Consensus Lung Cell Reference: The Collaborative Cross-Consortium and Country Lung Cell Nomenclature Project (C3LCN). An Official American Thoracic Society Workshop Report

Rapid advances in single-cell technologies now allow measurement of thousands of transcripts and other molecular features of individual cells offering unprecedented insight into lung biology in homeostasis and in disease. The accelerated generation of multimodal data has, however, been accompanied by the reporting of putatively "novel" cell types described without consensus regarding their ontogeny, identity, function, or defining markers. To fully realize the value of the technological advances and to enable rigorous comparison across studies, respiratory research will benefit from standardized, quantitative, and biologically grounded cell classifications and nomenclature. Achieving the transformative potential of the multimodal data will depend on common, machine- and human-readable nomenclature, structured and expandable dictionary and atlas resources, and clear methodological standards that ensure consistency as technologies evolve. The American Thoracic Society (ATS) recognized the importance of promoting a common nomenclature to enhance equitable access and utility of the vast amounts of multimodal data generated by the lung research community. The Collaborative Cross-Consortium and Country Lung Cell Nomenclature Project (C3LCN) was adopted as an ATS Assembly Project in 2024. This is the consensus report outlining the goals and framework of the Project to foster coordinated progressive lung cell research to include: 1) providing best practices for analysis, publication and reporting of lung single-cell transcriptomic datasets; 2) establishing a contemporary lexicon for healthy adult human cells of the lower respiratory tract with structured, persistent, and resolvable identifiers; 3) defining a scalable taxonomy to organize a common lung cell nomenclature; 4) offering tools to support collaboration, knowledge dissemination, and translational advances rooted in modern lung biology augmenting, not replacing, pre-genomic biological knowledge; and 5) describing an infrastructure capable of incorporating new ontological refinements as higher-resolution, multimodal single-cell and spatial datasets emerge, cellular heterogeneity is better defined, and disease-associated abnormal cell types and reactive cell states are increasingly recognized and mechanistically interrogated. Together, this coordinated effort aims to provide the foundation necessary for a robust, harmonized, and expandable nomenclature for lung science.

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Journal
American Journal of Respiratory Cell and Molecular Biology
Published
2026-08-14
DOI
https://doi.org/10.1093/ajrcmb/aanag144
Primary Topic
Single-cell and spatial transcriptomics
Type
article
Field-Weighted Citation Impact
0.00

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article

Consensus Lung Cell Reference: The Collaborative Cross-Consortium and Country Lung Cell Nomenclature Project (C3LCN). An Official American Thoracic Society Workshop Report

Gloria Pryhuber, Jonathan A. Kropski, Terren K. Niethamer, Kevin A. Burns et al.
American Journal of Respiratory Cell and Molecular Biology
Single-cell and spatial transcriptomics
article

Consensus Lung Cell Reference: The Collaborative Cross-Consortium and Country Lung Cell Nomenclature Project (C3LCN). An Official American Thoracic Society Workshop Report

Gloria Pryhuber, Jonathan A. Kropski, Terren K. Niethamer, Kevin A. Burns, Kathryn A. Wikenheiser‐Brokamp, Enikö Sajti, Minzhe Guo, Gerard H. Koppelman, Gail H. Deutsch, Bruce Aronow, Denise Al Alam, Martijn C. Nawijn, Joseph D. Planer, Jayaraj Rajagopal, Martin Banchero, Richard H. Scheuermann, Christos Samakovlis, Thu Elizabeth Duong, Ravi Misra, Rod Rahimi, Laure‐Emmanuelle Zaragosi, Joshua D. Fortriede, Alexandra–Chloé Villani, Mingxia Gu, Malte D. Luecken, Nathan Salomonis, Aleix Puig-Barbe, Bruce J. Aronow, Anne‐Karina T. Perl, Xin Sun, Wellington V. Cardoso, Matthew S. Walters, Ellen M. Quardokus, Raphael Kfuri‐Rubens, Soula Danopoulos, Gérémy Clair, Susan M. Majka, Purushothama Rao Tata, Yan Xu, Qing S. Lin, Kerstin B. Meyer, Pascal Barbry, Maria Basil, Janine Schniering, Nicholas Banovich, Martijn Nawijn, Gail Deutsch, Geremy Clair, David Frank, Scott Randell, Enid Neptune, Susan Majka, Thu Elizabeth Duong, the American Thoracic Society Assembly on Respiratory Cell and Molecular Biology, Kerstin Meyer, Malte D Luecken, Elizabeth Redente, Kenichi Okuda, James Hagood, Wellington V Cardoso, Clare Lloyd, Rachel Clifford, Joshua Fortriede, Alexander Misharin, Kevin Burns, Gerard H Koppelman, Janette Burgess, Raphael Kfuri-Rubens, Anna Karina Perl, Reinoud Gosens, David Osumi-Sutherland, Ana Mora, Stephanie Krick
article en

Abstract

Rapid advances in single-cell technologies now allow measurement of thousands of transcripts and other molecular features of individual cells offering unprecedented insight into lung biology in homeostasis and in disease. The accelerated generation of multimodal data has, however, been accompanied by the reporting of putatively "novel" cell types described without consensus regarding their ontogeny, identity, function, or defining markers. To fully realize the value of the technological advances and to enable rigorous comparison across studies, respiratory research will benefit from standardized, quantitative, and biologically grounded cell classifications and nomenclature. Achieving the transformative potential of the multimodal data will depend on common, machine- and human-readable nomenclature, structured and expandable dictionary and atlas resources, and clear methodological standards that ensure consistency as technologies evolve. The American Thoracic Society (ATS) recognized the importance of promoting a common nomenclature to enhance equitable access and utility of the vast amounts of multimodal data generated by the lung research community. The Collaborative Cross-Consortium and Country Lung Cell Nomenclature Project (C3LCN) was adopted as an ATS Assembly Project in 2024. This is the consensus report outlining the goals and framework of the Project to foster coordinated progressive lung cell research to include: 1) providing best practices for analysis, publication and reporting of lung single-cell transcriptomic datasets; 2) establishing a contemporary lexicon for healthy adult human cells of the lower respiratory tract with structured, persistent, and resolvable identifiers; 3) defining a scalable taxonomy to organize a common lung cell nomenclature; 4) offering tools to support collaboration, knowledge dissemination, and translational advances rooted in modern lung biology augmenting, not replacing, pre-genomic biological knowledge; and 5) describing an infrastructure capable of incorporating new ontological refinements as higher-resolution, multimodal single-cell and spatial datasets emerge, cellular heterogeneity is better defined, and disease-associated abnormal cell types and reactive cell states are increasingly recognized and mechanistically interrogated. Together, this coordinated effort aims to provide the foundation necessary for a robust, harmonized, and expandable nomenclature for lung science.

American Journal of Respiratory Cell and Molecular Biology
Broad Institute (US), Northwestern University (US), University of North Carolina at Chapel Hill (US), Translational Genomics Research Institute (US), Cincinnati Children's Hospital Medical Center (US), Bern University of Applied Sciences (CH), University Medical Center Groningen (NL), University of Central Oklahoma (US), University of Nottingham (GB), Pacific Northwest National Laboratory (US), Johns Hopkins University (US), University of California, Los Angeles (US), Stockholm University (SE), Duke University (US), University of Cambridge (GB), Columbia University Irving Medical Center (US), Johns Hopkins Medicine (US), United States National Library of Medicine (US), The Francis Crick Institute (GB), The Ohio State University Wexner Medical Center (US), University of Rochester Medical Center (US), Helmholtz Zentrum München (DE), National Jewish Health (US), University of Alabama at Birmingham (US), Yale University (US), University of California San Diego (US), Massachusetts General Hospital (US), Bridge University (SS), National Heart, Lung, and Blood Institute (US), Seattle Children's Hospital (US), Indiana University Bloomington (US), Bioinformatics Institute (RU), Institut de Pharmacologie Moléculaire et Cellulaire (FR), Technical University of Munich (DE), University of Pennsylvania (US), Vanderbilt University Medical Center (US), University of Colorado Denver (US)
U.S. Department of Health and Human Services, American Thoracic Society, Cincinnati Children's Hospital Medical Center, University of Rochester, Georgia Clinical and Translational Science Alliance, European Commission, National Institutes of Health, Horizon 2020 Framework Programme, HORIZON EUROPE Framework Programme, National Center for Advancing Translational Sciences, Common Fund
Industry, innovation and infrastructure
Openalex Percentile: Top 16%
Single-cell and spatial transcriptomics
DOIOpen Access PDFOpenAlex
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