Biology subjects

Kendall, T. J.

Publications and source records attributed to Kendall, T. J..

12 recordsLinked to original sources

bioRxiv2026

Mapping vascular plasticity in liver fibrogenesis identifies novel fibrosis-associated endothelial cells in early-stage liver disease

Vascular plasticity is a crucial biological asset enabling our bodies to rapidly adapt to infections and acute inflammation. However, repeated insult during chronic disease can result in these vascular adaptations becoming irreversible, thereby driving disease progression and fibrosis. This study aimed to understand if phenotypic changes in endothelial cell (EC) identity could be indicative of progressive fibrosis and thereby offer new diagnostic and therapeutic opportunities for patients with metabolic dysfunction-associated steatotic liver disease (MASLD). Previous research has documented that a significant shift in EC transcriptomic signature occurs during liver fibrosis in both pre-clinical models and patients. However, the protein expression profile, phenotype and functional role of these new EC subpopulations that are induced during fibrogenesis is unclear. In this study, we integrate high-resolution imaging, proteomic and transcriptomic analysis which collectively highlight a central role for endothelial-to-mesenchymal transition (EndMT)-induced EC plasticity in the derivation of fibrosis-associated EC (FAEC). We demonstrate that: 1) full spectrum flow cytometry can provide new opportunities to categorize and phenotype EC subpopulations, 2) two distinct EndMT-derived FAEC subpopulations expand during fibrogenesis; THY1.2+ICAM1+ and TAGLN+MCAM+ EC that display unique immunomodulatory and metabolic phenotypes, 3) TAGLN+ FAEC are a conserved, pro-fibrotic cell type arising at early stages of MASLD, and 4) increased hepatic expression of TAGLN is significantly associated with detrimental patient outcomes at all stages of liver disease. This study will pave the way for the development of FAEC-specific diagnostic and therapeutic approaches to tackle progressive fibrotic disease. One Sentence SummaryPhenotyping fibrosis-associated endothelial cells reveals pro-fibrotic and immunomodulatory subpopulations at early stages of liver disease. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=112 SRC="FIGDIR/small/710459v2_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@dc91fforg.highwire.dtl.DTLVardef@f526d9org.highwire.dtl.DTLVardef@c9783borg.highwire.dtl.DTLVardef@f469e4_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

DUCK-Net: Automated deep learning segmentation of Ductular Reaction in murine liver injury captures multicellular niche dynamics from H&E morphology

Ductular Reactions (DRs) are dynamic and complex multicellular responses that occur as a result of various hepatic injuries. Precise identification and quantification of the extent of DRs is a cornerstone of pre-clinical modelling of liver disease, with links to inflammation, fibrosis, regeneration, and disease severity. Here, we apply a deep learning model, Deep Understanding Convolutional Kernel or DUCK-Net, to the automated detection and segmentation of DRs in whole-slide histopathological images of murine models of liver damage. Following annotation of a training dataset by a specialist liver histopathologist, we demonstrate accelerated performance and accurate detection, achieving a mean Dice coefficient (model-expert segmentation overlap) of 85.4% and a specificity of 98%, indicating minimal false positives. Evaluation of model validity and utility was achieved with a histological time course of cholestatic injury and recovery using 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine diet (DDC) in mice. When assessed against a multiple linear regression model incorporating core epithelial and stromal components of the DR as quantified using IHC, DUCK-Net predicted the spatiotemporal response to injury and repair/resolution with a coefficient of determination (R2) of 0.88. Moreover, DUCK-Net kinetics strongly correlated with published spatial transcriptomic (Stereo-seq) analysis of the DDC model, demonstrating that H&E-based segmentation captures molecular DR dynamics comparable to, or exceeding that of individual IHC markers without the need for immunostaining. DUCK-Net provides a novel and accessible platform for rapid, accurate histological quantification of liver injury reflective of the matrix-rich, multicellular regenerative niche observed in DRs.

cell biology↗

bioRxiv2025

A Human Single-cell Atlas Identifies OLR1+ Scar-associated Macrophages as a Therapeutic Target for Chronic Liver Disease

Chronic liver disease (CLD) is a major global healthcare problem. Irrespective of cause, chronic damage to the liver results in fibrosis, which is associated with adverse clinical outcomes. Immune cells, in particular monocyte-derived macrophages (MDMs), are key regulators of fibrosis and represent an attractive therapeutic target for CLD. However, it has remained unclear which specific subpopulation of MDMs drives pro-inflammatory and pro-fibrotic functions in human CLD and how they might be selectively modulated. Here, we generate an annotated human liver single cell atlas from 42 healthy and 35 CLD patients, identifying 125 transcriptionally distinct cellular states. Leveraging large patient and cell numbers, our atlas resolves rare liver cell states and distinguishes two types of disease-expanded scar-associated macrophages (SAMac), including a specific subpopulation with a pro-inflammatory pro-fibrotic phenotype. The scavenger receptor OLR1 was enriched in pro-inflammatory SAMacs and high hepatic OLR1 expression was associated with increased mortality in CLD patients. A corresponding monocyte-derived OLR1+ SAMac subpopulation expanded in a mouse model of CLD and exhibited a pro-inflammatory phenotype based on single-cell RNA-seq, single-cell ATAC-seq, and flow cytometry analyses. Primary human OLR1+ MDMs promoted fibrogenic signalling in multilineage liver spheroid cultures, whilst specific targeting of OLR1 reduced IL-1{beta} production by human macrophages and attenuated myofibroblast activation. Overall, our annotated human liver single-cell atlas provides a valuable reference to study disease-associated cell states in CLD. We utilise this resource to identify a distinct pro-inflammatory subpopulation of SAMacs and highlight OLR1 as a potential therapeutic target to specifically modulate SAMac function and attenuate liver fibrosis.

immunology↗

bioRxiv2025

Epithelial state-transitions permit inflammation-induced tumorigenesis.

Chronic inflammation across tissues is associated with an increased risk of developing cancer1-3. While potentially oncogenic somatic mutations have been demonstrated to persist and expand in healthy organs4-6, what triggers a subset of cells harbouring deleterious mutations to transition into a neoplasm or an aggressive adenoma with poor prognosis7,8 is not well-understood. Unlike normal, healthy cells, benign cells harbouring mutations perceive inflammation in chronic disease differently, potentiating the progression from physiological inflammation to tumorigenesis9. Here, we reveal that a subset of epithelial cells with mutations are poised to transition from pre-neoplastic state to early neoplasm, through rewiring of epithelial IL-1{beta} responses and inflammatory macrophage recruitment. We characterise this process by leveraging a mouse model of biliary tract cancer (cholangiocarcinoma), in which deleterious mutations are introduced to tumour suppressor genes in common cancer pathways (Trp53 and Pten), and by quantifying differences in cell states and corresponding gene expression dependencies in the absence or presence of liver inflammation. Critically, we find that targeting the epithelial-derived signals of tissue-wide inflammation (namely COX2) is insufficient to limit tumorigenesis; rather, targeting the reactivation of oncogene-induced developmental signals, such as NOTCH, prevents this pre-neoplastic to neoplastic transition, demonstrating that oncofoetal switching is a pharmacologically-tractable target in patients with a high risk of developing cancers on the background of inflammation.

cancer biology↗

bioRxiv2025

Tissue scarring provides a biomechanical framework to promote mammalian bile duct regeneration through the activation of integrin-SRC/FAK signalling.

Following chronic injury, the adult mammalian bile duct regenerates by forming new branches, essentially replumbing the ductular system to overcome blockages and breaks. To regenerate effectively, biliary epithelial cells (BECs) receive a range of pro-mitogenic signals from myofibroblasts, which concurrently deposit a collagen-rich scar around the duct as it regrows. Despite epithelial regeneration and scarring occurring side-by-side, whether the deposition of scar tissue regulates ductular regeneration per se remains unclear. By inducing ductular fibrosis and regeneration in vivo, we show that the formation of collagen-I-rich scars around regenerating ducts changes the local biomechanical properties of these tissues, promoting the growth of ducts. Critically, this changing structural landscape is perceived by a spatially restricted population of biliary epithelial cells which forms a "leading-tip" of integrin-2-high cells. This leading-tip undergoes partial-EMT-type reprogramming, allowing it to become migratory and coordinate ductular regeneration. We show that this process is directly driven through an integrin-2-SRC/FAK signalling axis; thereby connecting epithelial regeneration directly to the changing fibrotic environment in chronic ductular disease. HighlightsO_LIChronic liver disease results in the formation of stiff, collagen scars around ducts. C_LIO_LINew ducts acquire high levels of integrin-2 which is spatially localised to a "leading-tip", which loses epithelial features. C_LIO_LIIntegrin-2{beta}1-SRC/FAK signalling regulates ductular migration by linking changes in the bio-structural composition of the liver with ductular cells. C_LI

cell biology↗

bioRxiv2025

Regulatory T cell stability determines the efficiency of bile duct regeneration during cholangitis.

Background and AimsCholangiopathies such as Primary Sclerosing Cholangitis (PSC) cause damage to the bile ducts and fibrosis with no effective cure. A reduction and impairment in the function of regulatory T cells (Tregs) occurs in PSC. Yet, it is currently unknown what consequence this has on bile duct regeneration. We investigate whether Tregs regulate bile duct regeneration and the dynamics of Tregs turnover during bile duct injury. Approach and ResultsWe used the transgenic Foxp3GFPDTR model to mimic reduced Tregs infiltration to the liver during bile duct injury and showed that reduced intrahepatic Tregs limits bile duct regeneration. Fate mapping of Tregs (Foxp3CreERTAi14) showed that Tregs acquire a pro-inflammatory phenotype within the inflammatory microenvironment, even after IL2 mediated Tregs expansion. Ox40L expression correlates with fibrosis in PSC patients. In the 3,5-Diethoxycarbonyl-1,4-Dihydrocollidine (DDC)-diet mouse model of experimental cholangiopathy, combining IL2-complex administration and blocking Ox40L decreases periportal fibrosis level, increases Treg number and reduces the pro-inflammatory phenotype of Tregs. ConclusionsThese results indicate that Tregs mediate cholangiocyte response to biliary injury, and Tregs downregulate Foxp3 and acquire an inflammatory phenotype in an inflammatory microenvironment. Enhancing Treg numbers through IL2 complex administration and blocking Ox40 signalling simultaneously suppress the inflammatory phenotype of Tregs and reduces bile duct damage and fibrosis.

immunology↗

bioRxiv2023

Multimodal decoding of human liver regeneration

The liver has a unique ability to regenerate1,2, however in the setting of acute liver failure (ALF) this regenerative capacity is often overwhelmed and emergency liver transplantation is the only curative option3-5. To advance our understanding of human liver regeneration and to inform design of pro-regenerative therapies, we use paired single-nuclei RNA sequencing (snRNA-seq) combined with spatial profiling of healthy and ALF explant human livers to generate the first single-cell, pan-lineage atlas of human liver regeneration. We uncover a novel ANXA2+ migratory hepatocyte subpopulation which emerges during human liver regeneration, and a corollary migratory hepatocyte subpopulation in a mouse model of acetaminophen (APAP)-induced liver regeneration. Importantly, interrogation of necrotic wound closure and hepatocyte proliferation across multiple timepoints following APAP-induced liver injury in mice demonstrates that wound closure precedes hepatocyte proliferation. 4-D intravital imaging of APAP-induced mouse liver injury identifies motile hepatocytes at the edge of the necrotic area, enabling collective migration of the hepatocyte sheet to effect wound closure. Depletion of hepatocyte ANXA2 expression reduces HGF-induced human and mouse hepatocyte migration in vitro, and abrogates necrotic wound closure following APAP-induced mouse liver injury. Taken together, our work dissects unanticipated aspects of liver regeneration, demonstrating an uncoupling of wound closure and hepatocyte proliferation and uncovering a novel migratory hepatocyte subpopulation which mediates wound closure following liver injury. Therapies designed to promote rapid reconstitution of normal hepatic microarchitecture and reparation of the gut-liver barrier may open up new areas of therapeutic discovery in regenerative medicine.

cell biology↗

bioRxiv2022

Primary cilia loss promotes reactivation of morphogenesis and cyst-fission through a deregulated TGFβ-ECM-Integrin axis in polycystic liver disease.

Pathological liver cysts are an important comorbidity in multiple diseases and syndromes(1, 2) driven by dysfunction of the primary cilium (PC), a complex sensory organelle that protrudes from the apical surface of biliary epithelial cells (BECs)(3, 4). The essential nature of PC in liver development(5, 6) makes understanding the molecular role of this organelle in the structural maintenance of the adult bile duct challenging. Here, we show that PC loss deletion of Wdr35 in adult mouse BECs is sufficient to cause bile duct expansion, driving cyst formation through the de novo production of a fibronectin-rich pro-cystic microenvironment. This newly formed niche promotes both cell-autonomous changes in cell shape and duct-level mechanical rearrangements that converge to drive cyst-fission, a novel process whereby single, large cysts undergo morphological splitting. This process gives rise to many, smaller polycystic progeny and can be halted by pharmacological inhibition of a specific pro-cystic integrin receptor.

cell biology↗

bioRxiv2022

Single Nucleus RNA Sequencing of Pre-Malignant Liver Reveals Disease-Associated Hepatocyte State with HCC Prognostic Potential

Current approaches to stage chronic liver diseases have limited utility to directly predict liver cancer risk. Here, we employed single nucleus RNA sequencing (snRNA-seq) to characterize the cellular microenvironment of healthy and chronically injured pre-malignant livers using two distinct mouse models. Analysis of 40,748 hepatic nuclei unraveled a previously uncharacterized disease-associated hepatocyte transcriptional state (daHep). These cells were absent in healthy livers, but were increasingly prevalent as chronic liver disease progressed towards hepatocarcinogenesis. Gene expression deconvolution of 1,439 human liver transcriptomes from publicly available datasets revealed that daHep frequencies highly correlate with current histopathological liver disease staging systems. Importantly, we show that high daHep levels precede carcinogenesis in mice and humans and predict a higher risk of hepatocellular carcinoma (HCC) development. This novel transcriptional signature with diagnostic and, more importantly, prognostic significance has the potential to change the way chronic liver disease patients are staged, surveilled and risk-stratified.

cancer biology↗

bioRxiv2021

In vivo modelling of patient genetic heterogeneity identifies concurrent Wnt and PI3K activity as a potent driver of invasive cholangiocarcinoma growth.

Intrahepatic cholangiocarcinoma (ICC) is an aggressive and lethal malignancy of the bile ducts within the liver characterised by high levels of genetic heterogeneity. In the context of such genetic variability, determining which oncogenic mutations drive ICC growth has been difficult and developing modes of patient stratification and targeted therapies remains challenging. As a result, survival rates following a diagnosis with ICC have remained static since the late 1970s, whilst incidence of ICC has increased. Here, we performed the first functional in vivo study into the role that genetic heterogeneity plays in drivinga ICC via modelling of interactions between rare mutations with more common driver genes. By leveraging human ICC sequencing data to stratify and then model genetic heterogeneity in the mouse, we uncovered numerous novel tumour suppressors which, when lost, cooperate with the RAS oncoprotein to drive ICC growth. In this study, we specifically focus on a set of driver mutations that interact with KRAS to initiate aggressive, sarcomatoid-type ICC. We show that tumour growth of this cancer relies on both Wnt and PI3K signalling to drive proliferation and suppress apoptosis. Finally, we demonstrate that pharmacological co-inhibition of Wnt and PI3K in vivo substantially impedes the growth of ICC, regardless of mutational profile. As such, Wnt and PI3K activity should be considered as a signature by which patients can be stratified for treatment and inhibitors of these pathways should be levied as a treatment for patients diagnosed with ICC.

cancer biology↗

bioRxiv2019

qPaLM: quantifying occult microarchitectural relationships in histopathological landscapes

Optimal tissue imaging methods should be easy to apply, not require use-specific algorithmic training, and should leverage feature relationships central to subjective gold-standard assessment. We reinterpret histological images as landscapes to describe quantitative pathological landscape metrics (qPaLM), a generalisable framework defining topographic relationships in tissue using geoscience approaches. qPaLM requires no user-dependent training to operate on all image datasets in a classifier-agnostic manner to quantify occult abnormalities, derive mechanistic insights, and define a new feature class for machine-learning diagnostic classification.

pathology↗

bioRxiv2018

Non-invasive Assessment of Liver Disease in Rats Using Multiparametric Magnetic Resonance Imaging: A Feasibility Study

Background & AimsNon-invasive quantitation of chronic liver disease using multiparametric MRI has the potential to refine clinical care pathways, trial design and preclinical drug development. The aim of the study was to evaluate the use of multiparametric liver MRI in experimental rat models of chronic liver disease. Methods: Liver injury was induced in male wild-type Sprague-Dawley rats using 4 or 12 weeks carbon tetrachloride (CCl4) intoxication and 4 or 8 weeks methionine and choline deficient (MCD) diet. Liver MRI was performed using a 7.0 Tesla small animal scanner at baseline and specified timepoints after liver injury. Multiparametric liver MRI parameters (T1 mapping, T2* mapping and proton density fat fraction (PDFF)) were correlated with gold standard histopathological measures, assessed by a blinded expert adjudicator. One-way analysis of variance with Tukeys post-hoc test was used to assess differences between groups and Spearmans rank-order correlation to examine associations.\n\nResultsMean hepatic T1 increased significantly in rats treated with CCl4 for 12 weeks compared to controls (1122{+/-}78 ms vs. 959{+/-}114 ms; d=162.7, 95% CI (11.92, 313.4), P=0.038) and correlated strongly with histological collagen content (rs=0.717, P=0.037). In MCD diet-treated rats, hepatic PDFF correlated strongly with histological fat content (rs=0.819, P<0.0001), steatosis grade (rs=0.850, P<0.0001) and steatohepatitis score (rs=0.818, P<0.0001). Although there was minimal histological iron, progressive fat accumulation in MCD diet-treated liver significantly shortened T2*.\n\nConclusionsIn preclinical models, quantitative MRI markers correlated with histopathological assessments, especially for fatty liver disease. Validation in longitudinal studies is required.\n\nKey pointsO_LINon-invasive quantitative measures of chronic liver injury are needed for stratification and monitoring of disease in clinical practice and in drug development\nC_LIO_LIWe adapted and applied a clinically-relevant non-contrast multiparametric MRI protocol in well-established preclinical liver disease models, for simultaneous quantitation of hepatic fat, fibro-inflammatory injury and iron\nC_LIO_LIMultiparametric liver MRI was feasible at 7.0 Tesla in experimental rat models and imaging parameters correlated with gold standard histopathological assessments, especially characteristics of fatty liver disease\nC_LIO_LIFurther development of multiparametric liver MRI could refine drug development strategies and impact upon trial design and clinical care pathways\nC_LI

pathology↗