Immune cells adapt to distinct stem cell niches to govern tissue homeostasis

Keywords

● Stem cell niches

● Skin homeostasis

● Dendritic epidermal T cells

Main Findings

Epithelial stem cells exist within distinct microenvironments (niches) which support their capacity to regenerate and maintain tissue homeostasis. For example, in this skin, interfollicular epidermis (IFE) stem cells must drive continuous barrier renewal.  whereas upper hair follicle stem cells help replenish and rejuvenate the epithelium at the follicle opening, a region with high microbial burden. Immune cells are key components of epithelial stem cell niches, but a detailed understanding of immune-stem cell interactions is lacking. Using the skin as a model, Parigi et al. combine the uLIPSTIC (universal labelling immune partnerships by SorTagging intercellular contacts) in vivo labelling system with single-cell RNA sequencing to map immune cells that physically interact with Sox9+ hair follicle stem cells (HFSC). Their data reveal that intraepithelial dendritic epidermal T cells (DETC; Vγ5Vδ1 T cells) adopt distinct transcriptional and functional programs depending on the stem cell niche they occupy.

uLIPSTIC+DETCs are enriched in the upper hair follicle (uHF) and exhibit an immune-activating signature, including high expression of lymphotoxin- β (LTB). Notably, LTB expression is enriched across multiple lymphocytes in the uHF. In parallel, uHF stem cells show elevated expression of the lymphotoxin- β receptor (Ltbr) and downstream effector molecule nuclear factor kappa B subunit 2 (NFkb2) relative to other epithelial compartments, suggesting a uHF niche-specific LTB-LTBR axis. Experimentally stimulating LTBR signalling in uHF stem cells increases chemokine production and promotes T recruitment in vitro and in vivo. Conversely, depleting LTB-expressing immune cells and stem-cell specific deletion of Ltbr reduce chemokine production, decrease CD8+ T cell accumulation in hair follicles, and impairs control of Staphylococcus epidermis skin colonization. Overall, the results support a model in which LTB-LTBR signalling between lymphocytes and SC in the uHF help establish an immune competent niche that recruits T cells and restrains bacterial expansion.

As DETCs are intraepithelial, the authors reason that uLIPSTIC- DETC represent DETCs residing in the interfollicular epidermis (IFE), where they interact with a distinct stem cell population. In this IFE niche, DETCs preferentially express amphiregulin (AREG) and the immune checkpoint molecule (LAG-3). In addition, IFE stem cells show higher expression of LAG-3-interacting proteins MHC-II and Galectin-3. Blocking LAG-3 increases DETC abundance specifically in the IFE and elevates intraepithelial levels of AREG as well as the proliferation of IFE stem cells but not uHF stem cells. In line with this, increasing AREG availability by administering recombinant AREG boosts IFE stem cell proliferation, whereas conditional loss of AREG in DETC dampens it. Altogether, these results suggest that IFE DETC expression of AREG and LAG-3 form a circuit in which AREG promotes epidermal stem cell proliferation while LAG-3 limits DETC abundance and, therefore, AREG levels, preventing excessive proliferative responses in the epidermis.

The study further demonstrates that when DETCs are absent, dermal Vγ5- Vδ T cells or innate lymphoid cells can move into the IFE and acquire AREG and LAG-3 expression, maintaining overall intraepithelial AREG levels. This indicates that the IFE niche can imprint a shared functional program onto distinct immune cell subsets to preserve tissue homeostasis.

Notably, DETC acquisition of niche-specific LTB, AREG, and LAG-3 expression occurs after their migration to the skin from the thymus and is similar between specific pathogen-free and germ-free mice, suggesting that stem cell niche itself is a dominant driver of DETC reprogramming.

Overall, the preprint demonstrates that DETCs are actively reprogrammed by the skin SC niche in which they reside and, in turn, can tune niche function to meet local tissue demands. Furthermore, when DETCs are absent, dermal lymphocyte populations can repopulate and adapt niche-specific functions, highlighting that niche-specific adaptations are not restricted to ontogenically related cells, but are rather governed by stem cell niches and vacancies within them.

Limitations

● The data about the LTB-LTBR circuit in the upper hair follicle is compelling, but there are additional mechanistic experiments would strengthen the authors claims about the necessity of this circuit to maintain an immune-competent niche. For example, LTB expression by lymphocytes and LTBR expression by uHF stem cells does not conclusively show the cell types are interacting with each other. Additionally, the diphtheria toxin-mediated loss of LTB-expressing lymphocytes cannot separate the effects of LTB signalling from other immune mechanisms that lymphocytes employ to control bacterial burden. A conditional knockout of LTB from DETC (similar to the mouse model generated to test AREG function in DETC) would better resolve the DETC-specific role of LTB. Additionally, the link between reduced CD8+ T cell recruitment and increased bacterial colonization is suggestive but not causal.

● DETC are a critical population of epidermal lymphocytes in mice that are not present in humans. The authors demonstrate there is remarkable plasticity and other immune cells adopt AREG/LAG-3 programs when DETC are absent. Therefore, it would be interesting to test if analogous LTB-LTBR and AREG-LAG-3 circuits exist in human skin with human-resident lymphocyte populations.

● The data demonstrating that DETC acquire LAG-3, AREG, and LTB expression after migrating to the skin and independently of microbial colonization, suggesting a role for the stem cell niche they localize to in endowing heterogeneity to the DETC. There is opportunity within this window to profile the SC within the IFE and uHF niche and compare thymic DETC to epidermal DETC subsets to explore how regional imprinting occurs.

● Most experiments are done in steady-state. It would be interesting to see how the functional adaptation of DETCs (or other lymphocytes) play out during additional perturbations of the skin (e.g. colonization with a pathogen or age)

Significance/Novelty

The authors apply a newly developed in vivo contact labelling system (uLIPSTIC) to the skin for the first time and uncover key details governing immune cell-stem cell interactions in the skin. First, skin-resident DETCs are regionally imprinted by distinct epithelial stem cell niches and adopt specific effector programs that in turn help maintain stem cell homeostasis and meet local tissue demands. Secondly, there is plasticity and resilience within the niche. In the absence of DETCs, other lymphocytes expand into the IFE and adapt similar functions. The authors support their model with several complementary approaches and establish a framework for exploring immune-stem cell cross-talk in other tissues such as the bone marrow or the intestine.

Credit

Reviewed by Preya Patel as part of a cross-institutional journal club between the Icahn School of Medicine at Mount Sinai, the University of Oxford, the Karolinska Institute and the University of Toronto.

The author declares no conflict of interests in relation to their involvement in the review.