IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-024-55129-6.html
   My bibliography  Save this article

A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens

Author

Listed:
  • Gina Bouchard

    (Stanford University)

  • Weiruo Zhang

    (Stanford University)

  • Ilayda Ilerten

    (Stanford University)

  • Irene Li

    (Stanford University)

  • Asmita Bhattacharya

    (Stanford University)

  • Yuanyuan Li

    (Stanford University)

  • Winston Trope

    (Stanford University)

  • Joseph B. Shrager

    (Stanford University
    Veterans Affairs Palo Alto Health Care System)

  • Calvin Kuo

    (Stanford University)

  • Michael G. Ozawa

    (Stanford University)

  • Amato J. Giaccia

    (Stanford University
    University of Oxford)

  • Lu Tian

    (Stanford University)

  • Sylvia K. Plevritis

    (Stanford University
    Stanford University)

Abstract

Spatial omics is enabling unprecedented tissue characterization, but the ability to adequately compare spatial features across samples under different conditions is lacking. We propose a quantitative framework that catalogs significant, normalized, colocalizations between pairs of cell subpopulations, enabling comparisons among a variety of biological samples. We perform cell-pair colocalization analysis on multiplexed immunofluorescence images of assembloids constructed with lung adenocarcinoma (LUAD) organoids and cancer-associated fibroblasts derived from human tumors. Our data show that assembloids recapitulate human LUAD tumor-stroma spatial organization, justifying their use as a tool for investigating the spatial biology of human disease. Intriguingly, drug-perturbation studies identify drug-induced spatial rearrangements that also appear in treatment-naïve human tumor samples, suggesting potential directions for characterizing spatial (re)-organization related to drug resistance. Moreover, our work provides an opportunity to quantify spatial data across different samples, with the common goal of building catalogs of spatial features associated with disease processes and drug response.

Suggested Citation

  • Gina Bouchard & Weiruo Zhang & Ilayda Ilerten & Irene Li & Asmita Bhattacharya & Yuanyuan Li & Winston Trope & Joseph B. Shrager & Calvin Kuo & Michael G. Ozawa & Amato J. Giaccia & Lu Tian & Sylvia K, 2025. "A quantitative spatial cell-cell colocalizations framework enabling comparisons between in vitro assembloids and pathological specimens," Nature Communications, Nature, vol. 16(1), pages 1-17, December.
  • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55129-6
    DOI: 10.1038/s41467-024-55129-6
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-024-55129-6
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-024-55129-6?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Loukia G. Karacosta & Benedict Anchang & Nikolaos Ignatiadis & Samuel C. Kimmey & Jalen A. Benson & Joseph B. Shrager & Robert Tibshirani & Sean C. Bendall & Sylvia K. Plevritis, 2019. "Mapping lung cancer epithelial-mesenchymal transition states and trajectories with single-cell resolution," Nature Communications, Nature, vol. 10(1), pages 1-15, December.
    2. Yi-Ing Chen & Chin-Chun Chang & Min-Fen Hsu & Yung-Ming Jeng & Yu-Wen Tien & Ming-Chu Chang & Yu-Ting Chang & Chun-Mei Hu & Wen-Hwa Lee, 2022. "Homophilic ATP1A1 binding induces activin A secretion to promote EMT of tumor cells and myofibroblast activation," Nature Communications, Nature, vol. 13(1), pages 1-20, December.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Guidantonio Malagoli Tagliazucchi & Anna J. Wiecek & Eloise Withnell & Maria Secrier, 2023. "Genomic and microenvironmental heterogeneity shaping epithelial-to-mesenchymal trajectories in cancer," Nature Communications, Nature, vol. 14(1), pages 1-20, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-024-55129-6. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.