Skip to main content

Thank you for visiting You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Spatial atlas reveals insight into lung immunity

The cell types of the lung enable gas exchange and protect against infection. Our spatial atlas of the human lung and airways revealed 11 new cell types and mapped their anatomical locations. In particular, we defined the gland-associated immune niche (GAIN), which is involved in fighting respiratory infections.

This is a preview of subscription content, access via your institution

Access options

Buy article

Get time limited or full article access on ReadCube.


All prices are NET prices.

Fig. 1: Spatial profiling of the lungs and airways.


  1. Schiller, H. B. et al. The human lung cell atlas: a high resolution reference map of the human lung in health and disease. Am. J. Respir. Cell Mol. Biol. 61, 31–41 (2019). A review article that provides a roadmap for the human lung cell atlas, including the rationale, approach and expected impact.

    Article  CAS  Google Scholar 

  2. Vieira Braga, F. A. A cellular census of human lungs identifies novel cell states in health and in asthma. Nat. Med. 25, 1153–1163 (2019). An early single-cell sequencing study of the lung and airways of healthy individuals and those with asthma.

    Article  CAS  Google Scholar 

  3. Hewitt, R. J. & Lloyd, C. M. Regulation of immune responses by the airway epithelial cell landscape. Nat. Rev. Immunol. 21, 347–362 (2021). This paper reviews how transcriptomic analyses have advanced our understanding of epithelial and immune cell regulation in the airways.

    Article  CAS  Google Scholar 

  4. Kleshchevnikov, V. et al. Cell2location maps fine-grained cell types in spatial transcriptomics. Nat. Biotechnol. 40, 661–671 (2022). This paper presents cell2location, a method for integrating single-cell and spatial transcriptomic data in order to resolve the spatial contexts of cells.

    Article  CAS  Google Scholar 

  5. Sikkema, L. et al. An integrated cell atlas of the human lung in health and disease. Preprint at bioRxiv (2021). This preprint presents the integrated human lung cell atlas, which comprises more than 400 donor lungs and airways profiled by single-cell transcriptomics, including those presented here.

Download references

Additional information

Publisher’s note Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

This is a summary of: Madissoon, E. et al. A spatially resolved atlas of the human lung characterizes a gland-associated immune niche. Nat. Genet. (2022).

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Spatial atlas reveals insight into lung immunity. Nat Genet 55, 10–11 (2023).

Download citation

  • Published:

  • Issue Date:

  • DOI:


Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing