Biology subjects

Gordon, M.

Publications and source records attributed to Gordon, M..

17 recordsLinked to original sources

bioRxiv2026

SCN1A haploinsufficiency disrupts neural progenitor networks and accelerates neurogenesis in human Dravet syndrome forebrain assembloids

Dravet syndrome is a severe childhood neurological disorder caused mostly due to mutations in the sodium channel gene SCN1A. Although the disorder is widely attributed to dysfunction of inhibitory neurons, growing evidence suggests that disease mechanisms may begin much earlier during brain development. To investigate the developmental consequences of SCN1A haploinsufficiency, we generated patient-derived dorsal-ventral forebrain assembloids that model key features of human corticogenesis. We found that SCN1A was expressed in ventricular zone neural progenitors and that its reduced expression was associated with impaired growth, disrupted ventricular zone organization, and progressive depletion of progenitor populations. We further demonstrated reduced progenitor proliferation and self-renewal, accelerated cell-cycle exit, and premature neuronal differentiation, leading to increased production of excitatory neurons and enhanced network excitability. Single cell transcriptomic analyses revealed reduced cycling radial glial cells, accelerated progenitor maturation, and dysregulation of gap junction and calcium signaling pathways. Following these findings, we examined progenitor calcium activity and found that SCN1A haploinsufficiency disrupted coordinated functional network organization, resulting in reduced recurrent connectivity and fragmentation of functional cellular assemblies. These abnormalities occurred despite preserved intrinsic electrophysiological properties of individual progenitors, indicating a defect in population-level coordination rather than single cell electrophysiology. Together, our findings identify disrupted progenitor communication as an early developmental consequence of SCN1A haploinsufficiency and suggest that abnormalities within neural progenitor populations contribute to altered corticogenesis, excitatory neurogenesis, and circuit hyperexcitability in Dravet syndrome. This work expands current disease models beyond interneuron dysfunction and highlights the developing ventricular zone as a potential therapeutic target.

neuroscience↗

bioRxiv2026

Pan-Coronavirus Protease Engagement and Differentiated Pharmacology of Antiviral Candidate CMX990

COVID-19 highlighted the need for antivirals that can be rapidly deployed against both current and future coronavirus threats. CMX990 is a clinical stage coronavirus main protease (Mpro) inhibitor bearing a unique trifluoromethoxymethyl ketone warhead. Here, we broadly evaluate its pan-coronavirus target engagement, antiviral breadth, and pharmacologic differentiation. Across a reporter panel of 24 Mpro enzymes spanning alpha-, beta-, delta-, and gamma-coronaviruses, CMX990 retained robust potent activity, including against nirmatrelvir-resistant SARS-CoV-2 variants. In direct comparison, nirmatrelvir and ensitrelvir showed diminished potency against non-SARS-CoV-2 coronaviruses. Live-virus assays corroborated this breadth, with potent, selective activity against SARS-CoV-2, SARS-CoV-1, MERS-CoV, and additional human coronaviruses. Structural studies revealed a conserved covalent binding mode centered on the catalytic Cys of coronavirus Mpro. In serial-passage studies, resistance emerged only after approximately twice as many serial passages under CMX990 selection as under nirmatrelvir selection, without selecting for the canonical nirmatrelvir-resistance substitution E166V. Extracellular washout experiments revealed superior persistence of antiviral activity relative to nirmatrelvir, consistent with durable target engagement. In a murine SARS-CoV-2 infection model, once-daily CMX990 protected against weight loss and reduced lung viral titers to near baseline levels. Collectively, these findings identify CMX990 as a structurally and functionally validated pan-coronavirus protease inhibitor supporting its potential as a pandemic-ready antiviral candidate.

pharmacology and toxicology↗

bioRxiv2026

APOE4 disrupts the central dogma by arresting neuronal proteome dynamics

Apolipoprotein E4 (APOE4) is the strongest genetic risk factor for late-onset Alzheimers disease and promotes neuronal dysfunction through incompletely understood mechanisms. Here, we integrated transcriptomic, translatomic, and proteomic profiling of isogenic APOE3 and APOE4 human iPSC-derived neurons and found that APOE4 fundamentally impairs neuronal proteome renewal. Although transcriptional changes were modest, APOE4 disrupted ribosome occupancy, altered translational dynamics, and uncoupled protein abundance from transcript levels. Proteome-wide turnover measurements revealed a global extension of protein half-lives and widespread accumulation of long-lived proteins. Functional proteomic analyses demonstrated concurrent lysosomal and proteasomal impairments associated with reduced proteasome activity and increased association of APOE with neuronal proteasomes. Longitudinal proteomics further showed that protein accumulation emerges during neuronal maturation and precedes a senescence-like cellular stress state. Together, these findings identify impaired proteome renewal as a central mechanism underlying neuronal vulnerability to APOE4 and establish defective proteostasis as an early pathogenic event in Alzheimers disease.

neuroscience↗

bioRxiv2025

Functional diversification of the cephalopod proteome by RNA-editing

Coleoid cephalopods exhibit the highest levels of ADAR-mediated RNA editing of any known animal, yet the functional consequences of most recoding events remain largely unknown. We integrate proteomics with biochemical and cellular assays to characterize thousands of recoding events across the Doryteuthis pealeii proteome. Using quantitative and functional mass spectrometry, we show that RNA edit-driven recoding reshapes the cellular proteome to alter protein stability, subcellular localization, post-translational modifications, and enzymatic activity. --Recoding can regulate post-translational modifications through their creation or ablation, and this has direct effects on protein function and protein-protein interactions. Recoding of the E3 ligase MARCHF5 drives widespread changes in substrate ubiquitylation and perturbs mitochondrial homeostasis, illustrating how RNA editing can influence organelle function. These data provide the first proteome-scale view of how extensive RNA recoding diversifies protein function in coleoid cephalopods and offers a new framework for understanding how RNA-level plasticity shapes protein function and cellular physiology.

molecular biology↗

bioRxiv2025

KeySDL: Sparse Dictionary Learning for Keystone Microbe Identification

Identification of microbes with large impacts on their microbial communities, known as keystone microbes, is a topic of long-standing interest in microbiome research. However, many approaches to identify keystone microbes are limited by the inherent nonlinearity and state-dependence of microbial dynamics. Machine learning approaches have been applied to address these shortcomings but often require more data than is available for a given microbial system. We propose a keystone identification approach called KeySDL which reduces the amount of data required by incorporating assumptions about the type of microbial dynamics present in the experimental system. The data are modeled as originating from a Generalized Lotka-Volterra (GLV) model, an architecture commonly used to simulate microbial systems. The parameters of this model are then estimated using Sparse Dictionary Learning (SDL) Compared to existing methods, this approach allows accurate prediction of keystone microbes from small numbers of samples and provides an output interpretable as reconstructed system dynamics. We also propose a self-consistency score to help evaluate whether the assumption of GLV dynamics is reasonable for a given dataset, either through the application of KeySDL or other analysis tools validated using GLV simulation.

bioinformatics↗

bioRxiv2025

Coronavirus protein interaction mapping in bat and human cells identifies molecular and genetic switches for immune evasion and replication

Coronaviruses, including SARS-CoV-2, can cause severe disease in humans, whereas reservoir hosts like Rhinolophus bats remain asymptomatic. To investigate how host-specific protein-protein interactions (PPIs) influence infection, we generated comparative PPI maps for SARS-CoV-2 and its bat-origin relative RaTG13 using affinity purification-mass spectrometry (AP-MS) in human and Rhinolophus ferrumequinum (RFe) bat cells. This approach identified both conserved and virus- and host-specific interactions that regulate infection dynamics. Notably, SARS-CoV-2 required a non-synonymous mutation in nucleocapsid to replicate in bat cells expressing human ACE2 and TMPRSS2. Analysis of the viral protein Orf9b revealed differential interactions with mitochondrial proteins Tom70 and MTARC2. A single residue difference in Orf9b between SARS-CoV-2 and RaTG13 functions as a molecular switch, weakening Tom70 binding and immune evasion in human cells while enhancing interaction with the bat-specific restriction factor MTARC2. These findings demonstrate how a single-residue substitution can reshape virus-host interactions and contribute to immune evasion and host adaptation.

systems biology↗

bioRxiv2024

Enhanced RNA replication and pathogenesis in recent SARS-CoV-2 variants harboring the L260F mutation in NSP6

The COVID-19 pandemic has been driven by SARS-CoV-2 variants with enhanced transmission and immune escape. Apart from extensive evolution in the Spike protein, non-Spike mutations are accumulating across the entire viral genome and their functional impact is not well understood. To address the contribution of these mutations, we reconstructed genomes of recent Omicron variants with disabled Spike expression (replicons) to systematically compare their RNA replication capabilities independently from Spike. We also used a single reference replicon and complemented it with various Omicron variant Spike proteins to quantify viral entry capabilities in single-round infection assays. Viral entry and RNA replication were negatively correlated, suggesting that as variants evolve reduced entry functions under growing immune pressure on Spike, RNA replication increases as a compensatory mechanism. We identified multiple mutations across the viral genome that enhanced viral RNA replication. NSP6 emerged as a hotspot with a distinct L260F mutation independently arising in the BQ.1.1 and XBB.1.16 variants. Using mutant and revertant NSP6 viral clones, the L260F mutation was validated to enhance viral replication in cells and increase pathogenesis in mice. Notably, this mutation enhanced host lipid droplet consumption by NSP6 without impacting its known ER-zippering function or double-membrane vesicle morphology. Collectively, a systematic analysis of RNA replication of recent Omicron variants defined NSP6s key role in viral RNA replication that provides insight into evolutionary trajectories of recent variants with possible therapeutic implications. Author SummaryAs SARS-CoV-2 continues to spread and adapt in humans, viral variants with enhanced spread and immune evasion have emerged throughout the COVID-19 pandemic. While most of the mutations occur in the Spike protein and have been extensively studied, non-Spike mutations have been accumulating and are not as well understood. Here, we constructed Spike-defective genomes of recent Omicron variants and systematically compared their RNA replication capabilities independently from Spike. We also performed single-round infection assays with various Omicron variant Spike proteins to quantify viral entry capabilities. Interestingly, viral entry and RNA replication were negatively correlated, suggesting that as variants evolved reduced entry functions under growing immune pressure on Spike, RNA replication increased as a compensatory mechanism. We focused on a viral protein NSP6 that acquired mutations that significantly enhanced RNA replication. We validated that a frequently accessed L260F mutation in NSP6 enhanced viral infection in cells and increased pathogenesis in mice. While the mutation did not alter NSP6s role in maintaining a membranous network of viral replication factories, the mutation enhanced viral hijacking of the host lipid droplet machinery. Collectively, we highlight the important role of non-Spike mutations in the evolutionary trajectories of SARS-CoV-2 variants with possible monitoring and therapeutic implications.

microbiology↗

bioRxiv2024

Preclinical Proof of Concept for SNAPTM-TIL: a personalized, next-generation tumor-infiltrating lymphocyte therapy platform

Tumor-infiltrating lymphocyte (TIL) therapy, which involves extracting, expanding, and reinfusing immune cells to target cancer cells, has shown promise in melanoma treatment, but requires optimization for broader efficacy. The success of TIL therapy depends on the recognition of tumor-associated antigens, but neoantigen-reactive T-cells are often rare and exhausted in less immunogenic malignancies. Isolating T cells enriched in neoantigen reactivity prior to in vitro expansion and reinfusion may improve the response rates. To this end, our proprietary Specific Neo-Antigen Peptides (SNAP) technology platform improves the accuracy of neoantigen prediction and validation by combining advanced computational modeling and PepSeq, a high-throughput screen for the physical credentialing of putative neoantigens based on their affinity to bind patient-specific HLA class II proteins. This approach allows for the education and enrichment of TILs (SNAP-TILs) with personalized, predefined, highly immunogenic neoantigens prior to expansion. Using the SNAP platform, we consistently achieved, on average, an SNAP-TIL product comprising 96% CD3+ cells, with a mixture of 75% effector and 23% central memory cells. SNAP-TILs exhibited greater efficacy and selectivity in immune infiltration than TIL, which was expanded by the rapid expansion protocol alone using ex vivo models. SNAP-TIL was also reactive in highly and poorly immunogenic tumors, with 70% and 50% tumor growth inhibition in melanoma and pancreatic patient-derived xenograft models, respectively. This study demonstrates the novel benefit of our Personalized Neoantigen Pipeline approach, potentially providing a durable antitumor immune response for a larger proportion of cancer patients.

immunology↗

bioRxiv2024

Development of a Cloud-Based IoT System for Livestock Health Monitoring Using AWS and Python

The agriculture industry is currently facing significant challenges in effectively monitoring the health of livestock. Traditional methods of health monitoring are often labor-intensive, inefficient, and insufficiently responsive to the needs of modern farming. As the number of IoT devices in agriculture proliferates, issues of scalability and computational load have become prominent, necessitating efficient and scalable solutions. This research introduces a cloud-based architecture aimed at enhancing livestock health monitoring. This system is designed to track critical health indicators such as movement patterns, body temperature, and heart rate, utilizing AWS for robust data handling and Python for data processing and real-time analytics. The proposed system incorporates Narrow Band IoT (Nb IoT) technology, which is optimized for low-bandwidth, long-range communication, making it suitable for rural and remote farming locations. The architectures scalability allows for the effective management of varying numbers of IoT devices, which is essential for adapting to changing herd sizes and farm scales. Preliminary experiments conducted to assess the systems performance have demonstrated its durability and effectiveness, indicating a successful integration of AWS IoT Cloud services with the deployed IoT devices. Furthermore, the study explores the implementation of predictive analytics to facilitate proactive health management in livestock. By predicting potential health issues before they become apparent, the system can offer significant improvements in animal welfare and farm efficiency. The integration of cloud computing and IoT not only meets the growing technological needs of modern agriculture but also sets a new benchmark in the development of sustainable farming practices. The findings from this research could have broad implications for the future of livestock management, potentially leading to widespread adoption of technology-driven health monitoring systems in agriculture. This would help in optimizing the health management of livestock globally, thereby enhancing productivity and sustainability in the agricultural sector.

animal behavior and cognition↗

bioRxiv2023

Modulation of FGF pathway signaling and vascular differentiation using designed oligomeric assemblies

Growth factors and cytokines signal by binding to the extracellular domains of their receptors and drive association and transphosphorylation of the receptor intracellular tyrosine kinase domains, initiating downstream signaling cascades. To enable systematic exploration of how receptor valency and geometry affects signaling outcomes, we designed cyclic homo-oligomers with up to 8 subunits using repeat protein building blocks that can be modularly extended. By incorporating a de novo designed fibroblast growth-factor receptor (FGFR) binding module into these scaffolds, we generated a series of synthetic signaling ligands that exhibit potent valency- and geometry-dependent Ca2+ release and MAPK pathway activation. The high specificity of the designed agonists reveal distinct roles for two FGFR splice variants in driving endothelial and mesenchymal cell fates during early vascular development. The ability to incorporate receptor binding domains and repeat extensions in a modular fashion makes our designed scaffolds broadly useful for probing and manipulating cellular signaling pathways. HighlightsO_LIDe novo designed cyclic oligomers with tunable geometric properties C_LIO_LICyclic, homo-oligomeric FGFR binding modules induce geometry- and valency-dependent activity of isoform-specific FGF signaling C_LIO_LIModulation of FGFR isoform activity controls bifurcation of endothelial and mesenchymal fate during vascular development C_LIO_LIC-isoform activation favors arterial endothelial cell formation while B-isoform induces pericyte differentiation C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=135 SRC="FIGDIR/small/532666v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@151f6eforg.highwire.dtl.DTLVardef@2ae877org.highwire.dtl.DTLVardef@103e0d1org.highwire.dtl.DTLVardef@19cd695_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2022

Receptor-like kinases FER and SRK mediate Lotus japonicus freezing tolerance and climate adaptation

Many plant species have succeeded in colonizing a wide range of diverse climates through local adaptation, but the underlying molecular genetics remain obscure. We previously found that winter survival was a direct target of selection during colonization of Japan by the perennial legume Lotus japonicus and identified associated candidate genes. Here, we show that two of these, the FERONIA-receptor like kinase (LjFER) and a novel S-receptor-like kinase (LjSRK) are required for non-acclimated freezing tolerance and show haplotype-dependent cold-responsive expression. Our work demonstrates that recruiting a conserved growth regulator, FER, and a novel receptor-like kinase, SRK, into the set of cold-responsive genes has contributed to freezing tolerance and local climate adaptation in L. japonicus, offering new functional genetic insight into perennial herb evolution.

plant biology↗

bioRxiv2021

Positive Selection and Heat-Response Transcriptomes Reveal Adaptive Features of the Arabidopsis Desert Relative, Anastatica hierochuntica

O_LIPlant adaptation to a desert environment and its endemic heat stress is poorly understood at the molecular level. The naturally heat-tolerant Brassicaceae species Anastatica hierochuntica is an ideal extremophyte model to identify genetic adaptations that have evolved to allow plants to tolerate heat stress and thrive in deserts. C_LIO_LIWe generated an A. hierochuntica reference transcriptome and pinpointed extremophyte adaptations by comparing Arabidopsis thaliana and A. hierochuntica transcriptome responses to heat and identifying positively selected genes in A. hierochuntica. C_LIO_LIThe two species exhibit similar transcriptome adjustment in response to heat and the A. hierochuntica transcriptome does not exist in a constitutive heat "stress-ready" state. Furthermore, the A. hierochuntica global transcriptome as well as heat-responsive orthologs, display a lower basal and higher heat-induced expression than in A. thaliana. Genes positively selected in multiple extremophytes are associated with stomatal opening, nutrient acquisition, and UV-B induced DNA repair while those unique to A. hierochuntica are consistent with its photoperiod-insensitive, early-flowering phenotype. C_LIO_LIWe suggest that evolution of a flexible transcriptome confers the ability to quickly react to extreme diurnal temperature fluctuations characteristic of a desert environment while positive selection of genes involved in stress tolerance and early flowering could facilitate an opportunistic desert lifestyle. C_LI

plant biology↗

bioRxiv2020

A closed-loop optogenetic screen for neurons controlling feeding in Drosophila

Feeding is an essential part of animal life that is impacted greatly by the sense of taste. Although the characterization of taste-detection at the periphery is extensive, higher-order taste and feeding circuits are still being elucidated. Here, we use an automated closed-loop optogenetic activation screen for novel taste and feeding neurons in Drosophila melanogaster. Out of 122 Janelia FlyLight Project GAL4 lines preselected based on expression pattern, we identify six lines that acutely promote feeding and 35 lines that inhibit it. As proof of principle, we follow up on the R70C07-GAL4 neuron population, which strongly inhibits feeding. Using split-GAL4 lines to isolate subsets of the R70C07-GAL4 population, we find both appetitive and aversive neurons. We also show that R70C07-GAL4 labels a population of putative second-order taste interneurons that contact both sweet and bitter sensory neurons. These results serve as a resource for further functional dissection of fly feeding circuits.

neuroscience↗

bioRxiv2020

Lamin C regulates genome organization after mitosis

The dynamic 3D organization of the genome is central to the regulation of gene expression and developmental progression, with its disruption being implicated in various diseases. The nuclear lamina, a proteinaceous meshwork underlying the nuclear envelope (NE), provides both structural and regulatory influences on genome organization through the tethering of large inactive genomic regions, called Lamina Associated Domains (LADs), to the nuclear periphery. Evidence suggests that the A type lamins, lamins A and C, are the predominant lamins involved in the peripheral association of LADs, with these two isotypes forming distinct networks and potentially involved in different cellular processes. Here we tested whether lamins A and C have distinct roles in genome organization by examining chromosome architecture in cells in which lamin C or lamin A are specifically down-regulated. We find that lamin C (not lamin A) is required for the 3D organization of LADs and overall chromosome organization in the cell nucleus. Striking differences in the localization of lamin A and lamin C are present as cells exit mitosis that persist through early G1. Whereas lamin A associates with the nascent NE during telophase, lamin C remains in the interior surrounding nucleoplasmic LAD clusters. Lamin C association with the NE is delayed until several hours into G1 and correlates temporally and spatially with the post-mitotic NE association of LADs. Post-mitotic LAD association with the NE, and consequently global 3D genome organization, is perturbed only in cells depleted of lamin C, and not in cells depleted of lamin A. We conclude that lamin C regulates LAD dynamics after mitosis and is a key regulator of genome organization in mammalian cells. These findings reveal an unexpectedly central role for lamin C in genome organization, including both inter-chromosomal LAD-LAD segregation and LAD scaffolding at the NE.

cell biology↗

bioRxiv2019

Mapping the micro-proteome of the nuclear lamina and lamin associated domains

The nuclear lamina is a proteinaceous network of filaments that provide both structural and gene regulatory functions by tethering proteins and large domains of DNA, so-called lamin associated domains (LADs), to the periphery of the nucleus. LADs are a large fraction of the mammalian genome that are repressed, in part, by their association to the nuclear periphery. The genesis and maintenance of LADs is poorly understood as are the proteins that participate in these functions. In an effort to identify proteins that reside at the nuclear periphery and potentially interact with LADs, we have taken a two-pronged approach. First, we have undertaken an interactome analysis of the inner nuclear membrane bound LAP2{beta} to further characterize the nuclear lamina proteome. To accomplish this, we have leveraged the BioID system, which previously has been successfully used to characterize the nuclear lamina proteome. Second, we have established a system to identify proteins that bind to LADs by developing a chromatin directed BioID system. We combined the BioID system with the m6A-tracer system which binds to LADs in live cells to identify both LAD proximal and nuclear lamina proteins. In combining these datasets, we have further characterized the protein network at the nuclear lamina, identified putative LAD proximal proteins and found several proteins that appear to interface with both micro-proteomes. Importantly, several proteins essential for LAD function, including heterochromatin regulating proteins related to H3K9 methylation, were identified in this study.

genomics↗

bioRxiv2019

Development of a Comprehensive Antibody Staining Database using a Standardized Analytics Pipeline

Large-scale immune monitoring experiments (such as clinical trials) are a promising direction for biomarker discovery and responder stratification in immunotherapy. Mass cytometry is one of the tools in the immune monitoring arsenal. We propose a standardized workflow for the acquisition and analysis of large-scale mass cytometry experiments. The workflow includes two-tiered barcoding, a broad lyophilized panel, and the incorporation of a fully automated, cloud-based analysis platform. We applied the workflow to a large antibody staining screen using the LEGENDScreen kit, resulting in single-cell data for 350 antibodies over 71 profiling subsets. The screen recapitulates many known trends in the immune system and reveals potential markers for delineating MAIT cells. Additionally, we examine the effect of fixation on staining intensity and identify several markers where fixation leads to either gain or loss of signal. The standardized workflow can be seamlessly integrated into existing trials. Finally, the antibody staining data set is available as an online resource for researchers who are designing mass cytometry experiments in suspension and tissue.

immunology↗

bioRxiv2017

NeatSeq-Flow: A Lightweight Software for Efficient Execution of High Throughput Sequencing Workflows

Nowadays, it has become almost a necessity for many biologists to execute bioinformatics workflows (WFs) as part of their research. However, most WF-management software packages require for their operation at least some programming expertise. Here we describe NeatSeq-Flow, a platform that enables users with no programming knowledge to design and execute complex high throughput sequencing WFs. This is achieved by using a compendium of pre-built modules as well as a generic module, both do not require programming expertise. Nonetheless, NeatSeq-Flow retains the flexibility to generate sophisticated WF modules using templates and only basic Python programming abilities. NeatSeq-Flow is designed to enable easy sharing of WFs and modules by conceptually separating modules, WF design, sample information and execution. Moreover, NeatSeq-Flow works hand in hand with CONDA environments for easy installation of the WFs analysis programs in one go. NeatSeq-Flow enables efficient WF execution on computer clusters by parallelizing on both samples and WF steps. NeatSeq-Flow operates by shell-script generation; thus it allows full transparency of the WF process. NeatSeq-Flow offers real-time WF execution monitoring, detailed documentation and self-sustaining WF backups for reproducibility. All of these features make NeatSeq-Flow an easy-to-use WF platform while not compromising for flexibility, reproducibility, transparency and efficiency.\n\nAvailabilityhttp://neatseq-flow.readthedocs.io/en/latest/\n\nContactsklarz@bgu.ac.il

bioinformatics↗