Biology subjects

Leung, S.

Publications and source records attributed to Leung, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Novel Target Combinations in Lung Squamous Cell Carcinoma proposed by the Emet AI Research Environment and supported by discovery stage experimentation

Early drug discovery is frequently bottlenecked by target identification, a challenge that becomes particularly difficult in complex diseases driven by overlapping, redundant pathways rather than a single dominant driver. Lung squamous cell carcinoma (LUSC) is one such disease: mutationally complex, lacking a dominant actionable target, and marked by a long series of failed single-agent targeted trials. We hypothesized a research environment, capable of reasoning across interconnected datasets, would be well-suited to generate novel, mechanistically grounded therapeutic hypotheses for LUSC. Emet, an AI research environment utilizing a biomedical knowledge graph of more than 1.5 billion triples connected to over 100 specialised biological databases, was paired with an Agentic Research Director that pursues each hypothesis through a graph-of-thoughts search, invoking scoped link-prediction and retrieval tools and committing every round of findings to persistent memory. The top-ranked hypotheses were two-target combinations rather than a single target. The four highest-ranked combinations were advanced to dose-matrix testing in NCI-H520 and SK-MES-1 cells, and two produced combination effects exceeding either single agent; to our knowledge neither of these two pairings had previously been evaluated in LUSC. Dual inhibition of CDC7 (TAK-931) and PKMYT1 (RP-6306) produced statistically significant synergy in both lines that strengthened from day 5 to day 7 (HSA 19.24 to 24.19 in NCI-H520; 11.07 to 13.73 in SK-MES-1). Dual inhibition of USP13 (spautin-1) and PI3K (alpelisib) produced an additive, cell-line-dependent effect, and immunoblotting confirmed the predicted mechanism: time-dependent depletion of MCL-1, c-Myc and SOX-2 driven by the USP13 arm. Agentic reasoning over multi-domain biomedical evidence can therefore nominate testable, mechanism-bearing combination hypotheses that survive experimental scrutiny.

bioinformatics↗

bioRxiv2025

Feeding a low-protein diet exacerbates the susceptibility to Citrobacter rodentium and Dextran Sulfate Sodium-induced intestinal injury in mice.

Globally, almost half of all early childhood deaths are linked to severe undernutrition, herein referred to as severe malnutrition. Mortality in severely malnourished children is often attributed to common infectious diseases, including enteric infections. It has been proposed that impaired intestinal barrier function contributes to mortality, but direct evidence is limited and thus there exists a need to develop improved preclinical models to test these and other mechanistic hypotheses. In this study, we aimed to describe differences in response to enteric inflammation and infection in the colon of malnourished mice compared to well-nourished littermates. C57Bl/6 male weanlings were fed isocaloric diets, either a low 1% protein diet (LPD) or a control 18% protein diet (CPD) for 2-weeks either in combination with oral administration of dextran sodium sulfate (DSS), or Citrobacter rodentium (C. rodentium). LPD-fed mice were more susceptible to DSS or C. rodentium as evidenced by increased clinical severity scores, and reaching their humane endpoints. LPD-fed mice also showed more signs of colonic dysfunction with reduced levels of tight junction proteins, higher colonic pathogen load, and increased systemic inflammation and bacterial spread. Taken together, these observations show that malnourished animals have increased susceptibility to intestinal dysfunction caused by either chemical exposure or infection. These novel preclinical models can be used to further elucidate the processes involved in enteric dysfunction in malnutrition and to test therapies to improve intestinal repair and outcomes.

microbiology↗

bioRxiv2025

Local thalamic interneurons drive spindle termination and enable sleep-dependent learning

The thalamus is central to fundamental brain functions including sensation, attention, and sleep through the precise generation and regulation of neuronal ensemble oscillatory activity. Sensory thalamic circuits are considered feedforward structures, lacking lateral connectivity, while recurrence in the network is mediated by interactions with inhibitory neurons of the thalamic reticular nucleus. Here, we define previously uncharacterized functional roles of local thalamic interneurons, a component of the sensory thalamus whose function has remained unexplored. We demonstrate that local interneuron activation induces rebound oscillations in thalamocortical relay neurons ex vivo and neocortical spindles in vivo, while their inhibition increases spindle occurrence, overall spindle duration and impairs sensory learning. Our findings reveal that local thalamic interneurons have shared and complementary functions to those of thalamic reticular neurons and are required for proper spindle formation and sleep-dependent learning. Together, this work establishes an important neural substrate of thalamocortical circuit function.

neuroscience↗

bioRxiv2025

Spatial gene expression of human coronary arteries revealed the molecular features of diffuse intimal thickening in explanted hearts

BackgroundDiffuse intimal thickening (DIT) is a pre-clinical stage of atherosclerosis characterized by thickened intima. The molecular basis of its susceptibility to atherogenesis is unknown, and mechanistic investigations cannot be performed in commonly used mouse models, in which DIT does not exist. Vascular smooth muscle cells (SMCs) are the predominant cell type that occupies the intima and media of DIT. The molecular differences between these two layers may reveal the earliest phenotypic changes in SMCs to promote atherosclerosis. MethodsWe benchmarked the RNA quality of human coronary arteries from autopsies (n=7) and freshly explanted hearts (n=7) and performed Visium spatial gene expression on tissue sections with DIT. SMC-enriched intima and media were compared to find differentially expressed genes. The gene ontology features of SMC-enriched intima in this study were also compared to those in the atherosclerotic lesions, as previously revealed by single-cell RNA-sequencing studies. ResultsAlthough autopsy samples met the RNA quality standard for Visium (DV200 [≥] 30%), only arteries from freshly explanted hearts exhibited reliable performance. Genes enriched in TGF-{beta}-mediated remodeling of the extracellular matrix were overrepresented in the intima, including versican and biglycan. SMCs enriched in the intima are dedifferentiated, but unlike those in the lesions, they are not proinflammatory. ConclusionsOur findings indicate that autopsy samples are not ideal to distinguish subtle differences among cell phenotypes. Dedifferentiated SMCs in the DIT are distinct from the proinflammatory SMCs in atherosclerotic lesions. SMCs in thickened intima may lead to lipid retention but not necessarily the onset of atherosclerosis. Research Perspective1) What is New? O_LIPostmortem coronary arteries, which are frequently collected by biobanks, have degraded RNA, which are not suitable for identifying subtle differences in the transcriptome profiles. C_LIO_LICoronary arteries from explanted hearts allow for more faithful representation of spatial gene expression across the vessel wall as compared to ones from autopsy hearts. C_LIO_LIThickened intima in diffuse intimal thickening, which exists in everyone, is unlikely to undergo atherogenesis without additional stimuli such as inflammation. C_LI 2) What Question Should be Addressed Next? O_LIThe current RNA quality standard of spatial transcriptomics needs to be carefully benchmarked in biobank samples to control sequencing performance and meaningful data interpretation. C_LIO_LIHow inflammation changes smooth muscle cell phenotypes may explain why everyone has diffuse intimal thickening, but those with chronic inflammatory disease have a high risk of coronary artery disease. C_LIO_LIFuture research should focus on the interplay between smooth muscle cell phenotypes and the extracellular matrix to understand the etiology of coronary artery disease. C_LI

pathology↗

bioRxiv2023

Palmitic acid reduces viability and increases production of reactive oxygen species and respiration in rat tendon-derived cells

Clinically, there is a positive correlation between BMI and the risk of tendinopathy. However, the underlying mechanisms are not understood. Dyslipidaemia and increased circulating free fatty acids (FFA) are associated with increased BMI. We hypothesised that increased FFA concentrations negatively affect rat tendon-derived cells (rTDCs) through mitochondrial-mediated mechanisms. rTDCs were isolated and treated with oleic acid (OA), stearic acid (SA), and palmitic acid (PA). Cell viability was assessed using AlamarBlue assay, and gene expression using real-time PCR. Cell respiration and reactive oxygen species (ROS) production were measured using high-resolution respirometry and MitoSox staining. PA transport into the mitochondria was blocked by pre-treatment with 50{micro}M etomoxir. Treatment with SA and PA at 10 {micro}g/ml decreased rTDC viability by 40% and 60%, respectively. PA decreased the gene expression of the tendon markers Scx and Tnmd, and increased the expression of Mmp3, Mmp13, and Ptgs2 (encoding Cox-2). FFA treatment increased the expression of Cpt1 and Pdk4, indicating an increase in mitochondrial FFA oxidation. PA, at 10 {micro}g/ml, increased cellular respiration and ROS production. Pre-treatment with etomoxir partially inhibited the effects of PA on cell viability, Mmp3 gene expression, ROS production, and cell respiration, but did not affect PA-induced inhibition of Scx or Tnmd expression. We found that increased saturated FFA concentrations in the microenvironment reduce cell viability and alter ROS production, respiration, and gene expression. Blocking PA transport into mitochondria partially reversed the negative effects of PA. Overall, an increase in saturated FFA concentrations may contribute to poor tendon health.

cell biology↗

bioRxiv2021

Population replacement gene drive characteristics for malaria elimination in a range of seasonal transmission settings: a modeling study

Genetically engineering mosquitoes is a promising new vector control strategy to reinvigorate the fight against malaria in Sub-Saharan Africa. Using an agent-based model of malaria transmission with vector genetics, we examine the impacts of releasing population-replacement gene drive mosquitoes on malaria transmission and quantify the gene drive system parameters required to achieve local elimination within a spatially-resolved, seasonal Sahelian setting. We evaluate the performance of two different gene drive systems: "classic" and "integral." Various transmission regimes (low, moderate, and high - corresponding to annual entomological inoculation rates of 10, 30, and 80 infectious bites per person) and other simultaneous interventions, including deployment of insecticide-treated nets (ITNs) and passive healthcare seeking, are also simulated. Local elimination probabilities decreased with pre-existing population target site resistance frequency, increased with transmission-blocking effectiveness of the introduced antiparasitic gene and drive efficiency, and were context dependent with respect to fitness costs associated with the introduced gene. Of the four parameters, transmission-blocking effectiveness may be the most important to focus on for improvements to future gene drive strains because a single release of classic gene drive mosquitoes is likely to locally eliminate malaria in low to moderate transmission settings only when transmission-blocking effectiveness is very high (above ~80-90%). However, simultaneously deploying ITNs and releasing integral rather than classic gene drive mosquitoes significantly boosts elimination probabilities, such that elimination remains highly likely in low to moderate transmission regimes down to transmission-blocking effectiveness values as low as ~50% and in high transmission regimes with transmission-blocking effectiveness values above ~80-90%. Thus, a single release of currently achievable population replacement gene drive mosquitoes, in combination with traditional forms of vector control, can likely locally eliminate malaria in low to moderate transmission regimes within the Sahel. In a high transmission regime, higher levels of transmission-blocking effectiveness than are currently available may be required. Author summaryMalaria remains a significant health burden in Sub-Saharan Africa. The mass deployment of insecticide-treated nets and antimalarial drugs have drastically reduced malaria incidence, but insecticide and drug resistance threaten to stall these efforts. The genetic engineering of mosquito populations is a promising new vector control strategy to reinvigorate the fight against malaria. Releases of engineered gene drive mosquitoes that can spread introduced antimalarial genes quickly throughout the mosquito population may be a particularly effective new method for reducing malaria transmission. Important questions arise, however, about how well these gene drive systems must work in order to deliver substantial reductions in transmission. Here we use a spatial model of individual humans and vectors to simulate the effects of releasing gene drive mosquitoes with antimalarial properties on malaria transmission in a Sahelian setting. We quantify the gene drive system parameters required to achieve local elimination and find that when deployed in combination with traditional forms of vector control, a single release of gene drive mosquitoes with realistically achievable characteristics is highly likely to locally eliminate malaria in low to moderate transmission regimes. In a high transmission regime, improved strains of gene drive mosquitoes may be required. In all settings, releasing gene drive mosquitoes with antimalarial properties helps create a window of opportunity during which malaria prevalence is suppressed and other interventions can be ramped up to achieve elimination, even when a single gene drive mosquito release by itself cannot.

genetics↗

bioRxiv2021

Immune and malignant cell phenotypes of ovarian cancer are determined by distinct mutational processes

High-grade serous ovarian cancer (HGSOC) is an archetypal cancer of genomic instability patterned by distinct mutational processes, intratumoral heterogeneity and intraperitoneal spread. We investigated determinants of immune recognition and evasion in HGSOC to elucidate co- evolutionary processes underlying malignant progression and tumor immunity. Mutational processes and anatomic sites of tumor foci were key determinants of tumor microenvironment cellular phenotypes, inferred from whole genome sequencing, single-cell RNA sequencing, digital histopathology and multiplexed immunofluorescence of 160 tumor sites from 42 treatment-naive HGSOC patients. Homologous recombination-deficient (HRD)-Dup (BRCA1 mutant-like) and HRD- Del (BRCA2 mutant-like) tumors harbored increased neoantigen burden, inflammatory signaling and ongoing immunoediting, reflected in loss of HLA diversity and tumor infiltration with highly- differentiated dysfunctional CD8+ T cells. Foldback inversion (FBI, non-HRD) tumors exhibited elevated TGF{beta} signaling and immune exclusion, with predominantly naive/stem-like and memory T cells. Our findings implicate distinct immune resistance mechanisms across HGSOC subtypes which can inform future immunotherapeutic strategies. HIGHLIGHTSO_LIMulti-region, multi-modal profiling of malignant and immune cell phenotypes in ovarian cancer C_LIO_LIAnatomic site specificity is a determinant of cancer cell and intratumoral immune phenotypes C_LIO_LITumor mutational processes impact mechanisms of immune control and immune evasion C_LIO_LISpatial topology of HR-deficient tumors is defined by immune interactions absent from immune inert HR-proficient subtypes C_LI

cancer biology↗

bioRxiv2021

Matrix stiffness controls ciliogenesis and centriole position

Mechanical stress and the stiffness of the extracellular matrix are key drivers of tissue development and homeostasis. Aberrant mechanosensation is associated with a wide range of pathologies, including diseases such as osteoarthritis. Substrate stiffness is one of the well-known mechanical properties of the matrix that enabled establishing the central dogma of an integrin-mediated mechanotransduction using stem cells. However, how specific cells feel or sense substrate stiffness requires further study. The primary cilium is an essential cellular organelle that senses and integrates mechanical and chemical signals from the extracellular environment. We hypothesised that the primary cilium dynamically alters its length and position to fine-tune cell mechanosignalling based on substrate stiffness alone. We used a hydrogel system of varying substrate stiffness to examine the role of substrate stiffness on cilia frequency, length and centriole position as well as cell and nuclei area over time. Contrary to other cell types, we show that chondrocyte primary cilia shorten on softer substrates demonstrating tissue-specific mechanosensing which is aligned with the tissue stiffness the cells originate from. We further show that stiffness alone determines centriole positioning to either the basal or apical membrane during attachment and spreading, with centriole positioned towards the basal membrane on stiffer substrates. These phenomena are mediated by force generation actin-myosin stress fibres in a time-dependent manner. Based on these findings, we propose that substrate stiffness plays a central role in cilia positioning, regulating cellular response to external forces, and may be a key driver of mechanosignalling-associated diseases. Significance StatementThe primary cilium has been thrust into the limelight owing to its role as a cellular sensor in embryonic development and adult tissue maintenance. How the primary cilium interacts with the mechanical environment still remains unclear. We show that substrate stiffness dynamically regulates primary cilium length and position through integrin-mediated traction forces, the cilia are a key determinant of cell shape on certain stiffnesses. Our data support the promising potential of primary cilia as a novel target in mechanotherapy for improved clinical outcomes in cartilage pathobiology.

cell biology↗

bioRxiv2021

Evolutionary tracking of cancer haplotypes at single-cell resolution

Cancer genomes exhibit extensive chromosomal copy number changes and structural variation, yet how allele specific alterations drive cancer genome evolution remains unclear. Here, through application of a new computational approach we report allele specific copy number alterations in 11,097 single cell whole genomes from genetically engineered mammary epithelial cells and 21,852 cells from high grade serous ovarian and triple negative breast cancers. Resolving single cell copy number profiles to individual alleles uncovered genomic background distributions of gains, losses and loss of heterozygosity, yielding evidence of positive selection of specific chromosomal alterations. In addition specific genomic loci in maternal and paternal alleles were commonly found to be altered in parallel with convergent phenotypic transcriptional effects. Finally we show that haplotype specific alterations trace the cyclical etiology of high level amplifications and reveal clonal haplotype decomposition of complex structures. Together, our results illuminate how allele and haplotype specific alterations, here determined across thousands of single cell cancer genomes, impact the etiology and evolution of structural variations in human tumours.

cancer biology↗

bioRxiv2021

The impact of mutational processes on structural genomic plasticity in cancer cells

Structural genome alterations are determinants of cancer ontogeny and therapeutic response. While bulk genome sequencing has enabled delineation of structural variation (SV) mutational processes which generate patterns of DNA damage, we have little understanding of how these processes lead to cell-to-cell variations which underlie selection and rates of accrual of different genomic lesions. We analysed 309 high grade serous ovarian and triple negative breast cancer genomes to determine their mutational processes, selecting 22 from which we sequenced >22,000 single cell whole genomes across a spectrum of mutational processes. We show that distinct patterns of cell-to-cell variation in aneuploidy, copy number alteration (CNA) and segment length occur in homologous recombination deficiency (HRD) and fold-back inversion (FBI) phenotypes. Widespread aneuploidy through induction of HRD through BRCA1 and BRCA2 inactivation was mirrored by continuous whole genome duplication in HRD tumours, contrasted with early ploidy fixation in FBI. FBI tumours exhibited copy number distributions skewed towards gains, widespread clone-specific variation in amplitude of high-level amplifications, often impacting oncogenes, and break-point variability consistent with progressive genomic diversification, which we termed serriform structural variation (SSV). SSVs were consistent with a CNA-based molecular clock reflecting a continual and distributed process across clones within tumours. These observations reveal previously obscured genome plasticity and evolutionary properties with implications for cancer evolution, therapeutic targeting and response.

cancer biology↗

bioRxiv2020

Immunological and pathological outcomes of SARS-CoV-2 challenge after formalin-inactivated vaccine immunisation of ferrets and rhesus macaques

There is an urgent requirement for safe and effective vaccines to prevent novel coronavirus disease (COVID-19) caused by SARS-CoV-2. A concern for the development of new viral vaccines is the potential to induce vaccine-enhanced disease (VED). This was reported in several preclinical studies with both SARS-CoV-1 and MERS vaccines but has not been reported with SARS-CoV-2 vaccines. We have used ferret and rhesus macaques challenged with SARS-CoV-2 to assess the potential for VED in animals vaccinated with formaldehyde-inactivated SARS-CoV-2 (FIV) formulated with Alhydrogel, compared to a negative control vaccine in ferrets or unvaccinated macaques. We showed no evidence of enhanced disease in ferrets or rhesus macaques given FIV except for mild transient enhanced disease seen at seven days post infection in ferrets. This increased lung pathology was observed early in the infection (day 7) but was resolved by day 15. We also demonstrate that formaldehyde treatment of SARS-CoV-2 reduces exposure of the spike receptor binding domain providing a mechanistic explanation for suboptimal immunity.

pathology↗

bioRxiv2020

Comparison of Rhesus and Cynomolgus macaques as an authentic model for COVID-19.

A novel coronavirus, SARS-CoV-2, has been identified as the causative agent of the current COVID-19 pandemic. Animal models, and in particular non-human primates, are essential to understand the pathogenesis of emerging diseases and to the safety and efficacy of novel vaccines and therapeutics. Here, we show that SARS-CoV-2 replicates in the upper and lower respiratory tract and causes pulmonary lesions in both rhesus and cynomolgus macaques, resembling the mild clinical cases of COVID-19 in humans. Immune responses against SARS-CoV-2 were also similar in both species and equivalent to those reported in milder infections and convalescent human patients. Importantly, we have devised a new method for lung histopathology scoring that will provide a metric to enable clearer decision making for this key endpoint. In contrast to prior publications, in which rhesus are accepted to be the optimal study species, we provide convincing evidence that both macaque species authentically represent mild to moderate forms of COVID-19 observed in the majority of the human population and both species should be used to evaluate the safety and efficacy of novel and repurposed interventions against SARS-CoV-2. Accessing cynomolgus macaques will greatly alleviate the pressures on current rhesus stocks.

microbiology↗

bioRxiv2020

ENSO drives lateral separation of FAD-associated skipjack and bigeye tuna in the Western Tropical Pacific

Incidental capture of juvenile bigeye tuna in fish aggregating device (FAD)-associated purse seine fisheries targeting skipjack tuna have contributed significantly to the degradation of bigeye stocks in the Western Tropical Pacific (WTP) Ocean. One way to reduce this incidental catch is to simply limit purse seine fishing effort; however, skipjack tuna stocks are healthy and economically important to many small island nations in the region. Here we assess whether there is sufficient lateral separation of skipjack and bigeye within FAD-associated purse seine fisheries in the WTP to allow limiting bigeye catch while maintaining a robust skipjack fishery. Based on monthly 5{degrees}-longitude-by-5{degrees}-latitude catch and effort data, FAD-associated bigeye and skipjack catch per unit effort (CPUE) covary tightly throughout the WTP, such that lateral separation between the two species is generally small. There are, however, significant variations in the amount of separation over both space and time. Waters within the Party to the Nauru Agreement exclusive economic zones (EEZs) belonging to Palau, Solomon Islands, and Tuvalu regularly exhibit some of the smallest bigeye-to-skipjack catch ratios, especially during El Nino. In contrast, waters within Kiribatis Phoenix Islands EEZ regularly exhibit some of the largest bigeye-to-skipjack catch ratios, which are particularly high during La Nina. In general, El Nino lowers bigeye-to-skipjack catch ratios east of 170{degrees}E, while La Nina lowers bigeye-to-skipjack catch ratios west of 170{degrees}E. These ENSO-driven variations in separability are larger and more widespread than those driven by seasonality, due to larger associated variations in environmental conditions. Sea surface height anomalies may be particularly useful for demarcating the different environments preferred by skipjack and bigeye throughout the WTP. Sea surface temperatures, temperatures at 100 m, and thermocline depths may also help distinguish between the two species preferred habitats in many areas. These analyses can help better inform the complex decisions made by both fishers during operations and fisheries managers during creation of effective, dynamic policies to preserve bigeye stocks in the WTP. They also show that climate variability can have substantial effects on the spatial distributions of top pelagic predators and their interactions with one another.

ecology↗

bioRxiv2020

Primary platinum resistance and immune exclusion in ovarian carcinomas with high expression of the homologous recombination mediator RAD51

BackgroundHomologous recombination deficiency (HRD) in ovarian cancer confers increased sensitivity to Poly-ADP-Ribose-Polymerase (PARP) inhibitors and platinum. The homologous recombination (HR) mediator RAD51, however, is commonly overexpressed, potentially driving unregulated HR. Due to non-quantitative measurements and heterogeneous cohorts, the clinical relevance of RAD51 expression in ovarian cancer is unclear. MethodsFluorescent immunohistochemistry and multispectral imaging were used to quantitate RAD51 expression, in relation to other markers, in independent cohorts of ovarian carcinomas from British Columbia Cancer (BCC n=284) and the phase III SCOTROC4 trial (n=268). Independent cohorts (TCGA n=566, GSE9891 n=267, GSE26712 n=185 and GSE3149 n=146) were used for mRNA expression and immune infiltration analyses. ResultsRAD51-High tumours had shorter progression-free and overall survival compared to RAD51-Low cases in both BCC and SCOTROC4. The negative prognostic significance of high RAD51 was primarily evident in cases classified "HRD negative" by the Myriad genomic scar assay. Unexpectedly, overexpression of RAD51 in ovarian cancer cell lines did not affect sensitivity to platinum or PARP inhibitors, but modified the expression of immune-regulatory genes. Accordingly, tumours with high RAD51 mRNA showed consistent changes in immunomodulatory transcripts across four independent ovarian cancer cohorts. In-situ multiplexed imaging confirmed that high RAD51 tumours correlated with tumour exclusion of cytotoxic-T-cells, possibly explaining their poor outcomes after chemotherapy. ConclusionsHigh RAD51 expression, in conjunction with a HRD score <42, identifies a subgroup of EOC cases with platinum resistance and an immune excluded tumour microenvironment. Tumours with high RAD51 may require alternate or additional adjuvant therapeutic strategies to overcome immune exclusion. Statement of Translational RelevanceHomologous recombination deficiency (HRD) in ovarian cancer confers increased sensitivity to Poly-ADP-Ribose-Polymerase (PARP) inhibitors and platinum. Currently, methods to identify patients who do poorly on first-line platinum based chemotherapy in ovarian cancer represent an unmet clinical need. In this report we show that RAD51 expression can identify patients with primary platinum resistance in two large cohorts, including a unique phase-III trial of carboplatin as adjuvant monotherapy. The clinical relevance of a positive genomic scar HRD score, a biomarker for assessing HRD status, in predicting benefit to PARP inhibitors has been established following recent phase 3 trials in first line and 2nd line maintenance treatment of ovarian cancer. Our findings suggest that HRD negative ovarian tumours may be further stratified by RAD51 expression status in the context of platinum sensitivity, and may serve to guide future trials of HRD targeted agents.

cancer biology↗

bioRxiv2020

Dose-dependent response to infection with SARS-CoV-2 in the ferret model: evidence of protection to re-challenge

In December 2019 an outbreak of coronavirus disease (COVID-19) emerged in Wuhan, China. The causative agent was subsequently identified and named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) which rapidly spread worldwide causing a pandemic. Currently there are no licensed vaccines or therapeutics available against SARS-CoV-2 but numerous candidate vaccines are in development and repurposed drugs are being tested in the clinic. There is a vital need for authentic COVID-19 animal models to further our understanding of pathogenesis and viral spread in addition to pre-clinical evaluation of candidate interventions. Here we report a dose titration study of SARS-CoV-2 to determine the most suitable infectious dose to use in the ferret model. We show that a high (5x106 pfu) and medium (5x104 pfu) dose of SARS-CoV-2 induces consistent upper respiratory tract (URT) viral RNA shedding in both groups of six challenged animals, whilst a low dose (5x102 pfu) resulted in only one of six displaying signs of URT viral RNA replication. The URT shedding lasted up to 21 days in the high dose animals with intermittent positive signal from day 14. Sequential culls revealed distinct pathological signs of mild multifocal bronchopneumonia in approximately 5-15% of the lung, observed on day 3 in high and medium dosed animals, with presence of mild broncho-interstitial pneumonia on day 7 onwards. No obvious elevated temperature or signs of coughing or dyspnoea were observed although animals did present with a consistent post-viral fatigue lasting from day 9-14 in the medium and high dose groups. After virus shedding ceased, re-challenged ferrets were shown to be fully protected from acute lung pathology. The endpoints of URT viral RNA replication in addition to distinct lung pathology and post viral fatigue were observed most consistently in the high dose group. This ferret model of SARS-CoV-2 infection presents a mild clinical disease (as displayed by 80% of patients infected with SARS-CoV-2). In addition, intermittent viral shedding on days 14-21 parallel observations reported in a minority of clinical cases.

microbiology↗

bioRxiv2020

Expansion of Functional Regulatory T Cells Using Soluble RAGE Prevents Type 1 Diabetes

Type 1 diabetes (T1D) is an autoimmune disease with no cure. Therapeutic translation has been hampered by preclinical reproducibility. Here, short-term administration of an antagonist to the receptor for advanced glycation end products (sRAGE) protected against murine diabetes at two independent centers. Treatment with sRAGE increased regulatory T cells (Tregs) within islets, pancreatic lymph nodes and spleen, increasing islet insulin expression and function. Diabetes protection was abrogated by Treg depletion and shown to be dependent on antagonizing RAGE using knockout mice. Human Tregs treated with a RAGE ligand downregulated genes for suppression, migration and Treg homeostasis (FOXP3, IL7R, TIGIT, JAK1, STAT3, STAT5b, CCR4). Loss of suppressive function was reversed by sRAGE, where Tregs increased proliferation and suppressed conventional T cell division, confirming that sRAGE expands functional human Tregs. These results highlight sRAGE as an attractive treatment to prevent diabetes, showing efficacy at multiple research centers and in human T cells.

immunology↗

bioRxiv2019

Arginine depletion through ADI-PEG20 to treat argininosuccinate synthase deficient ovarian cancer, including small cell carcinoma of the ovary, hypercalcemic type

PurposeMany rare ovarian cancer subtypes such as small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) have poor prognosis due to their aggressive nature and resistance to standard platinum and taxane based chemotherapy. The development of effective therapeutics has been hindered by the rarity of such tumors. We sought to identify targetable vulnerabilities in rare ovarian cancer subtypes. Experimental DesignWe compared the global proteomic landscape of six cases each of endometrioid ovarian cancer (ENOC), clear cell ovarian cancer (CCOC), and SCCOHT to the most common subtype high grade serous ovarian cancer (HGSC) to identify potential therapeutic targets. Immunohistochemistry of tissue microarrays were used as validation of ASS1 deficiency. The efficacy of arginine-depriving therapeutic ADI-PEG20 was assessed in vitro using cell lines and patient derived xenograft mouse models representing SCCOHT. ResultsGlobal proteomic analysis identified low ASS1 expression in ENOC, CCOC, and SCCOHT compared to HGSC. Low ASS1 levels were validated through IHC in a large patient cohort. The lowest levels of ASS1 were observed in SCCOHT, where ASS1 was absent in 2/15 cases, and expressed in less than 5% of the tumor cells in 8/15 cases. ASS1 deficient ovarian cancer cells were sensitive to ADI-PEG20 treatment regardless of subtype in vitro. Furthermore, in two cell line mouse xenograft models and one patient derived mouse xenograft model of SCCOHT, once a week treatment of ADI-PEG20 (30mg/kg and 15mg/kg) inhibited tumor growth in vivo. ConclusionsPreclinical in vitro and in vivo studies identified ADI-PEG20 as a potential therapy for patients with rare ovarian cancers including SCCOHT. Translational relevanceMany rare ovarian cancers lack effective management strategies and are resistant to the standard platinum- and taxane-based chemotherapy. Thus, for a rare ovarian cancer subtype like small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) - an aggressive malignancy affecting young women in their twenties, effective targeted therapeutics are urgently needed. We used global proteomics to identify a deficiency in arginosuccinate synthase (ASS1) as a common feature among some rare ovarian cancer subtypes. Using in-vitro and in-vivo models, we demonstrated that the arginine-depriving investigational agent ADI-PEG20 effectively inhibited cell growth in ASS1 deficient ovarian cancers including SCCOHT, establishing it as a potential therapeutic agent for rare ovarian cancer subtypes deficient in ASS1. Further clinical investigation is warranted.

cancer biology↗

bioRxiv2018

Prediction-error signals to violated expectations about person identity and head orientation are doubly-dissociated across the dorsal and ventral visual streams

Predictive coding theories of perception suggest the importance of constantly updated internal models of the world in predicting future sensory inputs. One implication of such models is that cortical regions whose function is to resolve particular stimulus attributes should also signal prediction violations with respect to those same stimulus attributes. Previously, through carefully designed experiments, we have demonstrated early-mid latency EEG/MEG prediction-error signals in the dorsal visual stream to violated expectations about stimulus orientation/trajectory, with localisations consistent with cortical areas processing motion and orientation. Here we extend those methods to simultaneously investigate the predictive processes in both dorsal and ventral visual streams. In this MEG study we employed a contextual trajectory paradigm that builds expectations using a series of image presentations. We created expectations about both face orientation and identity, either of which can subsequently be violated. Crucially this paradigm allows us to parametrically test double dissociations between these different types of violations. The study identified double dissociations across the type of violation in the dorsal and ventral visual streams, such that the right fusiform gyrus showed greater evidence of prediction-error signals to Identity violations than to Orientation violations, whereas the left angular gyrus and postcentral gyrus showed the opposite pattern of results. Our results suggest comparable processes for error checking and context updating in high-level expectations instantiated across both perceptual streams. Perceptual prediction-error signalling is initiated in regions associated with the processing of different stimulus properties.\n\nSignificance StatementVisual processing occurs along what and where information streams that run, respectively along the ventral and dorsal surface of the posterior brain. Predictive coding models of perception imply prediction-error detection processes that are instantiated at the level where particular stimulus attributes are parsed. This implies that, for instance, when considering face stimuli, signals arising through violated expectations about the person identity of the stimulus should localise to the ventral stream, whereas signals arising through violated expectations about head orientation should localise to the dorsal stream. We test this in a magnetoencephalography source localisation study. The analysis confirmed that prediction-error signals to identity versus head-orientation occur with similar latency, but activate doubly-dissociated brain regions along ventral and dorsal processing streams.

neuroscience↗