2024/07/27 by Joana F. Neves · 1 voice
Immunology and Microbiology · #Immunotherapy and Immune Responses #T-cell and B-cell Immunology #Immune Cell Function and Interaction
paper · pdf · doi:10.1093/cei/uxae067
openalex publication_date 2024/07/27 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/30
Historically, immunological research, especially when involving human cells, has relied heavily on the use of in vitro cultures. While this has led to countless discoveries, in vitro cultures tend to lack physiological structure and cellular diversity, which limits their ability to recapitulate in vivo tissue. This barrier has been bridged by advances in stem cell research that led to development of organoids, i.e. self-assembling 3D tissue cultures whose cell composition, structure, and functions resemble the tissue/organ of origin, which currently can be established from a constantly increasing list of tissues and organs [1]. Intestinal organoids were some of the first organoids to be developed, with a single stem cell from murine small-intestinal crypts being shown to support formation of organoids with the architecture of intestinal crypts and presence of multiple epithelial cell types [2]. Subsequent studies derived intestinal organoids from human intestinal crypts [3] and from human-induced pluripotent cells, with the last ones containing mesenchymal cells in addition to epithelial cells [4, 5]. Given the experimental flexibility of gut organoids, coupled with the continuous emergence of studies documenting the close interactions between immune, microbiota, and epithelial cells in the gut [6], these 3D cultures caught the attention of mucosal immunologists as a powerful system enabling the detailed study of these cellular interactions in the intestine and their importance in health and disease. Organoid research, which was initially focused on stem cell and tissue development, has therefore since been adopted and adapted by immunologists that have been recognizing the advantages of using these models for their studies. That is the main focus of this review series, which covers the use of intestinal organoid models in different aspects of immunological research. Initially, immunological studies with intestinal organoids mainly involved the addition of cytokines to the culture media to assess the impact of immune components on the epithelial compartment. Subsequent studies started increasing the complexity of these systems, including by adding immune cells to the organoid cultures, enabling the elucidation of the bidirectional interactions between the epithelium and the immune compartment. Kromann et al. review several models of immune-organoid co-cultures available nowadays, which are suitable to address different research questions [7]. These systems can incorporate a variety of immune cells, including CD4+ T cells, innate lymphoid cells, dendritic cells, monocytes and macrophages [7]. Importantly, these co-cultures are leading to the discovery of new mechanisms that regulate immune-epithelial interactions during homeostasis and disease, including inflammation, infection, and cancer [7]. Furthermore, they discuss how organoids can be used to generate immune cells with tissue-specific phenotypes, which may facilitate immunotherapeutic approaches [7]. The gastrointestinal immune system is constantly being challenged by commensal and pathogenic microorganisms. Pauzuolis et al. review how the incorporation of bacteria, viruses, and parasites in organoid models has been used to study the interactions between pathogens, epithelial, and immune cells in the gut [8]. Some of these pathogens have host tropism and/or organ tropism, and the use of human organoids from different regions of the gastrointestinal tract (e.g. stomach, small intestinal, and colon) has enabled the detailed characterization of the interactions between pathogens and different host tissues [8]. In addition, organoids have the different types of epithelial cells present in the intestine and can even be enriched for particular cell types, allowing to dissect the cellular tropism of various pathogens [8]. Such studies can be challenging because intestinal organoids are closed 3D structures in which the apical side faces the lumen/inside of the organoid, which can make it difficult to access and requires microinjection of the microbes/microbial products into the lumen of the organoids. However, the 3D structures can be disrupted and placed in transwells to form organoid monolayers providing easy access to both the apical and basal sides, which has been widely adopted for host–pathogen interactions models [8]. In addition to studying infections, organoids are also being increasingly used for modelling other diseases, as they maintain characteristics of the diseased tissue origin and can be manipulated (e.g. genome editing, addition of environmental clues) to display disease phenotypes [9]. Papp et al. review how using organoids that incorporate immune cells increases the physiological relevance of these disease models, including for intestinal inflammation and cancer [9]. Furthermore, they highlight how these increasingly complex disease models are starting to be used for drug screening and safety testing. For example, organ-on-chip and microfluidic systems that incorporate organoids are being adopted to increase the capacity and applicability of these models allowing for automated and high-throughput approaches, which is particularly important for industrial R&D [9]. They also argue that, as organoid technology is now widely used in several areas of research, appropriate infrastructure and technical support must be provided to achieve maximum impact and efficiency of these novel applications and facilitate sharing of resources, including through the establishment of organoid facilities and organoid biobanks. The reviews in this series demonstrate the exponential development of organoids as a tool for immunological research, a continuously expanding field with plenty of room for growth. These articles highlight how the complexity of these systems continues to increase, including by adding different subsets of immune cells, establishing co-cultures of organoids with immune and microbial cells, and modulating cellular composition. Future studies are likely to continue to expand organoid complexity to further advance immunology research, including by increasing the organoid lifespan, improving tissue architecture and functions, incorporating other cellular components (such as neurons), and developing robust models that recapitulate disease phenotypes, all of which will enable the use of organoids models to tackle a wider range of questions in immunology. In addition to these future technical developments, there are other challenges that need to be overcome so that organoids reach their full potential to advance immunology research. Currently, adoption of organoids models in low- and middle-income countries can be challenging due to multiple reasons, including costs, difficulties in importing reagents and materials, and lack of technical expertise. Therefore, it is important that the community continues to work together to develop and share reliable and reproducible methods and materials that contribute to the affordability of organoid models to disseminate their use. For example, access to organoid biobanks and cell lines used to produce certain components required for growing organoids can be facilitated, and training networks can be established to share technical know-how. Furthermore, there is a need to engage with other communities to debate more widely the ethical considerations linked to various aspects of the use of organoids in research, from obtaining consent to establish organoids to their use in precision medicine. Overall, the articles in this series demonstrate that organoids are already an essential tool to study human diseases that enable the detailed characterization of new mechanisms of immune–epithelial–microbial interactions in the gut. By continuing to improve on these models, including by expanding their complexity and broadening their use and applications, organoids have the potential to accelerate the translation of immunology research for the benefit of the patients. None declared. Joana F. Neves acknowledges funding from the Lister Institute of Preventive Medicine.