Human intestinal organoids with an autologous tissue-resident immune compartment

Published: 4 June 2024| Version 1 | DOI: 10.17632/5h3ym82bnb.1
, Bruno Gjeta,
, Lukas Adam, Kristina Kromer, Marisa Pimentel Mendes, Marina Almatò Bellavista, Mikhail Nikolaev, Giacomo Lazzaroni, Rok Krese, Umut Kilik, Doris Popovic, Bilgenaz Stoll, Regine Gerard, Michael Bscheider, Marc Bickle, Lauriane Cabon, Gray Camp, Nikolche Gjorevski


The intimate relationship between the epithelium and the immune system is crucial for maintaining tissue homeostasis, with perturbations in epithelial-immune interactions linked to autoimmune disease and cancer. Whereas stem cell-derived organoids are powerful models of tissue-specific epithelial function, these structures lack tissue-resident immune cells that are essential for capturing organ-level processes. We describe human intestinal immuno-organoids (IIOs), formed through self-organization of epithelial organoids and autologous tissue-resident memory T cells (TRMs), a portion of which integrate within the IIO epithelium and survey the barrier. IIO formation was driven by TRM migration and interaction with epithelial cells, as orchestrated by TRM-enriched transcriptomic programs governing cell motility and epithelial inspection. We combined IIOs and single-cell transcriptomics to investigate intestinal inflammation triggered by cancer-targeting biologics in patients, and found that the system produces outcomes that are consistent with aspects of clinically observed adverse events. The tractability of the system allowed dissection of the cellular mechanisms underlying these effects. Inflammation was associated with the emergence of an activated population of CD8+ T cells, which progressively acquired intraepithelial and cytotoxic features. The appearance of this effector population was preceded and likely orchestrated by a Th1-like CD4+ population, which initially displayed a cytokine-producing character and subsequently became cytotoxic itself. A system amenable to direct perturbation and interrogation, IIOs allowed us to identify the Rho pathway as a novel target for mitigating immunotherapy-associated intestinal inflammation. Given that they recapitulate both the phenotypic outcomes and the underlying inter-lineage immune interactions, IIOs can be used to broadly study tissue-resident immune responses in the context of tumorigenesis, infectious and autoimmune diseases. Data provided here reprent the raw count matrices for all 10x scRNA-seq experiments showcased in this study. Specifically P1-3 are three human individuals whose samples provided materials three experimental conditions each (TRM alone, IIO, Epithelial organoid + PBMC) sequenced after 24h of in vitro culture. P4 is a human individual whose tissues provided material for three experimental conditions probing IIO model response to EpCAM-TCB stimulation at 4h and 48h after treatment as well as a control condition (DP47) at 4h of culture. Count matrices are provided in CSV file format while the Supplementary Information Table 1 file collects metadata around the single cells that contributed to the results supporting the conclusions of this study.



Medizinische Hochschule Hannover, F Hoffmann-La Roche AG Research and Development Division, Universite Paris-Saclay Departement de Biologie, Universitat Basel


Single-Cell RNA Sequencing