TY  - JOUR
AU  - Sikkema, Lisa
AU  - Ramírez-Suástegui, Ciro
AU  - Strobl, Daniel C
AU  - Gillett, Tessa E
AU  - Zappia, Luke
AU  - Madissoon, Elo
AU  - Markov, Nikolay S
AU  - Zaragosi, Laure-Emmanuelle
AU  - Ji, Yuge
AU  - Ansari, Meshal
AU  - Arguel, Marie-Jeanne
AU  - Apperloo, Leonie
AU  - Banchero, Martin
AU  - Bécavin, Christophe
AU  - Berg, Marijn
AU  - Chichelnitskiy, Evgeny
AU  - Chung, Mei-I
AU  - Collin, Antoine
AU  - Gay, Aurore C A
AU  - Gote-Schniering, Janine
AU  - Hooshiar Kashani, Baharak
AU  - Inecik, Kemal
AU  - Jain, Manu
AU  - Kapellos, Theodore S
AU  - Kole, Tessa M
AU  - Leroy, Sylvie
AU  - Mayr, Christoph H
AU  - Oliver, Amanda J
AU  - von Papen, Michael
AU  - Peter, Lance
AU  - Taylor, Chase J
AU  - Walzthoeni, Thomas
AU  - Xu, Chuan
AU  - Bui, Linh T
AU  - De Donno, Carlo
AU  - Dony, Leander
AU  - Faiz, Alen
AU  - Guo, Minzhe
AU  - Gutierrez, Austin J
AU  - Heumos, Lukas
AU  - Huang, Ni
AU  - Ibarra, Ignacio L
AU  - Jackson, Nathan D
AU  - Kadur Lakshminarasimha Murthy, Preetish
AU  - Lotfollahi, Mohammad
AU  - Tabib, Tracy
AU  - Talavera-López, Carlos
AU  - Travaglini, Kyle J
AU  - Wilbrey-Clark, Anna
AU  - Worlock, Kaylee B
AU  - Yoshida, Masahiro
AU  - van den Berge, Maarten
AU  - Bossé, Yohan
AU  - Desai, Tushar J
AU  - Eickelberg, Oliver
AU  - Kaminski, Naftali
AU  - Krasnow, Mark A
AU  - Lafyatis, Robert
AU  - Nikolic, Marko Z
AU  - Powell, Joseph E
AU  - Rajagopal, Jayaraj
AU  - Rojas, Mauricio
AU  - Rozenblatt-Rosen, Orit
AU  - Seibold, Max A
AU  - Sheppard, Dean
AU  - Shepherd, Douglas P
AU  - Sin, Don D
AU  - Timens, Wim
AU  - Tsankov, Alexander M
AU  - Whitsett, Jeffrey
AU  - Xu, Yan
AU  - Banovich, Nicholas E
AU  - Barbry, Pascal
AU  - Duong, Thu Elizabeth
AU  - Falk, Christine S
AU  - Meyer, Kerstin B
AU  - Kropski, Jonathan A
AU  - Pe'er, Dana
AU  - Schiller, Herbert B
AU  - Tata, Purushothama Rao
AU  - Schultze, Joachim L
AU  - Teichmann, Sara A
AU  - Misharin, Alexander V
AU  - Nawijn, Martijn C
AU  - Luecken, Malte D
AU  - Theis, Fabian J
TI  - An integrated cell atlas of the lung in health and disease.
JO  - Nature medicine
VL  - 29
IS  - 6
SN  - 1078-8956
CY  - New York, NY
PB  - Nature America Inc.
M1  - DZNE-2023-00690
SP  - 1563 - 1577
PY  - 2023
AB  - Single-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.
KW  - Humans
KW  - COVID-19
KW  - Lung
KW  - Pulmonary Fibrosis
KW  - Lung Neoplasms: genetics
KW  - Macrophages
LB  - PUB:(DE-HGF)16
C6  - pmid:37291214
C2  - pmc:PMC10287567
DO  - DOI:10.1038/s41591-023-02327-2
UR  - https://pub.dzne.de/record/258918
ER  -