Biology subjects

Nguyen, P. T.

Publications and source records attributed to Nguyen, P. T..

At least 19 recordsLinked to original sources

bioRxiv2026

A Compendium of 49 Experimental SBS Signatures for Decoding Human Cancer Mutational Processes

Human cancer genomes harbor distinct mutational patterns that reflect past processes of DNA damage and repair. However, the precise attribution of these signatures to specific chemical carcinogens lacks a standardized experimental reference framework. To address this gap, we curated 4,282 genome-wide sequencing datasets from 42 model systems across five species exposed to 146 cancer-risk agents. This platform yielded 49 robust experimental single-base substitution signatures (eSS), with 28 matching 19 established COSMIC signatures and 21 defining novel mutational processes. We reconstructed 24 COSMIC signatures, assigning candidate etiologies to five signatures of unknown origin and revising two contested assignments. Pan-cancer decomposition detected four eSS-like mutational processes enriched in smokers across 4,951 tumors. Lastly, independent single-molecule sequencing of primary human organoids reproduced these profiles with high fidelity, confirming true platform-independent biological reproducibility across complex human models. This eSS repertoire provides a reference that links human mutational processes to mechanistic classes of DNA damage.

genomics↗

bioRxiv2026

The liver compensates for zonal loss of glucose 6-phosphatase to prevent glycogen storage disease

The liver is organized into spatial zones with distinct metabolic roles, but how this architecture contributes to disease remains unclear. Glucose production is concentrated in periportal hepatocytes and depends on G6PC1; loss of this enzyme causes glycogen storage disease type Ia (GSD1a). We tested whether G6PC1 loss in specific zones, including its primary periportal location, is sufficient to cause disease. Unexpectedly, loss of G6pc1 in any single zone caused local glycogen accumulation but did not produce the systemic metabolic abnormalities or liver tumors seen after whole-liver deletion. Instead, disease developed only after near-complete loss of G6pc1 across the entire liver. These findings show that organ-wide compensation preserves metabolic homeostasis and suppresses tumorigenesis despite localized disruption. TeaserSpatial G6pc1 loss causes local glycogen storage without systemic metabolic disease.

physiology↗

bioRxiv2026

Impact of temperature on patient-derived dengue virus breakthrough infections in wMel-infected Aedes aegypti.

The wMel strain of the insect endosymbiont Wolbachia reduces the potential for Aedes aegypti to transmit mosquito-borne viruses such as dengue (DENV). Field trials that have introgressed wMel into Ae. aegypti populations have shown this approach significantly reduces dengue incidence. In a laboratory setting some wMel-Ae. aegypti develop infectious saliva following a viremic blood meal. Additionally, studies have demonstrated that exposing wMel-Ae. aegypti to heat treatment, particularly during the larval stage, reduces wMel density in key tissues such as the ovaries, midgut and salivary glands. Here we build on these studies, using viremic blood collected from 13 dengue inpatients at the Hospital for Tropical Diseases in Ho Chi Minh City (Viet Nam), to assess how temperature affects the protection afforded to Ae. aegypti by wMel. We found that, compared to wMel-Ae. aegypti reared at 28 {+/-} 4{degrees}C, those reared at 31 {+/-} 4{degrees}C developed infectious saliva more frequently, but the risk of this occurring was still reduced compared to WT mosquitoes reared at the same temperature. Heat treatment reduced the density of wMel in all tissues tested, decreased the magnitude of wMels protection against DENV replication in the head/thorax, and significantly increased the amount of DENV replication in wMel-Ae. aegypti. When comparing cohorts of wMel-Ae. aegypti that did or did not develop infectious saliva, DENV levels in the head/thorax were associated with increased odds of mosquitoes developing infectious saliva, but wMel density was not. Overall, these findings show that elevated rearing temperatures increase the risk of patient-derived DENV breakthrough infections in wMel-Ae. aegypti, potentially due to increased DENV replication in these mosquitoes. This limitation suggests it would be prudent to increase surveillance in regions using wMel for dengue control when daily mean temperatures remain above 30{degrees}C for multiday periods. Author SummaryThe mosquito species Ae. aegypti can be infected with the bacterium Wolbachia (wMel strain), reducing its capacity to transmit viruses like dengue (DENV). Wolbachia is now being used as a biocontrol tool to reduce the burden of dengue in communities. However, some mosquitoes with Wolbachia can still transmit DENV. Here we utilised a natural infection model using dengue patient-derived blood to examine how temperature may increase the risk of DENV transmission occurrence in mosquitoes with wMel. Mosquitoes with wMel were more likely to transmit virus when reared at an average temperature of 31{degrees}C compared to those reared at an average temperature of 28{degrees}C but these mosquitoes still had a lower risk of developing infectious saliva compared to their wMel-free counterparts. Higher temperatures reduced the amount of wMel in mosquito tissues and increased the amount of DENV replicating in the head/thorax. Increasing levels of DENV RNA in these tissues were found to be associated with increased risk of mosquitoes with wMel developing infectious saliva. This finding indicates surveillance is warranted in high temperature settings or during heat waves, to monitor for changes in wMel frequency and DENV infection in Ae. aegypti.

microbiology↗

bioRxiv2026

UFMylation of Pyruvate Dehydrogenase Regulates Mitochondrial Metabolism

The ubiquitin-fold modifier 1 (UFM1) post-translational modification (PTM), or UFMylation, regulates protein homeostasis and is essential for human development. Yet the roles of the de-UFMylase, UFM1-specific peptidase 2 (UFSP2), which removes UFM1 from UFMylated proteins, remain poorly characterized. Here, we demonstrate that UFMylation and UFSP2 regulate mitochondrial metabolism. Quantitative proteomics in UFSP2-deficient cells revealed the accumulation of many proteins previously unknown to be impacted by UFMylation. These included components of the mitochondrial ribosome, electron transport chain (ETC), and pyruvate dehydrogenase (PDH) complex. Functional analyses demonstrated that excessive UFMylation in UFSP2-deficient cells increases mitochondrial respiration, glucose oxidation in the tricarboxylic acid (TCA) cycle, and PDH enzymatic activity. We identified dihydrolipoamide S-acetyltransferase (DLAT), the E2 component of PDH, as a direct UFMylation substrate, with lysine 118 (K118) as the primary conjugation site. Mutating K118 to arginine (K118R) abolished DLAT UFMylation and reduced pyruvate oxidation, identifying this modification as an activator of PDH. These findings reveal a UFMylation-based regulatory mechanism that controls mitochondrial function by inducing utilization of pyruvate as a TCA cycle fuel.

biochemistry↗

bioRxiv2025

Myelin maintenance and addition regulate synaptic plasticity in the adult mouse cortex

Myelination of the developing central nervous system (CNS) increases action potential conduction velocity but can also act as a plasticity brake, limiting neurite reorganisation and synaptic plasticity. As myelination is a life-long process, the myelin laid down in development or adulthood could also affect synapse number or plasticity across the lifespan. We report that conditionally deleting the transcription factor, myelin regulatory factor (Myrf), to disrupt the myelin maintenance program in oligodendrocytes (OLs) from P57 (Plp-CreERT2 :: Myrf fl/fl mice), led to significant myelin loss and impaired action potential conduction and gross motor performance. By sparsely labelling layer V pyramidal neurons in the primary motor cortex, we could visualise the apical and basal dendrites and their excitatory post-synaptic dendritic spines and determined that spine density was normal in P57+60 Plp-CreERT2 :: Myrf fl/fl mice. However, a higher proportion of the dendritic spines were large, stable mushroom spines and generated larger amplitude miniature excitatory post-synaptic currents. These data indicate that the myelin maintenance program is critical for preserving neuron adaptability, homeostasis and glutamate sensitivity. When we instead prevented the addition of new OLs and myelin from P57, action potential conduction velocity and gross motor performance appeared normal. Spine density was also normal in Pdgfr-CreERTM :: Myrf fl/fl mice, however, spine morphology was changed along the basal dendrites of layer V M1 pyramidal neurons. At P117, the basal dendrites were frozen in a state that resembled P57 dendrites, as they retained a higher proportion of thin, plastic spines. These data suggest that adult myelination supports the life-long accumulation of stable spines within the basal but not apical dendritic compartment and have important implications for understanding dendritic plasticity rules in the motor circuit. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=140 SRC="FIGDIR/small/695322v1_ufig1.gif" ALT="Figure 1"> View larger version (77K): org.highwire.dtl.DTLVardef@1a7928org.highwire.dtl.DTLVardef@83e7borg.highwire.dtl.DTLVardef@13e1e14org.highwire.dtl.DTLVardef@128e2df_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIAdult myelin maintenance regulates synaptic plasticity and neuron homeostasis C_LIO_LIExisting myelin regulates layer V pyramidal neuron glutamate sensitivity C_LIO_LIOligodendrocytes born in young adulthood undergo age-related loss C_LIO_LINew myelin stabilises synapses in the basal but not apical dendritic compartment C_LI eTOC blurbMyelin regulates axon branching, metabolism and action potential conduction speed. We report that myelin also preserves neuron adaptability, homeostasis and glutamate sensitivity in the adult motor cortex. Furthermore, new myelin allows the accumulation of stable synapse on basal but not apical layer V pyramidal neuron dendrites over time.

neuroscience↗

bioRxiv2025

Imputation and polygenic score performance of low coverage whole-genome sequencing and genotyping arrays in diverse human populations

Genome-wide association studies and polygenic score analysis rely on large-scale genotypic data, traditionally obtained through SNP arrays and imputation. However, low coverage whole-genome sequencing has emerged as a promising alternative. This study presents a comprehensive comparison of imputation accuracy and polygenic score performance between eight high-performance genotyping arrays and six low coverage whole-genome sequencing coverage levels (0.5-2x) across diverse populations. We analyze data from 2,504 individuals in the 1000 Genomes Project using a 10-fold cross-imputation strategy to evaluate imputation accuracy and polygenic score performance for four complex traits. Our results demonstrate that low-pass whole-genome sequencing performs competitively with population-specific arrays in both imputation accuracy and polygenic score estimation. Interestingly, low coverage whole-genome sequencing shows superior performances compared to arrays in underrepresented populations and for rare and low-frequency variants. Our findings suggest that low coverage whole-genome sequencing offers a flexible and powerful alternative to genotyping arrays for large-scale genetic studies, particularly in diverse or underrepresented populations.

genomics↗

bioRxiv2025

Mgl2+ cDC2 triggering of fungal allergic inflammation depends on a spore induced glycolytic shift fuelled by local availability of glucose

Fungal spores are a major cause of severe asthmatic disease. However, the precise events that cause individuals to become sensitised to spores are poorly understood. Mgl2+ type 2 conventional dendritic cells (Mgl2+ cDC2s) are critical in coordinating allergic airway inflammation in mice following repeated exposure to inhaled spores. Yet, whether these DCs are directly acquiring spores from the airway, and the downstream mechanism(s) upon fungal uptake causing DCs to trigger allergic inflammation are unknown. Here we find that spores are acquired by lung DCs after inhalation although these events are rare ([~] 0.5% of the cDC2 population). Transcriptomics on isolated spore+ Mgl2+ cDC2s, compared to spore- Mgl2+ cDC2s from the same environment, revealed that a major consequence of fungal uptake was a boost in metabolic activity. Single-cell metabolic profiling revealed this increase in Mgl2+ cDC2 metabolism upon spore acquisition was fuelled by a glycolytic shift. To pinpoint if nutrient availability and acquisition is an important determinant of this response, mass spectrometry-based metabolomics revealed that, during fungal allergic inflammation, the local airway nutrient environment is altered. To ascertain which of these could be fuelling DC responses, we identified which substrates that feed into glycolysis were crucial. Of these, we found that glucose availability acts as a key rheostat in shaping cDC2 responses to spores. These data highlight a crucial role for glycolytic metabolism in driving cDC2 responses to spores, which is governed by glucose availability, defining novel targets for future therapeutic development of fungal allergic inflammation.

immunology↗

bioRxiv2025

An early evolutionary stage of mutualistic endosymbiosis reveals a parasitic aspect of endosymbionts

Mutualistic endosymbiosis is a cornerstone of evolutionary innovation, enabling organisms to exploit diverse niches unavailable to individual species. However, our knowledge about the early evolutionary stage of this relationship remains limited. The association between the ciliate Tetrahymena utriculariae and its algal endosymbiont Micractinium tetrahymenae indicates an incipient stage of endosymbiosis. Although T. utriculariae cells rely on endosymbiotic algae to grow in low-oxygen conditions, they gradually lose the endosymbionts in aerobic conditions. Our comparative genomics reveals that the mitochondria-related genes of T. utriculariae are fast-evolving. Symbiotic cells display elongated mitochondria, which interact intimately with endosymbionts. Moreover, inhibiting mitochondrial fatty acid oxidation reduces host fitness but increases the endosymbiont population. Time-series transcriptomics reveal physiological fine-tuning of the host during day and night, underscoring adaptations for nutrient exchange and regulation. Notably, endosymbiotic algae downregulate photosynthesis-related genes compared with free-living cells, correlated with a substantially reduced chlorophyll content. These findings indicate that the endosymbionts exploit host metabolites to supplement reduced photosynthesis. Consistently, symbiotic Tetrahymena cells exhibit lower fitness under aerobic conditions than aposymbiotic cells. Our results support that mutualistic and parasitic relationships between symbiotic organisms are condition-dependent, especially at an early evolutionary stage.

evolutionary biology↗

bioRxiv2025

The Effects of Antidepressants on the Hippocampus: A Meta-Analysis of Public Transcriptional Profiling Data

Depression can be treated with traditional pharmaceuticals targeting monoaminergic function, non-traditional drug classes and neuromodulatory interventions. To identify mechanisms of action shared across clinically-effective antidepressant treatment categories, we performed two systematic meta-analyses of public transcriptional profiling data from adult laboratory rodents (rats, mice). The outcome variable was gene expression, measured by microarray or RNA-Seq from bulk-dissected tissue from two depression-related brain regions (hippocampus, cortex). Relevant datasets were identified in the Gemma database of curated, reprocessed transcriptional profiling data using predefined search terms and inclusion/exclusion criteria (hippocampus: 6-24-2024, cortex: 7-10-2024). Differential expression results were extracted for all genes, minimizing bias. For each gene, a random effects meta-analysis model was fit to antidepressant vs. control effect sizes (Log2 Fold Changes) from each study for each brain region, with follow-up analyses exploring sources of effect heterogeneity. For the hippocampus, 15 relevant studies were identified, containing 22 antidepressant vs. control group comparisons (collective n=313 samples), with approximately half representing traditional versus non-traditional antidepressants. Of 16,439 analyzed genes, 58 were consistently differentially expressed (False Discovery Rate (FDR)<0.05) following treatment. Antidepressant effects were enriched in the dentate gyrus and in gene sets related to stress regulation, brain growth and plasticity, vasculature and glia, and immune function. Comparisons with single nucleus RNA-Seq confirmed effects on specific hippocampal cell types, including potential rejuvenation of dentate granule neurons. For the cortex, 13 studies were identified, containing 16 antidepressant vs. control group comparisons (collective n=233 samples). Of 15,583 analyzed genes, only one was consistently differentially expressed (FDR<0.05: Atp6v1b2), but overall expression patterns moderately resembled the hippocampus. These genes and pathways showing consistent differential expression across treatment categories may be promising targets for novel therapies. Future work should explore relevance to human clinical populations and potential heterogeneity introduced by sex and subregion. Key PointsO_LIDepression can be treated with traditional antidepressants targeting monoaminergic function, as well as other drug classes and non-pharmaceutical interventions. C_LIO_LIUnderstanding the congruent effects of different types of antidepressant treatments on sensitive brain regions, such as the hippocampus and cortex, can highlight essential mechanisms of action. C_LIO_LIA meta-analysis of public transcriptional profiling datasets identified genes and functional gene sets that are differentially expressed across antidepressant categories. C_LI Plain Language SummaryMajor depressive disorder is characterized by persistent depressed mood and loss of interest and pleasure in life. Worldwide, an estimated 5% of adults suffer from depression, making it a leading cause of disability. The current standard of care for depressed individuals includes psychotherapy and antidepressant medications that enhance signaling by monoamine neurotransmitters, such as serotonin and norepinephrine. Other treatments include non-traditional antidepressants that function via alternative, often unknown, mechanisms. To identify mechanisms of action shared across different categories of antidepressants, we performed a meta-analysis using public datasets to characterize changes in gene expression (mRNA) following treatment with both traditional and non-traditional antidepressants. We focused on the hippocampus and cortex, which are two brain regions that are sensitive to both depression and antidepressant usage. We found 59 genes that had consistently higher or lower levels of expression (mRNA) across antidepressant categories. The functions associated with these genes were diverse, including regulation of stress response, the immune system, brain growth and adaptability. These genes are worth investigating further as potential linchpins for antidepressant efficacy or as targets for novel therapies. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=104 SRC="FIGDIR/small/648805v3_ufig1.gif" ALT="Figure 1"> View larger version (29K): org.highwire.dtl.DTLVardef@14538e3org.highwire.dtl.DTLVardef@199c5e3org.highwire.dtl.DTLVardef@8ed8a6org.highwire.dtl.DTLVardef@31b1f8_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2025

NUDT5 regulates purine metabolism and thiopurine sensitivity by interacting with PPAT

Cells generate purine nucleotides through both de novo purine biosynthesis (DNPB) and purine salvage. Purine accumulation represses energetically costly DNPB through feedback inhibition of the enzymatic steps that produce the precursor phosphoribosylamine. Excessive DNPB is associated with human diseases including neurological dysfunction and hyperuricemia. However, the mechanisms explaining how cells balance DNPB and purine salvage are incompletely understood. Data from a genome-wide CRISPR loss-of-function screen and extensive stable isotope tracing identified Nudix hydrolase 5 (NUDT5) as a suppressor of DNPB during purine salvage. NUDT5 ablation allows DNPB to persist in the presence of either native purines or thiopurine drugs; this renders NUDT5-deficient cells insensitive to thiopurine treatment. Surprisingly, this regulation occurs independently of NUDT5s known function in hydrolyzing ADP-ribose to AMP and ribose-5-phosphate. Rather, NUDT5 interacts with phosphoribosyl pyrophosphate amidotransferase (PPAT), the rate-limiting enzyme in DNPB that generates phosphoribosylamine. Upon induction of purine salvage, the PPAT-NUDT5 interaction is required to trigger disassembly of the purinosome, a cytosolic metabolon involved in efficient DNPB. Mutations that disrupt NUDT5s interaction with PPAT but leave its catalytic activity intact permit excessive DNPB during purine salvage, inducing thiopurine resistance. Collectively, our findings identify NUDT5 as a regulator governing the balance between DNPB and purine salvage, underscoring its impact on nucleotide metabolism and efficacy of thiopurine treatment.

biochemistry↗

bioRxiv2025

Antidepressants promote developmental-like plasticity through remodeling of extracellular matrix

Antidepressants are widely used to treat mood and anxiety disorders, yet the cellular and molecular mechanisms underlying their therapeutic effects remain poorly understood. Here, we show that the selective serotonin reuptake inhibitor (SSRI) fluoxetine rejuvenates the dentate gyrus (DG) by reactivating a latent developmental plasticity program in mature neurons, which is required for re-engaging critical period-like synaptic remodeling and antidepressant-like behavioral effects. Single nuclei transcriptomic profiling across all hippocampal cell types revealed a strikingly selective response in the DG, where mature neurons re-engaged a developmental-like transcriptional state, an effect distinct from adult neurogenesis. Chronic fluoxetine treatment induced expression of SOX11, a developmental transcription factor involved in neurodevelopment and axonal regeneration that is normally silenced in the adult brain. Reactivation of SOX11 in mature DG neurons was necessary for both the antidepressant-like behavioral effects of fluoxetine and the re-engagement of critical period-like synaptic remodeling. Notably, SOX11 reactivation was also induced by physiological stimuli, including environmental enrichment and peripheral axon regeneration, suggesting that mature neurons retain access to a conserved developmental plasticity program throughout adulthood. We further identified evidence of this form of developmental plasticity in the adult human brain, an effect distinct from adult neurogenesis. At the structural level, fluoxetine remodeled novel extracellular matrix (ECM) structures within the DG distinct from canonical perineuronal nets, and targeted ECM degradation was sufficient to reactivate SOX11 in mature neurons, identifying the ECM as a key regulator of neuronal rejuvenation. Altogether, these findings demonstrate that mature neurons retain an intrinsic capacity to re-engage dormant developmental programs, and that antidepressants harness this regenerative plasticity to drive neural circuit remodeling and antidepressant-like effects.

neuroscience↗

bioRxiv2024

Unravelling the Impact of miR-21 Overexpression on the MicroRNA Network and Cancer Pathways

AbstractMicroRNAs (miRNA, miRs) are small noncoding RNAs that are ubiquitously expressed in all mammalian cells. Their primary function is the regulation of nascent RNA transcripts by direct binding to regions on the target. There is now exciting data to suggest that these miRNAs can bind to other miRNAs, and this may have a broader impact on gene regulation in disease states. The oncomiR miR-21 is one of the highest-expressing miRNAs in cancer cells, and in this study, we characterise which miRNAs could be potential targets of miR-21. In cancer cells delivered with a miR-21 mimic, there was an observable shift of the miRNA milieu. We demonstrate that the miR-17-92a cluster, which harbours six miRNA members, may be a target of miR-21 regulation. Additionally, the primary transcript of miR-17-92a was reduced in the presence of miR-21. In the broader context of gene regulation, overexpression of miR-21 shifted the expression of more than 150 miRNAs, including those known to regulate genes encoding proteins in cancer pathways such as the MAPK signalling and FoxO pathways. This study expands upon our limited understanding of miR:miR regulatory network and reinforces the concept that miRNAs can regulate each other, thereby influencing broader gene regulatory networks.

cell biology↗

bioRxiv2024

Autophagy is suppressed in peripheral blood mononuclear cells during chronic obstructive pulmonary disease.

Assessing autophagy may offer insights into the pathogenesis of chronic obstructive pulmonary disease (COPD). However, measuring the dynamic aspect of autophagy is challenging, and sample manipulation can cause signal fluctuations that deviate from physiological conditions. We applied an organotypic method to quantify autophagy in COPD, where it frequently demonstrates disease-related dysregulation. Blood from control and COPD participants were treated with or without chloroquine. LC3B-II abundance was quantified in peripheral blood mononuclear cells, and findings were validated by transmission electron microscopy. Our observations show that while basal LC3B-II abundance was similar between groups (P = 0.60), autophagic flux was significantly lower in the COPD cohort, suggesting disruption in the regulatory factors that direct autophagosome clearance (P = 0.004). This was supported by less frequent observations of autophagy-related vacuoles in the cytosol of COPD-derived PBMCs. Our findings indicate that the suppression of autophagy can be detected in the blood of individuals with COPD, which warrants further investigation into its contribution to extrapulmonary disease processes.

molecular biology↗

bioRxiv2024

Towards high-resolution modeling of small molecule-ion channel interactions

Ion channels are critical drug discovery targets for a wider range of pathologies, such as epilepsy, chronic pain, itch, autoimmunity, and cardiac arrhythmias. To develop effective and safe therapeutics, it is necessary to design small molecules with high potency and selectivity for specific ion channel subtypes. There has been increasing implementation of structure-guided drug design for the development of small molecules targeting ion channels. We evaluated the performance of two Rosetta ligand docking methods, RosettaLigand and GALigandDock, on structures of known ligand - cation channel complexes. Ligands were docked to voltage-gated sodium (NaV), voltage-gated calcium (CaV), and transient receptor potential vanilloid (TRPV) channel families. For each test case, RosettaLigand and GALigandDock methods were able to frequently sample a ligand binding pose within 1-2 [A] root mean square deviation (RMSD) relative to the native ligand - channel structure. However, RosettaLigand and GALigandDock scoring functions cannot consistently identify native drug binding poses as top-scoring models. Our study reveals that the proper scoring criteria for RosettaLigand and GALigandDock modeling of ligand - ion channel complexes should be assessed on a case-by-case basis using sufficient ligand and receptor interface sampling, knowledge about state specific interactions of the ion channel and inherent receptor site flexibility that could influence ligand binding.

biophysics↗

bioRxiv2024

An artificial intelligence accelerated virtual screening platform for drug discovery

Structure-based virtual screening is a key tool in early drug discovery, with growing interest in the screening of multi-billion chemical compound libraries. However, the success of virtual screening crucially depends on the accuracy of the binding pose and binding affinity predicted by computational docking. Here we developed a highly accurate structure-based virtual screen method, RosettaVS, for predicting docking poses and binding affinities. Our approach outperforms other state-of-the-art methods on a wide range of benchmarks, partially due to our ability to model receptor flexibility. We incorporate this into a new open-source artificial intelligence accelerated virtual screening platform for drug discovery. Using this platform, we screened multi-billion compound libraries against two unrelated targets, a novel ubiquitin ligase target KLHDC2 and the human voltage-gated sodium channel NaV1.7. On both targets, we discover hits, including seven novel hits (14% hit rate) to KLHDC2 and four novel hits (44% hit rate) to NaV1.7 with single digit micromolar binding affinities. Screening in both cases was completed in less than seven days. Finally, a high resolution X-ray crystallographic structure validates the predicted docking pose for the KLHDC2 ligand complex, demonstrating the effectiveness of our method in lead discovery.

biochemistry↗

bioRxiv2024

Low intensity repetitive transcranial magnetic stimulation enhances remyelination by newborn and surviving oligodendrocytes in the cuprizone model of toxic demyelination

In people with multiple sclerosis (MS), newborn and surviving oligodendrocytes (OLs) can contribute to remyelination, however, current therapies are unable to enhance or sustain endogenous repair. Low intensity repetitive transcranial magnetic stimulation (LI-rTMS), delivered as an intermittent theta burst stimulation (iTBS), increases the survival and maturation of newborn OLs in the healthy adult mouse cortex, but it is unclear whether LI-rTMS can promote remyelination. To examine this possibility, we fluorescently labelled oligodendrocyte progenitor cells (OPCs; Pdgfr-CreER transgenic mice) or mature OLs (Plp-CreER transgenic mice) in the adult mouse brain and traced the fate of each cell population over time. Multiple consecutive daily sessions of iTBS (600 pulses; 120 mT), delivered during cuprizone (CPZ) feeding, did not alter new or pre- existing OL survival but increased the number of myelin internodes elaborated by new OLs in the primary motor cortex (M1). This resulted in each new M1 OL producing [~]471{micro}m more myelin. When LI-rTMS was delivered after CPZ withdrawal (during remyelination), it significantly increased the length of the internodes elaborated by new M1 and callosal OLs and increased the number of surviving OLs that contributed to remyelination in the corpus callosum (CC). As LI-rTMS can non-invasively promote remyelination by modifying the behaviour of new and surviving OLs, it may be suitable as an adjunct intervention to enhance remyelination in people with MS.

neuroscience↗

bioRxiv2023

KRAS inhibition activates an actionable CD24 do-not-eat-me signal in pancreas cancer

KRASG12C inhibitors (G12Ci) have produced encouraging, albeit modest and transient, clinical benefit in pancreatic ductal adenocarcinoma (PDAC). Identifying and targeting resistance mechanisms to G12Ci treatment is therefore crucial. To better understand the function of KRASG12C and possible G12Ci bypass mechanisms, we developed an autochthonous KRASG12C- driven PDAC model. Compared to the classical KRASG12D PDAC model, the G12C model exhibits slower tumor growth, yet similar histopathological and molecular features. Aligned with clinical experience, G12Ci treatment of KRASG12C tumors produced modest impact despite stimulating a hot tumor immune microenvironment. Immunoprofiling revealed that CD24, a dont eat me signal, is significantly upregulated on cancer cells upon G12Ci treatment. Blocking CD24 enhanced macrophage phagocytosis of cancer cells and significantly sensitized tumors to G12Ci treatment. Similar findings were observed in KRASG12D-driven PDAC. Together, this study reveals common and distinct oncogenic KRAS allele-specific biology and identifies a clinically actionable adaptive mechanism that may improve the efficacy of oncogenic KRAS inhibitor therapy in PDAC. SignificanceGeneration of an autochthonous KRASG12C-driven pancreatic cancer model enabled elucidation of specific effects of KRASG12C during tumor development, revealing CD24 as an actionable adaptive mechanism in cancer cells induced upon KRASG12C inhibition.

cancer biology↗

bioRxiv2023

Electron transport inhibition increases cellular dependence on purine transport and salvage

Cancer cells reprogram their metabolism to support cell growth and proliferation in harsh environments. While many studies have documented the importance of mitochondrial oxidative phosphorylation (OXPHOS) in tumor growth, some cancer cells experience conditions of reduced OXPHOS in vivo and induce alternative metabolic pathways to compensate. To assess how human cells respond to mitochondrial dysfunction, we performed metabolomics in fibroblasts and plasma from patients with inborn errors of mitochondrial metabolism, and in cancer cells subjected to inhibition of the electron transport chain (ETC). All these analyses revealed extensive perturbations in purine-related metabolites; in non-small cell lung cancer (NSCLC) cells, ETC blockade led to purine metabolite accumulation arising from a reduced cytosolic NAD+/NADH ratio (NADH reductive stress). Stable isotope tracing demonstrated that ETC deficiency suppressed de novo purine nucleotide synthesis while enhancing purine salvage. Analysis of NSCLC patients infused with [U-13C]glucose revealed that tumors with markers of low oxidative mitochondrial metabolism exhibited high expression of the purine salvage enzyme HPRT1 and abundant levels of the HPRT1 product inosine monophosphate (IMP). ETC blockade also induced production of ribose-5 phosphate (R5P) by the pentose phosphate pathway (PPP) and import of purine nucleobases. Blocking either HPRT1 or nucleoside transporters sensitized cancer cells to ETC inhibition, and overexpressing nucleoside transporters was sufficient to drive growth of NSCLC xenografts. Collectively, this study mechanistically delineates how cells compensate for suppressed purine metabolism in response to ETC blockade, and uncovers a new metabolic vulnerability in tumors experiencing NADH excess.

biochemistry↗