doi-asserted-by":"crossref","first-page":"5706","DOI":"10.1158\/0008-5472.CAN-21-0536","article-title":"TGFBI Production by Macrophages Contributes to an Immunosuppressive Microenvironment in Ovarian Cancer","volume":"81","author":"Lecker","year":"2021","journal-title":"Cancer Res."},{"key":"10.1016\/j.celrep.2024.113689_bib56","doi-asserted-by":"crossref","first-page":"2233","DOI":"10.1056\/NEJMra0910061","article-title":"Airway mucus function and dysfunction","volume":"363","author":"Fahy","year":"2010","journal-title":"N.\u00a0Engl. J. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib57","doi-asserted-by":"crossref","first-page":"1078","DOI":"10.1038\/s41422-020-00435-z","article-title":"Mucus production stimulated by IFN-AhR signaling triggers hypoxia of COVID-19","volume":"30","author":"Liu","year":"2020","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2024.113689_bib58","doi-asserted-by":"crossref","first-page":"883","DOI":"10.1016\/j.chom.2020.04.017","article-title":"Heightened Innate Immune Responses in the Respiratory Tract of COVID-19 Patients","volume":"27","author":"Zhou","year":"2020","journal-title":"Cell Host Microbe"},{"key":"10.1016\/j.celrep.2024.113689_bib59","doi-asserted-by":"crossref","first-page":"1336","DOI":"10.1164\/rccm.202111-2606OC","article-title":"Prevalence and Mechanisms of Mucus Accumulation in COVID-19 Lung Disease","volume":"206","author":"Kato","year":"2022","journal-title":"Am. J. Respir. Crit. Care Med."},{"key":"10.1016\/j.celrep.2024.113689_bib60","doi-asserted-by":"crossref","DOI":"10.1016\/j.lfs.2021.119046","article-title":"The proteomic characteristics of airway mucus from critical ill COVID-19 patients","volume":"269","author":"Zhang","year":"2021","journal-title":"Life Sci."},{"key":"10.1016\/j.celrep.2024.113689_bib61","doi-asserted-by":"crossref","first-page":"345","DOI":"10.1038\/s41577-020-0328-z","article-title":"COVID-19: a case for inhibiting IL-17?","volume":"20","author":"Pacha","year":"2020","journal-title":"Nat. Rev. Immunol."},{"key":"10.1016\/j.celrep.2024.113689_bib62","doi-asserted-by":"crossref","DOI":"10.1084\/jem.20201129","article-title":"SARS-CoV-2-triggered neutrophil extracellular traps mediate COVID-19 pathology","volume":"217","author":"Veras","year":"2020","journal-title":"J.\u00a0Exp. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib63","doi-asserted-by":"crossref","first-page":"3025","DOI":"10.1172\/JCI68782","article-title":"Type 2 alveolar cells are stem cells in adult lung","volume":"123","author":"Barkauskas","year":"2013","journal-title":"J.\u00a0Clin. Invest."},{"key":"10.1016\/j.celrep.2024.113689_bib64","article-title":"Lung epithelial and endothelial damage, loss of tissue repair, inhibition of fibrinolysis, and cellular senescence in fatal COVID-19","volume":"13","author":"D'Agnillo","year":"2021","journal-title":"Sci. Transl. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib65","doi-asserted-by":"crossref","first-page":"1007","DOI":"10.1038\/s41379-020-0536-x","article-title":"Pathological study of the 2019 novel coronavirus disease (COVID-19) through postmortem core biopsies","volume":"33","author":"Tian","year":"2020","journal-title":"Mod. Pathol."},{"key":"10.1016\/j.celrep.2024.113689_bib66","doi-asserted-by":"crossref","first-page":"708","DOI":"10.1038\/s41422-020-0369-7","article-title":"Pulmonary alveolar regeneration in adult COVID-19 patients","volume":"30","author":"Chen","year":"2020","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2024.113689_bib67","doi-asserted-by":"crossref","first-page":"417","DOI":"10.1016\/j.cels.2015.12.004","article-title":"The Molecular Signatures Database (MSigDB) hallmark gene set collection","volume":"1","author":"Liberzon","year":"2015","journal-title":"Cell Syst."},{"key":"10.1016\/j.celrep.2024.113689_bib68","doi-asserted-by":"crossref","first-page":"1895","DOI":"10.1016\/j.cell.2021.01.053","article-title":"COVID-19 immune features revealed by a large-scale single-cell transcriptome atlas","volume":"184","author":"Ren","year":"2021","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib69","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1038\/s41580-021-00418-x","article-title":"Mechanisms of SARS-CoV-2 entry into cells","volume":"23","author":"Jackson","year":"2022","journal-title":"Nat. Rev. Mol. Cell Biol."},{"key":"10.1016\/j.celrep.2024.113689_bib70","doi-asserted-by":"crossref","first-page":"1219","DOI":"10.1038\/s41564-021-00958-0","article-title":"Cellular host factors for SARS-CoV-2 infection","volume":"6","author":"Baggen","year":"2021","journal-title":"Nat. Microbiol."},{"key":"10.1016\/j.celrep.2024.113689_bib71","doi-asserted-by":"crossref","first-page":"600","DOI":"10.1038\/s41422-022-00654-6","article-title":"Receptome profiling identifies KREMEN1 and ASGR1 as alternative functional receptors of SARS-CoV-2 (vol 32, pg 24, 2022)","volume":"32","author":"Gu","year":"2022","journal-title":"Cell Res."},{"key":"10.1016\/j.celrep.2024.113689_bib72","doi-asserted-by":"crossref","first-page":"4584","DOI":"10.1038\/s41467-021-24817-y","article-title":"IFITM proteins promote SARS-CoV-2 infection and are targets for virus inhibition in\u00a0vitro","volume":"12","author":"Prelli Bozzo","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib73","doi-asserted-by":"crossref","first-page":"271","DOI":"10.1016\/j.cell.2020.02.052","article-title":"SARS-CoV-2 Cell Entry Depends on ACE2 and TMPRSS2 and Is Blocked by a Clinically Proven Protease Inhibitor","volume":"181","author":"Hoffmann","year":"2020","journal-title":"Cell"},{"key":"10.1016\/j.celrep.2024.113689_bib74","doi-asserted-by":"crossref","first-page":"431","DOI":"10.1016\/j.tips.2021.03.006","article-title":"Therapeutic Potential of Targeting Plasminogen Activator Inhibitor-1 in COVID-19","volume":"42","author":"Kellici","year":"2021","journal-title":"Trends Pharmacol. Sci."},{"key":"10.1016\/j.celrep.2024.113689_bib75","doi-asserted-by":"crossref","first-page":"146","DOI":"10.1038\/s41586-020-2600-6","article-title":"Association of COVID-19 inflammation with activation of the C5a-C5aR1 axis","volume":"588","author":"Carvelli","year":"2020","journal-title":"Nature"},{"key":"10.1016\/j.celrep.2024.113689_bib76","doi-asserted-by":"crossref","first-page":"4888","DOI":"10.1038\/s41467-021-25191-5","article-title":"The cytokines HGF and CXCL13 predict the severity and the mortality in COVID-19 patients","volume":"12","author":"Perreau","year":"2021","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib77","doi-asserted-by":"crossref","DOI":"10.1126\/science.abd4570","article-title":"Inborn errors of type I IFN immunity in patients with life-threatening COVID-19","volume":"370","author":"Zhang","year":"2020","journal-title":"Science"},{"key":"10.1016\/j.celrep.2024.113689_bib78","doi-asserted-by":"crossref","first-page":"579","DOI":"10.1038\/nm.4307","article-title":"Oncostatin M drives intestinal inflammation and predicts response to tumor necrosis factor-neutralizing therapy in patients with inflammatory bowel disease","volume":"23","author":"West","year":"2017","journal-title":"Nat. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib84","doi-asserted-by":"crossref","DOI":"10.15252\/emmm.202317459","article-title":"Quantitative multiorgan proteomics of fatal COVID-19 uncovers tissue-specific effects beyond inflammation","volume":"15","author":"Schweizer","year":"2023","journal-title":"EMBO Mol. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib85","article-title":"System-wide transcriptome damage and tissue identity loss in COVID-19 patients","volume":"3","author":"Park","year":"2022","journal-title":"Cell Rep. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib79","doi-asserted-by":"crossref","first-page":"6319","DOI":"10.1038\/s41467-020-20139-7","article-title":"Temporal and spatial heterogeneity of host response to SARS-CoV-2 pulmonary infection","volume":"11","author":"Desai","year":"2020","journal-title":"Nat. Commun."},{"key":"10.1016\/j.celrep.2024.113689_bib80","doi-asserted-by":"crossref","first-page":"531","DOI":"10.1038\/nm.4073","article-title":"Inflammatory signaling in human tuberculosis granulomas is spatially organized","volume":"22","author":"Marakalala","year":"2016","journal-title":"Nat. Med."},{"key":"10.1016\/j.celrep.2024.113689_bib83","doi-asserted-by":"crossref","first-page":"D543","DOI":"10.1093\/nar\/gkab1038","article-title":"The PRIDE database resources in 2022: a hub for mass spectrometry-based proteomics evidences","volume":"50","author":"Perez-Riverol","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"10.1016\/j.celrep.2024.113689_bib81","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1038\/s41596-018-0006-9","article-title":"Reproducible workflow for multiplexed deep-scale proteome and phosphoproteome analysis of tumor tissues by liquid chromatography-mass spectrometry","volume":"13","author":"Mertins","year":"2018","journal-title":"Nat. Protoc."}],"container-title":["Cell Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124724000172?httpAccept=text\/xml","content-type":"text\/xml","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/api.elsevier.com\/content\/article\/PII:S2211124724000172?httpAccept=text\/plain","content-type":"text\/plain","content-version":"vor","intended-application":"text-mining"}],"deposited":{"date-parts":[[2024,10,2]],"date-time":"2024-10-02T12:14:51Z","timestamp":1727871291000},"score":1,"resource":{"primary":{"URL":"https:\/\/linkinghub.elsevier.com\/retrieve\/pii\/S2211124724000172"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2]]},"references-count":85,"journal-issue":{"issue":"2","published-print":{"date-parts":[[2024,2]]}},"alternative-id":["S2211124724000172"],"URL":"https:\/\/doi.org\/10.1016\/j.celrep.2024.113689","relation":{},"ISSN":["2211-1247"],"issn-type":[{"value":"2211-1247","type":"print"}],"subject":[],"published":{"date-parts":[[2024,2]]},"assertion":[{"value":"Elsevier","name":"publisher","label":"This article is maintained by"},{"value":"Deep spatial proteomics reveals region-specific features of severe COVID-19-related pulmonary injury","name":"articletitle","label":"Article Title"},{"value":"Cell Reports","name":"journaltitle","label":"Journal Title"},{"value":"https:\/\/doi.org\/10.1016\/j.celrep.2024.113689","name":"articlelink","label":"CrossRef DOI link to publisher maintained version"},{"value":"article","name":"content_type","label":"Content Type"},{"value":"\u00a9 2024 The Author(s).","name":"copyright","label":"Copyright"}],"article-number":"113689"}}