Intestinal lamina propria supports acquired eTreg suppressor function

Yisu Gu, Raquel Bartolomé-Casado, Chuan Xu, Alina Janney, Cornelia Heuberger, Claire Pearson, Sarah Teichmann, Emily E Thornton, Fiona Powrie

Posted on: 3 November 2022 , updated on: 9 May 2024

Preprint posted on 21 October 2022

Spatial mechanisms of tolerance in the intestine – how networking with the local niche informs Treg function

Selected by Marina Schernthanner

Categories: immunology

Updated 9 May 2024 with a postLight by Marina Schernthanner

The previously highlighted preprint “Intestinal lamina propria supports acquired eTreg suppressor function” by the Powrie group has recently been published in Nature. Besides a change in title (“Immune microniches shape intestinal Treg function” – admittedly more intriguing and all-encompassing), the figures have undergone substantial re-formatting and the authors’ findings have been supplemented with additional spatial transcriptomic experiments.

The core message of the manuscript – how your tissue neighborhood determines cell function – still pertains. The authors took advantage of Helicobacter hepaticus (Hh) infection in mice. Hh establishes lifelong colonization of the caecum and thus can be repurposed as a model to study how tolerance is induced and maintained in the intestine. Regulatory T cells (Tregs) and their production of immunosuppressive IL-10 are crucial in this process. To enable longitudinal tracking of Hh-specific Tregs across lymphoid and non-lymphoid tissue compartments, the authors transferred Hh-specific T cells into Hh-colonized hosts. Complemented by various reporter mouse strains, 2-photon live imaging, photoactivation-guided singe cell RNA-sequencing (NICHE-seq) and now (in the peer-reviewed paper) spatial transcriptomics of Hh-infected mice in the settings of tolerance and inflammation, the authors provide a spatiotemporal atlas of Treg development and adaptation. Clonotype analysis confirmed that transferred Hh-specific T cells can be used as sentinels, which accurately reflect host immune responses to Hh infection.

As shown in the preprint, Treg activation was highest in the lamina propria, the only non-lymphoid tissue compartment the authors surveilled. Indeed, NICHE-seq revealed compartmentalization of such effector Treg (eTreg) phenotypes and diverging cellular networks, driven by different interaction partners, across tissue microniches. Receptor:ligand analyses for instance pinpointed a sustained interaction between highly motile eTregs and CD206+ macrophages, which was specific for the lamina propria and absent in lymphoid aggregates. Intriguingly, inflammation perturbed such compartmentalized programs.

Without doubt, the integration of spatial transcriptomic data on inflamed and non-inflamed Hh-infected mouse intestines in the peer-reviewed paper has added new insights into how spatially coordinated circuits go awry upon perturbation. While my original question of how such processes may affect epithelial turnover, an important determinant of tissue regeneration, remains unaddressed, the authors did delve into eTreg:macrophage interactions in more detail via 2-photon live imaging.

In conclusion, this paper elegantly demonstrates how Tregs adopt their effector phenotype directly within the tissue. More importantly, however, it showcases the need for tailored cell:cell communication in specialized microniches across the tissue to fuel efficient immune responses, while maintaining tissue homeostasis. It’s all about being in the right place at the right time.

1. Background to the preprint

The intestine serves as an important barrier tissue that must balance between nutrient absorption and microbial colonization, while protecting against pathogens. Perhaps not surprisingly, the intestine harbors the largest number of immune cells of any tissue in our body. Consequently, efficient and well-controlled immune mechanisms need to be at play during homeostasis to maintain tolerance, while minimizing long-term consequences of and enabling tissue repair following inflammation. Regulatory T cells (Tregs), a specialized subset of T cells, are a central player in a network of stromal niche cells inhabiting the intestine. They generally act to suppress immune responses, thereby ensuring homeostasis and tissue integrity. In the case of life-long Helicobacter hepaticus (Hh) infection of the mouse caecum for instance, Tregs are pivotal for immune homeostasis and upon loss of Treg function Hh infection triggers murine colitis. While initial Treg induction has been shown to occur in the tissue-draining mesenteric lymph nodes, knowledge about the subsequent steps in Treg adaptation, function and maintenance is still lacking – thus prompting a robust spatiotemporal characterization of Treg development as was done in this preprint by Gu, Bartolomé-Casado and colleagues.


2. Key findings of the preprint

Within the framework of this preprint, the authors combined state-of-the-art mouse genetic models, two-photon in vivo imaging of antigen-specific Tregs in intestinal tissue and NICHE-sequencing to generate a spatiotemporal atlas characterizing Treg induction, adaptation and maintenance in the context of Hh colonization. Key findings of this preprint include the following:

  1. While Treg induction in the intestine was dependent on secondary lymphoid organs, Treg activation, as measured by active TCR-signaling and IL-10 production, mostly happened locally in the non-lymphoid lamina propria.
  2. NICHE-seq of cells from mesenteric lymph nodes, cryptopatches, lymphoid aggregates within colonic tissue and non-lymphoid lamina propria revealed transcriptional differences between Tregs dependent on tissue localization, with non-lymphoid Tregs being associated with the expression of effector-like molecules such as Ctla4, Maf and Tnfrsf4.
  3. NICHE-seq coupled with receptor:ligand analysis through CellPhoneDB revealed differences in Treg interaction in lymphoid versus non-lymphoid microniches.
    • On the one hand, Tregs exhibited different interacting myeloid partners. In lymphoid tissue, Tregs mostly engaged in TCR-MHCII interactions with IL-1βhigh CD103+ Sirpα+ dendritic cells. In comparison, Tregs in the lamina propria mostly interacted with IL-1β+ CD206+ macrophages and IL-1βmonocytes.
    • On the other hand, the molecular pathways involving Tregs and their interaction partners were different in lymphoid versus non-lymphoid tissue.
  4. The lamina propria microniche ensured effector Treg survival and function.
  5. Despite disruption of positive IL-10 feedback signaling between effector Tregs and macrophages in the lamina propria, effector Tregs were not compromised in their expansion and suppressor function in an inflammatory setting.


3. What I like about this preprint

What I appreciate about this preprint is that the authors have taken the spatial tissue context into account when characterizing the step-by-step development of Hh-specific effector Tregs upon adoptive transfer into an Hh-colonized host. In general, classical immunological approaches, such as flow cytometric analysis, do not account for the relative position of immune cells within the tissue. However, a complete understanding of where immune cells become activated and which of their surrounding niche cells might dictate their function, becomes more and more relevant, particularly in the context of infections and inflammatory disorders. In line with that, the field of tissue immunology is on the rise, looking at interactions between immune cells and other tissue-resident cells and focusing on the areas which oftentimes represent the central seat of disease. Naturally, studies like this preprint will highlight new therapeutic targets by identifying new, tissue-specific immune effector subsets and their unique molecular crosstalk with cells within their microniche.


4. Future directions and questions for the authors

In this preprint, the authors generated quite a comprehensive spatiotemporal transcriptional atlas of multiple lymphoid and non-lymphoid tissue compartments, including cells of non-leukocyte identity such as mesenchymal and epithelial cells. A suggested future direction following this work could be a more in-depth receptor:ligand analysis between Tregs (or additional immune cells) and other cellular interaction partners aside from the myeloid compartment. Epithelial cells emerge as an interesting candidate, since they are closest to the majority of microbial inhabitants in the gut and only separated from them by layer(s) of mucus.

Coming from a stem cell-centric background, I could not help but ask myself the following questions:

  1. How would the effector Tregs (eTregs), characterized in this preprint and shown to be predominantly active in the lamina propria of the intestine, influence local tissue dynamics by for instance signaling to tissue-resident stem cells in their vicinity?
    • In figure 4l there appears to be a spike in epithelial proliferation upon treatment with anti-IL-10R in the lamina propria, yet the authors do not report any overt inflammation. They argue eTregs are functioning properly and proliferating more following anti-IL-10R treatment – to what extent might increased Treg proliferation directly impact epithelial turnover?
    • How would local expansion of eTregs in an inflammatory setting influence stem cell-driven epithelial turnover and differentiation?
  2. What might be the molecular pathways through which Tregs communicate with intestinal stem cells?
  3. Regarding the cellular interaction pairs the authors looked at within the context of their work: Where, relative to the crypts, can you find IL-1β+ CD206+ macrophages? And how persistent are macrophage:eTreg interactions? How long do cell contact-dependent interactions last? Are interactions like these present in an uncolonized wild-type mouse as well?


Tags: intestine, niche-seq, tregs


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