Biology subjects

Lee, D.

Publications and source records attributed to Lee, D..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

A plant virus, TYLCV, up-regulates an endocrine oxylipin signal in its insect vector, Bemisia tabaci, via the viral C2 virulence factor for viral transmission

To survive and efficiently transit between plant and insect hosts, circulative plant viruses have evolved sophisticated strategies to exploit insect vector factors. Tomato yellow leaf curl virus (TYLCV) is transmitted by Bemisia tabaci through a circulative and replicative pathway. In insects, C20 oxylipin (eicosanoid) and C18 oxylipin (EpOME) antagonistically regulate antiviral responses. Upon TYLCV infection, the intestinal apoptosis of B. tabaci facilitated the viral multiplication. The apoptosis was suppressed by eicosanoid but induced by EpOME. EpOME treatment also upregulated other proviral factors, including defensin, PGRP, and cathepsins, while eicosanoid signaling exerted opposite effects. TYLCV infection suppressed eicosanoid biosynthetic enzymes but induced a cytochrome P450 gene involved in EpOME biosynthesis, consistent with elevated EpOME levels in the viruliferous B. tabaci detected by LC-MS/MS. Individual RNA interference treatments specific to each of the TYLCV genes in the viruliferous insects revealed that only silencing of the viral C2 gene abolished EpOME-mediated proviral effects. These findings uncover a lipid-mediated mechanism by which TYLCV enhances vector competence to promote transmission. IMPORTANCEVarious plant viruses depend on insect vectors for their horizontal transfer. Some of them exhibit a circulative and propagative transmission by multiplying the viral titers within the insects using the host machinery. Here is a fascinating manipulation of the host immunity by a plant virus, tomato yellow leaf curl virus (TYLCV), which uses the insect endocrine signals associated with immunity of its vector, Bemisia tabaci. Two types of oxylipins, eicosanoid and EpOME, antagonistically act to insect immunity, in which eicosanoid induces immune responses while EpOME, as an insect immune resolvin, suppresses them. TYLCV uses its C2 gene component as a virulent factor to induce the EpOME biosynthesis of B. tabaci. The elevated EpOME levels in the vector insect led to proviral responses by inducing intestinal apoptosis and selectively suppressing the immune-associated genes. These findings demonstrate the viral manipulation of the host endocrine signal for inducing proviral responses.

plant biology↗

bioRxiv2026

Generative single-cell transcriptomics via large language models

Single-cell and spatial transcriptomics have generated vast atlases of cellular states, yet these data are almost exclusively used for analysis rather than generation. Here we introduce the LLM-based model PGL, Portraying Gene Language, a framework that reframes single-cell transcriptomes as a language generation modeling problem. PGL represents each cell as a long sequence of gene-expression tokens and uses a large language model to synthesize complete single-cell RNA-seq profiles from metadata alone, such as tissue and disease context. PGL-generated cells recapitulate dataset-specific transcriptomic structure, align with known cancer subtype biology, and mix coherently with real single-cell datasets. Notably, generated cells can be used as effective references for spatial transcriptomics, enabling accurate cell-type mapping without matched single-cell atlases. By shifting single-cell modeling from representation learning to cell generation, PGL enables virtual cohort construction, hypothesis generation, and reference-on-demand analysis, positioning generative language models as foundational tools for in silico single-cell biology.

bioinformatics↗

bioRxiv2026

Ultrafast Frame-Free Imaging of Neural Activity with Event Cameras

Frame-based fluorescence imaging has long defined how neural activity is optically measured. This approach requires acquiring all pixels within an image, regardless of whether they carry meaningful neural dynamics, thereby intrinsically coupling spatial and temporal resolution while increasing data output. Here, we introduce an entirely different, frame-free approach that leverages the sparse nature of neural activity using event-based cameras, which asynchronously report fluorescence changes as spatiotemporal events. Compared with a frame-based camera, our method preserves signal fidelity while eliminating the fixed trade-off between spatial resolution, temporal resolution and data rate, thereby reducing data output by orders of magnitude. Applied to hippocampal preparations we demonstrate that the frame-free approach can resolve both single action potentials and fast network dynamics over large fields of view at kilohertz rates, enabling scalable, ultrafast optical recordings.

neuroscience↗

bioRxiv2025

A machine learning framework for predicting and modulating condition-dependent protein phase separation

Protein phase separation is a fundamental process in organizing membraneless organelles and is implicated in a wide range of pathological conditions. Importantly, rather than being a static feature of specific proteins, phase separation is a condition-dependent phenomenon governed by environmental parameters, including protein concentration, temperature, and solvent composition. However, most existing machine learning models infer phase-separation propensity solely from amino-acid sequences, failing to capture these context-dependent behaviors. Here, we present LLPSense, a machine learning framework that integrates pre-trained protein language model embeddings with environmental parameters to achieve accurate, condition-aware predictions of protein phase separation. We demonstrate LLPSenses predictive power and utility through three key experimental demonstrations. First, the model revealed that SGTA, previously unrecognized as a phase-separating protein, exhibits complex, temperature-dependent reentrant phase behavior. Second, LLPSense accurately predicted mutations in -synuclein that either enhance or suppress phase separation, enabling systematic mapping of residues potentially relevant to Parkinsons disease. Third, using model-guided mutagenesis, we inverted the phase behavior of UBQLN4, shifting it from high-temperature to low-temperature separation. Collectively, LLPSense provides a robust computational tool for interrogating the condition-dependent landscape of protein phase separation, enabling mechanistic studies of disease-associated phase separation and the rational design of programmable condensates.

bioinformatics↗

bioRxiv2025

APE1 Coordinates Its Disordered Region and Metal Cofactors to Drive Genome Surveillance

Efficient recognition of DNA lesions such as apurinic/apyrimidinic (AP) sites is essential for maintaining genome stability. Apurinic/apyrimidinic endonuclease 1 (APE1) is the primary eukaryotic AP endonuclease, yet how it identifies rare lesions among vast stretches of undamaged DNA remains incompletely understood. Using single-molecule imaging combined with molecular dynamics simulations, we reveal that APE1 employs a distinctive dual mechanism to search DNA. First, Mg{superscript 2} coordination at the active site neutralizes clustered negative charges, stabilizing electrostatic contacts during scanning. Second, its N-terminal intrinsically disordered region (IDR)--a feature conserved only in eukaryotic homologs but absent in prokaryotic ExoIII--not only forms DNA through transient IDR contacts but also engages continuous interactions via the unprecedented 177 arginine residue within the structured nuclease domain, thereby prolonging residence time and enabling long-range diffusion. Together, these two modules synergize to promote a sliding-based search strategy tailored to the complexity of eukaryotic genomes. Consistent with this model, IDR deletion restricts APE1 to 3D collisions, whereas IDR duplication enhances 1D scanning. Thus, APE1 exemplifies how structural disorder and metal-ion coordination integrate to enable long-range lesion recognition, highlighting an evolutionary innovation in eukaryotic DNA repair.

molecular biology↗

bioRxiv2025

The landscape of allele-specific expression in human kidneys

Allele-specific expression (ASE), the preferential expression of one gene copy, is a key mechanism of genomic regulation. However, its role in human kidney disease remains poorly understood. In this study, we generated a high-quality, genome-wide ASE map using paired whole-genome sequencing and RNA-seq from microdissected glomerular (GLOM) and tubulointerstitial (TUBE) compartments of patients with proteinuric kidney disease. We showed that the majority of common ASE events were deterministic and sequence-mediated. We also found that diseased kidneys exhibited significantly more ASE in GLOM than TUBE, compared to controls. Unexpectedly, higher ASE in GLOM than TUBE was significantly associated with improved kidney disease outcomes in the disease cohort. Differential gene expression analysis suggested this was the result of an active, protective transcriptional response, including ribosome and ATP synthesis upregulation, rather than pathogenic dysregulation. Our work reveals glomerular ASE as a marker of adaptive transcriptional activity in proteinuric kidney disease.

genomics↗

bioRxiv2025

Lemborexant Reduces Infarct Volume and Improves Long-Term Functional Recovery in a Murine Model of Ischemic Stroke

IntroductionRecovery following ischemic stroke is highly variable and often incomplete, underscoring the urgent need to develop novel targeted poststroke treatments. While the mechanisms underlying poststroke recovery remain incompletely understood, sleep fragmentation, a common consequence of stroke, has been linked to worse patient outcomes. Lemborexant is a dual orexin receptor antagonist that promotes sleep by suppressing wakefulness and enhancing sleep continuity. We hypothesized that lemborexant would reduce poststroke sleep disturbances and promote recovery in a rodent model of stroke. MethodsWe examined the effects of lemborexant (10 mg/kg and 30 mg/kg) and zolpidem (30 mg/kg) on sleep macrostructure, fragmentation, and EEG spectra in both healthy mice and in stroke model mice, which underwent photothrombotic ischemia of the forelimb somatosensory cortex. We also evaluated whether 12 days of drug administration altered infarct volume and functional recovery following the experimental induction of stroke in model mice. ResultsLemborexant treatment (30 mg/kg) increased the percentage of NREM sleep, while preserving sleep continuity, in both healthy and stroke model mice. In contrast, zolpidem increased NREM sleep after stroke, but also increased sleep fragmentation in both groups. Lemborexant treatment at 10 mg/kg and 30 mg/kg significantly reduced infarct volume eight weeks after the induction of stroke. In addition, lemborexant-treated mice showed greater use of the impaired limb four weeks after stroke. InterpretationThese preclinical findings suggest that lemborexant stabilizes sleep and promotes structural and functional recovery following the experimental induction of stroke in model mice, supporting its potential as a novel therapeutic intervention following ischemic stroke. Summary for Social Media if PublishedO_LIIf you and/or a co-author has a X handle that you would like to be tagged, please enter it here. (format: @AUTHORSHANDLE). @EricLandsness C_LIO_LIWhat is the current knowledge on the topic? Sleep plays a critical role in structural and functional recovery after stroke, but most pharmacologic sleep aids, such as benzodiazepines and zolpidem, can fragment sleep and impair neuroplasticity. Dual orexin receptor antagonists like lemborexant may offer a newer, mechanistically distinct approach with potential neuroprotective benefits. C_LIO_LIWhat question did this study address? This study investigated whether the dual orexin receptor antagonist lemborexant could improve sleep quality, reduce ischemic injury, and enhance functional recovery following stroke in adult mice, compared with the sleep-promoting agent zolpidem. C_LIO_LIWhat does this study add to our knowledge? Lemborexant increased NREM sleep without causing fragmentation, reduced infarct volume, and improved motor recovery when administered. These findings suggest that modulating sleep architecture through orexin antagonism during the subacute phase after stroke can promote neural repair and functional recovery. C_LIO_LIHow might this potentially impact on the practice of neurology? Since lemborexant is already FDA-approved for insomnia, these results could be rapidly translated into a therapeutic opportunity to improve stroke recovery through targeted sleep modulation. This approach may shift poststroke care toward integrating neurorestorative, sleep-based interventions during the subacute phase. C_LI

neuroscience↗

bioRxiv2025

A foundation model for microbial growth dynamics

Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engineering. However, the high dimensionality of growth data and the scarcity of large, task-specific datasets have limited generalizable modeling analysis across systems. Here, we develop a foundation model for microbial growth dynamics. It is a large-scale, self-supervised representation model trained on [~]370,000 experimental and simulated growth curves spanning diverse microbial species, environmental conditions, and community contexts. The model learns lower-dimensional latent embeddings that capture essential dynamical features of raw growth data and enable accurate reconstruction of these data. The concise representations enhance predictive performance in diverse downstream applications. Using these embedding, we achieve few-shot learning for antibiotic classification and concentration prediction, accurate forecasting of simulated and experimental communities, and inference of total abundance from relative-abundance data. By extracting transferable representations from heterogeneous datasets, our model provides a general framework for analyzing and predicting microbial community dynamics from limited measurements.

synthetic biology↗

bioRxiv2025

Engineering the citrus phyllosphere microbiome for enhanced disease resistance to bacterial canker

Engineering phyllosphere microbiomes toward plant protection against pathogens on crops has shown promising effects. Here we tested the effect of application of beneficial bacteria individually and as a synthetic community (SynCom) on the phyllosphere microbiome and management of bacterial canker caused by Xanthomonas citri subsp. citri (Xcc). Foliar spray of a SynCom consisting of three citrus endophytic bacterial strains (Paenibacillus sp. ATY16, Bacillus megaterium PT6, and Bacillus subtilis PT26A, SynCom1) with mechanistically complemented plant-beneficial properties exerted a more profound effect on the leaf microbiota and suppression of citrus canker than single strains. Cultivation-dependent and bacterial 16S rRNA gene-sequence profiling analyses revealed that leaf endophytic Bradyrhizobium, Brevibacillus, Cellvibrio, Flavobacterium, and Pseudomonas were significantly enriched in the SynCom treated plants, in addition to Bacillus and Paenibacillus. The enriched Brevibacillus and Pseudomonas spp. were isolated, whole-genome sequenced, and confirmed to possess multiple beneficial traits including antimicrobial activity against Xcc, Moreover, the expression of citrus defense genes was induced by the SynCom1 inoculation. Foliar application of SynCom1 and a newly assembled SynCom (SynCom2; SynCom1 with representative Brevibacillus and Pseudomonas isolates) prior to Xcc inoculation significantly reduced the citrus canker disease severity in greenhouse assays, and SynCom2 had a better efficacy, comparable to a copper bactericide. Three-year field tests showed that both SynCom1 and SynCom2 effectively controlled citrus canker, with a 50% reduction of foliar and fruit canker incidence. Collectively, these findings provide novel insights and valuable clues for microbiome engineering to serve as a sustainable strategy for the control of phyllosphere pathogens on crops.

plant biology↗

bioRxiv2025

Precision at Every Scale: Efficiency in AI-Driven De Novo Antibody Design

The precise de novo design of antibodies remains a therapeutic challenge. The AI platform, GaluxDesign, was evaluated in a high-efficiency Precision-Scale Workflow by synthesizing and testing only 50 full-length IgG candidates per epitope across eight distinct epitopes from six therapeutic targets. This campaign yielded a 10.5% binder rate (estimated EC50 < 100 nM), identifying target-specific binders for seven of eight epitopes, with multiple candidates exhibiting sub-nanomolar to single-digit nanomolar dissociation constants (Kd). We further assessed the same workflow on nine shared benchmark targets selected for external comparison, where GaluxDesign identified target-specific binders for eight of nine targets, demonstrating strong target-level performance relative to previously reported de novo antibody design approaches. Together, these results establish a high-efficiency, precision-scale workflow for generating novel, high-affinity therapeutic antibodies.

bioengineering↗

bioRxiv2025

SHEST: Single-cell-level artificial intelligence from haematoxylin and eosin morphology for cell type prediction and spatial transcriptomics reconstruction

A comprehensive understanding of cancer progression requires integrating tissue morphol-ogy with spatial molecular profiles. We present SHEST, a multi-task profiling framework that leverages haematoxylin and eosin morphology to predict cellular composition and re-construct spatial gene expression at single-cell resolution. SHEST employs a quadruple-tile input capturing nuclear and contextual information, combined with a neighbourhood-informed clustering algorithm to filter ambiguous cellular signals. It comprises a shared morphological encoder with two task-specific heads: a classifier for cell type prediction and a reconstruc-tor for gene expression. Multi-task optimisation uses cross-entropy and zero-inflated negative binomial losses, specifically addressing the sparsity of spatial transcriptomic data. Evalua-tion on human lung adenocarcinoma datasets demonstrated high accuracy for the principal reciprocal constituents of the tumour-immune axis (F1: 0.97 for tumour cells and 0.91 for lym-phocytes). External validation confirmed its generalisability, revealing alveolar cells and their early neoplastic transitions. Reconstructed gene expression reproduced spatially resolved, cell-type-specific marker patterns--EPCAM in tumour cells, LTBP2 in fibroblasts, and CD3E in lymphocytes--recovering biologically coherent transcriptional architecture. SHEST also pre-served distance-dependent spatial relationships and gene-level autocorrelation, reflecting the multicellular niche structure of the tumour microenvironment. By unifying cell type iden-tification, gene expression reconstruction, and spatial mapping within a single interpretable framework, SHEST provides a synergistic and cost-efficient bridge between histopathology and spatial transcriptomics. This approach facilitates comprehensive tissue characterisation and forms a foundation for precision oncology through spatially informed, cell-level insights into tumour-immune ecosystems.

bioinformatics↗

bioRxiv2025

Compositional analysis of yellow fever virus induced stress granules reveals a functional connection to mitochondrial homeostasis

The phase separation of biomolecules into so-called stress granules (SGs) allows the cell to tightly regulate translation activity in response to different stimuli, such as oxidative stress, starvation, or the recognition of non-cellular RNA. Recent reports suggest SGs induced during viral infection, may act as a crossroad between the cellular stress response and the activation of the innate immune response. Here, we aimed to dissect the role of SGs in the context of yellow fever virus (YFV) infection. We found that YFV infection resulted in translational shut-off from 24 hpi on followed by the formation of SGs at 48 hpi, a delay potentially associated with the ability of the YFV capsid to inhibit SG formation, through an interaction with the major SG scaffolding protein G3BP1. To elucidate the role of YFV-induced SGs during infection, we inhibited SG assembly using a small-molecule inhibitor and find that SG formation does not influence viral replication. Uncovering the first proteome of virus-induced SGs, our compositional analysis revealed a specific enrichment of proteins associated with mitochondrial processes in YFV-induced SGs. Indeed, we show that YFV infection results in mitochondrial damage and dysfunction. Together, we propose that YFV-induced SGs may be involved not only in the modulation of cellular homeostasis but also in influencing mitochondrial functions. Author SummaryViruses impose a major burden on the infected host - from structural rearrangements needed to assemble replication complexes, to exploiting cellular energy resources and genetic rewiring associated with antiviral responses. The assembly of membrane-less organelles such as stress granules (SGs) enable cells to rapidly tune cellular processes upon sensing of stresses such as viruses. Moreover, the cells innate immune response is proposed to be regulated by SGs and in turn many viruses disrupt or highjack their components. Yet, the molecular basis for SG functions during infection remain ambiguous. Here we investigated the interplay between yellow fever virus (YFV) infection and SGs. We demonstrate that infection with attenuated or pathogenic viruses result in the formation of SGs. Their compositional analysis reveal that they sequester mitochondrial proteins, correlating with altered mitochondrial functions during infection. This highlights a novel complex interplay between membrane-bound and membrane-less organelles which could present novel opportunities for antiviral therapies.

microbiology↗

bioRxiv2025

Mus Musculus papillomavirus MmuPV1 resists restriction by human APOBEC3B

The single-stranded DNA deaminase APOBEC3B (A3B) is capable of potently restricting the replication of a range of viruses including retroviruses (cDNA) and herpesviruses (genomic DNA). However, these and likely other DNA virus families have evolved host species-specific counter-defenses that are equally potent and serve to protect viral DNA from restriction. Although high-risk human papillomavirus (HPV) infection triggers A3B upregulation, potentially as part of an antiviral response, the impact of this restriction factor on papillomavirus replication and pathogenesis has yet to be assessed. To study human A3B antiviral function in the absence of a species-specific counter-defense, here we ask whether human A3B is capable of restricting Mus musculus papillomavirus (MmuPV1) in cellulo and in vivo. First, we created human A3B and catalytic mutant A3B-E255A expressing FVB/N mice. Second, MmuPV1 gene expression and replication was quantified in primary keratinocytes from these animals and, surprisingly, enzymatically active human A3B caused no measurable impairment in viral transcript or DNA accumulation. Third, A3B, catalytic mutant A3B-E255A, and nontransgenic FVB/N animals were infected with MmuPV1 and similar pathologies were found regardless of A3B functionality. Thus, despite likely never being exposed to human A3B during evolution, MmuPV1 appears to be unaffected by this potent, primate-specific antiviral factor. These results suggest that MmuPV1 and perhaps papillomaviruses more broadly possess a conserved mechanism to efficiently escape restriction by human A3B and related DNA deaminases. IMPORTANCEHuman papillomaviruses (HPVs) are nearly ubiquitous, and persistent infection with high-risk types causes approximately 5% of cancers worldwide. Although HPV vaccination is effective for preventing infection, insufficient global coverage and a rising incidence of HPV-associated malignancies, such as oropharyngeal carcinoma, highlight the need to understand innate virus clearance mechanisms. APOBEC3 enzymes are a central component of the mammalian innate immune system and are hypothesized to restrict papillomavirus infection, particularly between species. Here, we establish mice that express the human antiviral enzyme APOBEC3B (A3B). Surprisingly, we find that human A3B is incapable of blocking the replication of a murine papillomavirus (Mus musculus papillomavirus 1, MmuPV1) in relevant primary cells from these animals or in infected tissues in vivo. These findings highlight the complexity of teasing apart host-pathogen interactions and suggest that papillomaviruses may have a general mechanism for escaping restriction by antiviral enzymes such as A3B.

microbiology↗

bioRxiv2025

Effect of Large Language Models on P300 Speller Performance with Cross-Subject Training

Amyotrophic lateral sclerosis (ALS), a progressive neurodegenerative disease, severely impairs communication, requiring assistive technologies that restore interaction. The P300 speller brain-computer interface (BCI) enables communication by translating EEG responses into text; however, its practical adoption is limited by slow typing speed and the need for subject-specific calibration. Recent work has demonstrated that large language models (LLMs), such as GPT-2, can significantly improve the performance of the P300 speller by predicting words. However, it remains unclear whether these gains are model-specific or represent a broader trend across language models. Furthermore, the fundamental performance limits of LLM-assisted P300 spellers have not been systematically characterized within a unified decoding framework. In this study, we address these gaps through a systematic multi-model theoretical analysis framework. We evaluate a wide range of language models and introduce an idealized LLM to establish upper bounds on achievable performance. In addition, we incorporate cross-subject classifier training to reduce calibration requirements and assess generalization across subjects. Using extensive simulations on EEG data from 78 subjects, we demonstrate that the evaluated models consistently achieve substantial improvements in typing speed, with gains of up to [~]40% (across-subject training) and [~]75% (within-subject training) over conventional approaches. More importantly, we show that multiple models, despite architectural differences, operate within 5% of the theoretical performance bound, indicating diminishing returns from further model scaling. These improvements generalize across both within-subject and across-subject classifiers. Our results suggest that LLM-assisted P300 spellers are approaching their fundamental performance limits within the considered decoding framework, shifting the primary bottleneck from language modeling to neural signal decoding. This work provides both a practical framework for improving BCI communication and a theoretical perspective on its achievable limits.

neuroscience↗

bioRxiv2025

Prognostic and Therapeutic Implications of BRAF Mutations in Acute Myeloid Leukemia

Mutations in the RAS/MAPK signaling pathway are recurrent in acute myeloid leukemia (AML), primarily involving NRAS and KRAS. In contrast, mutations in the gene encoding an effector protein, BRAF, occur at relatively lower frequencies in AML and are associated with poor outcomes. To date, no comprehensive analysis has assessed the clinical and molecular characteristics of BRAF-mutated AML. In this study, we report the identification of canonical and non-canonical BRAF mutations in [~]1% of 5,779 consecutive clinically and molecularly fully-annotated AML patients treated at two major United States Cancer Centers (50/5779 AML patients: 21 newly diagnosed AML; 9 relapsed/refractory; 20 newly diagnosed secondary AML). We performed single-cell multiomic analysis on a subset of AML samples. BRAF mutations were enriched in myelodysplasia-related AML (AML-MR), and most mutations were located outside the V600 hotspot. Single-cell multiomic profiling delineated BRAF mutation class-specific patterns of co-mutations, clonality, and immunophenotypes. Notably, BRAF mutations and other signaling co-mutation(s) could be found in the same cell, a finding that significantly diverges from prior studies of RAS-mutant AML. In this cohort, BRAF-mutant AML patients had poor overall survival with currently available treatments, including venetoclax-based regimens. Drug sensitivity data suggest possible avenues for targeted treatment of BRAF-mutated AML. Statement of SignificanceCanonical and non-canonical BRAF mutations are enriched in AML-MR and associate with poor survival outcomes. Single-cell multiomic profiling revealed unique co-mutation patterns and immunophenotypes that highlight RAS pathway addiction and nominate BRAF-mutated disease as a distinct subtype within RAS pathway-aberrated leukemias. Drug sensitivity screens suggest broad CDK or HSP90 inhibition in addition to BRAF/RAS-directed inhibition may be effective targeted therapies in this prognostically poor AML subtype.

cancer biology↗

bioRxiv2025

Property Enhancer - a data efficient multi-objective approach for functional antibody optimization

In-silico antibody lead optimization remains challenging due to scarce high-quality data, costly experimental validation, and the need to jointly optimize multiple developability properties. Discovery workflows often rely on high-throughput phage, ribosome or yeast display experiments, which yield large but noisy datasets; as leads emerge, strategies shift to low-throughput assays which are precise, yet unscalable. Deep-learning and language-model approaches are hindered by such limited, unreliable measurements. We introduce Property Enhancer (PropEn), a data-efficient framework for low-data, heterogeneous regimes that can simultaneously optimize multiple antibody properties. PropEn proposes a matching-based augmentation that expands the training data with sequence pairs differing by only a few mutations; within each pair the second sequence improves the target value, providing an implicit optimization signal. Extensive in silico and in vitro tests show 10-39x affinity gains across four targets and nine leads, and enable joint multi-property optimization, positioning PropEn as a scalable, general solution.

molecular biology↗

bioRxiv2025

A family of lethal exotoxins defined by cell entry via the Attractin receptor

Although bacterial genomes encode numerous potential toxins, it is unclear how evolution drives the specificity of these important virulence factors. Using an insect CRISPR screen, we identified the transmembrane protein Attractin (ATRN) as the receptor for Nigritoxin (Ntx), a Vibrio toxin that causes seasonal shrimp pandemics. We found that Ntxs effector "warhead" inhibits translation via a previously uncharacterized mechanism. Moreover, we show that two related toxins require ATRN for entry but possess unrelated effector domains. One has a Rho-GTPase AMPylation function and the other an actin-targeting/proteolysis function. Our findings reveal the mechanism of Ntx entry and toxicity and show that the ATRN-targeting domain can deliver disparate effector domains, strongly indicating that this class of exotoxins can evolve as modular proteins using a common entry domain.

microbiology↗

bioRxiv2025

ETV4 restrains the formation of CD74+ cytotoxic exhausted CD8+ T cells

Exhausted CD8+ T (Tex) cells comprise heterogeneous subsets with varying cytotoxic and dysfunctional properties, making inhibitory receptor profiles unreliable indicators of function. Therefore, it is essential to define transcriptional regulators or markers that accurately reflect these states. Here, we identified ETS variant 4 (ETV4) as a transcription factor that restricts cytotoxic Tex differentiation within tumors. ETV4 deficiency promotes the emergence of a CD74+ cytotoxic Tex subset while preserving the progenitor Tex (Tpex) pool. CD74 serves as both a marker and regulator, reinforcing Tpex features and enhancing Tex cytotoxicity. Mechanistically, ETV4 loss derepresses T-bet expression, thereby increasing IFN{gamma} production that induces CD74 expression in a paracrine manner. Single-cell analyses across human cancers revealed that CD74+ Tex cells are enriched for proliferative and metabolic programs and correlate with improved survival. Collectively, we establish the ETV4-CD74 axis as a regulator of Tex fate and promising therapeutic target to augment anti-tumor immunity.

immunology↗