Biology subjects

Hu, A.

Publications and source records attributed to Hu, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Whole Blood Deep Immunophenotyping and Platelet-Leukocyte Aggregate Quantification by Spectral Flow Cytometry

Platelet-leukocyte aggregates (PLAs) are a proposed interface between coagulation and immune regulation, but their distribution across leukocyte subsets beyond monocytes and neutrophils, and their behavior in acute disorders of immune regulation, such as sepsis and severe trauma, remain largely undefined. The study of thromboimmune mechanisms in these acute conditions has relied heavily on murine sepsis models, whose species differences in platelet and leukocyte biology limit translation to human disease. Direct measurement in human whole blood is needed yet reported PLA frequencies vary widely because quantification is highly sensitive to sample handling. Here we present a robust, minimally manipulative 27-color spectral flow cytometry protocol that allows simultaneous deep immunophenotyping and classification of PLAs across >40 leukocyte subpopulations. In healthy donors, PLA frequency ranged from 1.7% on memory CD4 T cells to over 50% on monocyte subsets, with monocytes contributing 25% of all PLAs. We also found novel platelet-binding leukocyte populations, including Th9 and Th22 CD4+ T cells. Optimization identified anticoagulant choice, centrifugation conditions, dilution, and sample processing time as key determinants of reproducible measurement; PLA quantification was validated by imaging flow cytometry. In a small validation cohort of sepsis and trauma patients, the assay recapitulated established immunophenotypic features of critical illness, including neutrophilia and myeloid-derived suppressor cells (MDSC) expansion, and quantified PLAs within each subset. This protocol provides a reference framework for studying thromboinflammation and other dysregulated immune response diseases directly in human blood, and a foundation for further studies, defining the mechanisms and clinical relevance of platelet-leukocyte interactions in disease.

immunology↗

bioRxiv2026

Toward a global chemogeography of dissolved organic matter: a molecular trait dataset across Earth systems

Dissolved organic matter (DOM) is a central component of biogeochemical cycling, but molecular observations generated by ultrahigh-resolution mass spectrometry remain fragmented across studies, limiting quantitative comparisons among ecosystems. Here, we compile and harmonize a global dataset of DOM molecular traits comprising 3,999 samples from 337 studies published between 2005 and 2026. The dataset includes eight intensity-weighted molecular traits: hydrogen-to-carbon (H/C), oxygen-to-carbon (O/C), nitrogen-to-carbon (N/C), and sulfur-to-carbon (S/C) ratios; molecular mass; double-bond equivalents (DBE); modified aromaticity index (AImod); and nominal oxidation state of carbon (NOSC). Samples span aquatic, terrestrial, atmospheric, plant-associated, petroleum-related, and other environments, and are linked, where available, to geographic, physicochemical, nutrient, and climatic metadata. Molecular data were harmonized using common definitions and restricted to negative-mode electrospray-ionization FT-ICR MS to improve cross-study comparability. This resource enables cross-system comparisons of DOM molecular traits and supports analyses of environmental gradients, geographic coverage, and global DOM chemogeography.

ecology↗

bioRxiv2026

Tumor-tropic E. coli engineered as living T and NK cell engagers

Despite advances in immunotherapy, most solid tumors remain resistant to treatment. Immune cell engagers redirect cytotoxic lymphocytes against cancer, but limited tumor access, immunosuppressive microenvironments and systemic immune activation limit efficacy. Here we develop live immune modulating engagers (LIME), a modular platform where non-pathogenic, tumor-tropic Escherichia coli display tandem single-chain variable fragments targeting a tumor-associated antigen and an activating receptor on T or natural killer cells. LIME bridged effector and tumor cells, induced transcriptional programs of T cell activation, metabolism and proliferation, and enhanced cytotoxicity across cancer cell lines and patient-derived organoids. In mouse models, LIME safely accumulated in tumors, outperformed tarlatamab in small cell lung cancer, and induced durable immunity in lymphoma. RAS inhibition and PD-L1 blockade enhanced LIME activity in pancreatic cancer and induced humoral responses. Multi-lineage immune modulation remained tumor-confined, without organ toxicity. These findings establish LIME as a versatile living therapeutic platform for programmable, tumor-restricted immune orchestration.

bioengineering↗

bioRxiv2026

CovSite: A High-Throughput Blind Covalent Screening Framework for Reactive Site Detection

Targeted covalent inhibitors are a powerful, yet underexplored, class of therapeutics, and current computational covalent screeners are constrained in early drug discovery due to the need for prior knowledge of the target site and limited throughput. We present CovSite, a blind covalent screening tool that identifies candidate reactive residues across the entire protein surface, utilizing only the protein structure and electrophile SMILES. CovSite applies a pipeline of four orthogonal physicochemical filters (nucleophile identification, solvent accessibility, environment-dependent deprotonation prediction, and semi-quantum-mechanical reactivity ranking) to identify potential small-molecule candidate inhibitors. Validated against 2,062 diverse covalent protein-ligand complexes spanning six nucleophilic residue types, CovSite achieves a 98.5% blind target site hit on a held-out benchmark set of 207 cysteine-targeted complexes while reducing the search space by 97.8%. The target-site hit detection exceeds the 53-62% accuracy of popular covalent screening tools operating under non-blind conditions on the same benchmark set. By extending nucleophilic coverage beyond cysteine to include serine, threonine, lysine, histidine, and tyrosine, and completing a screening of a 200-residue protein in two to three minutes on standard hardware, CovSite serves as a platform technology with the potential to address critical gaps in throughput, generalizability, and accuracy in this field of covalent screening. We demonstrate this capability by using CovSite as a blind, ligand-specific approach that enables iterative, machine-learning-driven covalent inhibitor generation that is impractical with existing tools, establishing a foundation for computationally guided covalent drug discovery for novel and understudied targets. TOC Figure O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/739288v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@139335forg.highwire.dtl.DTLVardef@5bd9feorg.highwire.dtl.DTLVardef@44d6c8org.highwire.dtl.DTLVardef@1710154_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2026

Chorismate and isochorismate turnover reveal hidden dynamics of aromatic metabolism in Arabidopsis

The shikimate pathway provides precursors for phenolic metabolites in plant primary and secondary metabolism. Carbon flux measurements in intact Arabidopsis leaves using a novel isotopologue MS/MS methodology revealed unexpected dynamics between chorismate and isochorismate pools. 13CO2 labeling kinetics point to chloroplast-derived shikimate as a major bifurcation point, with approximately one third diverted away from the chloroplast. In contrast, the small pool of chorismate was almost exclusively chloroplast-localized and turned over rapidly, reaching more than 70% labeling within minutes. Isochorismate, a precursor to salicylic acid (SA) in the Brassicales, was present at 50-fold molar excess over chorismate but labeled much more slowly and appeared primarily extra-chloroplastic. Total isochorismate declined by 90% in the Arabidopsis enhanced disease susceptibility mutant, which lacks the isochorismate exporter. Non-aqueous fractionation further supported a primarily chloroplast-localized chorismate pool but extra-plastidic isochorismate. Populus trichocarpa and Nicotiana benthamiana leaves contained chorismate but only trace isochorismate, consistent with their use of the benzoyl-CoA route to SA. Carbon commitment calculations indicated that one third of the total chorismate pool in Arabidopsis leaves is diverted to isochorismate. Global leaf calculations based on elemental analysis-isotope ratio mass spectrometry and targeted isotope recovery indicate that only 0.03% of total assimilated carbon (5.27 pmol{middle dot}mg-1 D.W.{middle dot}min-1) enters the shikimate pathway in photosynthetically active mesophyll. For comparison [~]0.05% (7.75 pmol{middle dot}mg-1 D.W.{middle dot}min-1) enters the 2-C-methyl-D-erythritol 4-phosphate pathway, which provides precursors for photosynthetic pigments and electron carriers. The compartmentalization and turnover dynamics of shikimate, chorismate, and isochorismate suggest continuous demand for aromatic precursors in mesophyll tissue is comparable to demand for MEP-pathway derived pigments.

plant biology↗

bioRxiv2026

Reconstituting Mouse Embryogenesis Ex Utero from Gastrulation to Fetal Development Reveals Maternally Independent Metabolic Programs

Mammalian development takes place inside the maternal uterus, creating technological constraints that make difficult the study of embryogenesis in live developing embryos. A central challenge for understanding the role of metabolism in mammalian development is discriminating placental and uterine-regulated signals from embryo-intrinsic processes independent of maternal influence, a process that until now has remained inseparable during gastrulation and organogenesis1-3. Ex utero culture systems allowing continuous growth of embryos during pre-gastrulation to organogenesis4,5 offer a promising solution to this challenge. Here, we present optimized ex utero culture platforms that support faithful development of mouse embryos from gastrulation (embryonic day 6.5/7.5) through the fetal period (embryonic day [~]12.5) and harnessed these platforms for dissecting metabolic transitions in vivo during embryogenesis independently of uterus and placenta. We characterized the metabolome of in utero and ex utero whole embryos, fetal organs and culture medium between embryonic days E6.5 and E12.5 by liquid chromatography mass-spectrometry (LC-MS) metabolomics, isotope tracing, and single cell transcriptomics. These datasets present a comprehensive overview of the dynamic embryonic metabolism during gastrulation and organogenesis in utero and ex utero. This analysis revealed that the midgestational metabolic switch occurring at E10.5-E11.5 is faithfully recapitulated ex utero, indicating that this transition is intrinsically programmed in embryonic tissues and does not require direct maternal or placental cues. Notably, oxygen availability modulated the extent of this transition, but elevated oxygen was insufficient to induce it prematurely, demonstrating that the switch is developmentally timed and only partially environmental-responsive. We further harnessed the ex utero platform for identifying and perturbing a mitochondrial redox shift at E7.5-E8.5 that is critical for developmental progress after gastrulation. These findings uncover the remarkable metabolic plasticity of the mammalian embryo, demonstrating its capacity to sustain growth independently of maternal inputs from the establishment of the body plan through the onset of the fetal period. Moreover, they highlight the use of long-term ex utero culture as a unique framework for dissecting the mechanisms that shape embryogenesis under physiological and experimentally perturbed conditions, while functionally uncoupling embryonic programs from maternal and placental influences.

developmental biology↗

bioRxiv2025

Modeling neurodegenerative diseases in Drosophila is conditioned by stress resistance and gut microbiome composition of the reference line

Drosophila is widely used to study the pathological mechanisms of human diseases in vivo, including metabolic and neurological disorders. In these models, disease-induced alterations in locomotion and stress resistance are generally monitored in comparison to healthy control flies, such the white-eyed strain w1118, used as a reference for normal physiology and behavior. Here we compared two independent w1118 lines and found that they differed strikingly in their susceptibility to oxidative stress and nutrient starvation, and less markedly in their locomotor performance. Interestingly, modulating the gut microbiome by rearing these flies under axenic conditions increased oxidative stress resistance of the more susceptible, but not the more resistant line, while it had no effect on starvation resistance for both lines. We also found that the stress-sensitive line had higher levels of Clostridiales bacteria and of the intracellular endosymbiont Wolbachia in the gut microbiota, as well as lower expression levels of immune effectors (antimicrobial peptides and lysozymes) in the head and gut. Both lines nevertheless showed similar susceptibility to pathogenic bacterial infections. In a transgenic Parkinsons disease model, the stress-resistant background strongly attenuated the progressive locomotor defects induced by pan-neuronal expression of human mutant -synuclein, but intriguingly not when -synuclein expression was restricted to a subset of brain dopaminergic neurons in the protocerebral anterior medial (PAM) cluster. These results suggest that taking into account unapparent features of the reference lines could improve the reproducibility and consistency of neurodegenerative disease models in Drosophila.

neuroscience↗

bioRxiv2025

Imaging cellular activity simultaneously across all organs of a vertebrate reveals body-wide circuits

All cells in an animal collectively ensure, moment-to-moment, the survival of the whole organism in the face of environmental stressors1,2. Physiology seeks to elucidate the intricate network of interactions that sustain life, which often span multiple organs, cell types, and timescales, but a major challenge lies in the inability to simultaneously record time-varying cellular activity throughout the entire body. We developed WHOLISTIC (WHole Organism Live Imaging System for recording Tissue and IntraCellular activity), a method to image second-timescale, time-varying intracellular dynamics across cell-types of the vertebrate body. By advancing and integrating volumetric fluorescence microscopy, machine learning, and pancellular transgenic expression of calcium sensors in transparent young Danio rerio (zebrafish) and with proof of concept in adult Danionella, the method enables real-time recording of cellular dynamics across the organism. Calcium is a universal intracellular messenger, with a large array of cellular processes depending on changes in calcium concentration across varying time-scales, making it an ideal proxy of cellular activity3. Using this platform to screen the dynamics of most cells in the body, we discovered unexpected responses of specific cell types to stimuli, such as chondrocyte reactions to cold, meningeal responses to ketamine, and state-dependent activity, such as oscillatory ependymal-cell activity during periods of extended motor quiescence. At the organ scale, the method uncovered pulsating traveling waves along the kidney nephron. At the multi-organ scale, we uncovered muscle synergies and independencies, as well as muscle-organ interactions. Integration with optogenetics allowed us to all-optically determine the causal direction of brain-body interactions. At the whole-organism scale, the method captured the rapid brainstem-controlled redistribution of blood flow across the body. Finally, we advanced Whole-Body Expansion Microscopy4 to provide ground-truth molecular and ultrastructural anatomical context, explaining the spatiotemporal structure of activity captured by WHOLISTIC. Together, these innovations establish a new paradigm for systems biology, bridging cellular and organismal physiology, with broad implications for both fundamental research and drug discovery.

neuroscience↗

bioRxiv2025

Mutation or deletion of the Avr6 avirulence effector gene of Fulvia fulva leads to breakdown of the Cf-6 leaf mold resistance locus in tomato

Genetic resistance mediated by Cf cell-surface receptors is a cornerstone of tomato breeding against leaf mold disease caused by the fungal pathogen Fulvia fulva. After widespread deployment of the Cf-9 resistance locus, breeders increasingly relied on Cf-6, yet Cf-6-mediated resistance has already been overcome in multiple regions. The molecular basis of this breakdown, and the identity of the matching avirulence (Avr) effector, have remained unresolved. Here, we use comparative genomics and functional genetics to identify the F. fulva effector Avr6 as the previously described apoplastic protein Ecp5. Sequencing of Cf-6-breaking strains revealed either deletion of the Ecp5 locus or non-synonymous mutations in its coding sequence. Using transient expression, targeted gene knockout, and complementation assays, we show that Ecp5 is both necessary and sufficient for Cf-6-mediated recognition and defence activation. We then use Avr6-triggered cell death as a phenotypic marker in a bulked segregant analysis combined with Comparative Subsequence Sets analysis (CoSSa) to map Cf-6 to a [~]2 Mb interval on the short arm of chromosome 12 that overlaps the previously described Cf-Ecp5.12 locus. Sequencing of Avr6 in a broad strain collection reveals a predominantly conserved allele under apparent purifying selection, with recent independent loss-of-function variants in Europe and South America that confer virulence on Cf-6 plants. Together, these findings establish the Avr6-Cf-6 gene-for-gene pair, explain the erosion of Cf-6-mediated resistance, and illustrate how effector loss or mutation provides a rapid route for F. fulva adaptation, with important implications for designing more durable resistance strategies against tomato leaf mold.

microbiology↗

bioRxiv2025

TEMI: Tissue Expansion Mass Spectrometry Imaging

The spatial distribution of diverse biomolecules in multicellular organisms is essential for their physiological functions. High-throughput in situ mapping of biomolecules is crucial for both basic and medical research, and requires high scanning speed, spatial resolution, and chemical sensitivity. Here, we developed a Tissue Expansion method compatible with matrix-assisted laser desorption/ionization Mass spectrometry Imaging (TEMI). TEMI reaches single-cell spatial resolution without sacrificing voxel throughput and enables the profiling of hundreds of biomolecules, including lipids, metabolites, peptides (proteins), and N-glycans. Using TEMI, we mapped the spatial distribution of biomolecules across various mammalian tissues and uncovered metabolic heterogeneity in tumors. TEMI can be easily adapted and broadly applied in biological and medical research, to advance spatial multi-omics profiling.

molecular biology↗

bioRxiv2024

Companion to: A molecular basis for milk allergen immune recognition in eosinophilic esophagitis

BackgroundEosinophilic esophagitis (EoE) is a chronic, type 2 inflammatory disease that is increasing in incidence and has substantial morbidity. Despite being clinically defined as a food allergy, the molecular details of food antigen presentation and recognition by the immune system are unknown. ObjectiveThe objective of this study was to identify and characterize the molecular basis of milk antigen presentation and T cell recognition in a patient with EoE milk allergy. MethodsMilk-expanded TCR clonotypes were identified using ex vivo stimulation followed by single cell RNA with linked, paired TRA and TRB sequencing. HLA restriction and antigen specificity of TCRs were identified using a combination of lentiviral expression, HLA sequencing, antibody blockade, and a peptide library screen. ResultsWe isolated a {beta}-casein specific TCR clonotype (eoeTCR-4) and determined its HLA restriction (HLA-DRB1*07:01) and cognate antigen ({beta}-casein AA 59-78). EoeTCR-4 was not detected among a larger group of subjects and is likely private to EoE Subject 1. ConclusionIn conjunction with the parent manuscript, this companion article provides the first molecular identity of food antigen presentation and immune recognition in EoE. SUMMARYThis manuscript is a companion to the parent manuscript "A molecular basis for milk allergen immune recognition in eosinophilic esophagitis". It provides additional data and detailed methods not provided in the parent manuscript. It is designed to supplement and support the findings and conclusions of the parent manuscript.

immunology↗

bioRxiv2024

Microbial strategies of environmental adaptation revealed by trait-environmental relationships

Microbial trait variation along environment gradients is crucial to understanding their ecological adaptation mechanisms. With the increasing availability of microbial genomes, making full use of the genome-based traits to decipher their adaptation strategies becomes promising and urgent. Here, we examined microbial communities in water and sediments of 20 East African lakes with pH values ranging from 7.2 to 10.1 through taxonomic-profiling and genome-centric metagenomics. We identified functional traits important for microbial adaptation to the stresses of alkalinity and salinity based on the significant trait-environment relationships (TERs), including those involved in cytoplasmic pH homeostasis, compatible solute accumulation, cell envelope modification and energy requisition. By integrating these significant-TER traits, we further developed an environmental adaptation index to quantify the species-level adaptive capacity for environmental stresses, such as high pH environments. The adaptation index of pH showed consistently significant positive relationships with species pH optima across regional and global genomic datasets from freshwater, marine and soda lake ecosystems. The generality of the index for quantifying environmental adaptation was demonstrated by showing significant relationships with the species niche optima for the gradients of soil temperature and seawater salinity. These results highlight the importance of trait-environment relationships in facilitating the inference of microbial genomic-based adaptation mechanisms, and expand our understanding of ecological adaptative strategies along environmental gradients.

ecology↗

bioRxiv2024

Molecular activity mediates the composition and assembly of dissolved organic matter in lake sediments

Lake sediments are hotspots for carbon transformation and burial, where dissolved organic matter (DOM) interacts with microorganisms to regulate global carbon cycling. The potential for individual DOM molecules to undergo biochemical transformations, i.e., their activity, is a critical molecular trait affecting DOM turnover in environment. However, the composition of sediment DOM and how its assembly mechanisms are related to molecular activity remains poorly understood. Here, 63 freshwater sediments were collected from tropical to cold temperate climatic zones in China. We explored the molecular composition and assembly of sediment DOM and the underlying mechanisms driven by climate, physicochemical factors, and microbes along the molecular activity gradient. Sediment DOM was dominated by lipid- (34.8%) and lignin-like compounds (33.01%), and the latter were enriched as molecular activity of DOM increased. Besides, DOM composed of more active molecules had greater compositional similarity across different climatic zones, and was inclined to assemble deterministically. This was supported by the fact that as potential transformations of molecular assemblages increased from 0.4 to 14, the assembly of these molecules was structured by a shift from stochastic to deterministic processes, with the latter accounting for [≥] 75% thereafter. Overall, the molecular assemblage was primarily structured by physicochemical factors, including sediment total organic carbon and electrical conductivity. As molecular activity increased, however, assemblage was increasingly affected by climate and bacterial communities, consistent with the enhanced complexity of bacterial-molecular networks. Collectively, our study highlights that the intrinsic activity of DOM molecules determines their fate through distinct biotic and abiotic mechanisms.

biochemistry↗

bioRxiv2024

Photochemical processes drive thermal responses of dissolved organic matter in the dark ocean

How dissolved organic matter (DOM) responds to climate warming is critical for understanding its role in future ocean carbon cycling. Here, we use a highly resolved dataset of over 800 DOM samples covering the surface waters to the deep Atlantic, Southern, and Pacific oceans to examine the changes in DOM molecular composition in response to warming water temperatures, referred to as DOM thermal responses. Towards the deep waters, the strength (i.e., overall magnitude) and diversity (i.e., variation among molecules) of these thermal responses both decline. However, these responses show opposite trends with the concentration of more recalcitrant molecules, decreasing and increasing, respectively. These contrasting trends concur with the observation that, compared to the strength of thermal responses, their diversity is more strongly explained by photochemical processes of DOM. By projecting global ocean thermal responses from 1950 to 2020 using environmental temperature, salinity and radiation, we predict that increases in the diversity of thermal responses are unexpectedly largest at deeper depths (> 1,000 m). Such increases could elevate the recalcitrant deep-ocean carbon sink by approximately 10 Tg C yr-1, which accounts for > 5% of the carbon flux reaching and persisting in the deep ocean. Our findings highlight the role of photochemical processes in imprinting DOM thermal responses, offering new insights into the future capacity of the oceanic carbon sink under global climate change.

ecology↗

bioRxiv2024

Deep-Tissue Spatial Omics: Imaging Whole-Embryo Transcriptomics and Subcellular Structures at High Spatial Resolution

The inherent limitations of fluorescence microscopy, notably the restricted number of color channels, have long constrained comprehensive spatial analysis in biological specimens. Here, we introduce cycleHCR technology that leverages multicycle DNA barcoding and Hybridization Chain Reaction (HCR) to surpass the conventional color barrier. cycleHCR facilitates high-specificity, single-shot imaging per target for RNA and protein species within thick specimens, mitigating the molecular crowding issues encountered with other imaging-based spatial omics techniques. We demonstrate whole-mount transcriptomics imaging of 254 genes within an E6.5[~]7.0 mouse embryo, achieving precise three-dimensional gene expression and cell fate mapping across a specimen depth of [~] 310 {micro}m. Utilizing expansion microscopy alongside protein cycleHCR, we unveil the complex network of 10 subcellular structures in primary mouse embryonic fibroblasts. Furthermore, in mouse hippocampal slice, we image 8 protein targets and profile the transcriptome of 120 genes, uncovering complex gene expression gradients and cell-type specific nuclear structural variances. cycleHCR provides a unifying framework for multiplex RNA and protein imaging, offering a quantitative solution for elucidating spatial regulations in deep tissue contexts for research and potentially diagnostic applications.

developmental biology↗

bioRxiv2024

Axo-axonic synaptic input drives homeostatic plasticity by tuning the axon initial segment structurally and functionally

The stability of functional brain network is maintained by homeostatic plasticity, which restores equilibrium following perturbation. As the initiation site of action potentials, the axon initial segment (AIS) of glutamatergic projection neurons (PyNs) undergoes dynamic adjustment that exerts powerful control over neuronal firing properties in response to changes in network states. Although AIS plasticity has been reported to be coupled with the changes of network activity, it is poorly understood whether it involves direct synaptic input to the AIS. Here we show that changes of GABAergic synaptic input to the AIS of cortical PyNs, specifically from chandelier cells (ChCs), are sufficient to drive homeostatic tuning of the AIS within 1-2 weeks, while those from parvalbumin-positive basket cells do not. This tuning is reflected in the morphology of the AIS, the expression level of voltage-gated sodium channels, and the intrinsic neuronal excitability of PyNs. Interestingly, the timing of AIS tuning in PyNs of the prefrontal cortex corresponds to the recovery of changes in social behavior caused by alterations of ChC synaptic transmission. Thus, homeostatic plasticity of the AIS at postsynaptic PyNs may counteract deficits elicited by imbalanced ChC presynaptic input. TeaserAxon initial segment dynamically responds to changes in local input from chandelier cells to prevent abnormal neuronal functions.

neuroscience↗

bioRxiv2024

Visualizing the Spatio-Temporal Dynamics of Clonal Evolution with LinG3D software

Cancer clonal evolution, especially following anti-cancer treatments, depends on the locations of the mutated cells within the tumor tissue. Cells near the vessels, exposed to higher concentrations of drugs, will undergo a different evolutionary path than cells residing far from the vasculature in the areas of lower drug levels. However, classical representations of cell lineage trees do not account for this spatial component of emerging cancer clones. Here, we propose the LinG3D (Lineage Graphs in 3D) algorithms to trace clonal evolution in space and time. These are an open-source collection of routines (in MATLAB, Python, and R) that enables spatio-temporal visualization of clonal evolution in a two-dimensional tumor slice from computer simulations of the tumor evolution models. These routines draw traces of tumor clones in both time and space, with an option to include a projection of a selected microenvironmental factor, such as the drug or oxygen distribution within the tumor. The utility of LinG3D has been demonstrated through examples of simulated tumors with different number of clones and, additionally, in experimental colony growth assay. This routine package extends the classical lineage trees, that show cellular clone relationships in time, by adding the space component to show the locations of cellular clones within the 2D tumor tissue patch from computer simulations of tumor evolution models.

systems biology↗

bioRxiv2023

Atenolol reduces cardiac-mediated mortality in a genetic mouse model of sudden unexpected death in epilepsy

Sudden Unexpected Death in Epilepsy (SUDEP) is the leading cause of premature mortality in epilepsy. Genetic cardiac risk factors, including loss-of-function KCNH2 variants, have been linked to SUDEP. We hypothesised that seizures and LQTS interact to increase SUDEP risk. To investigate this, we crossed Kcnh2+/- and Gabrg2R43Q/+ mice that model LQTS and genetic epilepsy, respectively. Electrocorticography and electrocardiogram confirmed that Kcnh2+/- mice had a LQTS phenotype, while Gabrg2R43Q/+ mice displayed spontaneous seizures. Double mutant mice (Gabrg2R43Q/+/Kcnh2+/-) had both seizure and LQTS phenotypes that were indistinguishable from the respective single mutant mice. Survival analysis revealed that Gabrg2R43Q/+/Kcnh2+/- mice experienced a disproportionate higher rate of seizure-related death. Long-term oral administration of atenolol, a cardiac-selective {beta}-blocker, significantly improved survival in the Gabrg2R43Q/+/Kcnh2+/- mice. An additional mouse model, Hcn1M294L/+/Kcnh2+/-, based on a HCN1 developmental epileptic encephalopathy variant, also experienced a disproportionately higher rate of premature death that was rescued by atenolol. Kcnh2+/- mice also spent more time in ventricular arrhythmia during proconvulsant-induced seizures. Overall, the data implicates cardiac and loss-of-function KCNH2 variants as an important risk factor, and the potential repurposing of {beta}- blockers as a prevention strategy, for SUDEP in a subset of epilepsy patients.

neuroscience↗