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000258918 1001_ $$00000-0001-9686-6295$$aSikkema, Lisa$$b0
000258918 245__ $$aAn integrated cell atlas of the lung in health and disease.
000258918 260__ $$aNew York, NY$$bNature America Inc.$$c2023
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000258918 520__ $$aSingle-cell technologies have transformed our understanding of human tissues. Yet, studies typically capture only a limited number of donors and disagree on cell type definitions. Integrating many single-cell datasets can address these limitations of individual studies and capture the variability present in the population. Here we present the integrated Human Lung Cell Atlas (HLCA), combining 49 datasets of the human respiratory system into a single atlas spanning over 2.4 million cells from 486 individuals. The HLCA presents a consensus cell type re-annotation with matching marker genes, including annotations of rare and previously undescribed cell types. Leveraging the number and diversity of individuals in the HLCA, we identify gene modules that are associated with demographic covariates such as age, sex and body mass index, as well as gene modules changing expression along the proximal-to-distal axis of the bronchial tree. Mapping new data to the HLCA enables rapid data annotation and interpretation. Using the HLCA as a reference for the study of disease, we identify shared cell states across multiple lung diseases, including SPP1+ profibrotic monocyte-derived macrophages in COVID-19, pulmonary fibrosis and lung carcinoma. Overall, the HLCA serves as an example for the development and use of large-scale, cross-dataset organ atlases within the Human Cell Atlas.
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000258918 650_2 $$2MeSH$$aHumans
000258918 650_2 $$2MeSH$$aCOVID-19
000258918 650_2 $$2MeSH$$aLung
000258918 650_2 $$2MeSH$$aPulmonary Fibrosis
000258918 650_2 $$2MeSH$$aLung Neoplasms: genetics
000258918 650_2 $$2MeSH$$aMacrophages
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000258918 7001_ $$aRamírez-Suástegui, Ciro$$b1
000258918 7001_ $$aStrobl, Daniel C$$b2
000258918 7001_ $$00000-0002-5447-1727$$aGillett, Tessa E$$b3
000258918 7001_ $$00000-0001-7744-8565$$aZappia, Luke$$b4
000258918 7001_ $$aMadissoon, Elo$$b5
000258918 7001_ $$00000-0002-3659-4387$$aMarkov, Nikolay S$$b6
000258918 7001_ $$00000-0001-6747-7928$$aZaragosi, Laure-Emmanuelle$$b7
000258918 7001_ $$aJi, Yuge$$b8
000258918 7001_ $$aAnsari, Meshal$$b9
000258918 7001_ $$00000-0002-8725-2555$$aArguel, Marie-Jeanne$$b10
000258918 7001_ $$aApperloo, Leonie$$b11
000258918 7001_ $$aBanchero, Martin$$b12
000258918 7001_ $$00000-0003-1555-3153$$aBécavin, Christophe$$b13
000258918 7001_ $$aBerg, Marijn$$b14
000258918 7001_ $$aChichelnitskiy, Evgeny$$b15
000258918 7001_ $$aChung, Mei-I$$b16
000258918 7001_ $$aCollin, Antoine$$b17
000258918 7001_ $$00000-0002-1593-2674$$aGay, Aurore C A$$b18
000258918 7001_ $$aGote-Schniering, Janine$$b19
000258918 7001_ $$aHooshiar Kashani, Baharak$$b20
000258918 7001_ $$00000-0001-7379-9093$$aInecik, Kemal$$b21
000258918 7001_ $$aJain, Manu$$b22
000258918 7001_ $$aKapellos, Theodore S$$b23
000258918 7001_ $$aKole, Tessa M$$b24
000258918 7001_ $$aLeroy, Sylvie$$b25
000258918 7001_ $$aMayr, Christoph H$$b26
000258918 7001_ $$00000-0003-1690-9027$$aOliver, Amanda J$$b27
000258918 7001_ $$00000-0001-5030-1643$$avon Papen, Michael$$b28
000258918 7001_ $$aPeter, Lance$$b29
000258918 7001_ $$aTaylor, Chase J$$b30
000258918 7001_ $$aWalzthoeni, Thomas$$b31
000258918 7001_ $$aXu, Chuan$$b32
000258918 7001_ $$00000-0003-3152-8978$$aBui, Linh T$$b33
000258918 7001_ $$aDe Donno, Carlo$$b34
000258918 7001_ $$00000-0001-5697-6991$$aDony, Leander$$b35
000258918 7001_ $$aFaiz, Alen$$b36
000258918 7001_ $$00000-0002-5502-9172$$aGuo, Minzhe$$b37
000258918 7001_ $$00000-0003-2977-2189$$aGutierrez, Austin J$$b38
000258918 7001_ $$aHeumos, Lukas$$b39
000258918 7001_ $$aHuang, Ni$$b40
000258918 7001_ $$00000-0002-0582-002X$$aIbarra, Ignacio L$$b41
000258918 7001_ $$aJackson, Nathan D$$b42
000258918 7001_ $$aKadur Lakshminarasimha Murthy, Preetish$$b43
000258918 7001_ $$00000-0001-6858-7985$$aLotfollahi, Mohammad$$b44
000258918 7001_ $$aTabib, Tracy$$b45
000258918 7001_ $$aTalavera-López, Carlos$$b46
000258918 7001_ $$00000-0003-3164-6448$$aTravaglini, Kyle J$$b47
000258918 7001_ $$aWilbrey-Clark, Anna$$b48
000258918 7001_ $$00000-0002-5656-7634$$aWorlock, Kaylee B$$b49
000258918 7001_ $$00000-0002-3521-5322$$aYoshida, Masahiro$$b50
000258918 7001_ $$aConsortium, Lung Biological Network$$b51$$eCollaboration Author
000258918 7001_ $$avan den Berge, Maarten$$b52
000258918 7001_ $$00000-0002-3067-3711$$aBossé, Yohan$$b53
000258918 7001_ $$00000-0002-8794-5319$$aDesai, Tushar J$$b54
000258918 7001_ $$aEickelberg, Oliver$$b55
000258918 7001_ $$00000-0001-5917-4601$$aKaminski, Naftali$$b56
000258918 7001_ $$00000-0002-1976-5471$$aKrasnow, Mark A$$b57
000258918 7001_ $$00000-0002-9398-5034$$aLafyatis, Robert$$b58
000258918 7001_ $$00000-0001-6304-6848$$aNikolic, Marko Z$$b59
000258918 7001_ $$aPowell, Joseph E$$b60
000258918 7001_ $$aRajagopal, Jayaraj$$b61
000258918 7001_ $$aRojas, Mauricio$$b62
000258918 7001_ $$00000-0001-6313-3570$$aRozenblatt-Rosen, Orit$$b63
000258918 7001_ $$00000-0002-8685-4263$$aSeibold, Max A$$b64
000258918 7001_ $$00000-0002-6277-2036$$aSheppard, Dean$$b65
000258918 7001_ $$aShepherd, Douglas P$$b66
000258918 7001_ $$00000-0002-0756-6643$$aSin, Don D$$b67
000258918 7001_ $$00000-0002-4146-6363$$aTimens, Wim$$b68
000258918 7001_ $$aTsankov, Alexander M$$b69
000258918 7001_ $$00000-0003-1668-5174$$aWhitsett, Jeffrey$$b70
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000258918 7001_ $$00000-0001-7464-7921$$aLuecken, Malte D$$b85
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000258918 7001_ $$aChen, Yuexin$$b87$$eContributor
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000258918 773__ $$0PERI:(DE-600)1484517-9$$a10.1038/s41591-023-02327-2$$gVol. 29, no. 6, p. 1563 - 1577$$n6$$p1563 - 1577$$tNature medicine$$v29$$x1078-8956$$y2023
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