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Review
. 2025 Mar;155(3):678-687.
doi: 10.1016/j.jaci.2025.01.009. Epub 2025 Jan 19.

Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation

Haihan Zhang  1 , Matthew T Patrick  2 , Jingyu Zhao  1 , Xintong Zhai  1 , Jialin Liu  3 , Zheng Li  1 , Yiqian Gu  4 , Joshua Welch  5 , Xiang Zhou  1 , Robert L Modlin  4 , Lam C Tsoi  6 , Johann E Gudjonsson  7
Affiliations
Review

Techniques and analytic workflow for spatial transcriptomics and its application to allergy and inflammation

Haihan Zhang et al. J Allergy Clin Immunol. 2025 Mar.

Abstract

Spatial profiling, through single-cell gene-level expression data paired with cell localization, offers unprecedented biologic insights within the intact spatial context of cells in healthy and diseased tissue, adding a novel dimension to data interpretation. This review summarizes recent developments in this field, its application to allergy and inflammation, and recent single-cell resolution platforms designed for spatial transcriptomics with a focus on data processing and analyses for efficient biologic interpretation of data. By preserving spatial context, these technologies provide critical insights into tissue architecture and cellular interactions that are unattainable with traditional transcriptomics methods, such as revealing localized inflammatory cell network in atopic dermatitis and T-cell interactions in the lung in chronic obstructive pulmonary disease. Spatial profiling offers opportunities for discovering novel biomarkers, defining compartmentalization of immune responses within tissues and individual diseases, and accelerating novel discoveries toward a greater understanding of fundamental disease mechanisms and, eventually, toward the development of future targeted therapies.

Keywords: Spatial profiling; allergy and skin biology; spatial transcriptomics.

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Conflict of interest statement

Disclosure statement Disclosure of potential conflict of interest: J. E. Gudjonsson has served as a consultant to AbbVie, Eli Lilly, Almirall, Celgene, BMS, Janssen, Prometheus, TimberPharma, Galderma, Novatis, MiRagen, and AnaptysBio and has received research support from AbbVie, SunPharma, Eli Lilly, Kyowa Kirin, Almirall, Celgene, BMS, Janssen, Prometheus, and TimberPharma. L. C. Tsoi has received support from Galderma and Janssen. The rest of the authors declare that they have no relevant conflicts of interest.

References

    1. Larsson L, Frisén J, Lundeberg J. Spatially resolved transcriptomics adds a new dimension to genomics. Nature methods. 2021;18(1):15–8. - PubMed
    1. Moor AE, Itzkovitz S. Spatial transcriptomics: paving the way for tissue-level systems biology. Current opinion in biotechnology. 2017;46:126–33. - PubMed
    1. Stuart T, Satija R. Integrative single-cell analysis. Nature reviews genetics. 2019;20(5):257–72. - PubMed
    1. Ståhl PL, Salmén F, Vickovic S, Lundmark A, Navarro JF, Magnusson J, et al. Visualization and analysis of gene expression in tissue sections by spatial transcriptomics. Science. 2016;353(6294):78–82. - PubMed
    1. Marx V Method of the Year: spatially resolved transcriptomics. Nature methods. 2021;18(1):9–14. - PubMed