Biology subjects

Chen, W.

Publications and source records attributed to Chen, W..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Ultramutagenesis through combined Msh2 depletion and proofreading-deficient DNA polymerase ε expression enhances small molecule target identification in forward genetic screens

DNA mismatch repair (MMR) deficiency has been widely utilized in forward genetic screens to identify drug resistance mutations and elucidate the mechanisms of action of cytotoxic small molecules. However, MMR deficiency generates a characteristic mutational signature enriched for C>T transitions that precludes saturation of mutagenesis. We hypothesized that expression of proofreading deficient DNA polymerase epsilon, as has been observed in patients with biallelic MMR deficiency, would enhance mutagenesis and enable identification of new resistance mutations and cytotoxin mechanisms. Here, we combine auxin-inducible degradation of Msh2 with doxycycline-inducible expression of the proofreading-deficient Pol{varepsilon}P286R mutant in murine small cell lung cancer (SCLC) cells. Simultaneous MMR deficiency and mutant Pol{varepsilon} expression markedly increased the emergence of bortezomib-resistant clones relative to either perturbation alone and targeted sequencing of Psmb5 in bortezomib-resistant clones identified recurrent mutations previously reported in chemical mutagenesis-based resistance screens. We next applied this platform to investigate resistance to lurbinectedin, a clinically relevant therapy for SCLC. Whole-exome sequencing revealed recurrent loss-of-function alterations in nucleotide excision repair (NER) genes, most notably Ercc5 and Ercc4, implicating NER deficiency as a major mechanism of lurbinectedin resistance and supporting a central role for NER in mediating lurbinectedin-induced cytotoxicity. Collectively, these findings establish inducible ultramutagenesis as a powerful and versatile platform for the unbiased discovery of drug resistance mechanisms and therapeutic vulnerabilities.

Cancer Biology↗

bioRxiv2026

Bamsnap-LRS: an automated batch visualization tool for long-read sequencing alignments

SummaryLong-read sequencing (LRS) has become essential for genome assembly, structural variations (SVs) detection, haplotype phasing and transcript isoform characterization. However, these applications often require manual inspection of read alignment for validation. Existing visualization tools are either interactive genome browsers that are difficult to scale to large datasets or batch-oriented tools that are not optimized for the unique alignment patterns of long-read data. We developed Bamsnap-LRS, an automated command-line tool for high-throughput LRS alignment visualization. It supports long-read-specific features, phased SNP inspection, and publication-ready batch figure generation within a unified framework for genomic, transcriptomic, and haplotype-aware analyses. Availability and ImplementationAll codes and examples are freely available at https://github.com/comery/Bamsnap-LRS. ContactChentao Yang (yangchentao@genomics.cn) and Yang Zhou (zhouyang@genomics.cn). Supplementary informationSupplementary Table 1 and Supplementary Figures 1-8 are available at xxx online.

bioinformatics↗

bioRxiv2026

Prenatal e-cigarette exposure induces region- and cell type-specific metabolic and developmental reprogramming

Prenatal e-cigarette exposure (PeCE) is increasingly prevalent and has been associated with adverse neurodevelopmental outcomes, yet how maternal vaping perturbs early brain development remains poorly understood. We integrated spatial transcriptomics, snRNA-seq and lipidomics to define neonatal rat brain responses to PeCE in rats at regional and cellular resolution. PeCE induced pronounced spatial heterogeneity in vulnerability, with the striatum exhibiting the strongest developmental transcriptional disruption. PeCE disrupts lipid metabolic homeostasis and induced molecular signatures suggestive of enhance Ca2+ signaling, dopaminergic responsiveness and region-specific synaptic stress programs. In the striatum, PeCE induced transcriptional programs consistent with altered lipid utilization, silent synapse-like molecular features, suppressed dendritic spine development and delayed D1-medium spiny neuron maturation. PeCE-sensitive genes were enriched in human autism spectrum disorders and neurodevelopment risk loci. Together, these findings identify disrupted metabolic and developmental reprogramming as a central feature of neonatal brain vulnerability to maternal vaping and provide a mechanistic framework linking PeCE to neurodevelopmental disease risk.

neuroscience↗

bioRxiv2026

Iron Regulates CD4 T Cell Quiescence by Controlling TGF-β Production

Transforming growth factor-{beta} (TGF-{beta}) regulates CD4 T cell quiescence, activation, and regulatory T cell differentiation, but its role in T cell iron metabolism is poorly defined. Here, we investigated whether TGF-{beta} regulates iron homeostasis and how iron overload alters TGF-{beta} responsiveness. During T cell activation, TGF-{beta} enhanced survival but markedly reduced proliferation. These effects were accompanied by decreased CD71 expression and cytosolic iron availability, as well as increased mitochondrial iron accumulation. Genetic deletion of TGF{beta}R1 reversed these changes, demonstrating that TGF-{beta} regulates CD4 T cell iron homeostasis through TGF{beta}R1-dependent signaling. Iron-overloaded CD4 T cells lacking the heme exporter FLVCR1 exhibit hypersensitivity to TGF-{beta}, increased TGF-{beta} secretion, and sustained TGF{beta}R1 expression upon activation. Pharmacologic inhibition of TGF{beta}R1restored proliferation, CD71 expression, and iron levels in FLVCR1-deficient cells. Although TGF-{beta} selectively induced total and mitochondrial ROS levels in FLVCR1-deficient cells, antioxidant treatment or Nox2 inhibition did not rescue this phenotype, suggesting that ROS is associated with, but not sufficient to explain, TGF-{beta} hypersensitivity. Acute FeSO4-induced iron overload partially recapitulated the phenotype of FLVCR1-deficient cells, although TGF{beta}R1 expression and TGF-{beta} production differed. Finally, regulatory T cells generated in vitro in the presence of TGF-{beta} displayed reduced iron acquisition, and excess iron impaired FoxP3 induction. Together, this work identifies TGF-{beta} as a context-dependent regulator of CD4 T cell iron homeostasis.

immunology↗

bioRxiv2026

Fibulin-2 transduces a matrix-to-metabolism signal in kidney fibrosis

Fibrotic extracellular matrix (ECM) is not merely a structural scaffold but an instructive signaling interface that shapes epithelial cell state. However, the molecular cues by which matrix remodeling controls tubular metabolism during kidney fibrosis remain poorly defined. Here, we identify Fibulin-2 (FBLN2) as a fibroblast-derived matrix cue that transduces fibrotic ECM remodeling into tubular mitochondrial metabolic reprogramming. Using fibroblast-selective deletion of Smoothened (Smo) across distinct fibroblast subpopulations, we found that loss of fibroblast Smo preserved kidney function and attenuated fibrosis in mouse models of chronic kidney injury. Multi-omics profiling revealed coordinated remodeling of the fibrotic matrisome, highlighted by suppression of FBLN2, an ECM glycoprotein genetically linked to kidney function in humans. Mechanistically, FBLN2 engaged EGFR in tubular epithelial cells and activated EGFR-AKT signaling in a non-canonical ligand-like manner. This signaling axis suppressed acetyl-CoA acetyltransferase 1 (ACAT1), a mitochondrial regulator of fatty acid oxidation and amino acid metabolism. Disruption of fibroblast Smo-FBLN2 signaling restored ACAT1-dependent oxidative metabolism and reduced tubular fibrotic activation. Spatial lipidomics revealed compartment-specific lipid remodeling associated with altered mitochondrial fatty acid metabolism, including acylcarnitine and phospholipid changes linked to reduced fibrotic injury. Together, these findings define a Fibulin-2-EGFR-ACAT1 matrix-to-metabolism signaling axis that couples fibrotic ECM remodeling to tubular mitochondrial metabolism during kidney fibrosis.

cell biology↗

bioRxiv2026

A Brugada-related KCNT1 mutation unveils its conductance-independent activation of store-operated Ca 2+ entry

BackgroundPotassium sodium-activated channel subfamily T member 1 (KCNT1) is a Na+-activated K+ channel, associated with epilepsy and cardiac diseases. Besides K+ conductance, KCNT1 is also involved in Ca2+ handling. KCNT1:R1106Q was identified in a Brugada Syndrome (BrS) patient; however, its pathological characteristics regarding either K+ or Ca2+ homeostasis remain to be fully elucidated. MethodsFura-2-loaded HEK293T cells were used for intracellular Ca2+ investigations, and whole-cell patch-clamp technique were used as complementary tests. Stromal interaction molecule 1 (STIM1) aggregation and endoplasmic reticulum (ER)-plasma membrane (PM) junctions in HeLa cells were visualized using spinning disc confocal microscope. Multielectrode array (MEA) assays were utilized to assess the field potential duration (FPD) and spontaneous beating rate of human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs). ResultsKCNT1 overexpression increased SOCE, which was further upregulated by the KCNT1R1106Q mutant. Furthermore, KCNT1 upregulated ER Ca2+ release and was found to localize at ER-PM junctions. The ER Ca2+ dynamics in KCNT1R1106-overexpressing cells was disrupted, while its SOCE remained intact. The KCNT1 cytoplasmic tail alone sufficiently modulated Ca2+ homeostasis. Given that KCNT1 possesses prominent charge-concentrated segments within its cytoplasmic domain, we substituted charged amino acids in either the 740-DDE-742 or 1114-RRLSR-1118 motifs with alanine; these substitutions abolished the KCNT1-mediated increases in ER Ca2+ release and ER-PM contact formation. MEA recordings of hiPSC-CMs revealed that the overexpression of KCNT1 shortened the FPD and accelerated the cardiomyocyte beating rate compared to baseline. However, the magnitude of beating rate acceleration induced by KCNT1R1106Q was significantly attenuated compared to that of KCNT1WT. ConclusionsOur findings indicate that, independent of KCNT1-mediated ion conductance, the charged motifs located at both ends of the KCNT1 cytoplasmic tail serve as structural anchors to facilitate ER-PM contact formation. This non-conducting role endows KCNT1 with a K+ current-independent mechanism to modulate intracellular Ca2+ homeostasis and cardiomyocyte physiology. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/731813v1_ufig1.gif" ALT="Figure 1"> View larger version (31K): org.highwire.dtl.DTLVardef@104e234org.highwire.dtl.DTLVardef@19eceb3org.highwire.dtl.DTLVardef@1148512org.highwire.dtl.DTLVardef@2c8118_HPS_FORMAT_FIGEXP M_FIG C_FIG Novelty and SignificanceO_ST_ABSWhat is known?C_ST_ABSO_LIKCNT1 is a Na+-activated K+ channel, and mutations within this gene are often associated with epilepsy and epilepsy-related cardiac diseases. C_LIO_LIBesides functioning as a rectifier, KCNT1 is implicated in cellular Ca2+ handling, such as regulating Ca2+ oscillations in rat cortical neurons. C_LIO_LIKCNT1:R1106Q missense mutation has been identified in a patient with Brugada Syndrome (BrS); however, its pathophysiological characteristics and underlying mechanisms remain uncharacterized. C_LI What New Information Does This Article Contribute?O_LIKCNT1 overexpression upregulates both ER Ca2+ release and store-operated Ca2+ entry (SOCE). KCNT1R1106Q further increased SOCE intensity, however, its increase in ER Ca2+ release and [Ca2+]ER were attenuated. C_LIO_LIThe cytoplasmic tail of KCNT1 alone is suNicient to modulate Ca2+ closely mimicking the eNects of full-length KCNT1. C_LIO_LIThe charged clusters distributed along the KCNT1 cytoplasmic tail facilitate ER-PM contact. Alanine substitutions abolish the enhancements in ER Ca2+ release and ER-PM contact formation, while SOCE modulation remains intact. C_LIO_LIThe KCNT1 cytoplasmic tail alone shortens the field potential duration (FPD) and accelerates the spontaneous beating rate in hiPSC-CMs. However, the magnitude of beating rate acceleration induced by KCNT1R1106Q is significantly attenuated compared to KCNT1WT. C_LI This study uncovers a novel, conductance-independent role for the KCNT1 channel in structural organization, demonstrating that the charged motifs on its cytoplasmic tail serve as physical anchors facilitating ER-PM junctions. This structural mechanism regulates intracellular Ca2+ homeostasis and subsequently alters cardiomyocyte electrophysiology. By decoupling KCNT1s structural impact from its ion-conducting function, these findings provide new mechanistic insights into how specific KCNT1 variants, such as the BrS-associated KCNT1:R1106Q mutation, may contribute to arrhythmogenesis through imbalanced Ca2+ handling rather than classical K+ current alterations.

Molecular Biology↗

bioRxiv2026

eQTM (expression quantitative trait methylation) Atlas: a comprehensive resource of over 11 million DNA methylation-gene expression associations through across 11 tissues and 4 diseases

MotivationEpigenome-wide association studies (EWAS) have identified numerous DNA methylation (DNAm) CpG sites associated with complex traits and diseases, but interpretation of those CpG sites remains challenging because in EWAS, CpGs are mostly linked to nearby genes based only on genomic proximity. Expression quantitative trait methylation (eQTM) analyses connect DNAm CpGs with statistically associated gene expression levels. However, a comprehensive, searchable resource integrating eQTMs across diverse tissues and disease contexts has been lacking. ResultsWe developed the eQTM Atlas, a web-based resource that manually curates more than 11 million DNAm-gene expression associations from eight cohorts, covering 11 tissue types, four broad disease contexts, 173,886 unique CpG probes and 20,231 unique genes. The Atlas supports gene- or CpG-searches by tissue or disease type and finding associated CpG or genes, visualization of cis- and trans-eQTMs through genome browser, heatmap interfaces across various tissues, and cohort-level data downloads. By integrating eQTM results with EWAS resources, the eQTM Atlas enables users to connect disease- or trait-associated CpGs to statistically associated genes rather than relying solely on proximity-based gene annotation, supporting functional interpretation of EWAS findings and generation of disease-specific regulatory hypotheses. Availability and implementationThe eQTM Atlas is freely available at https://shiny.crc.pitt.edu/eqtm_browser/. The web interface is implemented in R Shiny and hosted through the University of Pittsburgh Center for Research Computing (CRC). Source code is available at https://github.com/ads303/eQTM-Atlas.

genetics↗

bioRxiv2026

Characterization of velvet DNA-binding region by Aspergillus nidulans VelB

Velvet regulators characterized by a conserved velvet domain function as a central hub that coordinately govern fungal development, secondary metabolism, stress adaptation, and pathogenicity. The velvet domain is organized into an N-terminal DNA-binding region of approximately 30 amino acids and a C-terminal dimerization region of roughly 100 amino acids. In this study, Aspergillus nidulans VelB was used as a paradigm to systematically dissect the velvet DNA-binding region. Three arginine residues R71, R80, and R81 in the N-terminal velvet domain indispensable for VelB function were identified through alanine-scanning mutagenesis of 15 conserved residues. Alanine substitutions at these positions caused severe defects in long-term spore viability, sexual development, and secondary metabolism. Further comparative characterization of electrostatic potential dynamics pre- and post-mutation revealed that the three individual substitutions markedly attenuate local electrostatic potential across the DNA-binding interface. Notably, these mutations drive comprehensive remodeling of the proteins electrostatic properties, whereby electrostatic perturbations propagate across the entire protein exterior. Analysis of 4,999 velvet-domain sequences across the fungal kingdom revealed extraordinary conservation of these positions: arginine was present at position 71 in 85% of sequences, at position 80 in 91%, and at position 81 in 84%. Cross-kingdom complementation experiments further demonstrated that the wild-type velvet DNA-binding region from Capsaspora owczarzaki, a unicellular holozoan lacking the equivalent of R71, failed to rescue the A. nidulans velB deletion phenotype, whereas introduction of arginine at this position conferred substantial functional restoration. These findings establish that a cluster of conserved arginine residues generates the positive electrostatic surface potential required for velvet-DNA interaction, and define the molecular basis of DNA recognition by this ancient family of fungal transcription factors.

microbiology↗

bioRxiv2026

Colchicine Directly Targets Aldehyde Dehydrogenase 2 (ALDH2) to Suppress Radiation-Induced Senescence and Atherosclerosis

BackgroundIonizing radiation (IR) accelerates atherosclerosis through induction of cellular senescence, DNA damage, defective efferocytosis, and dysregulation of clonal hematopoiesis (CH) drivers. Although low-dose colchicine reduces ischemic cardiovascular events in coronary artery disease, the precise molecular mechanisms underlying its vasculoprotective effects remain incompletely defined, and whether it mitigates radiation-associated vascular injury is unknown. MethodsBone marrow-derived macrophages (BMDMs) were pretreated with low-dose colchicine and exposed to 2 Gy IR. Molecular effects were assessed by RNA-seq, immunoblotting, and molecular docking. In vivo effects were tested in a partial carotid ligation (PLCL) model using spatial proteomics. Human monocyte-derived macrophages (HMDMs) from thoracic malignancy patients were analyzed before and after radiation therapy (RT). ResultsLow-dose colchicine suppressed IR-induced macrophage senescence signaling while preserving NRF2 activity. In a cell-free assay, colchicine directly activated aldehyde dehydrogenase 2 (ALDH2) in a dose-dependent manner (EC50 1-5 nM), identifying ALDH2 as a direct molecular target of colchicine. Following irradiation, colchicine restored ALDH2, reduced mitochondrial (mt)ROS-dependent p90 ribosomal S6 kinase (p90RSK) activation and lipid peroxidation, preserved TET2 and DNMT3A expression, and rescued impaired efferocytosis while preventing nicotinamide adenine dinucleotide (NAD) and adenosine triphosphate (ATP) depletion. These protective effects were ALDH2-dependent, as they were lost with ALDH2 inhibition or depletion and were mimicked by pharmacologic ALDH2 activation. In vivo, colchicine attenuated radiation-induced atherosclerosis and macrophage senescence-associated stemness (SAS). Consistently, macrophages from patients after RT showed reduced ALDH2 with increased mtROS, lipid peroxidation, and senescence. ConclusionThese findings identify ALDH2 as a previously unrecognized molecular target of colchicine that links mitochondrial redox control to suppression of radiation-induced macrophage senescence and atherosclerosis and may contribute to the efficacy of low-dose colchicine in cardiovascular disease.

cell biology↗

bioRxiv2026

Dominant resistance alleles accelerate population suppression by CRISPR-based gene drive

CRISPR-based gene drive is a promising strategy for pest control. However, when targeting a recessive fertility gene, nonfunctional resistance alleles generated by end-joining slow the spread of drive and can even impair suppressive power. It was recently discovered that a doublesex target site can result in dominant female-sterile alleles when disrupted. It could serve as an ideal target for suppression drives, as disrupted alleles are efficiently removed when inherited by a female, increasing the suppressive power of the drive. Here, to better understand how dominant sterile target sites can improve suppression, we used an individual-based, continuous space model to investigate chasing dynamics of homing drives that produce dominant female-sterile resistance. Our results indicate that dominant-sterile resistance allows homing drives to achieve higher population elimination rates and a lower probability of chasing over a broader range of performance parameters. In addition, we propose a confined gene drive system, termed TADFI (Toxin-Antidote Dominant Female Intersex), that is also based on formation of dominant female sterile alleles. TADFI has two variants, designed for population suppression and modification, respectively. We estimate the introduction frequency threshold of TADFI in a panmictic model, and evaluate its suppression dynamics in a spatial model. Though spreading less rapidly than Toxin-Antidote Dominant Embryo (TADE) suppression drive, it has similar favorable dynamics related to confinement and suppressive power, while potentially being easier to construct. Together these results show that drives generating dominant-female sterile alleles may be promising candidates for a variety of population suppression applications.

genetics↗

bioRxiv2026

PD-1 remodels SHP2 dynamics and drives the non-catalytic inhibition of T cell activation

The inhibitory receptor programmed cell death protein 1 (PD-1) suppresses T cell activation primarily by recruiting the src homology 2 domain-containing phosphatase 2 (SHP2), thereby unleashing its phosphatase activity. However, a purely enzymatic model struggles to fully explain the rapid and robust disruption of proximal T cell receptor (TCR) and CD28 signaling. Here, by integrating X-ray crystallography, single-molecule magnetic tweezers, supported lipid bilayers, TIRF imaging, liquid-liquid phase separation, and cellular assays, we uncover a dual-layered inhibitory mechanism of the PD-1/SHP2 axis. Mechanistically, we determine the crystal structure of SHP2 in complex with dually phosphorylated PD-1 cytoplasmic motifs (pPD-1), revealing a ligand-induced open conformation, which is distinct from the oncogenic E76K-associated state. We further directly resolve the closed-to-open conformational dynamics of individual SHP2 molecules, characterized by an 8-nm transition amplitude, and demonstrate that pPD-1 accelerates the transition by at least 94-fold. Crucially, the pPD-1-mediated highly open conformation exposes the tandem SH2 (t-SH2) domains to function as a biophysical barrier. Independent of phosphatase activity, these domains directly dismantle pTCR and pCD28 signaling condensates to suppress T cell activation. Together, our findings establish a model in which pPD-1 remodels SHP2 structural dynamics and drives a non-catalytic inhibitory mechanism of TCR and CD28 signaling, suggesting next-generation immunotherapy design to reverse T cell suppression.

immunology↗

bioRxiv2026

Astrocytic D1 Dopamine-Signaling Regulates Synaptic Remodeling and Cocaine Seeking

D1-type receptor (D1R)-mediated dopaminergic signaling within the nucleus accumbens shell (NAcSh) is essential for forming adaptive circuit changes that embed persistent memories associated with drug seeking and craving. While D1R is expressed in both NAcSh neurons and astrocytes, the specific contribution of astrocytic D1R to drug-related circuit plasticity remains poorly understood. Here, we demonstrate in mouse NAcSh slices that D1R agonists increase astrocytic Ca2+ activity, an effect that is attenuated by astrocyte-specific D1R knockdown. Furthermore, selective knockdown of astrocytic D1R in the NAcSh prior to cocaine self-administration inhibits cocaine-induced generation of silent synapses, therefore hampering the associated remodeling of NAcSh circuits. Behaviorally, knockdown of NAcSh astrocytic D1R expedites the extinction of cocaine seeking and reduces cue-induced reinstatement. These results identify astrocytic D1R as a fundamental component of NAcSh dopamine signaling during cocaine experience that remodels synaptic connections and neural networks underlying drug seeking and relapse.

neuroscience↗

bioRxiv2026

Hippocampus single-nucleus transcriptomics reveals coordinated regulation of social and spatial representation development by perinatal SERT expression in CA3 pyramidal neurons

The hippocampal formation (HPF) provides neural substrates integrating disparate sensory cues into episodic memories and coherent action. Whereas HPF structures are formed by birth, the functional circuits evolve over postnatal development. Our previous studies showed that transient perinatal expression of the serotonin (5-HT) transporter SERT/Slc6a4 in CA3 pyramidal neurons, which do not synthesize 5-HT but take up extracellular 5-HT thus termed "5-HT-absorbing neurons", exerts sex-biased effects on long-term activity-dependent HPF synaptic plasticity and behavior in mice. This study investigates SERT impact on circuit development, through single-nucleus transcriptomics of postnatal HPF from CA3-pyramidal neuron SERT knockout (SERTPyramid{Delta}) mice. We demonstrate that SERTPyramid{Delta} mice preserve cell identities across the HPF but alter gene expression in specific neuronal types in a sex-biased manner. We observed SERTPyramid{Delta} male-biased upregulation of genes preferentially in glutamatergic neurons, particularly affecting the CA2 and parasubiculum (PaS) when they develop social novelty and spatial representations, respectively. In both the CA2 and PaS, altered genes center on two categories -- modulators of gene expression patterning including chromatin plasticity, RNA processing and ubiquitin-dependent protein degradation, and aspects of synaptic transmission. >20% of the dysregulated genes in the CA2 and PaS are associated with Autism and engaged in cell-type distinct functional networks, showing CA3 SERT regulation of ASD-vulnerable genes in intersecting biological processes in specific neurons during social and spatial circuits development. The data, available at https://scviewer.shinyapps.io/hippocampus_sertKO, provide an entry map for further deducing anatomical neuronal origin and the molecular and cellular pathways impaired by 5-HT dysfunction during HPF circuits development leading to lifetime cognitive deficits.

neuroscience↗

bioRxiv2026

Genome-wide CRISPR knockout cell screening platform for the disease vector tick species Ixodes scapularis

The black legged tick, Ixodes scapularis, is a vector of the bacterium that causes Lyme disease and several other illnesses, including anaplasmosis, babesiosis, and tick-borne encephalitis. Although high-quality genome annotations are available for I. scapularis, functional understanding of I. scapularis genes is limited. To address this, we developed a platform for genome-wide CRISPR-Cas9 knockout screening in I. scapularis cells. To evaluate the platform, we performed a screen to identify genes associated with cellular fitness, and screens for resistance to treatment with copper chloride, Antimycin A, or Destruxin A (DA), a cyclic hexadepsipeptide produced by the pathogenic fungus Metarhizium anisopliae. In each case, the screens implicate specific sets of conserved and non-conserved I. scapularis genes in relevant cellular functions, providing the first experimental evidence of function for a large set of I. scapularis genes. Altogether, in this first-of-its-kind effort for the arthropod subclass Acari, we present an unbiased genome-wide CRISPR-Cas9 knockout cell screening platform, related resources, and datasets that will be broadly useful to efficiently uncover cellular functions of I. scapularis genes.

genetics↗

bioRxiv2026

Interpreting Omics Data Analysis with Large Language Models for Disease Target and Drug Discovery

In biomedical scientific discovery, synthesizing prior knowledge from the literature is an essential component of interpreting numerical omics data analyses for disease target identification and drug discovery. Large language models (LLMs) alone can rapidly retrieve disease mechanisms from biomedical text, but text-only outputs are general and unreliable for target and drug prioritization without cohort-specific quantitative evidence. Herein, we propose a provenance-aware Text-to-Target framework that couples schema-constrained multi-model LLM retrieval with numeric omics data analysis. The key design is a modality-aware fusion step: candidates are partitioned into overlap-supported anchors, retrieval-only hidden hubs, and network-emergent novelty nodes, then propagated into staged hypothesis and strategy generation under topology constraints. We evaluate the model in Alzheimers disease (AD) and pancreatic ductal adenocarcinoma (PDAC). In PDAC, the workflow produced a balanced 75-gene candidate universe and a 23-strategy portfolio, with significant DepMap support at both target level and strategy level. In AD, stricter candidate controls yielded a compact 34-gene universe and 14 strategies; under an expanded CRISPRbrain registry, both target-level axes were significant, with strong strategy-level enrichment. Across both diseases, final strategies preserved full provenance closure to the candidate pool, enabling end-to-end auditability from retrieval artifacts to validation outputs. These results support a transferable discovery architecture in which omics evidence constrains biological activity, LLM retrieval expands mechanistic search space, and network-aware fusion preserves interpretability. The framework provides a reproducible basis for dual-disease target prioritization and motivates continuous literature-mechanism concordance with agentic evidence-refresh loops.

bioinformatics↗

bioRxiv2026

MorphOTU: A universal image-based framework for delineating biodiversity discovery

Biodiversity can be quantified only after organisms are assigned to reproducible units, yet most individuals encountered in nature lack reliable species-level identifications. Molecular operational taxonomic units can organize unnamed diversity, whereas image-based approaches generally depend on predefined species levels. Here, we show that operational biodiversity units can be derived directly from phenotypes. We developed morphOTU, a framework combining self-supervised representation learning, operational metric supervision, and adaptive hierarchical clustering to organize specimen images in continuous phenotypic space. Across five benchmark datasets comprising flowers, wood anatomy, and beetle habitus, morphOTUs recovered coherent species-level structure and produced -diversity estimates close to those obtained from expert identifications. This structure remained informative when species were excluded from representation learning, when labeled data were sparse, and per-species sampling was limited. In a heterogeneous field-survey dataset of 4,717 insects representing 269 species across 12 orders, fine-tuning on only 28 common species produced diversity estimates close to expert labels (Shannon index, 3.75 versus 3.53). Visual explanations localized variation to biologically meaningful structures, including body outliers, surface sculpture, floral symmetry, and wood vessels. Morphological units therefore provide an operational layer for organizing and quantifying biodiversity before, alongside, or in the absence of formal species names.

bioinformatics↗

bioRxiv2026

Global Acetylome Profiling Reveals Extensive Lysine Acetylation in Acinetobacter baumannii Bacteriophage Proteins

Post-translational modifications (PTMs) are increasingly recognized as potential regulators of bacteriophage-host interactions, yet their functions remain largely undefined. Here, we present the first proteome-wide characterization of lysine acetylation in a bacteriophage, using Acinetobacter baumannii myovirus vB_AbaM_DLP3 as a model to investigate host-imposed modification during infection. An optimized proteomic workflow that eliminates chemical artifacts and improves peptide identification accuracy enabled detection of 86 acetylated proteins, representing nearly one-third of the DLP3 proteome. Comparative analysis of purified virions and infected host cells revealed distinct acetylation profiles, consistent with host-driven, transient modifications that are removed or lost after lysis. Functional annotation showed that acetylation predominantly targets proteins involved in DNA replication, genome packaging, and structural assembly. Structural modeling of the major capsid and replication-associated proteins demonstrated that acetylation neutralizes positive surface charges, potentially weakening DNA binding and intercapsomer interactions critical for replication and capsid cohesion. Together, these findings establish lysine acetylation as a widespread and dynamic feature of phage infection and identify host-imposed acetylation as a potential regulatory mechanism that modulates phage replication, assembly, and infectivity. This work expands the molecular framework of phage-host interactions, providing a foundation for future studies aimed at understanding how bacterial PTMs influence phage function and for engineering phages resistant to host-mediated inhibition. ImportanceBacteriophages are being developed as alternatives to antibiotics, yet little is known about how bacterial hosts chemically modify phage proteins during infection. This study reveals that A. baumannii imposes extensive lysine acetylation on its infecting phage DLP3, affecting proteins involved in DNA replication and structural assembly. By demonstrating that acetylation neutralizes positive surface charges and is largely absent after phage release, this work identifies host-driven acetylation as a previously unrecognized, reversible mechanism that may influence phage infectivity. Understanding how bacteria use post-translational modifications to interfere with phage function provides new insight into phage-host molecular interactions and informs strategies for engineering therapeutic phages resistant to host-imposed inhibition.

microbiology↗

bioRxiv2026

Prenatal THC exposure disrupts mitochondrial respiratory gene programs and delays medium spiny neuron maturation in the nucleus accumbens

Prenatal cannabis exposure (PCE) is increasingly prevalent and has been associated with adverse neurodevelopmental outcomes, yet its molecular impact on brain reward circuitry remains poorly defined. Here, we investigated transcriptional and epigenomic alterations in the nucleus accumbens (NAc) following prenatal {Delta}9-tetrahydrocannabinol exposure in a rat model using snRNA-seq and snATAC-seq analyses. PCE markedly suppressed the expression of genes involved in mitochondrial oxidative phosphorylation (OXPHOS) in the NAc on postnatal day 24 (P24), indicating reduced mitochondrial respiration capacity. This disrupted mitochondrial respiratory gene programming was accompanied by coordinated alterations in ribosomal and proteasomal pathways regulating protein homeostasis in NAc medium spiny neurons (MSNs), suggesting coupled disruption of cellular metabolism and neuronal maturation. snATAC-seq analysis revealed altered chromatin accessibility at promoter regions enriched for Nrf1 and Yy2 binding motifs, implicating Hrf1- and Yy2-associated transcriptional regulation of mitochondrial genes in MSNs following PCE. Moreover, an acute THC challenge in PCE offspring at P24 further exacerbated the suppression of genes involved in mitochondrial OXPHOS and MSN maturation. Together, these findings define a transcriptional and epigenetic framework through which PCE may perturb mitochondrial function and impair MSN maturation trajectories in the NAc, providing mechanistic insights into how PCE may alter the development of reward circuitry.

neuroscience↗