Biology subjects

Lacy-Hulbert, A.

Publications and source records attributed to Lacy-Hulbert, A..

10 recordsLinked to original sources

bioRxiv2026

Lineage-specific chromatin poising enforced by ETS-IRF composite elements determines the divergent interferon responses of plasmacytoid dendritic cells and epithelial cells

Plasmacytoid dendritic cells (pDCs) produce robust type I interferons (IFN-I) within hours of viral sensing, while epithelial cells at mucosal surfaces mount a delayed response dominated by type III interferons (IFN-III). Both cell types express pattern recognition receptors that activate similar downstream transcription factors, yet they produce distinct subsets of IFNs. The mechanisms underlying these differences have remained unclear. Here, using Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq) in primary human pDCs and intestinal epithelial cells, we show that IFN-I and IFN-III gene loci carry opposing, constitutively established chromatin accessibility landscapes that determine cell-type-specific interferon induction. The IFN-I locus is broadly open in pDCs and constitutively closed in epithelial cells, while the IFN-III locus displays the reciprocal pattern. Motif enrichment analysis of accessible regions at the IFN-I locus in pDCs revealed unexpected and significant enrichment of ETS family binding motifs alongside IRF motifs, which determines the cell-type-specific locus accessibility. The ETS factor PU.1 and IRF8 bind IFN-I promoters, at composite ETS-IRF elements positioned at the Positive Regulatory Domain IV (PRDIV) site of IFNB1 promoter and adjacent to the TATA-proximal IRF motif of IFNA promoters. IFNL gene promoters lack ETS recognition sequences. PU.1-IRF8 composite factor binding extends across intergenic regions of the IFN-I locus, where candidate enhancer elements marked by H3K4me1, H3K27ac, and RNA Pol II occupancy were identified. We propose that this network of ETS-IRF composite-element-anchored enhancers maintains the IFN-I locus in a constitutively poised state in pDCs, licensing the rapid and robust IFN-I response that defines pDCs. In epithelial cells, the absence of PU.1 and IRF8 renders the IFN-I locus epigenetically silent, while the IFN-III locus is constitutively open. Despite this, the delayed IFN-III gene expression in epithelial cells is due to intrinsically weaker promoter activity relative to IFN-I. These findings reveal that the divergent IFN induction of pDCs and epithelial cells is determined by the chromatin architecture prior to infection. Overall, these observations show that lineage-specific ETS-IRF regulatory factors and promoter strength determine the cell-type-specific IFN activation.

immunology↗

bioRxiv2026

Coincident epithelial signals restrain commensal-specific CD8αβ+ T cells in the intestine

The intestinal epithelium harbors a large population of microbiota-dependent CD8{beta}+ T cells whose antigen specificity and regulation are ill-defined. By identifying MHCIa-restricted TCRs and generating tetramers against the gut commensal Segmented Filamentous Bacteria, we demonstrate that a single commensal species drives a clonally expanded, antigen-specific CD8{beta}+ T cell within the intraepithelial lymphocyte compartment. Mechanistically, the intestinal epithelium coordinates coincident signals governing this population: peptide:MHC-dependent TCR engagement drives pIEL accumulation, while v{beta}6-mediated TGF{beta} activation restraints effector cell differentiation. Perturbation of epithelial cell-mediated TGF{beta} activation diverts commensal-specific CD8+ T cells toward inflammatory differentiation states transcriptionally convergent with those observed in ulcerative colitis. The intestinal epithelium thus functions as a dual-signal organizer of commensal-specific CD8+ T cell responses, coupling differentiation to restraint through spatially coincident molecular cues.

immunology↗

bioRxiv2026

UC-associated autoantibodies to αvβ6 inhibit mucosal TGFβ activation and predispose to intestinal inflammation

Ulcerative colitis (UC) is characterized by epithelial barrier dysfunction and dysregulated mucosal immune responses; however, the mechanisms driving disease onset remain poorly defined. Autoantibodies against the epithelial-restricted integrin v{beta}6 are a highly specific biomarker of UC that can precede clinical diagnosis by up to 10 years. Because v{beta}6 activates TGF{beta} at epithelial surfaces, we hypothesized that UC-associated v{beta}6 autoantibodies inhibit mucosal TGF{beta} activation and disrupt epithelial homeostasis. We showed that v{beta}6 autoantibodies were enriched in UC and that IgG from autoantibody-positive individuals inhibited v{beta}6-dependent activation of TGF{beta}. v{beta}6 blockade dampened TGF{beta} signaling and altered differentiation-associated gene programs in human intestinal epithelial cells. In mice, deletion of v caused expansion of inflammation-associated goblet cells in the colon and changes in intestinal immune cells. Using a novel mouse model, we showed that v{beta}6-specific autoantibody disrupted epithelial-immune crosstalk and increased susceptibility to DSS colitis. Together, these findings establish anti-v{beta}6 autoantibodies as active inhibitors of epithelial TGF{beta} signaling, constituting a de facto anti-cytokine response, rather than passive biomarkers. By linking preclinical seropositivity to impaired epithelial signaling and heightened susceptibility to colitis, this work identifies epithelial v{beta}6-dependent TGF{beta} activation as a pathway that may be leveraged to modify disease risk or limit disease severity. One Sentence SummaryUC-associated autoantibodies impair epithelial TGF{beta} activation, alter mucosal homeostasis, and predispose to colitis.

immunology↗

bioRxiv2024

B cell αv integrin regulates germinal center derived lung-resident IgA B cell responses following influenza virus infection

Lung-resident B cells are increasingly recognized as key contributors to protective immunity against respiratory viruses, yet the mechanisms that govern their generation and specialization remain poorly understood. Here, we identify B cell-intrinsic v integrin as a critical negative regulator of germinal center (GC) dynamics and memory B cell formation in the lung following influenza A virus (IAV) infection. Using B cell-specific v knockout mice, we show that loss of B cell v integrin leads to persistent GC activity within the inducible bronchus-associated lymphoid tissue and expansion of lung-resident memory B cells, including IgA+ and cross-reactive B cells capable of recognizing heterologous influenza variants. Single-cell transcriptomic and B cell receptor (BCR) sequence analyses reveal that v restricts clonal expansion and antigenic diversification of GC and memory B cells in the lung, but not in draining lymph nodes, indicating a spatially restricted mechanism of mucosal B cell regulation. These findings position v integrin as a key checkpoint that constrains local mucosal B cell evolution and suggest new strategies to improve mucosal vaccine efficacy by enhancing GC activity directly in the lung.

immunology↗

bioRxiv2024

Unsupervised generative AI discovers pan-leukocyte dysregulated pathways in single-cell lupus data

Comparisons of single-cell RNA-sequencing (scRNA-seq) data from healthy and diseased tissues are widely used to identify cell-type-specific dysregulated genes, pathways, and processes. Accordingly, many sophisticated methods have been developed for this purpose. However, such tools generally require considerable user expertise for optimal performance. Here, we show that unsupervised application of a linearly-decoded Variational Auto Encoder (a generative AI model) to scRNA-seq data recapitulates and extends findings from a seminal recent lupus study and leads to new insights. Thanks to existing software libraries, our approach is straightforward to implement, computationally efficient, methodologically robust, and produces consistent and reproducible results.

bioinformatics↗

bioRxiv2023

Flow cytometry methods for targeted isolation of ctenophore cells

Cell suspension fluidics, such as flow cytometry (FCS) and fluorescence-activated cell sorting (FACS), facilitates the identification and precise separation of individual cells based on phenotype. Since its introduction, flow cytometry has been used to analyze cell types and cellular processes in diverse non-vertebrate taxa, including cnidarians, molluscs, and arthropods. Ctenophores, which diverged very early from the metazoan stem lineage, have emerged as an informative clade for the study of metazoan cell type evolution. We present standardized methodologies for flow cytometry-mediated identification and analyses of cells from the model ctenophore Mnemiopsis leidyi that can also be applied to isolate targeted cell populations. Here we focus on the identification and isolation of ctenophore phagocytes. Implementing flow cytometry methods in ctenophores allows for fine scale analyses of fundamental cellular processes conserved broadly across animals, as well as potentially revealing novel cellular phenotypes and behaviors restricted to the ctenophore lineage.

cell biology↗

bioRxiv2023

A rapid, inexpensive, non-lethal method for detecting disseminated neoplasia in a bivalve

Disseminated neoplasia (DN) is a form of cancer in bivalve molluscs that has been reported in some cases to be a transmissible cancer. Neoplastic cells are highly proliferative, and infection is often lethal. Some commercially valuable bivalve species (mussels, cockles, soft-shell clams, oysters) are affected by outbreaks of disseminated neoplasia, making disease diagnosis and mitigation an important issue in aquaculture and ecological restoration efforts. Here we describe a minimally invasive, non-lethal method for high-throughput screening for disseminated neoplasia in basket cockles (Clinocardium nuttallii). Basket cockles are native to the North American Pacific coast from California to Alaska. There is recent concern from some Coast Salish Tribes regarding an observed long-term decline in cockle populations in Puget Sound, WA. This has led to increased interest in monitoring efforts and research to improve our understanding of the mechanisms of observed basket cockle population dynamics, including assessing prevalence of disease, such as disseminated neoplasia. The rapid, non-lethal hemolymph smear screening method presented here to diagnose DN in adult C. nuttallii can be applied at field sites at low financial cost, and in a validation study of 29 animals the results were identical to that of the gold standard method, tissue histology. Due to the similar morphology of DN in different bivalves, this method can likely be generally applied for use in any bivalve species.

cell biology↗

bioRxiv2021

Transcriptomic analysis of pathways associated with alpha(v) integrin-related non-canonical autophagy in human B cells

Autophagy proteins have been linked with development of immune-mediated diseases including lupus, but the mechanisms for this are unclear. We have previously shown that non-canonical autophagy induced by v-integrins regulates B cell activation by viral and self-antigens in mice. Here we investigated the involvement of this pathway in B cells from human tissue. Our data revealed that autophagy is specifically induced in germinal-center and memory B cell sub-populations from human tonsil and spleen. Transcriptomic analysis showed that induction of autophagy is related to unique aspects of activated B cells such as mitochondrial metabolism. To understand the function of non-canonical autophagy in B cells, we used CRISPR-mediated knockdown of autophagy genes. Integrating data from primary B cells and knockout cells we found that v-integrin-related non-canonical autophagy limits activation of specific pathways while promoting others. These data provide new mechanistic links for autophagy and immune dysregulation in diseases such as lupus.

immunology↗

bioRxiv2020

Ctenophore immune cells produce chromatin traps in response to pathogens and NADPH-independent stimulus

The formation of extracellular DNA traps (ETosis) is a first response mechanism by specific immune cells following exposure to microbes 1,2. Initially characterized in vertebrate neutrophils, cells capable of ETosis have been discovered recently in diverse non-vertebrate taxa 3 4-6. To assess the conservation of ETosis between evolutionarily distant non-vertebrate phyla, we observed and quantified ETosis using the model ctenophore Mnemiopsis leidyi and the oyster Crassostrea gigas. Here we report that ctenophores - thought to have diverged very early from the metazoan stem lineage 7-10- possess immune cell types capable of phagocytosis and ETosis. We demonstrate that both Mnemiopsis and Crassostrea immune cells undergo ETosis after exposure to diverse microbes and chemical agents that stimulate ion flux. Our results support ETosis as an evolutionarily ancient metazoan defense against pathogens.

evolutionary biology↗

bioRxiv2020

Apoptotic cells induce CD103 expression and immunoregulatory function in myeloid dendritic cell precursors through integrin αv and TGF-β activation

In the mammalian gut CD103+ve myeloid DCs are known to suppress inflammation threatened by luminal bacteria, but stimuli driving DC precursor differentiation towards this beneficial phenotype are incompletely understood. We isolated CD11+ve DCs from mesenteric lymph nodes (MLNs) of healthy mice; CD103+ve DCs were 8-24 fold more likely than CD103-ve DCs to exhibit extensive of prior phagocytosis of apoptotic intestinal epithelial cells. However, CD103+ve and CD103-ve MLN DCs exhibited similar ex vivo capacity to ingest apoptotic cells, indicating that apoptotic cells might drive immature DC differentiation towards the CD103+ve phenotype. When cultured with apoptotic cells, myeloid DC precursors isolated from murine bone marrow and characterised as lineage-ve CD103-ve, displayed enhanced expression of CD103 and {beta}8 integrin and acquired increased capacity to induce Tregs after 7d in vitro. However, DC precursors isolated from v-tie2 mice lacking v integrins in the myeloid line exhibited reduced binding of apoptotic cells and complete deficiency in the capacity of apoptotic cells and/or latent TGF-{beta}1 to enhance CD103 expression in culture, whereas active TGF-{beta}1 increased DC precursor CD103 expression irrespective of v expression. Fluorescence microscopy revealed clustering of v integrin chains and latent TGF-{beta}1 at points of contact between DC precursors and apoptotic cells. We conclude that myeloid DC precursors can deploy v integrin to orchestrate binding of apoptotic cells, activation of latent TGF-{beta}1 and acquisition of the immunoregulatory CD103+ve {beta}8+ve DC phenotype. This implies that a hitherto unrecognised consequence of apoptotic cell interaction with myeloid phagocytes is programming that prevents inflammation.

immunology↗