Biology subjects

Clatworthy, M. R.

Publications and source records attributed to Clatworthy, M. R..

At least 19 recordsLinked to original sources

bioRxiv2025

Childhood brain tumours instruct cranial haematopoiesis and immunotolerance

Recent research has revealed a remarkable role for immunosurveillance in healthy and diseased brains, dispelling the notion that this organ is a passive immune-privileged site1-3. Better understanding of how this immunosurveillance operates could improve the treatment of neurological diseases. Here, using a novel genetically engineered mouse model of ZFTA-RELA ependymoma4-a childhood brain tumour-we characterised an immune circuit between the tumour and antigen presenting, haematopoietic stem/progenitor cells (HSPCs) in the skull bone marrow. The presentation of antigens in the cerebrospinal fluid (CSF) by HSPCs to CD4+ T cells, biased HSPC lineages toward myelopoiesis and polarised CD4+ T-cells to regulatory T cells (T- regs), culminating in tumour immunotolerance. Remarkably, a single infusion of antibodies directed against cytokines enriched in the CSF of mice bearing ZFTA-RELA ependymomas, choroid plexus carcinomas or Group-3 medulloblastoma-all aggressive childhood brain tumours-disrupted this process and caused profound tumour regression. These data unmask a mechanism by which skull bone marrow-derived HSPCs and CD4+ T cells cooperate to promote the immunotolerance of childhood brain tumours. Antibodies that disrupt this immunosurveillance could prove an effective therapy for these cancers that are less toxic than current treatments.

immunology↗

bioRxiv2025

Intestinal challenges shape the polarisation of protective dural memory CD4 T cells

The meninges house several innate and adaptive immune cell populations1-3. These predominantly localise within the dura mater and include gut-derived IgA-secreting plasma cells4. Whether T cell adaptive memory in the dura is similarly linked to the gut is currently unknown. Here we show that dural CD4 T cell polarisation to a T helper (Th) 1, Th2 and Th17 state is determined by the nature of the immunological challenge encountered in the gastrointestinal tract. We find that intestinally polarised CD4 T cells seed to the dura in a CXCR6-CXCL16-dependent manner, express tissue-residency markers and are long-lived. Functionally, these orally-primed dural CD4 T are capable of a rapid antigen-specific recall response that limits pathogen spread into the brain following intravenous re-challenge. Our work reveals how linked intestinal and dural immunity enables the central nervous system to accrue immunological memory of gut microbes, the most likely source of life-threatening bloodborne pathogens.

immunology↗

bioRxiv2025

Mapping and reprogramming microenvironment-induced cell states in human disease using generative AI

Tissue microenvironments reprogram local cellular states in disease, yet current computational spatial methods remain descriptive and do not simulate tissue perturbation. We present MintFlow, a generative AI algorithm that learns how the tissue microenvironment influences cell states and predicts how tissue perturbations can reprogram them. Applied to three human diseases, MintFlow uncovered distinct pathogenic spatial reprogramming in inflammatory and tumor microenvironments. In atopic dermatitis, MintFlow identified a novel, spatially-imprinted, type 2 (IL13+ITGAE+) epidermal T resident memory cell population (type 2 TRM), and decoded signaling pathways within the perivascular lymphoid niche. In melanoma, MintFlow identified fibrotic stroma resembling keloid scar tissue. In kidney cancer, MintFlow resolved immunosuppressed CD8+ T cell states within tertiary lymphoid structures. Furthermore, MintFlow enabled in silico perturbations of disease-relevant cell states and tissue environments. Regulatory T cell modulation in atopic dermatitis was predicted to suppress the pro-inflammatory tissue environment, supporting manipulation of these cells as a therapeutic target. In kidney cancer, in silico T cell replacement recapitulated immune checkpoint blockade, while spatially targeted macrophage depletion reverted immunosuppressed T cell states. The corresponding gene programs correlated with survival in large kidney cancer patient cohorts. Together, these findings position MintFlow as a tool for unbiased disease mechanism prediction and in silico perturbation, accelerating translational hypothesis generation and guiding therapeutic strategies.

genomics↗

bioRxiv2024

Multifaceted B-cell response to transient HIV viraemia in elite controllers

Chronic HIV infection drives B-cell dysfunction associated with the accumulation of tissue-like memory (TLMs) and activated memory B cells (MBCs) but decline in resting memory B cells. TLMs express multiple inhibitory receptors and lack response to soluble antigens. However, their origin and the mechanisms driving their expansion in HIV infection remain unclear. By using bulk BCR sequencing of memory B cell subsets from elite HIV controllers and an ART-controlled cohort, we revealed that TLMs (CD21- CD27- B cells) were significantly less mutated but also less diverse than other MBCs, suggesting an enrichment for innate-like B cells or that they belong to a less mature subset. Subsequent detailed multi-omics study of an immune response in an elite controller to a transient HIV viraemia demonstrated a functional increase in Env-reactive IgG and MBCs with non-TLM phenotype. Single-cell RNA/BCR sequencing of PMBCs enriched for B cells revealed an orchestrated TNF-alpha response followed by interferon alpha and gamma response across all B cells subsets. We noted an emergence of innate-like extrafollicular PLD4+ plasmablasts and previously undepreciated heterogeneity of a stable TLM population. We identified two distinct TLM subsets: TLM1 (T-betlow) and TLM2 (T-bethi) that differed in their differentiation stage, isotype use and mutational burden. Surprisingly, both subsets (TLM1 more than TLM2) were enriched for IGHV4-34 segment use (associated with self-reactivity) and displayed a persistent activation and BCR signalling signature, indicating (with other BCR indices) a strong presence of innate-like B cells. However, pseudotime analyses revealed that TLMs contained not only innate-like B cells but also cells from the conventional memory B cell lineages, further highlighting the complexity of the whole TLM compartment. This study provides a new insight into multifaceted functional B-cell response to transient HIV viraemia as likely happens during the early phase of anti-retroviral therapy cessation, highlighting the TLM heterogeneity and the contribution of innate-like B cells which might have important clinical implications for anti-HIV vaccine and therapy design.

immunology↗

bioRxiv2024

C1q and immunoglobulins mediate activity-dependent synapse loss in the adult brain

C1q, the initiating protein of the classical complement cascade, mediates synapse loss in development and disease. In various mouse models of neurologic diseases, including Alzheimer's disease, C1q, which is secreted by microglia, the brain's resident macrophages, is found deposited on synapses in vulnerable brain regions. However, what underlies C1q deposition on synapses in the adult brain is unclear. Using in vivo chemogenetics, we demonstrate that neuronal hyperactivity acts as a trigger for region-specific deposition of C1q, which is required for activity-dependent synapse loss. Further, using spatial transcriptomics, live cell tracking, super-resolution microscopy and other molecular and cellular tools, we report a role for B lymphocyte lineage cells and immunoglobulins in the activity-dependent C1q deposition and synapse loss. Overall, our work suggests a link between neuronal hyperactivity and C1q-mediated synapse loss in the adult brain and introduces immunoglobulins as players in this process.

neuroscience↗

bioRxiv2024

Chronic social defeat stress induces meningeal neutrophilia via type I interferon signaling

Animal models of stress and stress-related disorders are also associated with blood neutrophilia. The mechanistic relevance of this to symptoms or behavior is unclear. We used cytometry, immunohistochemistry, whole tissue clearing, and single-cell sequencing to characterize the meningeal immune response to chronic social defeat (CSD) stress in mice. We find that chronic, but not acute, stress causes meningeal neutrophil accumulation, and CSD increases neutrophil trafficking in vascular channels emanating from skull bone marrow (BM). Transcriptional analysis suggested CSD increases type I interferon (IFN-I) signaling in meningeal neutrophils. Blocking this pathway via the IFN-I receptor (IFNAR) protected against the anhedonic and anxiogenic effects of CSD stress, potentially through reduced infiltration of IFNAR+ neutrophils into the meninges from skull BM. Our identification of IFN-I signaling as a putative mediator of meningeal neutrophil recruitment may facilitate development of new therapies for stress-related disorders. One sentence summaryType I interferon sensing neutrophils accumulate in meninges of psychosocially stressed mice via skull bone marrow channels and are associated with the negative behavioral sequelae of stress; blockade of this pathway inhibits neutrophil trafficking and improves behavioral outcomes.

neuroscience↗

bioRxiv2024

A unique subset of pericystic endothelium associates with aberrant microvascular remodelling and impaired blood perfusion early in polycystic kidney disease

Hallmarks of autosomal dominant polycystic kidney disease (ADPKD), the most common hereditary kidney anomaly, include expanding fluid-filled epithelial cysts, inflammation, and fibrosis. Despite previous work showing the potential of vascular-based therapies, renal microvascular alterations in ADPKD, and their timing, are poorly understood. Using single-cell transcriptomics of human kidney microvasculature, we identify a population of endothelial cells adjacent to cysts in ADPKD. This pericystic endothelium, distinguishable by its expression of osteopontin (SPP1), has a distinct molecular profile compared to the common endothelial cell injury signature in other kidney diseases. SPP1+ pericystic endothelium was also present in an orthologous mouse model of ADPKD before overt kidney functional decline. By interrogating geometric, topological and fractal properties from three-dimensional imaging of early ADPKD mouse kidneys, we show that pericystic endothelium associates with disorganisation and non-uniformity of the renal cortical microvasculature. Concurrently, we detected region-specific reductions in cortical blood flow within ADPKD murine kidneys using arterial spin labelling. We conclude that ADPKD kidneys contain a unique subset of endothelium manifesting with aberrant remodelling and impaired blood perfusion. Its detection, prior to renal functional decline, advocates the vasculature as a therapeutic target to modulate or preserve renal function in early ADPKD.

pathology↗

bioRxiv2023

Multifocal, multiphenotypic tumours arising from an MTOR mutation acquired in early embryogenesis

Embryogenesis is a vulnerable time. Mutations in developmental cells can result in the wide dissemination of cells predisposed to disease within mature organs. We characterised the evolutionary history of four synchronous renal tumours from a 14-year-old girl, timing their shared origin to a multipotent embryonic cell committed to the right kidney, around 4 weeks post-conception. Their shared MTOR mutation, absent from normal tissues, enhances protein flexibility, which enables a FAT domain hinge to dramatically increase activity of mTORC1 and mTORC2. Developmental mutations, not usually detected in traditional genetic screening, have vital clinical importance in guiding prognosis, targeted treatment, and family screening decisions for paediatric tumours.

cancer biology↗

bioRxiv2023

Temporal profiling of human lymphoid tissues reveals coordinated defence to viral challenge

Adaptive immunity is generated in lymphoid organs, but how these structures defend themselves during infection in humans is unknown. The nasal epithelium is a major site of viral entry, with adenoid nasal-associated lymphoid tissue (NALT) generating early adaptive responses. Here, using a nasopharyngeal biopsy, we examined longitudinal immune responses in NALT following viral challenge, using SARS-CoV-2 infection as a natural experimental model. In acute infection, infiltrating monocytes formed a subepithelial and peri-follicular shield, recruiting NET-forming neutrophils, whilst tissue macrophages expressed pro-repair molecules during convalescence to promote the restoration of tissue integrity. Germinal centre B cells expressed anti-viral transcripts that inversely correlated with fate-defining transcription factors. Among T cells, tissue-resident memory CD8 T cells alone showed clonal expansion and maintained cytotoxic transcriptional programmes into convalescence. Together our study provides a unique insight into how human nasal adaptive immune responses are generated and sustained in the face of viral challenge.

immunology↗

bioRxiv2023

Rapid establishment of a tumor-retained state curtails the contribution of conventional NK cells to anti-tumor immunity in solid cancers

Immune cell dysfunction within the tumor microenvironment undermines the control of cancer progression. NK cells play critical roles in limiting early tumor growth and metastatic disease, however, established cancers contain a phenotypically distinct, tumor-specific NK cell compartment. The temporal dynamics, mechanistic underpinning and functional significance of this tumor NK pool remains incompletely understood. To address this, we exploited photo-labeling, combined with longitudinal transcriptomic and cellular analyses, to interrogate the fate of NK cells after tumor entry. In multiple murine cancer models we reveal that conventional NK cells are continuously recruited into tumors, but rapidly adopt a distinct phenotypic state with features associated with tissue-residency and complete loss of effector functions (including chemokine and cytokine production and cytotoxicity), within 48-72 hrs of entering the tumor. Depletion of NK cells from established tumors did not alter tumor growth, indicating that intratumoral NK cells cease to actively contribute to anti- tumor responses. Furthermore, comparable NK populations were identified in human colorectal cancers, confirming translational relevance and raising the possibility that interventions to reactivate NK cells within tissues may boost anti-tumor immunity in established cancers. Indeed, administration of IL-15:IL-15Ra complexes prevented the loss of NK cell function and improved tumor control, generating intratumoral NK cells with both enhanced tissue-residency characteristics and effector function. Collectively, our data reveals the fate of cNK cells after recruitment into tumors and provides insight into how intratumoral NK cell functions may be revived. SummaryConventional NK cells recruited from the circulation rapidly establish a tissue-resident phenotype defined by impaired cytotoxicity and chemokine production after tumor entry; administration of IL- 15:IL-15R complexes further promotes this tissue-residency programme but maintains core NK cell effector functions within the tumor.

immunology↗

bioRxiv2023

Time-, tissue- and treatment-associated heterogeneity in tumour-residing migratory DCs

Tumour dendritic cells (DCs) internalise antigen and upregulate CCR7, which directs their migration to tumour-draining lymph nodes (dLN). CCR7 expression is coupled to a maturation programme enriched in regulatory molecule expression, including PD-L1, termed mRegDC. However, the spatio- temporal dynamics and role of mRegDCs in anti-tumour immune responses remain unclear. Using photoconvertible mice to precisely track DC migration, we found that mRegDCs were the dominant DC population arriving in the dLN, but a subset remained tumour-resident despite CCR7 expression. These tumour-retained mRegDCs were phenotypically and transcriptionally distinct from their dLN counterparts and were heterogeneous. Specifically, they demonstrated a progressive reduction in the expression of antigen presentation and pro-inflammatory transcripts with more prolonged tumour dwell-time. Tumour mRegDCs spatially co-localised with PD-1+CD8+ T cells in human and murine solid tumours. Following anti-PD-L1 treatment, tumour-residing mRegDCs adopted a state enriched in lymphocyte stimulatory molecules, including OX40L, which was capable of augmenting anti- tumour cytolytic activity. Altogether, these data uncover previously unappreciated heterogeneity in mRegDCs that may underpin a variable capacity to support intratumoural cytotoxic T cells, and provide insights into their role in cancer immunotherapy.

immunology↗

bioRxiv2023

PAX8 and transient Wnt signalling are critical for induction and completion of human renal mesenchymal-to-epithelial transition

During kidney development, nephron epithelia arise de novo from fate-committed mesenchymal progenitors through a mesenchymal-to-epithelial transition (MET). Downstream of fate specification, transcriptional mechanisms that drive establishment of epithelial morphology through MET are poorly understood. We used human renal organoids derived from induced pluripotent stem cells, which recapitulate nephrogenesis, to investigate mechanisms controlling the renal MET programme. Multi-ome profiling of organoids revealed dynamic changes in gene expression and chromatin accessibility driven by transcriptional activators and repressors throughout renal MET. CRISPR-interference-based gene perturbation revealed that PAX8 is essential for initiation of MET in human renal organoids, contrary to mouse, by activating a cell adhesion programme. Furthermore, while Wnt/{beta}-Catenin signalling specifies nephron fate, we find that it must be attenuated to allow HNF1B and TEAD transcription factors to drive completion of MET. These results reveal how the developing kidney balances fate-commitment and morphogenesis with implications for understanding both developmental kidney diseases and aberrant epithelial plasticity following adult renal tubular injury.

developmental biology↗

bioRxiv2023

Spatially resolved multiomics of human cardiac niches

A cells function is defined by its intrinsic characteristics and its niche: the tissue microenvironment in which it dwells. Here, we combine single-cell and spatial transcriptomic data to discover cellular niches within eight regions of the human heart. We map cells to micro-anatomic locations and integrate knowledge-based and unsupervised structural annotations. For the first time, we profile the cells of the human cardiac conduction system, revealing their distinctive repertoire of ion channels, G-protein coupled receptors, and cell interactions using a custom CellPhoneDB.org module. We show that the sinoatrial node is compartmentalised, with a core of pacemaker cells, fibroblasts and glial cells supporting paracrine glutamatergic signalling. We introduce a druggable target prediction tool, drug2cell, which leverages single-cell profiles and drug-target interactions, providing unexpected mechanistic insights into the chronotropic effects of drugs, including GLP-1 analogues. In the epicardium, we show enrichment of both IgG+ and IgA+ plasma cells forming immune niches which may contribute to infection defence. We define a ventricular myocardial-stress niche enriched for activated fibroblasts and stressed cardiomyocytes, cell states that are expanded in cardiomyopathies. Overall, we provide new clarity to cardiac electro-anatomy and immunology, and our suite of computational approaches can be deployed to other tissues and organs.

genomics↗

bioRxiv2022

Early human lung immune cell development and its role in epithelial cell fate

During human development, lungs develop their roles of gas exchange and barrier function. Recent single cell studies have focused on epithelial and mesenchymal cell types, but much less is known about the developing lung immune cells, although the airways are a major site of mucosal immunity after birth. An open question is whether tissue-resident immune cells play a role in shaping the tissue as it develops in utero. In order to address this, we profiled lung immune cells using scRNAseq, smFISH and immunohistochemistry. At the embryonic stage, we observed an early wave of innate immune cells, including ILCs, NK, myeloid cells and lineage progenitors. By the canalicular stage, we detected naive T lymphocytes high in cytotoxicity genes, and mature B lymphocytes, including B1 cells. Our analysis suggests that fetal lungs provide a niche for full B cell maturation. Given the abundance of immune cells, we investigated their possible effect on epithelial maturation and found that IL-1{beta} drives epithelial progenitor exit from self-renewal and differentiation to basal cells in vitro. In vivo, IL-1{beta}-producing myeloid cells were found adjacent to epithelial tips, suggesting that immune cells may direct the developing lung epithelium.

immunology↗

bioRxiv2022

Single cell antigen receptor analysis reveals lymphocyte developmental origins

Assessment of single-cell gene expression (scRNA-seq) and adaptive immune receptor sequencing (scVDJ-seq) has been invaluable in studying lymphocyte biology. Here, we introduce Dandelion, a computational pipeline for scVDJ-seq analysis. It enables the application of standard V(D)J analysis workflows to single-cell datasets, delivering improved V(D)J contig annotation and the identification of non-productive and partially spliced contigs. We devised a novel strategy to create an adaptive immune receptor feature space that can be used for both differential V(D)J usage analysis and pseudotime trajectory inference. The application of Dandelion improved the alignment of human thymic development trajectories of double positive T cells to mature single-positive CD4/CD8 T cells, with important new predictions of factors regulating lineage commitment. Dandelion analysis of other cell compartments provided novel insights into the origins of human B1 cells and ILC/NK cell development, illustrating the power of our approach. Dandelion is an open access resource (https://www.github.com/zktuong/dandelion) that will enable future discoveries.

immunology↗

bioRxiv2022

Three-dimensional imaging and single-cell transcriptomics of the human kidney implicate perturbation of lymphatics in alloimmunity

Studies of the structural and molecular features of the lymphatic vasculature, which clears fluid, macromolecules and leukocytes from the tissue microenvironment, have largely relied on animal models, with limited information in human organs beyond traditional immunohistochemical assessment. Here, we use three-dimensional imaging and single-cell RNA-sequencing to study lymphatics in the human kidney. We found a hierarchical arrangement of lymphatic vessels within human kidneys, initiating along specialised nephron epithelium in the renal cortex and displaying a distinct, kidney-specific transcriptional profile. In chronic transplant rejection we found kidney allograft lymphatic expansion alongside a loss of structural hierarchy, with human leukocyte antigen-expressing lymphatic vessels infiltrating the medulla, presenting a putative target for alloreactive antibodies. This occurred concurrently with lymphatic vessels invading and interconnecting tertiary lymphoid structures at early stages of lymphocyte colonisation. Analysis of intercellular signalling revealed upregulation of co-inhibitory molecule-mediated CD4+ T cell-lymphatic crosstalk in rejecting kidneys, potentially acting to limit local alloimmune responses. Overall, we delineate novel structural and molecular features of human kidney lymphatics and reveal perturbations to their phenotype and transcriptome in the context of alloimmunity. SUMMARYLymphatics regulate fluid balance and immune cell accumulation but are under-studied in human organs such as the kidney. Jafree and colleagues profiled human kidney lymphatics using three-dimensional imaging and single-cell RNA-sequencing, revealing structural and transcriptional perturbations in rejecting kidney transplants.

immunology↗

bioRxiv2022

Obesity associated with attenuated tissue immune cell responses in COVID-19

Obesity is common and associated with more severe COVID-19, proposed to be in part related to an adipokine-driven pro-inflammatory state. Here we analysed single cell transcriptomes from bronchiolar lavage in three adult cohorts, comparing obese (Ob, body mass index (BMI) >30m2) and non-obese (N-Ob, BMI <30m2). Surprisingly, we found that Ob subjects had attenuated lung immune/inflammatory responses in SARS-CoV-2 infection, with decreased expression of interferon (IFN), IFN{gamma} and tumour necrosis factor (TNF) alpha response gene signatures in almost all lung epithelial and immune cell subsets, and lower expression of IFNG and TNF in specific lung immune cells. Analysis of peripheral blood immune cells in an independent adult cohort showed a similar, but less marked, reduction in type I IFN and IFN{gamma} response genes, as well as decreased serum IFN, in Ob patients with SARS-CoV-2. Nasal immune cells from Ob children with COVID-19 also showed reduced enrichment of IFN and IFN{gamma} response genes. Altogether, these findings show blunted tissue immune responses in Ob COVID-19 patients, with clinical implications.

immunology↗

bioRxiv2022

Mapping the developing human immune system across organs

Recent advances in single cell genomics technologies have facilitated studies on the developing immune system at unprecedented scale and resolution. However, these studies have focused on one or a few organs and were thus limited in understanding the developing immune system as a distributed network across tissues. Here, we profiled prenatal haematopoietic organs, lymphoid organs and non-lymphoid tissues using a combination of single-cell RNA sequencing, paired antigen-receptor sequencing and spatial transcriptomics to reconstruct the developing human immune system. Our analysis revealed the acquisition of immune effector transcriptome profiles in macrophages, mast cells and NK cells from the second trimester, and the transcriptomic changes accompanying the late-stage maturation of developing monocytes and T cells that extended from their organ of origin to peripheral tissues. We uncovered system-wide blood and immune cell development beyond the conventional primary haematopoietic organs. We further identified, extensively characterised and functionally validated the human prenatal B1 cells. Finally, we provide evidence for thymocyte-thymocyte selection origin for {beta}TCR- expressing unconventional T cells based on TCR gene usage and an in vitro artificial thymic organoid culture model. Our comprehensive atlas of the developing human immune system provides both valuable data resources and biological insights that will facilitate cell engineering, regenerative medicine and disease understanding. One-Sentence SummaryBy performing a comprehensive single-cell RNA sequencing atlas of human developing immune system together with antigen-receptor sequencing and spatial transcriptomics, we explored the cross-gestation and cross-organ variability in immune cells, discovered system-wide blood and immune cell development, identified, characterised and functionally validated the properties of human prenatal B1 cells and the origin of unconventional T cells.

immunology↗