Biology subjects

Huang, Y.

Publications and source records attributed to Huang, Y..

At least 109 records · Page 6Linked to original sources

bioRxiv2026

Generation of three induced pluripotent stem cell lines from an immune checkpoint inhibitor-induced myocarditis patient and controls

Immune checkpoint inhibitor-associated myocarditis (ICIM) is an uncommon but potentially fatal inflammatory heart disease triggered by cancer immunotherapy, with up to 40% mortality. The underlying mechanisms are still elusive, partly due to the lack of appropriate human disease models. Here, we report the generation of three induced pluripotent stem cell (iPSC) lines derived from an ICIM patient, an ICI-treated patient without myocarditis, and a healthy donor. These lines exhibit typical pluripotent stem cell morphology, express pluripotency markers, maintain normal karyotypes, and differentiate into derivatives of the three germ layers, providing a valuable platform for mechanistic studies and therapeutic discovery.

Developmental Biology↗

bioRxiv2026

Healing cascades and infections in wounds monitored using a wearable sensor of gaseous flux

Capabilities for quantitative monitoring of chronic wounds remain an unmet clinical need, as existing diagnostic approaches rely on semiquantitative evaluation of symptoms that lack sensitivity especially during early stages of infection. Here we present a scheme for tracking wound physiology that leverages a miniature, wireless skin-interfaced device for non-contact, transient measurements of the flux of volatile organic compounds (VOCs) and water vapor from the wound microenvironment. Unlike emerging smart bandage platforms that rely on physical contact with the fragile wound bed to interrogate liquid-phase biomarkers, this strategy uses an engineered microclimate and suspended suite of sensors to measure the diffusive transport of wound-derived gases across the wound surface but separated from it. The result enables quantitative evaluation of metabolic activity and healing progression without perturbing the healing tissues. In biofilm growth models of Staphylococcus aureus, measurements demonstrate that trends in VOC flux correlate strongly with bacterial growth kinetics and precede any visible biofilm formation. Longitudinal monitoring in infected murine wound healing models shows that concurrent measurements of water vapor and VOC flux provide complementary physiological insights, capturing both the trajectory of barrier restoration and the dynamics of bacterial burden. The findings establish this non-contact sensing scheme as a distinct and clinically translatable paradigm for wound monitoring, with broad implications for non-invasive surveillance of disease states in which tissue metabolic activity and skin barrier integrity serve as actionable physiological readouts. Significance StatementLimited capabilities in continuous, quantitative assessment of a wound make early diagnosis and effective management challenging, particularly in cases of infection that rapidly progress before symptoms appear. Non-contact approaches for wound monitoring that preserve fragile tissue can transform wound care. In this context, gaseous flux from the wound bed provides an integrative measure of microbial activity and barrier restoration. This study establishes a wearable sensing platform that quantifies these fluxes in real time, enabling early infection detection and temporal tracking of wound healing. These results highlight a path toward personalized treatment strategies and reduced reliance on episodic clinical evaluation.

bioengineering↗

bioRxiv2026

Subregion-Specific Input Organization of Prefrontal-Projecting Basal Forebrain Cholinergic Neurons and Weakened Striatum-to-NBM Inhibitory Transmission in 5xFAD mice

Basal forebrain cholinergic neurons regulate cortical activity and cognition and are vulnerable in Alzheimers disease (AD). However, the upstream circuits controlling projection-defined basal forebrain cholinergic populations remain incompletely understood. Here, we used projection-specific rabies-mediated monosynaptic tracing to map whole-brain inputs to medial prefrontal cortex (mPFC)-projecting cholinergic neurons in the nucleus basalis of Meynert (NBM) and horizontal limb of the diagonal band of Broca (HDB). mPFC-projecting NBM and HDB cholinergic neurons received broad but distinct input patterns. NBM cholinergic neurons received prominent striatal input, including input from D1-expressing medium spiny neurons, whereas HDB cholinergic neurons showed proportionally weaker striatal input and broader non-striatal contributions. Optogenetic electrophysiology confirmed that striatal inputs formed monosynaptic GABAergic inhibitory synapses onto NBM cholinergic neurons. This inhibitory transmission was weakened in 5xFAD mice, indicating impairment of a striatal-NBM inhibitory circuit in an AD mouse model. Together, these findings reveal subregion-specific input organization of mPFC-projecting basal forebrain cholinergic neurons and identify a vulnerable striatal-NBM circuit in AD. HighlightsO_LIWhole-brain rabies tracing reveals input organization of mPFC-projecting BF cholinergic neurons. C_LIO_LINBM and HDB cholinergic neurons projecting to mPFC show distinct monosynaptic input profiles. C_LIO_LIStriatal D1-MSNs are a major input source to mPFC-projecting NBM cholinergic neurons. C_LIO_LIStriatal-NBM inhibitory transmission is functionally impaired in 5xFAD mice. C_LI

neuroscience↗

bioRxiv2026

Structural Basis of Nidovirus Replication Organelle Evolution Revealed by the Arterivirus DMV Pore Complex

Positive-strand RNA viruses of the order Nidovirales - which include coronaviruses and arteriviruses - remodel host membranes into double-membrane vesicles (DMVs) as replication organelle to shield viral RNA synthesis from immune sensors. In coronaviruses, newly synthesized RNA is exported to the cytoplasm through a massive DMV pore complex formed by viral non-structural proteins (nsps). However, it remains unknown whether this elaborate architecture is unique to large-genome coronaviruses or a universal hallmark of the order. Here, we integrate in situ cryo-electron tomography and single-particle cryo-electron microscopy to resolve the atomic structure of DMV pore complex within its native membrane environment, from Equine Arteritis Virus (EAV), a prototype arterivirus with small genome. Despite lacking obvious sequence homology, the minimal EAV pore shares conserved architectural principles with its elaborate coronavirus counterpart. EAV pore complex is formed by a 12:12 stoichiometry of nsp2 and nsp3 protomers organized into four stacked concentric rings on double-membrane, yet generating pronounced structure symmetry mismatch. Functionally, the complex displays a distinct pore profile while preserving a positively charged central channel, essential for viral replication and transport. These findings demonstrate that, despite diversity in genome size and virion morphology, nidovirus replication organelles exhibit striking evolutionary conservation at the atomic structural level. Collectively, we propose that the order Nidovirales can be unified at the ultrastructural level by this conserved signature pore complex on the DMV-based replication organelle.

microbiology↗

bioRxiv2026

Cardiomyocytes Undergo a Mesenchymal-Like Fate Transition in Myocardial Fibrosis

BACKGROUNDMyocardial fibrosis, a pathological hallmark of adverse cardiac remodeling and heart failure, has been conventionally attributed to the activation of resident fibroblasts. Although recent studies suggest contributions from non-fibroblast lineages, direct in vivo genetic evidence that cardiomyocytes can undergo a mesenchymal-like fate transition during myocardial fibrosis remains absent. This study aims to investigate whether such a transition occurs and to elucidate the underlying regulatory mechanisms. METHODSHuman myocardial infarction (MI) tissues were analyzed by immunohistochemistry and integrated with public single-nucleus RNA sequencing (snRNA-seq) data to detect mesenchymal-like signatures in cardiomyocytes. Genetic lineage-tracing was performed in MI mice, and in cardiomyocyte-specific Hgs (hepatocyte growth factor-regulated tyrosine kinase substrate) gene knockout mice, to map the fate of cardiomyocyte-derived cells. Mechanistic insights were obtained through proteomic and snRNA-seq analysis of Hgs knockout hearts and validated through gain- and loss-of-function experiments targeting Aldh1a2 (aldehyde dehydrogenase 1 family member A2). RESULTSIn human MI samples, a subset of cardiomyocytes showed reduced expression of cardiomyocyte markers concurrent with acquisition of mesenchymal-associated markers. Genetic lineage tracing demonstrated that adult cardiomyocytes can adopt a mesenchymal-like cell fate during post-MI remodeling. We identify HGS as a factor constraining this transition. Hgs knockout in adult cardiomyocytes upregulated Aldh1a2, triggered the mesenchymal-like fate transition, and gave rise to cells expressing markers of activated fibroblasts or osteoblasts, accompanied by pronounced myocardial fibrosis and calcification. Forced Aldh1a2 overexpression in cardiomyocytes drove the mesenchymal-like fate transition in vitro and in vivo, whereas Aldh1a2 deletion in cardiomyocytes mitigated MI-induced myocardial fibrosis. CONCLUSIONSThis study provides in vivo genetic evidence that adult cardiomyocytes possess the capacity to undergo a mesenchymal-like fate transition under pathological conditions. Our data suggest that HGS and ALDH1A2 serve as regulators of the transition, offering a new basis for understanding cellular and molecular mechanisms of myocardial fibrosis. Novelty and SignificanceO_ST_ABSWhat Is Known?C_ST_ABSO_LIMyocardial fibrosis is primarily driven by resident fibroblast activation, with additional contributions from cardiac CD34+ cells, pericytes, and macrophages. C_LIO_LIAdult cardiomyocytes exhibit phenotypic plasticity and transdifferentiate into epicardial-like or pacemaker cells under specific conditions. C_LI What New Information Does This Article Contribute?O_LIA subset of cardiomyocytes adopts a mesenchymal-like cell fate during myocardial fibrosis, marked by downregulation of cardiomyocyte identity markers and loss of aligned cell-cell contacts. C_LIO_LIThese cells acquire mesenchymal morphology and markers, ECM components, migratory gene signatures, and proliferative capacity. C_LIO_LIHGS and ALDH1A2 act as regulators of this mesenchymal-like fate transition. C_LI Myocardial fibrosis drives heart failure progression, yet the cellular sources of pathological fibroblasts remain incompletely defined. Here, we demonstrate that a subset of cardiomyocytes adopts a mesenchymal-like cell fate during myocardial fibrosis by using an integrated approach combining human MI samples, murine genetic lineage tracing, and snRNA-seq. Mechanistically, we identify HGS and ALDH1A2 as regulators of this transition. Cardiomyocyte-specific Hgs deletion upregulates Aldh1a2, triggering the mesenchymal-like fate transition. Furthermore, Aldh1a2 overexpression drives this transition, while its deletion attenuates MI-induced fibrosis. These findings reveal a previously unrecognized plasticity of adult cardiomyocytes and identify potential therapeutic targets for fibrotic heart disease.

genetics↗

bioRxiv2026

Oxidized protein states define metastatic fitness in lung cancer

AbstractReactive oxygen species (ROS) are a pervasive feature of human cancers, yet the protein targets through which ROS-regulated cell states shape tumor biology remains poorly understood. Here, using cysteine chemical proteomics, we define signatures of protein states under distinct cellular ROS environments that capture protein oxidation and conformational changes. Quantifying these signatures in primary lung tumors and brain metastases revealed a surprising enrichment of oxidative states in metastasis. To determine how these states support fitness, we performed genome-wide CRISPR screens and identified the mitochondrial Complex I subunit NDUFA10 as a key oxidation-dependent vulnerability. Oxidation of NDUFA10*Cys253 supports Complex I function through a previously unrecognized nucleotide kinase activity that maintains mitochondrial DNA levels. Enforcing a reduced conformation in NDUFA10 disrupts brain metastatic colonization in vivo. These findings establish ROS regulated protein states as a functional layer of tumor fitness, providing a framework for identifying redox-dependent mechanisms that support cancer progression.

Cancer Biology↗

bioRxiv2026

PanKbase Integrated Single-Cell Map: A Comprehensive Atlas of Human Pancreatic Islets

Single-cell RNA sequencing (scRNA-seq) of human pancreatic islet tissue is a powerful tool for investigating type 1 diabetes (T1D). However, individual datasets are limited in size and fragmented across donors, laboratories, and experimental conditions. To address this, we constructed a comprehensive, integrated scRNA-seq atlas of isolated human pancreatic islets by collating publicly available data generated from tissue provided by resources including the Human Pancreas Analysis Program, the Integrated Islet Distribution Program, and Prodo Labs. Systematic quality controls were implemented to select high-quality samples, reads, and cells. During integration, we accounted for important variables such as age, sex, body mass index, origin study, treatments, islet distribution resources, and sequencing chemistry. Our single-cell atlas comprises 191 high-quality samples from 140 donors (59 female, 81 male) across five phenotypic groups: no diabetes (controls, n=69), autoantibody positivity without diabetes (n=12), pre-diabetes (n=11), T1D (n=12), and type 2 diabetes (T2D) (n=36). In total, the atlas contains 448,935 cells, capturing 13 distinct populations, including alpha cells (43.3%) and beta cells (26.8%), as well as groups such as immune cells (0.6%). Publicly available at www.pankbase.org, this atlas provides a platform for hypothesis-driven investigation of diabetes pathophysiology and, given rigorous quality control, is well-suited for downstream machine-learning applications. Article HighlightsO_LICurrent scRNA-seq datasets of pancreatic islet tissue are limited in size and scattered across donors, laboratories, and experimental conditions, underscoring the need for a consolidated resource. C_LIO_LIWe harmonized datasets from multiple sources to build a comprehensive single-cell map of isolated human pancreatic islets. C_LIO_LIOur atlas captures 448,935 cells from 191 high-quality samples across 140 donors and multiple phenotypic groups, identifying 13 distinct cell populations. C_LIO_LIAvailable at www.pankbase.org, the atlas provides a scalable, rigorously curated platform to support hypothesis-driven diabetes research and can enable a broad range of downstream computational applications. C_LI

genomics↗

bioRxiv2026

Human tissue-resident CD8 T cells contribute to trophoblast homeostasis in health and during acute inflammation

Previous studies have highlighted that some T cell subsets in tissues can provide signals to support tissue cell homeostasis and differentiation. If and how T cell-tissue cell signaling is altered in healthy compared to inflamed tissues is poorly understood. Here, we address if communication between human T cells and tissue cells changes from steady state to an acutely inflamed state in the human placenta. We used single cell analysis strategies to examine invasive cytotrophoblasts (iCTBs) and immune cells isolated from third trimester healthy and acutely inflamed human placentas. We performed cell communication analysis to predict cell-cell communication networks, and found evidence that iCTBs provided signals to support the recruitment of T cells, as well as the formation of tissue-resident memory CD8 T cells (Trm). In exchange, Trm provide signals to support iCTB homeostasis. During acute inflammation, iCTBs and macrophages underwent profound transcriptional changes, while most T cell subsets only underwent limited transcriptional changes. This was not due to T cell exhaustion or tolerance, as T cells were functionally intact. Cell communication analysis and validation at the protein level provide evidence that T cells can maintain their homeostatic support to iCTBs during acute inflammation.

immunology↗

bioRxiv2026

Desert hedgehog enhances endothelial resilience and prevents atherosclerosis by mitigating PAI-1 signaling

BACKGROUNDAtherosclerotic cardiovascular disease remains the leading cause of death worldwide. Most current pharmacotherapies target conventional risk factors that promote atherosclerosis (e.g., hyperlipidemia) rather than intrinsic resilience factors that protect against atherosclerosis in the face of risk factors. Here, we investigated the role of desert hedgehog (DHH), a canonical ligand of the hedgehog signaling pathway, as a novel resilience factor that restrains endothelial mesenchymal transition (EndoMT) and protects against atherosclerosis. METHODSSingle-cell RNA sequencing (scRNA-seq) was performed on atheroprone and atheroprotective regions of the ApoE knockout mouse aorta to identify mechanoresponsive genes associated with atherosclerosis. Endothelial cell-specific Dhh knockout mice were subjected to partial carotid ligation and hypercholesterolemic conditions to investigate the role of endothelial Dhh in atherosclerosis progression. scRNA-seq, bulk RNA sequencing, endothelial lineage tracing, immunoprecipitation-coupled mass spectrometry, and surface plasmon resonance were used to in-vestigate the role and mechanism of DHH in EndoMT. Pharmacological interventions and recombinant DHH administration were performed in vivo to evaluate therapeutic potential of DHH targeting. DHH expression was also examined in human atherosclerotic arteries and serum samples from patients with coronary artery disease. RESULTSDHH protein expression was enriched in arterial endothelium from mice, porcine, and humans. However, DHH expression was significantly reduced in atherosclerotic arteries and serum from patients with coronary artery disease. scRNA-seq of atheroprone and atheroresistant region of mouse aorta identified Dhh as a novel mechanoresponsive gene enriched in aortic regions exposed to unidirectional laminar flow. Endothelial cell-specific Dhh knockout (DhhecKO) mice exhibited increased atherosclerotic lesion area, large necrotic cores, and reduced collagen content following partial carotid ligation. Similarly, under hypercholesterolemic conditions, both male and female DhhecKO mice showed aggravated atherosclerosis progression. scRNA-seq of DhhecKO mouse aortas revealed an increased proportion of endothelial cells undergoing mesenchymal transition, indicating enhanced EndoMT. These findings were corroborated by bulk RNA-sequencing of DHH depleted HUVECs and endothelial lineage tracing in inducible DhhecKO mice. Mechanistically, DHH directly interacted with plasminogen activator inhibitor type 1 (PAI-1) and suppressed PAI-1-induced EndoMT. PAI-1 promoted EndoMT in ECs through activation of canonical TGF-{beta} signaling (SMAD2/3) and noncanonical AKT/ERK1/2 signaling via interaction with low-density lipoprotein receptor-related protein (LRP1). Neutralization of PAI-1 or inhibition of LRP1, AKT/ERK1/2, or SMAD3 signaling abolished DHH deficiency-induced EndoMT. DHH competitively inhibited PAI-1 binding to LRP1, thereby attenuating downstream pro-EndoMT signaling. Intriguingly, treatment with PAI-1 inhibitor TM5275 mitigated endothelial Dhh deficiency induced EndoMT in vivo. Of translational relevance, recombinant mouse DHH protein administration reduced atherosclerosis progression, stabilized plaque, and decreased the expression of EndoMT markers in ApoE knockout mice. CONCLUSIONSDesert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 signaling. The present study implicates endothelial DHH as a potential therapeutic target for atherosclerotic cardiovascular disease. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=163 SRC="FIGDIR/small/729715v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@194c8a3org.highwire.dtl.DTLVardef@1004d52org.highwire.dtl.DTLVardef@d47c73org.highwire.dtl.DTLVardef@368866_HPS_FORMAT_FIGEXP M_FIG C_FIG Desert hedgehog (DHH) is an intrinsic endothelial cell-enriched resilience factor that protects against EndoMT and atherosclerosis by preventing PAI-1 binding to LRP1 and downstream AKT/ERK, as well as SMAD2/3 signaling. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIDHH was identified as a flow-responsive resilience gene that is downregulated by disturbed flow in endothelial cells. C_LIO_LIEndothelial-specific deletion of Dhh promoted endothelial-to-mesenchymal transition (En-doMT) and atherosclerosis. C_LIO_LIDHH directly interacts with PAI-1 and preclude PAI-1 mediated pro-EndoMT signaling. C_LI What Are the Clinical Implications?O_LIDHH maintains endothelial homeostasis during atherosclerosis. C_LIO_LITargeting endothelial DHH-PAI-1 axis may represent a potential therapeutic strategy to reduce EndoMT and limit plaque progression. C_LIO_LILower circulating DHH level may serve as a potential biomarker of endothelial dysfunction and plaque vulnerability in atherosclerotic disease. C_LI

biochemistry↗

bioRxiv2026

Collecting Duct-Targeted Lipid Nanoparticles Deliver Pkd2 mRNA to Restore Polycystin-2 and Attenuate ADPKD

Autosomal dominant polycystic kidney disease (ADPKD), a leading genetic cause of kidney failure, is caused by mutations in the PKD1 or PKD2 genes, resulting in functional polycystin 1 (PC1) or polycystin 2 (PC2) deficiency, and is characterized by progressive cyst expansion in the kidneys. However, no approved therapy directly restores polycystin expression, and current treatments target downstream pathways rather than the genetic defect. Gene replacement therapy offers a direct route to functional rescue, but efficient delivery to cyst-lining renal epithelia remains a major barrier. To meet this challenge, we developed a lipid nanoparticle (LNP) that incorporates a collecting duct (CD) targeting peptide (CD LNPs) to enable delivery of Pkd2 mRNA (CD-mPkd2) to renal CD epithelia, the predominant site of cyst origin. CD LNPs increased renal accumulation and targeted CD cells in vivo, outperforming non-targeted formulations. In a Pkd2-deficient mouse model, repeated administration of CD-mPkd2 induced reversal of established cystic disease, restored renal architecture, and reduced the fibrotic and inflammatory microenvironment characteristic of ADPKD. Furthermore, CD-mPkd2 was well tolerated without detectable off-target toxicity. Given that PC2 supplementation can attenuate disease in Pkd1-deficient models, we further demonstrate that a single dose of CD-mPkd2 reduces cyst burden and improves renal function across this distinct genetic background. These findings establish CD-mPkd2 as a potential therapeutic strategy for ADPKD across genetic backgrounds.

bioengineering↗

bioRxiv2026

Modeling the journey as well as the destination: a control theory account of rotational navigation

Navigation requires estimating heading and transforming these estimates into actions. Prior models explain how self-motion and landmark cues are combined into heading estimates, but less is known about how these estimates are iteratively transformed into motor commands to reach a goal. Here, we hypothesized that navigation operates as a closed-loop process in which ongoing movement is updated by sensory prediction errors. To test this hypothesis, participants performed a goal-directed rotation task in virtual reality. On select trials, visual landmarks were shifted during movement, inducing a prediction error between the heading expected from self-motion estimates and the heading observed from the shifted landmarks. In parallel, we developed a closed-loop model of turning behavior that represents heading and angular velocity as jointly estimated states over time. This model accounts not only for final position--the destination--but also for the movement dynamics that produce it--the journey. The model predicts that landmark-induced visual prediction errors should produce rapid corrective changes in movement. Participant turning behavior qualitatively paralleled these model dynamics: acceleration changed after visual feedback, with larger landmark mismatches producing larger corrective responses. Together, these findings suggest that naturalistic movement depends on continuously transforming heading estimates into motor command through closed-loop control.

neuroscience↗

bioRxiv2026

Ground Truth-Based Evaluation of False Discovery Rate and Statistical Power in DIA Proteomics

Data-independent acquisition (DIA) mass spectrometry enables rapid proteomic quantification, yet the reliability of statistical inference in DIA-based protein quantification remains incompletely understood. Here, we systematically evaluated missingness, false discovery rate (FDR), and statistical power, defined as true positive rate (i.e. sensitivity or recall), using technical replicates and a spike-in benchmark with known ground truth. Analysis of 18 HeLa replicates revealed persistent, abundance-dependent missingness. In the spike-in experiment with five replicates, human peptides were titrated against a stable yeast background, allowing fold changes (FCs) to be compared with expected values. Across comparisons with log2FCs ranging from 0.2 to 2.5, the nominal BH-FDR substantially underestimated the true FDR. For example, at a BH-FDR threshold of 0.05, the true FDR was [~]0.2. Statistical power was [~]40% for a log2FC of 0.2 and increased to nearly 100% for a log2FC of 2.5. Additional incorporation of FC thresholds improved the true FDR for large-FC comparisons, with slight loss of power, but markedly reduced sensitivity for small-FC comparisons. Together, these results indicate that nominal FDR does not necessarily reflect actual error rates in DIA proteomics and that DIA performance is influenced by protein abundance and expected fold changes. This study provides a framework for experimental design and data interpretation in DIA-based proteomic studies.

bioinformatics↗

bioRxiv2026

Multimodal dynamics control activity of a glial glutamate transporter

Membrane transporters move polar solutes across lipid bilayers to regulate cellular metabolism, signaling, and drug distribution. These proteins operate via an alternating-access mechanism, cycling between extracellular-, intermediate-, and intracellular-facing conformations. The human excitatory amino acid transporter 1 (EAAT1) protects neurons from excitotoxic damage by mediating the uptake of glutamate and aspartate into glial cells. Defects in EAAT1 function result in numerous pathologies, including epilepsy and ataxia, suggesting that positive modulation of these transporters might ameliorate glutamate neurotoxicity. However, developing EAAT1 activators requires understanding the timing of conformational changes, which remain largely unexplored. Here, we establish an experimental platform that combines single-molecule Forster resonance energy transfer (smFRET) to monitor real-time conformational dynamics, single-transporter activity assays to correlate dynamics with function, and cryogenic electron microscopy (cryoEM) to visualize discrete conformations at high resolution. This platform enables detection of [A]ngstrom-scale movements of single transporter molecules in real time, revealing that EAAT1 intersperses rapid conformational dynamics with long pauses. Slow and fast dynamics can be modulated by substrates, membrane composition, and mutations, and are correlated with the enrichment of specific structural states. We leverage this platform to investigate an EAAT1 mutation associated with severe episodic ataxia and show that it inhibits transport by stabilizing a paused cytoplasm-facing conformation. These results identify multimodal dynamics as an intrinsic, regulatable feature of EAAT1 function and, therefore, a potential therapeutic target. Henceforth, our integrated platform will facilitate investigations of other regulatory factors, including the effects of small-molecule and lipid modulators on the transport cycle.

biophysics↗

bioRxiv2026

A Monoclonal Antibody Panel to Track Ongoing Antigenic Evolution of SARS-CoV-2 Variants

SARS-CoV-2 continues to evolve, generating successive variants with enhanced resistance to antibody-mediated neutralization. However, many existing monoclonal antibody (mAb) repertoires were derived from exposures to ancestral or early Omicron strains and thus incompletely capture the antigenic landscape of newly emerging strains. Here, we generated a mAb panel by immunizing naive, unimprinted VelocImmune humanized mice with spike from the KP.3.1.1 variant, and isolated and characterized 11 neutralizing antibodies targeting diverse epitopes of recently evolved antigenic variants. We then integrated these antibodies with previously characterized mAbs to establish an expanded toolbox for profiling antigenic evolution among emerging variants. Application of this panel to currently emerging SARS-CoV-2 variants provided mechanistic insight into recent antigenic evolution, highlighting the potential role of altered receptor-binding domain conformation. Our data also revealed clear differences in antibody-evasion profiles between JN.1-derived lineages and BA.3.2 lineages. Together, our findings establish an updated mAb panel for monitoring SARS-CoV-2 antigenic evolution.

microbiology↗

bioRxiv2026

A Novel Drug Candidate that Selectively Targets the Critical Androgen Receptor-ELK1 Growth Axis in Advanced and Drug-Resistant Prostate Cancer

Androgen receptor (AR)-dependent prostate cancer (PCa) cells require co-activation of ELK1 by AR to activate a critical set of cell cycle and mitosis genes, regardless of hormone - sensitivity. A small molecule antagonist (KCI807) that inhibits AR-dependent growth by selectively binding to AR and blocking its association with ELK1 is limited as a drug by auto-induced metabolism. Using structure-activity data, consistent with modeling a physically mapped KCI807 binding pocket, we developed a new class of compounds with a different core structure comprising 5-Hydroxy-2-(3-hydroxyphenyl)-1-methylquinolin-4(1H)-one (KCI830), with variable N- substituents. The compound with a N-2,2,2-trifluoroethyl substitution (KCI838) was the fastest acting and most potent inhibitor of AR-dependent cell growth and colony formation in PCa model cells, including exclusively AR splice variant-dependent and other enzalutamide-resistant cells, without affecting growth of AR-negative cell lines. Critical tests were conducted to establish that KCI838 recapitulates the previously elucidated mode of action of KCI807. KCI838 selectively inhibited ELK1-dependent vs. androgen response element (ARE)-driven promoter and gene activation by AR. KCI838 blocked AR binding to ELK1 in situ tested by BRET assay. Increasing the total cellular AR by [~]2-fold using ectopic AR expression caused the predicted change in drug dose-response profile for growth, implicating AR as the exclusive target for the activity of KCI838. KCI838s molecular scaffold conferred reduced enzyme induction in primary human hepatocytes and weakened interactions with human UGT1A1 and CYP1A2. In mice bearing an aggressive, enzalutamide-resistant patient-derived PCa tumor xenograft characteristically overexpressing prostatic acid phosphatase, daily bolus injections of a soluble 3phosphate monoester prodrug of KCI838 (KCI838PME) progressively inhibited tumor growth, concomitant with tumor accumulation of active hydrophobic drug, without significant toxicity. Additionally, ALZET osmotic pumps were used to establish proof-of-concept for reversible in vivo anti-tumor activity of KCI838PME administered in a low dose, controlled release mode. The results warrant investigation of KCI838PME in a controlled-release formulation, to treat PCa that is resistant to current AR-targeted therapies while obviating the need for testosterone suppression.

cancer biology↗

bioRxiv2026

The Drosophila melanogaster Genetic Reference Panel, Version 3 (DGRP3)

Drosophila melanogaster is a leading animal model for understanding basic genetic principles for biomedical research and for quantitative, population and evolutionary genetics and genomics. The D. melanogaster Genetic Reference Panel (DGRP) of [~]200 inbred strains with full genome sequences is a publicly available resource for genome wide association (GWA) studies of quantitative traits, systems genetics, and population genomic analyses. However, the small size of the DGRP limits the power to map rare variants or variants with small effect sizes. Here, we describe the DGRP Version 3 (DGRP3), consisting of full genome sequences from 1,233 inbred lines, of which 1,037 are currently extant. The DGRP3 harbors extensive genetic diversity, with 8,760,339 molecular polymorphisms including single nucleotide polymorphisms, insertions, deletions, inversions, tandem duplications and complex rearrangements. We identified 80,894 damaging variants and 4,550 genes with at least one loss-of-function haplotype. We inferred 16 mitochondrial haplotype groups, determined the microbial composition, and quantified the numbers of sensory bristles for the DGRP3 lines. We performed GWA analyses for inbreeding depression, host control of microbiome composition, and numbers of sensory bristles, identifying novel candidate variants and genes for each. The accompanying online tool (flydgrp.org) implements state-of-the-art association mapping methods and provides results for users DGRP3 data.

genomics↗

bioRxiv2026

Gene-Specific Analysis of Clonal Hematopoiesis Identifies ASXL1 as a Risk Factor for Lung Cancer

IntroductionClonal hematopoiesis of indeterminate potential (CHIP) is a recognized risk factor for hematologic malignancies, but its contribution to different types of solid cancers remains incompletely defined. MethodsHere, we performed a systematic, gene-specific analysis of CHIP across 19 common solid cancer types using two large population-based cohorts, the UK Biobank and All of Us with Cox proportional hazards models and nested case-control logistic models. ResultsWe demonstrate that the relationship between CHIP and solid tumors is highly cancer-type specific, with lung cancer exhibiting the strongest association. In lung cancer, this association is largely driven by ASXL1-mutant clones. Specifically, high variant allele fraction (high-VAF) ASXL1 conferring a significantly increased risk (hazard ratio = 3.2), and the associations remained robust after adjustment for age, sex, body mass index (BMI), smoking status, and genetic ancestry. Notably, ASXL1 CHIP was substantially enriched among smokers, and its association with lung cancer risk was restricted to ever-smokers, highlighting a key interaction between CHIP and environmental exposure. The enrichment of ASXL1 CHIP in lung cancer was further validated in two independent cancer-only cohorts, including MSK-IMPACT and TCGA. In addition, rare germline variant association analysis revealed that germline variation in ASXL1 had the strongest association with lung cancer susceptibility among all solid tumors. ConclusionsCollectively, our findings support a model in which smoking-associated expansion of ASXL1-mutant clones contributes to lung cancer development and suggest that gene-specific CHIP metrics may enhance risk stratification and early detection strategies.

bioinformatics↗

bioRxiv2026

Integrated optimization of experimental and computational workflows improves genome recovery in long-read gut metagenomics

Short-read metagenomic sequencing has been widely applied in microbial research due to its high quality and decreasing cost. However, short reads are inherently fragmented, which limits assembly contiguity and the recovery of complete microbial genomes. In contrast, long-read sequencing, with significantly longer read lengths, helps overcome these limitations. Achieving complete and accurate genome recovery is the core goal of metagenomics. To address this challenge, we systematically evaluated and optimized the long-read metagenomic workflow, from sample processing to computational assembly, using the CycloneSEQ platform.

bioinformatics↗