Immune cell-stem cell interactions in regeneration and repair: who's calling the shots?

Both stem cells and immune cells have been long studied within their separate fields. In the past decade, however, immune cells have emerged as prominent modulators of stem cell niches in a wide range of tissues (Xing and Naik, 2020), highlighting their potential in the context of regenerative therapies. The recent symposium ‘Stem Cells & the Immune System: At the Crossroads of Regeneration’ focused on this influence of immune cells on stem cell biology, repair and regeneration. The welcome speech was delivered by Jon Epstein, Executive Vice Dean and Chief Scientific Officer of the Perelman School of Medicine (PA, USA), and E. John Wherry, Director of the Institute for Immunology at University of Pennsylvania (PA, USA). Both highlighted that the joining of their institutes to organize the symposium underlines the necessity to support interconnected work at the interface between both disciplines. The aim of the symposium was to showcase recent findings, explore relevant ideas and discuss the overall state of this emerging field. Here, we highlight some of the key trends and concepts that were discussed and provide a summary of the exciting science presented at the symposium.

The symposium touched on several key concepts and emerging trends. It is known that cells in the stem cell niche directly interact with stem cells to modulate their proliferation and direct their differentiation. This is already relatively well-examined in the case of fibroblasts, but we are learning more and more about how other cells, especially immune cells, can also directly impact stem cells. Indeed, the field is shifting away from the classical model, whereby stem cell-driven regeneration is primarily orchestrated by the stem cells themselves, to a model in which the niche dictates the behavior of stem cells, with immune cells forming a key part of this niche.

Throughout the symposium it was also highlighted that, although there are parallels between the general regulation of different stem cell niches, each tissue exhibits distinct immune cell-stem cell interactions (Xing and Naik, 2020). During homeostasis, different tissues display different levels of cellular replacement rates, e.g., rates are mostly constant in the intestine, limited in the brain and episodic in the lactating mammary gland. In the context of immune cells, tissue-specific differences in residency and turnover are also observed and these can vary with age and organ (Wijeyesinghe et al., 2021). For example, stem cell niches at epithelial barriers are exposed to a continuous turnover of resident immune cells. By contrast, other organs, such as the brain, contain tissue-specific immune cells (microglia) and the infiltration of blood immune cells only occurs during disease- or age-related disruption of the blood-brain barrier (Dulken et al., 2019).

Macrophages in particular were in the limelight during the symposium, emerging as a well-studied immune cell type that plays interesting functions in stem cell regulation. The field has moved away from the standard macrophage classification system, with pro-inflammatory M1 macrophages transitioning into M2 macrophages, and has embraced a more nuanced understanding of tissue macrophage function. In addition, new studies have revealed a broad spectrum of macrophage phenotypes with different roles in regeneration (Graney et al., 2020).

Finally, the symposium made it clear that the availability of and advances in single-cell RNA-sequencing, together with complex in vitro models such as organoids, are pivotal for understanding how cell networks function in concert to coordinate a response at the population level. These technologies allow us to better define cell populations in vivo and to define the impact of cell-cell interactions in vitro, revealing new cell populations that are implicated in tissue regeneration processes (Choi et al., 2020; Dulken et al., 2019; Evans and Lee, 2020; Kayisoglu et al., 2021; Melms et al., 2021).

Shruti Naik (NYU Grossman School of Medicine, NY, USA) opened the stage with the fundamental question: how does a tissue or organ recover after deviation from homeostasis? She urged us to discriminate between repair and regeneration. Repair is a fast response, involves the formation of scar tissue, and often comes at a cost of compromised organ function (which, in turn, comes with a significant health burden in humans). In the case of regeneration, however, the response is slower and is characterized by restoration of organ function and the original structure, such as the regenerating limbs of axolotl. Although it is clear that both repair and regeneration rely on the proliferative capacity of stem cells and their differentiating progeny, immune cells may be the linchpin actually defining stem cell function in these processes. She stressed that understanding the role of the immune system in this process can help us to use this knowledge as a lever to promote the desired recovery in regenerative therapies (Konieczny and Naik, 2021; Xing and Naik, 2020). Showing an in-depth analysis of skin lymphocyte populations in response to acute injury, together with elegant experiments in organoids, Dr Naik discussed molecular signals necessary for wound edge remodeling.

Epithelial cells can produce immunological effectors to recruit and influence immune cells. The classical example is pattern recognition receptor-driven pro-inflammatory cytokine secretion by epithelial cells. More recently, tuft cells have emerged as an epithelial cell type with important sensory and immunomodulatory functions (Schneider et al., 2019). Tuft cells are rare secretory epithelial cells, best known from the intestinal epithelium. Andy Vaughan (University of Pennsylvania) discussed tuft cell development and function in the lung in response to influenza infection and viral pneumonia. In the respiratory epithelium, severe injury induces partly dysplastic re-epithelialization. Dr Vaughan identified specialized chemosensory cells that are absent in uninjured lung tissue but appear adjacent to dysplastic epithelium after infection-induced injury. These cells express the classical tuft cell marker Dclk1 and also share transcriptomic signatures with intestinal tuft cells. The signals required for the expansion of lung tuft cells and their exact function after infection injury in the lung are not yet clear (Rane et al., 2019).

Epithelial innate immune signaling drives inflammation. But how does epithelial innate immune function develop? Sina Bartfeld (Technical University Berlin, Germany) emphasized the advantages of using adult stem cell-derived organoids to address this question. Comparing sequencing data from human and murine gastrointestinal organoids, her group identified that each gut segment along the anterior-posterior axis expresses a specific set of innate immune signaling components, such as Toll-like receptors or inflammasome components. Expression and function of a large part, but not all, of the innate immune-related genes did not depend on contact with microbial products but instead was regulated by developmental processes (Kayisoglu et al., 2021). The group further analyzed the interaction of pathogens with their host cells using organoids (Wallaschek et al., 2021). Exactly how location-specific epithelial innate immunity arises and how it contributes to immune cell recruitment, the resolution of infection, and injury repair remains an open question.

Although epithelial cells can express specific innate immune receptors, the cells best known for pathogen clearance and pattern recognition are macrophages. Joo-Hyeon Lee (University of Cambridge, UK) presented work connecting immune cell activation and epithelial reprogramming in lung regeneration. Using single-cell RNA-sequencing, elegant in vivo lineage-tracing and organoids, her group deciphered that injury-induced IL1β secreted from interstitial macrophages directly activates quiescent alveolar stem cells expressing Il1r1 and promotes their differentiation via an intermediate population named damage-associated transient progenitors (DATPs) (Choi et al., 2020). Markers for DATPs also emerged in diseased lungs, including lung cancers and SARS-CoV-2-infected lungs (Melms et al., 2021). The group also identified that inflammatory IL1β builds the stem cell niche by modulating Notch ligands in ciliated cells, which in turn drives the reprogramming of epithelial secretory cells (Choi et al., 2021).

Allie Greenplate (University of Pennsylvania) turned the focus of the symposium towards tracking the immune system in order to direct patient care. The idea, assembled around the Immune Health Project, is to immunoprofile patients’ blood throughout a specific treatment or a vaccine to generate a detailed picture of immune system function and coordination. The immunoprofiling analysis involves labeling antigen-specific cells, high-dimensional flow cytometry, metacluster analysis and longitudinal profiling of antibody response (Apostolidis et al., 2021; Painter et al., 2021). Teaming up with Amit Bar-Or (University of Pennsylvania), the group monitored cellular and humoral immune responses following SARS-CoV-2 mRNA vaccination in patients with multiple sclerosis during treatment with the B-cell depleting agent CD20, identifying that the ideal window for vaccination is rather towards the middle or end of a treatment cycle (Apostolidis et al., 2021). The techniques and analyses used for immunoprofiling have great potential and might also be helpful for studying crosstalk between the immune system and regenerative pathways.

Focusing on the modulation of immune cells, Kara Spiller (Drexel University, Philadelphia, PA, USA) shared her group's developments on the design of biomaterials for the promotion of tissue repair. She highlighted the importance and diversity of macrophage populations in repair, especially M2 macrophages in angiogenesis after tissue injury (Spiller and Koh, 2017). To influence macrophage differentiation, the group loaded IL4 and IL13 onto microspheres and embedded them within gelatin hydrogels. In vivo and in vitro, these microspheres enable constant release of the cytokines over days and weeks, opposed to very short boosts of cytokine levels after traditional injections. Subcutaneous transplantation of the microspheres led to an increase in the expression of M2 markers and extracellular matrix regulatory genes, and increased deposition of extracellular matrix with less aligned fibers (Witherel et al., 2021). The exact influence on macrophage differentiation and the function of the complex subpopulations are not yet understood.

The brain was long believed to be an immune-privileged and sterile organ, owing to the blood-brain barrier. It was therefore surprising when the group of Anne Brunet (Stanford University, CA, USA) identified CD8T cells within the murine brain (Dulken et al., 2019). CD8T cells are only present in aged mice, thus raising the question: is their presence a cause or consequence of aging? The group described the cells as clonally expanded cytotoxic T cells that are not located in blood vessels but instead are integrated within parenchymal tissue, in close proximity to the neural stem cell niche. The specific antigen recognized in the aged brain by the T cells, as well as the function of the cells, are topics of active investigation. Dr Brunet also shared exciting new data on defining the age of neural cells based on single-cell RNA-sequencing of the aging murine brain.

Also highlighting the influence of macrophages on stem cells and regeneration, Rumela Chakrabarti (University of Pennsylvania) examined the mammary gland – a tissue in which immune cell involvement is only starting to be appreciated. Here, mammary stem cells express the Notch ligand Dll1, which activates juxtacrine Notch signaling in macrophages. This then induces the production of Wnts by macrophages, which in turn promotes stem cell activity (Chakrabarti et al., 2018). Keeping with the recurring theme of tissue-specific immunity, Dr Chakrabarti confirmed that mammary macrophages are also different from other tissue macrophages. These data prompt investigation of how macrophages change their molecular character during mammary gland development.

Peter Currie (Australian Regenerative Medicine Institute, Monash University, Australia) presented direct, imaging-based observations of macrophage-stem cell interactions in zebrafish, in which it is possible to image the entire process of muscle regeneration from injury to fiber replacement in vivo. Imaging shows that local tissue-resident macrophages are recruited to the wound site. Every single division of a stem cell is preceded by intimate interactions with macrophages ∼5 h prior. Characterizing macrophages using single-cell RNA-sequencing defined a particular subset of macrophages, marked by MMP9. Ablation of this subset showed that it is necessary for wound healing, and more detailed analysis identified that this subset of macrophages secretes NAMPTA, which binds to the Ccr5 receptor on muscle stem cells. With this, macrophages provide a transient muscle stem cell niche (Ratnayake et al., 2021). Dr Currie underlined that the importance of macrophages is just one example of the role of the immune system as a crucial operator in regeneration, but there are several other cell types to be characterized systematically in the future.

Overall, this timely and exciting symposium emphasized the direct influence of immune cells on stem cells and thus on tissue repair and regeneration. The role of macrophages was highlighted as being key in regulating stem cell niches during regeneration. However, the complexity of not only macrophage populations but also other immune cell populations and their interactions with tissue-resident stem cells is only beginning to be understood. Technological advances, such as single cell RNA-sequencing, new biomaterials and in vitro organoid models, are contributing to the building momentum to decipher the beautifully elaborated invention of nature that we call regeneration and repair.

We thank the organizers of the meeting for commenting on the manuscript before submission and Shruti Naik and Joo-Hyeon Lee for reviewing the manuscript.