Revealing the grammar of small RNA secretion using interpretable machine learning

Small non-coding RNAs can be secreted through a variety of mechanisms, including exosomal sorting, in small extracellular vesicles, and within lipoprotein complexes. However, the mechanisms that govern their sorting and secretion are not well understood. Here, we present ExoGRU, a machine learning model that predicts small RNA secretion probabilities from primary RNA sequences. We experimentally validated the performance of this model through ExoGRU-guided mutagenesis and synthetic RNA sequence analysis. Additionally, we used ExoGRU to reveal cis and trans factors that underlie small RNA secretion, including known and novel RNA-binding proteins (RBPs), e.g., YBX1, HNRNPA2B1, and RBM24. We also developed a novel technique called exoCLIP, which reveals the RNA interactome of RBPs within the cell-free space. Together, our results demonstrate the power of machine learning in revealing novel biological mechanisms. In addition to providing deeper insight into small RNA secretion, this knowledge can be leveraged in therapeutic and synthetic biology applications.

Layilin Anchors Regulatory T Cells in Skin

Regulatory T cells (Tregs) reside in nonlymphoid tissues where they carry out unique functions. The molecular mechanisms responsible for Treg accumulation and maintenance in these tissues are relatively unknown. Using an unbiased discovery approach, we identified LAYN (layilin), a C-type lectin-like receptor, to be preferentially and highly expressed on a subset of activated Tregs in healthy and diseased human skin. Expression of layilin on Tregs was induced by TCR-mediated activation in the presence of IL-2 or TGF-β. Mice with a conditional deletion of layilin in Tregs had reduced accumulation of these cells in tumors. However, these animals somewhat paradoxically had enhanced immune regulation in the tumor microenvironment, resulting in increased tumor growth. Mechanistically, layilin expression on Tregs had a minimal effect on their activation and suppressive capacity in vitro. However, expression of this molecule resulted in a cumulative anchoring effect on Treg dynamic motility in vivo. Taken together, our results suggest a model whereby layilin facilitates Treg adhesion in skin and, in doing so, limits their suppressive capacity. These findings uncover a unique mechanism whereby reduced Treg motility acts to limit immune regulation in nonlymphoid organs and may help guide strategies to exploit this phenomenon for therapeutic benefit.

Dermal Adipocyte Lipolysis and Myofibroblast Conversion Are Required for Efficient Skin Repair

Mature adipocytes store fatty acids and are a common component of tissue stroma. Adipocyte function in regulating bone marrow, skin, muscle, and mammary gland biology is emerging, but the role of adipocyte-derived lipids in tissue homeostasis and repair is poorly understood. Here, we identify an essential role for adipocyte lipolysis in regulating inflammation and repair after injury in skin. Genetic mouse studies revealed that dermal adipocytes are necessary to initiate inflammation after injury and promote subsequent repair. We find through histological, ultrastructural, lipidomic, and genetic experiments in mice that adipocytes adjacent to skin injury initiate lipid release necessary for macrophage inflammation. Tamoxifen-inducible genetic lineage tracing of mature adipocytes and single-cell RNA sequencing revealed that dermal adipocytes alter their fate and generate ECM-producing myofibroblasts within wounds. Thus, adipocytes regulate multiple aspects of repair and may be therapeutic for inflammatory diseases and defective wound healing associated with aging and diabetes.

An Injectable Cytokine Trap for Local Treatment of Autoimmune Disease

Systemic cytokine therapy is limited by toxicity due to activation of unwanted immune cells in off-target tissues. Injectable nanomaterials that interact with the immune system have potential to offer improved pharmacokinetics and cell specificity compared to systemic cytokine therapy by instead capturing and potentiating endogenous cytokine. Here we demonstrate the use of high aspect ratio polycaprolactone nanowires conjugated to cytokine-binding antibodies that assemble into porous matrices when injected into the subcutaneous space. Nanowires are well tolerated in vivo over several weeks, incite minimal foreign body response and resist clearance. Nanowires conjugated with JES6-1, an anti-interleukin-2 (IL-2) antibody, were designed to capture endogenous IL-2 and selectively activate tissue resident regulatory T cells (Tregs). Together these nanowire-antibody matrices were capable of sequestering endogenous IL-2 in the skin and were successful in rebalancing local immune compartments to a more suppressive, Treg-mediated phenotype in both wild type and transgenic murine autoimmune disease models.

The TNFRSF members CD27 and OX40 coordinately limit TH17 differentiation in regulatory T cells

Regulatory T cells (T_regs) are closely related to T_H17 cells and use aspects of the T_H17-differentiation program for optimal immune regulation. In several chronic inflammatory human diseases, T_regs express IL-17A, suggesting that dysregulation of T_H17-associated pathways in T_regs may result in either loss of suppressive function and/or conversion into pathogenic cells. The pathways that regulate the T_H17 program in T_regs are poorly understood. We have identified two TNF receptor superfamily (TNFRSF) members, CD27 and OX40, that are preferentially expressed by skin-resident T_regs Both CD27 and OX40 signaling suppressed the expression of T_H17-associated genes from T_regs in a cell-intrinsic manner in vitro and in vivo. However, only OX40 played a nonredundant role in promoting T_reg accumulation. T_regs that lacked both CD27 and OX40 were defective in controlling skin inflammation and expressed high levels of IL-17A, as well as the master T_H17 transcription factor, RORγt. Last, we found that CD27 expression was inversely correlated with T_reg IL-17 production in skin of patients with psoriasis and hidradenitis suppurativa. Together, our results suggest that TNFRSF members play both redundant and distinct roles in regulating T_reg plasticity in tissues.

CD27 Promotes CD4+ Effector T Cell Survival in Response to Tissue Self-Antigen

Signaling through CD27 plays a role in T cell activation and memory. However, it is currently unknown how this costimulatory receptor influences CD4⁺ effector T (Teff) cells in inflamed tissues. In the current study, we used a murine model of inducible self-antigen expression in the epidermis to elucidate the functional role of CD27 on autoreactive Teff cells. Expression of CD27 on Ag-specific Teff cells resulted in enhanced skin inflammation when compared with CD27-deficient Teff cells. CD27 signaling promoted the accumulation of IFN-γ and IL-2-producing T cells in skin draining lymph nodes in a cell-intrinsic fashion. Surprisingly, this costimulatory pathway had minimal effect on early T cell activation and proliferation. Instead, signaling through CD27 resulted in the progressive survival of Teff cells during the autoimmune response. Using BH3 profiling to assess mitochondrial cell priming, we found that CD27-deficient cells were equally as sensitive as CD27-sufficient cells to mitochondrial outer membrane polarization upon exposure to either BH3 activator or sensitizer peptides. In contrast, CD27-deficient Teff cells expressed higher levels of active caspase 8. Taken together, these results suggest that CD27 does not promote Teff cell survival by increasing expression of antiapoptotic BCL2 family members but instead acts by preferentially suppressing the cell-extrinsic apoptosis pathway, highlighting a previously unidentified role for CD27 in augmenting autoreactive Teff cell responses.

Treg-Cell Control of a CXCL5-IL-17 Inflammatory Axis Promotes Hair-Follicle-Stem-Cell Differentiation During Skin-Barrier Repair

Restoration of barrier-tissue integrity after injury is dependent on the function of immune cells and stem cells (SCs) residing in the tissue. In response to skin injury, hair-follicle stem cells (HFSCs), normally poised for hair generation, are recruited to the site of injury and differentiate into cells that repair damaged epithelium. We used a SC fate-mapping approach to examine the contribution of regulatory T (Treg) cells to epidermal-barrier repair after injury. Depletion of Treg cells impaired skin-barrier regeneration and was associated with a Th17 inflammatory response and failed HFSC differentiation. In this setting, damaged epithelial cells preferentially expressed the neutrophil chemoattractant CXCL5, and blockade of CXCL5 or neutrophil depletion restored barrier function and SC differentiation after epidermal injury. Thus, Treg-cell regulation of localized inflammation enables HFSC differentiation and, thereby, skin-barrier regeneration, with implications for the maintenance and repair of other barrier tissues.

Fas ligand promotes an inducible TLR-dependent model of cutaneous lupus-like inflammation

Toll-like receptors TLR7 and TLR9 are both implicated in the activation of autoreactive B cells and other cell types associated with systemic lupus erythematosus (SLE) pathogenesis. However, Tlr9-/- autoimmune-prone strains paradoxically develop more severe disease. We have now leveraged the negative regulatory role of TLR9 to develop an inducible rapid-onset murine model of systemic autoimmunity that depends on T cell detection of a membrane-bound OVA fusion protein expressed by MHC class II+ cells, expression of TLR7, expression of the type I IFN receptor, and loss of expression of TLR9. These mice are distinguished by a high frequency of OVA-specific Tbet+, IFN-γ+, and FasL-expressing Th1 cells as well as autoantibody-producing B cells. Unexpectedly, contrary to what occurs in most models of SLE, they also developed skin lesions that are very similar to those of human cutaneous lupus erythematosus (CLE) as far as clinical appearance, histological changes, and gene expression. FasL was a key effector mechanism in the skin, as the transfer of FasL-deficient DO11gld T cells completely failed to elicit overt skin lesions. FasL was also upregulated in human CLE biopsies. Overall, our model provides a relevant system for exploring the pathophysiology of CLE as well as the negative regulatory role of TLR9.

Skin-Resident T Cells Drive Dermal Dendritic Cell Migration in Response to Tissue Self-Antigen

Migratory dendritic cell (DC) subsets deliver tissue Ags to draining lymph nodes (DLNs) to either initiate or inhibit T cell-mediated immune responses. The signals mediating DC migration in response to tissue self-antigen are largely unknown. Using a mouse model of inducible skin-specific self-antigen expression, we demonstrate that CD103⁺ dermal DCs (DDCs) rapidly migrate from skin to skin DLN (SDLNs) within the first 48 h after Ag expression. This window of time was characterized by the preferential activation of tissue-resident Ag-specific effector T cells (Teffs), with no concurrent activation of Ag-specific Teffs in SDLNs. Using genetic deletion and adoptive transfer approaches, we show that activation of skin-resident Teffs is required to drive CD103⁺ DDC migration in response to tissue self-antigen and this Batf3-dependent DC population is necessary to mount a fulminant autoimmune response in skin. Conversely, activation of Ag-specific Teffs in SDLNs played no role in DDC migration. Our studies reveal a crucial role for skin-resident T cell-derived signals, originating at the site of self-antigen expression, to drive DDC migration during the elicitation phase of an autoimmune response.

Elucidating the Role of CD27 in Treg Function during Th17 Responses

Tregs and Th17 cells have a very close and complex relationship. Tregs and Th17 cells share a dependence on TGFb for their differentiation and it has recently been shown that Tregs require the Th17-driving transcription factor STAT3 to regulate Th17 responses. Despite sharing a dependence on STAT3, Tregs within healthy tissue tend to produce very low amounts of IL-17. In contrast, in multiple Th17-driven diseases (including Multiple Sclerosis, Psoriasis and Crohn’s) Tregs within the diseased tissue produce increased levels of the IL-17. The costimulatory receptor CD27 and its ligand, CD70, have been shown to play a role in suppressing Th17 responses through the epigenetic suppression of IL-17 and CCR6. We have found that CD27 is highly expressed on Tregs in both human and murine skin, but whether CD27 plays a role in promoting Treg function (and suppressing acquisition of Th17-like traits) remains unknown. Utilizing CD27-deficient mice (CD27KO), we found that Tregs in the skin of CD27KO mice in the steady state produced more IL-17 compared to their wild-type (WT) counterparts. To test the role of CD27 specifically on Tregs during Th17-driven inflammation in vivo, we have developed an adoptive transfer model of cutaneous candida albicans infection where Tregs play an essential role in the development of productive Th17 responses. Using this model, we found that CD27 suppressed Treg expression of IL-17 and CCR6 in a cell-intrinsic manner. We also found that IL-6 could induce the production of IL-17 from Tregs in vitro which was suppressed when co-cultured with CD70 expressing BMDCs. Our studies suggest that the CD27-CD70 pathway promotes Treg function by limiting production of Th17 effector molecules.

A Role for the CD27-CD70 Pathway in T Cell Driven Skin Inflammation

The CD27-CD70 costimulatory pathway plays important roles in T cell function and has been implicated in multiple autoimmune diseases. It is currently unknown whether this costimulatory pathway influences T cell responses in the skin. To study the role of CD27 in CD4 T cells, we have utilized the previously described K5 TGO model of inducible tissue-antigen expression. In this model, mice with both K5 and TGO transgenes allow the expression of the model antigen ovalbumin (ova) to be stringently induced or extinguished in the epidermis through the application or withdrawal of doxycycline. After turning on antigen, the transfer of WT ova-specific CD4 (OTII) T cells into K5/TGO recipients induces an inflammatory dermatitis characterized by scaling and neutrophil influx. When CD27-deficient OTII T cells were transferred, skin disease was attenuated and neutrophil influx was decreased. CD27 costimulation promoted T cell accumulation in the skin draining lymph nodes and skin and IL-2 and IFNg production upon restimulation ex vivo. Using in vivo competition experiments, we found that CD27 promoted CD4 responses in a cell-intrinsic manner. CD27 had minimal effect on early T cell activation and proliferation but seemed instead to be involved in promoting survival. Our studies highlight a previously un-identified role for the CD27 pathway in promoting CD4 T cell responses in the skin.