Biology subjects

Palmer, M.

Publications and source records attributed to Palmer, M..

10 recordsLinked to original sources

bioRxiv2026

Leronlimab a humanized anti-CCR5 monoclonal antibody ameliorates hepatic fibrosis in two preclinical fibrosis mouse models

BackgroundChemokine receptor type 5 (CCR5) is expressed on hepatic stellate cells (HSCs), which, together with fibroblasts, are major producers of extracellular matrix during liver fibrosis. Leronlimab is a humanized IgG4{kappa} monoclonal antibody that binds to CCR5. The objective of the present study was to evaluate the antifibrotic effects of leronlimab in three independent preclinical studies using two mouse models of liver fibrosis. MethodsIn STAM (Stelic Animal Model) model 1, leronlimab was administered at doses of 5 or 10 mg/kg/week for 3 weeks. STAM model 2 was conducted as a confirmatory study to validate the antifibrotic effect observed with the 10 mg/kg/week dose in STAM model 1. In a third study, a carbon tetrachloride (CCl)-induced liver fibrosis mouse model was used to evaluate leronlimab administered at 10 mg/kg/week for 3 weeks. An isotype-matched control antibody was included in all studies for comparison. Evaluations included liver enzymes and histological assessment of liver fibrosis. ResultsIn STAM model 1, leronlimab at 10 mg/kg/week significantly reduced fibrosis area compared with the isotype control (p = 0.0005). These findings were confirmed in STAM model 2 (p < 0.0001). Consistent antifibrotic effects were also observed in the CCl-induced liver fibrosis model (p = 0.0006). ConclusionsCollectively, these preclinical results demonstrate that CCR5 blockade by leronlimab is associated with a significant reduction of established liver fibrosis in multiple mouse models and support further evaluation of leronlimab as a potential therapeutic option, either as monotherapy or in combination regimens, for chronic liver diseases with fibrosis.

pharmacology and toxicology↗

bioRxiv2025

The Carbon Starvation-Inducible Lipoprotein (Slp) Influences Differential Adherence of Escherichia coli O157:H7 at the Bovine Rectoanal Junction.

Shiga toxin-producing Escherichia coli O157:H7 (O157), a foodborne human pathogen, persists at the rectoanal junction (RAJ) of the bovine intestinal tract, in asymptomatic cattle reservoirs. Identifying mechanisms used by O157 for initial adherence before persistence at the RAJ could help develop effective O157 control modalities. We recently established the role of carbon starvation-inducible lipoprotein (Slp) in initial adherence of O157 to Caco-2 cells, with the human polymeric immunoglobulin receptor (pIgR) protein as the Slp-receptor. Here, we evaluated the role of Slp in O157 adherence to the bovine RAJ using the RAJ squamous epithelial (RSE) cell- and RAJ-In vitro Organ Culture (IVOC)- adherence assays. The wild-type O157 strain EDL932 (EDL932-WT), its isogenic slp deletion mutant (EDL932 {Delta}slp), and the slp complemented mutant (EDL932 {Delta}slp-p:slp), were tested with no bacteria controls. Adherence was verified by culture and immunofluorescence (IF) staining of O157. Tissue integrity was determined using nuclear/cell staining dyes and histopathological examination. All test strains adhered in a diffuse-moderate pattern on RSE cells. However, differential adherence was observed on the RAJ-IVOC with the strains preferentially adhering to the columnar cells. Additionally, EDL932- WT and EDL932 {Delta}slp-p:slp strains adhered in slightly greater numbers than the EDL932 {Delta}slp strain to the RAJ-IVOC, causing disruptions primarily in the columnar region of otherwise intact RAJ-IVOC tissues. Interestingly, pIgR was also predominantly detected by IF microscopy and RNAscope in situ hybridization at the columnar region of the RAJ-IVOC tissue. In silico modeling demonstrated the possibility of a bovine pIgR- bacterial Slp interaction. Hence, our observations support the role for Slp in the initial adherence of O157 to the columnar cells at the bovine RAJ, unlike the squamous cells where the loss of slp did not impact attachment. In addition, a possible mucosal immune-interference resulting from the bovine pIgR-Slp interaction could contribute towards long-term O157 colonization of cattle. AUTHOR SUMMARYEscherichia coli O157:H7 (O157) is a foodborne pathogen that causes disease in humans with symptoms ranging from watery/bloody diarrhea to kidney failure. Cattle are the main reservoirs of this human pathogen, where O157 tends to persist at the rectoanal junction (RAJ) of the bovine gastrointestinal tract. However, the exact mechanisms by which O157 adheres and persists at the bovine RAJ is not fully understood. Here, we identified that the O157 carbon starvation-inducible lipoprotein (Slp) allows O157 to attach to cells at the RAJ using polymeric immunoglobulin receptor (pIgR) protein as the Slp-receptor. Not only does this attachment of Slp to the cattle receptor allow O157 to colonize cattle, but the interaction could potentially interfere with intestinal immune responses, further promoting long-term O157 colonization of cattle. This makes Slp an attractive target for therapeutic interventions, such as vaccines that could interfere with O157 attachment to cattle intestinal cells.

microbiology↗

bioRxiv2025

Morpho-functional timeline of progressive cystic fibrosis pancreatic exocrine and endocrine pathology derived from semi-quantitative scoring and AI-driven quantitativeimage analysis

Cystic fibrosis (CF) is associated with pancreatic exocrine insufficiency (PEI) early in life and diabetes in up to 50% of adults. The underlying CF-related sequential changes within the pancreas associated with exocrine and endocrine insufficiency remain incompletely understood due to scarcity of available human tissue, protracted disease course and absence of established robust and reproducible analytical approaches. This study aimed to develop and apply a systematic analysis cross-sectionally to CF pancreatic tissue samples from donors over a wide age range to construct a timeline related to the main exocrine and endocrine changes underlying progressive disease. Based on a histopathological semi-quantitative scoring system and AI-driven quantitative image analysis pancreatic changes were individually evaluated and classified according to three patterns: fibrotic; fibrotic and lipotic; and lipoatrophic. This systematic evaluation was applied to 29 CF and 58 control donors without pancreatic disease. Rapid loss of acinar tissue with virtually complete absence by the age of 7 years was confirmed, mirrored by fatty tissue replacement - changes underlying PEI and likely preceding progression towards diabetes. Ductal blockage by thickened secretions was associated with increasing ductal dilatation accompanied by peri-ductal fibrosis, followed by ductal loss with involution of associated fibrosis in parallel with increasing adipocyte proportional area (PA). Remaining ducts were relatively small surrounded by residual fibrosis. Islets became increasingly clustered initially surrounded by activated pancreatic stellate cells (PSCs) and fibrosis and then disorganised by interposing fibrotic tissue between endocrine cell regions and surrounded by residual collagen stranding in a lipoatrophic pancreas. Overall islet mass was not significantly reduced but {beta}-cell PA was significantly reduced from birth without further loss over time. We concluded that the natural history of pancreatic CF progresses inexorably from peri-ductal fibrosis to global fat replacement with relatively well-maintained islet mass but PSC-associated fibrotic islet remodelling circumstantially implicated in {beta}-cell failure.

pathology↗

bioRxiv2022

Spatially resolved human kidney multi-omics single cell atlas highlights the key role of the fibrotic microenvironment in kidney disease progression

Kidneys possess one of the most intricate three-dimensional cellular structures in the body, yet the spatial and molecular principles of kidney health and disease remain inadequately understood. Here, we have generated high-quality datasets for 81 samples, including single cell (sc), single nuclear (sn), spot level (Visium) and single cell resolution (CosMx) spatial (sp)-RNA expression, and sn open chromatin, capturing cells from healthy, diabetic, and hypertensive diseased human kidneys. By combining the snRNA, snATAC and scRNA sequencing we identify cell types and map these cell types to their locations within the tissue. Unbiased deconvolution of the spatial data identifies 4 distinct spatial microenvironments: glomerular, immune, tubule and fibrotic. We describe the complex, heterogenous cellular and spatial organization of human microenvironments in health and disease. Further, we find that the fibrotic microenvironment spatial gene signature is not only able to molecularly classify human kidneys, but it also offers an improved prognosis prediction compared to traditional histopathological analysis. We provide a comprehensive spatially resolved molecular roadmap of the human kidney and the fibrotic process, demonstrating the clinical utility of spatial transcriptomics.

genetics↗

bioRxiv2022

Evaluation of PRKACA as a Therapeutic Target for Fibrolamellar Carcinoma

Background & AimsFibrolamellar carcinoma (FLC) is a rare, difficult-to-treat liver cancer primarily affecting pediatric and adolescent patients, and for which precision medicine approaches have historically not been possible. The DNAJB1-PRKACA gene fusion was identified as a driver of FLC pathogenesis. We aimed to assess whether FLC tumors maintain dependency on this gene fusion and determine if PRKACA is a viable therapeutic target. MethodsFLC patient-derived xenograft (PDX) shRNA cell lines were implanted subcutaneously into female NOD-SCID mice and tumors were allowed to develop prior to randomization to doxycycline (to induce knockdown) or control groups. Tumor development was assessed every 2 days. To assess the effect of treatment with novel selective PRKACA small molecule kinase inhibitors, BLU0588 and BLU2864, FLC PDX tumor cells were implanted subcutaneously into NOD-SCID mice and tumors allowed to develop. Mice were randomized to treatment (BLU0588 and BLU2864, orally, once daily) or control groups and tumor size determined as above. ResultsKnockdown of DNAJB1-PRKACA reversed a FLC-specific gene signature and reduced PDX tumor growth in mice compared to the control group. Furthermore, FLC PDX tumor growth was significantly reduced with BLU0588 and BLU2864 treatment versus control (P = 0.003 and P = 0.0005, respectively). ConclusionsWe demonstrated, using an inducible knockdown and small molecule approaches, that FLC PDX tumors were dependent upon DNAJB1-PRKACA fusion activity. In addition, this study serves as a proof-of-concept that PRKACA is a viable therapeutic target for FLC and warrants further investigation.

cancer biology↗

bioRxiv2021

Enhanced virus translation enables miR-122-independent Hepatitis C Virus propagation

The 5UTR of the Hepatitis C Virus genome forms RNA structures that regulate virus replication and translation. The region contains a viral internal ribosomal entry site and a 5 terminal region. Binding of the liver specific miRNA, miR-122, to two conserved binding sites in the 5 terminal region regulates viral replication, translation, and genome stability, and is essential for efficient virus replication, but its precise mechanism of its action is still under debate. A current hypothesis is that miR-122 binding stimulates viral translation by facilitating the viral 5 UTR to form the translationally active HCV IRES RNA structure. While miR-122 is essential for detectable virus replication in cell culture, several viral variants with 5 UTR mutations exhibit low level replication in the absence of miR-122. We show that HCV mutants capable of replicating independently of miR-122 also replicate independently of other microRNAs generated by the canonical miRNA synthesis pathway. Further, we also show that the mutant genomes display an enhanced translation phenotype that correlates with their ability to replicate independently of miR-122. Finally, we provide evidence that translation regulation is the major role for miR-122, and show that miR-122-independent HCV replication can be rescued to miR-122-dependent levels by the combined impacts of 5 UTR mutations that stimulate translation, and by stabilizing the viral genome by knockdown of host exonucleases and phosphatases that degrade the genome. Thus, we provide a model suggesting that translation stimulation and genome stabilization are the primary roles for miR-122 in the virus life cycle. IMPORTANCEThe unusual role of miR-122 in promoting HCV propagation is incompletely understood but is essential for an HCV infection. To better understand its role, we have analyzed HCV mutants capable of replicating independently of miR-122. Our data show that the ability of viruses to replicate independently of miR-122 correlates with enhanced virus translation, but that genome stabilization is required to restore efficient HCV replication. This suggests that viruses must gain both abilities to escape the need for miR-122 and impacts the possibility that HCV can evolve to replicate outside of the liver.

microbiology↗

bioRxiv2020

Mapping the genetic architecture of human traits to cell types in the kidney identifies mechanisms of disease and potential treatments

The functional interpretation of GWAS remains challenging due to cell-type dependent influences of genetic variants. Here, we generated comprehensive maps of expression quantitative trait loci (eQTL) for 659 microdissected human kidney samples and identified cell-type eQTLs by mapping interactions between cell type abundance and genotype. Separately, we generated single cell open chromatin maps (by snATAC-seq) for human kidney samples. We highlight critical enrichment of proximal tubules in kidney function and endothelial cells and distal tubule segments in blood pressure by partitioning heritability using stratified LD-score regression to integrate GWAS with scRNA-seq and snATAC-seq data. Bayesian colocalization analysis nominated more than 200 genes for kidney function and hypertension. Our study clarifies the mechanism of the most commonly used antihypertensive and renal protective drugs and identifies drug repurposing opportunities for kidney disease. One Sentence SummaryWe define causal cell types, genes and mechanism for kidney dysfunction.

genetics↗

bioRxiv2020

Mapping Drosophila insulin receptor structure to the regulation of aging through analysis of amino acid substitutions

Genetic manipulations of the Drosophila insulin/IGF signaling system slow aging, but it remains unknown how the insulin/IGF receptor acts to modulate lifespan or differentiate this control from that of growth, reproduction and metabolism. With homologous recombination we produced an allelic series of single amino acid substitutions in the fly insulin receptor (InR). Based on emerging biochemical and structural data, we map amino acid substitutions to receptor function to longevity and fecundity. We propose InR mutants generate bias in the process of asymmetric transphosphorylation when the receptor is activated. This induces specific kinase subdomains that modulate lifespan by additive processes, one involving survival costs of reproduction and the other involving reproduction-independent systems of longevity assurance. We identify a mutant in the kinase insert domain that robustly extends lifespan without affecting growth or reproduction, suggesting this element controls aging through unique mechanisms of longevity assurance.

genomics↗

bioRxiv2020

Diversity and Distribution of a Novel Genus of Hyperthermophilic Aquificae Viruses Encoding a Proof-reading Family-A DNA Polymerase

Despite the high abundance of Aquificae in many geothermal systems, these bacteria are difficult to culture and no viruses infecting members of this phylum have been isolated. Here, we describe the complete, circular dsDNA Uncultivated Virus Genome (UViG) of Thermocrinis Octopus Spring virus (TOSV), derived from metagenomic data, along with eight related UViGs representing three additional species, Thermocrinis Great Boiling Spring virus (TGBSV), Aquificae Josephs Coat Spring Virus (AJCSV), and Aquificae Conch Spring Virus (ACSV). Four near-complete UViGs, ranged from 37,256 bp to 41,208 bp and encoded 48 to 53 open reading frames. Despite low overall similarity between viruses from different hot springs, the genomes shared a high degree of synteny, and encoded numerous genes for nucleotide metabolism, including a polyprotein PolA-type polymerase with likely accessory functions, a DNA Pol III beta subunit (sliding clamp), a thymidylate kinase, a DNA gyrase, a helicase, and a DNA methylase. Also present were conserved genes predicted to code for phage capsids, large and small terminases, portal protein, holin, and lytic transglycosylase, all consistent with a distant relatedness to cultivated Caudovirales. TOSV and TGBSV had the highest coverage in their respective metagenomes and are predicted to infect Thermocrinis ruber and Thermocrinis jamiesonii, respectively, as multiple CRISPR spacers matching the viral genomes were identified within Thermocrinis ruber OC1/4T and Thermocrinis jamiesonii GBS1T. Based on the predicted, unusual bi-directional replication strategy, low sequence similarity to known viral genomes, and a unique position in gene-sharing networks, we propose a new putative genus, Pyrovirus, in the order Caudovirales.

microbiology↗

bioRxiv2018

Insight into the genetic architecture of back pain and its risk factors from a study of 509,000 individuals

Back pain (BP) is a common condition of major social importance and poorly understood pathogenesis. Combining data from the UK Biobank and CHARGE consortium cohorts allowed us to perform a very large GWAS (total N = 509,070) and examine the genetic correlation and pleiotropy between BP and its clinical and psychosocial risk factors. We identified and replicated three BP associated loci, including one novel region implicating SPOCK2/CHST3 genes. We provide evidence for pleiotropic effects of genetic factors underlying BP, height, and intervertebral disc problems. We also identified independent genetic correlations between BP and depression symptoms, neuroticism, sleep disturbance, overweight, and smoking. A significant enrichment for genes involved in central nervous system and skeletal tissue development was observed. The study of pleiotropy and genetic correlations, supported by the pathway analysis, suggests at least two strong molecular axes of BP genesis, one related to structural/anatomic factors such as intervertebral disk problems and anthropometrics; and another related to the psychological component of pain perception and pain processing. These findings corroborate with the current biopsychosocial model as a paradigm for BP. Overall, the results demonstrate BP to have an extremely complex genetic architecture that overlaps with the genetic predisposition to its biopsychosocial risk factors. The work sheds light on pathways of relevance in the prevention and management of LBP.

genetics↗