Biology subjects

Cao, Y.

Publications and source records attributed to Cao, Y..

At least 73 records · Page 4Linked to original sources

bioRxiv2026

Estrogen receptor-positive cell line xenograft models recapitulate metastatic dissemination and endocrine response of invasive lobular breast carcinoma

HighlightsO_LIER+, CDH1-deficient ILC xenografts recapitulate single-file histology in vivo C_LIO_LISpontaneous metastases faithfully mirror unique ILC clinical dissemination patterns C_LIO_LIER+ leptomeningeal metastases confirmed histologically in ILC xenograft models C_LIO_LIFulvestrant inhibits ILC tumor growth and metastatic burden, improving survival C_LIO_LIER signaling is enriched in ILC brain metastases, with upregulation of RET C_LI Invasive lobular breast carcinoma (ILC), the most common special histological subtype of breast cancer, is characterized by nearly universal expression of estrogen receptor alpha (ER) and unique sites of metastases, neither of which is fully recapitulated by genetically engineered mouse models. Using reporter-labeled ILC mouse xenografts, herein we used mammary fat pad, tail vein and intracardiac orthotopic growth to analyze spontaneous and experimental metastasis and gene expression. We observed ER-positive primary tumors with single-file histology and collagen deposition, and spontaneous metastasis from the mammary fat pad to bones, ovaries, and brain including the leptomeninges, thereby closely mirroring the growth and metastatic spread of human ILC. Brain metastases showed strong ER staining, confirmed by sequencing analyses which identified estrogen signaling as top activated pathway, and the lesions exhibited robust response to endocrine therapy. In summary, we report endocrine responsive mammary fat pad, tail vein and intracardiac xenografts that faithfully demonstrate unique ILC features and can serve as invaluable pre-clinical translational platforms for validating candidate ILC genetic drivers and testing novel therapeutics.

cancer biology↗

bioRxiv2026

Hierarchical control of cardiomyocyte maturation and ischaemia sensitivity by metabolic culture conditions

Ischaemic heart disease remains the leading cause of mortality worldwide, yet no therapies prevent cardiomyocyte death during acute ischaemia-reperfusion injury (IRI). Human induced pluripotent stem cell-derived cardiomyocytes (hiPSC-CMs) provide a platform for modelling cardiac injury, but their immature phenotype limits the physiological fidelity of in vitro models. Here, we systematically evaluated how experimental variables used during preparation of hiPSC-CM endpoint assays influence cardiomyocyte maturation and susceptibility to IRI. Integrating literature mining, molecular profiling, statistical genetics, and functional assays, we examined the effects of replating conditions, backbone media, metabolic substrates, and signalling modulators. We define the relationship between culture conditions and metabolic supplements in determining contractile maturation and sensitivity to IRI. Notably, we show that metabolic composition of the backbone medium establishes the baseline maturation state and determines responsiveness to additional maturation cues. These findings identify metabolic environment as a dominant regulator of injury susceptibility and provide a framework for improving the physiological fidelity of hiPSC-CM models of cardiac ischaemia.

cell biology↗

bioRxiv2026

A biofidelic Goat Model of Traumatic Optic Neuropathy with Optic Canal Fracture via Transnasal Endoscopy

Traumatic optic neuropathy (TON) is a major cause of irreversible vision loss following blunt cranial trauma, yet the absence of clinically relevant large animal models that faithfully recapitulate human TON has significantly impeded translational research. Current rodent models do not reproduce optic canal fracture, a key injury mechanism in many patients with TON. Here, we combined high-fidelity finite element analysis (FEA) with iterative engineering to establish a reproducible goat model of TON. We first built a high-resolution human-head finite element model to characterize force transmission to the optic nerve. Across clinically relevant periorbital impacts, stress preferentially concentrated in the intracanalicular segment, reaching a peak force density of approximately 500 N/m2 at 50.6 ms, about fivefold higher than in the intraorbital segment. Simulations further showed that direct optic canal impact reproduced comparable intracanalicular stress with a markedly lower input force: 195 N, compared with 3900 N for periorbital impact. Guided by these insights, we developed transnasal endoscopic impact systems capable of inducing optic canal fractures in goats. TON was confirmed within 24 hours by a characteristic relative afferent pupillary defect (RAPD), and at 1 month post-injury goats (n = 14) exhibited a 10%-20% reduction in ganglion cell complex (GCC) thickness and 40%-65% reductions in flash visual evoked potential (FVEP) and pattern electroretinogram (PERG) amplitude ratios (all P [≤] 0.001), with structural and functional preservation of the fellow eye. This study presents a robust, standardized, and clinically relevant large-animal platform for investigating TON pathophysiology.

neuroscience↗

bioRxiv2026

Anti-IL1RAP Antibodies for Pan-Inhibition of IL-1 Family Cytokine Signaling in Inflammatory Diseases and Oncology

The interleukin-1 (IL-1) superfamily of cytokines--comprising the IL-1, IL-33, and IL-36 subfamilies--orchestrates a vast array of innate and adaptive immune responses. While physiological activation of these pathways is essential for host defense and tissue repair, their chronic dysregulation is pathognomonic of a broad spectrum of autoimmune diseases and malignancies. Current therapeutic modalities largely rely on the neutralization of single cytokines, an approach often limited by the functional redundancy and compensatory signaling loops inherent to the IL-1 superfamily. The Interleukin-1 Receptor Accessory Protein (IL1RAP) serves as an obligatory co-receptor for IL-1, IL-33, and IL-36 subfamilies, functioning as a molecular bottleneck for pro-inflammatory signaling. Herein, we report the development and comprehensive characterization of two humanized monoclonal antibodies, DXP-006 and DXP-106, which target a unique epitope on domain 2 of IL1RAP. Cryo-electron microscopy studies at 3.55 [A] resolution reveal that these antibodies lock the critical c2d2 loop of IL1RAP, sterically occluding its recruitment to IL-1R1, ST2 and IL-36R binary complexes and potently blockade IL-1, IL33, and IL-36 signaling. DXP-006, engineered with a half-life-extended and effector-silenced Fc, exerts profound efficacy in murine models of psoriasis, superior to the clinical benchmark bimekizumab. Conversely, DXP-106, engineered with a defucosylated Fc to enhance antibody-dependent cellular cytotoxicity, exhibits potent antitumor activity in non-small cell lung cancer xenografts. These findings position DXP-006 and DXP-106 as ideal therapeutics for IL-1 family-driven autoimmunity and IL1RAP-positive cancers. One Sentence SummaryAnti-IL1RAP antibodies block multiple IL-1 family cytokines simultaneously, showing superior efficacy in inflammation and cancer models.

immunology↗

bioRxiv2026

Identification of a neural basis for anorexia nervosa

Anorexia nervosa (AN) is a severe, often fatal, psychiatric disorder characterized by self-imposed food restriction, hyperactivity, and profound affective disturbances. Despite its high morbidity and mortality, the neural mechanisms underlying AN remain poorly defined, largely because no animal model has fully recapitulated its core behavioral manifestations. Here, we demonstrate that aberrant activation of glutamatergic neurons in the mediobasal hypothalamus (MBH) is sufficient to induce AN-like phenotypes in mice, including self-starvation leading to death, hyperactivity, anhedonia, social avoidance, and heightened anxiety, which were reproduced by targeted activation of MBH neurons expressing steroidogenic factor 1 (SF1)/ estrogen receptor (ER). Mechanistically, the AN-like phenotypes were rescued by ablating release of glutamate or brain-derived neurotrophic factor (BDNF). Conversely, BDNF overexpression in SF1/ER neurons was sufficient to promote AN-like behaviors through increasing glutamate release. Thus, BDNF-dependent enhancement of glutamatergic signaling from SF1/ER neurons drives AN-associated phenotypes, providing a potential target for therapeutic intervention.

neuroscience↗

bioRxiv2026

ST-Analyzer: A Packaged Web and Command-Line Interface for Simulation Trajectory Analysis

As high-performance computing provides the ability to generate and analyze ever larger simulation trajectories, the challenges in learning, applying, and sharing the best analytical practices become more salient. Extracting reproducible scientific insights from simulation requires a thorough understanding of many computing topics unrelated to the molecular systems being modeled and simulated. While the rapid development of the technologies used for analysis makes previously impossible studies into routine work, the growing repertoire of software combined with the specificity of the ecosystems that they rely on can easily break the programs used in older studies. In this work, we present ST-Analyzer, a simulation trajectory analysis suite with command-line (CLI) and graphical (GUI) user interfaces. ST-Analyzer is distributed freely as an open-source conda-forge package with support for macOS, Linux, and Windows (via WSL2). Besides facilitating several common analysis tasks, the GUI shows users the exact commands necessary to repeat the same tasks on the command-line. We demonstrate ST-Analyzers capabilities by reproducing several results from previously published simulation studies on the lipid parameters of heterogeneous biomembranes and the behavior of a SARS-CoV-2 spike protein-antibody complex. We expect ST-Analyzer to be useful to experts for quickly setting up common analysis tasks and to nonexperts as a guided introduction to simulation analysis using both GUI and CLI. ST-Analyzer is freely available at https://github.com/nk53/stanalyzer.

biophysics↗

bioRxiv2026

An agentic framework turns patient-sourced records into a multimodal map of ALS heterogeneity

ALS progression is multidimensional, yet fragmented records and scalar outcomes obscure how patients move through disease states and how those states relate to molecular variation. MEDSTREM converts patient-held medical-record images into standardised longitudinal data, enabling bottom-up cohort construction. Using MEDSTREM-structured records from more than 8,000 AskHelpU participants together with PRO-ACT and Answer ALS, we developed DynaALS, the ALS Disease Dynamics Atlas. DynaALS represents ALS as a dynamic patient-state manifold that captures distinct directions of deterioration and patient movement between them over time. DynaALS retrieved population-referenced future states and decoded them into multidimensional clinical profiles without requiring patient-specific longitudinal histories. Motor-neuron RNA and chromatin profiles linked DynaALS states to developmental and regulatory programs, while neuromuscular-organoid single-cell multi-omics converged on a neural-developmental Netrin-DCC signalling axis across interacting cell types. By coupling MEDSTREM-enabled data construction to dynamic state modelling, DynaALS establishes a transferable patient-state engine for predictive and biologically interpretable disease models.

bioinformatics↗

bioRxiv2026

Monitoring Gene Expression in Retina with Synthetic Serum Markers

Gene expression underlies retinal development, function, and pathogenesis. However, monitoring retinal gene expression in vivo is challenging. In this study, we apply synthetic serum markers, called Released Markers of Activity, or RMAs, to quantify gene expression in an intact retina through a simple blood test. We show that RMAs can quantify transduction of multiple retinal cell-types and monitor cell implantation or cell loss. We found RMAs are sensitive enough to measure transduction of rare cell populations, such as retinal ganglion cells and could detect transplantation of as few as 100 stem cells. Expression of RMAs showed no evidence of cell loss or immune activation in the retina. Overall, these findings demonstrate that RMAs are highly sensitive, tissue non-destructive gene expression reporters that can continuously track gene delivery and cell survival in intact retina through a simple blood test.

bioengineering↗

bioRxiv2026

Cooperative Regulation of Membrane Domain Registration by Lipid Headgroup Size and Cholesterol Dynamics

The lateral organization of lipid domains and their coupling across the two leaflets are central to the structure of plasma membranes, yet the molecular determinants of domain registration and anti-registration remain incompletely understood. Here, we employ coarse-grained molecular dynamics simulations to investigate how lipid headgroup properties and cholesterol (CHOL) concentration regulate domain registration and anti-registration in symmetric model bilayers. Using a free energy perturbation (FEP)-like headgroup-interpolation approach to continuously interpolate between headgroup representations characteristic of phosphatidylethanolamine (PE) and phosphatidylcholine (PC) lipids at a fixed tail composition, we show that headgroup properties and CHOL concentration act cooperatively through their effects on lipid packing and membrane curvature. Simulations with restrained CHOL flip-flop further demonstrate that transbilayer CHOL exchange actively strengthens interleaflet coupling and promotes domain registration. These results identify headgroup-dependent packing, CHOL-induced curvature, and CHOL flip-flop as cooperative determinants of domain organization in model membranes. TOC Graphic O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=114 SRC="FIGDIR/small/699701v2_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1a78635org.highwire.dtl.DTLVardef@15c17f7org.highwire.dtl.DTLVardef@1295adaorg.highwire.dtl.DTLVardef@ba80a_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

EOLA1, a novel mitochondria-localized protein critical for heart functions via regulating mitochondrial translation

Mitochondria possess their own mRNA translation system, mediated by specialized mitoribosomes. Dysregulation of mitochondrial translation disrupts metabolic homeostasis and is linked to various pathologies, including metabolic syndromes, neurological disorders, and cardiac diseases. Using CRISPR/Cas9 screening, we identified EOLA1 (endothelial-overexpressed lipopolysaccharide-associated factor 1) as a novel mitochondrial matrix protein essential for metabolic homeostasis. Knockout of Eola1 severely affects mitochondrial translation and consequently the oxidative phosphorylation in mammalian cells. Mechanistically, EOLA1 physically interacts with mitochondrial 12S ribosomal RNA (12S mt-rRNA) and the mitochondrial Tu translation elongation factor (TUFM), facilitating efficient translation elongation of mitochondrial-encoded mRNAs. Furthermore, genetic ablation of Eola1 in mice induced severe cardiac dysfunction, demonstrating its indispensable role in maintaining heart function through mitochondrial translation control. Together, our findings establish EOLA1 as a key regulator of mitochondrial translation via its interactions with 12S mt-rRNA and TUFM, highlighting its importance in cellular metabolism and a potential role in cardiac disease pathogenesis.

molecular biology↗

bioRxiv2026

Multiplexed measurements of protein-protein interactions and protein abundance across cellular conditions using Prod&PQ-seq

Methods to profile protein-protein interactions (PPIs) have limited scalability and can only study a handful of conditions and/or targets. Here, we introduce Prod&PQ-seq, a framework for multiplexed detection and quantification of PPIs and proteins. Our framework uses cross-linked cells, antibody-oligonucleotide conjugates (ab-oligos), and captures PPIs by the DNA-caliper, a specialized oligonucleotide for bidirectional priming of proximal ab-oligos. We benchmarked Prod&PQ-seq using recombinant complexes, titrations and cell mixture experiments and show that our framework is quantitative, reproducible, sensitive and specific. Applying Prod&PQ-seq to study Polycomb Repressive Complex 2 (PRC2) shows that EZH2 inhibition and expression of the oncohistone H3.3K27M weakens both PRC2-H3K27me3 interactions and PPIs within PRC2. Further, H3.1K27M and H3.3K27M variants lead to distinct PPI profiles such as the intensity of H3K27ac-K27M or H3K27ac-EED. Together, Prod&PQ-seq enables detection of changes in PPI composition and intensity and protein quantification across biological conditions, small molecule inhibition and genetic perturbations. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=197 HEIGHT=200 SRC="FIGDIR/small/697286v2_ufig1.gif" ALT="Figure 1"> View larger version (59K): org.highwire.dtl.DTLVardef@1ed0805org.highwire.dtl.DTLVardef@a9c0d9org.highwire.dtl.DTLVardef@b411fborg.highwire.dtl.DTLVardef@8a12e_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

Tuning the open-close equilibrium of Cereblon with small molecules influences protein degradation

Most PROTACs and molecular glue degraders currently approved or in clinical trials recruit Cereblon (CRBN) as the ubiquitin E3 ligase. Upon binding ligands and molecular glues, CRBN undergoes a significant structural rearrangement from an open to closed state, defined by the positioning of the thalidomide-binding domain (TBD) with respect to the Lon domain. However, the exact molecular basis for this ligand-induced conformational change and its implication to neo-substrate degradation remain elusive. During our campaign to discover novel CRBN binders, we found hits exhibiting distinct biophysical behaviour from classical thalidomide-based ligands. By combining orthogonal biophysical methods of differential scanning fluorimetry, isothermal titration calorimetry, and small-angle X-ray scattering, supported by X-ray crystallography and cryo-EM structures of ligand-bound complexes, we classify CRBN binders between those that can induce CRBN closure, and those that cannot. Mutational studies identify key residues in the CRBN ligand binding pocket and N-terminal belt that are essential for the Lon and TBD domains to come together in the closed state. Finally, we show that the probability to yield active degrader molecules is greatly influenced by whether binders can or cannot induce CRBN closure. Together, our study reveals new molecular insights into the structural basis for how CRBN open-closed equilibrium is directly modulated by compound binding and impact target degradability by CRBN, with important implications to the design of PROTACs and molecular glue degraders.

biochemistry↗

bioRxiv2025

Helix: a structure-aware deep learning model for accurate prediction of A-to-I RNA editing by endogenous ADARs

Adenosine deaminase acting on RNA (ADAR) converts adenosine to inosine within double-stranded RNA (dsRNA) and can be co-opted for therapeutic RNA editing by introducing dsRNA substrates in trans using programmable guide RNAs (gRNAs). However, ADARs natural promiscuity necessitates sophisticated gRNA designs to achieve efficient and specific editing. Here we present Helix, a predictive model that achieves highly accurate, zero-shot per-adenosine editing predictions for any target sequence. Helixs performance arises from two architectural choices: a transformer framework that scales effectively with increasing and imbalanced training data; and a structure-aware attention mechanism that incorporates predicted RNA secondary structure, a key determinant of ADAR activity. Helixs predictive accuracy enables seamless integration with DeepREAD, our previously reported generative model, in a noisy-student distillation framework termed DeepHelix. This workflow supports both zero-shot gRNA design and the generation of complex, constraint-based designs. We demonstrate DeepHelixs utility by designing gRNAs that efficiently edit a therapeutically relevant adenosine and by leveraging its flexible design space to engineer species cross-reactive gRNAs to accelerate pre-clinical development.

bioengineering↗

bioRxiv2025

IGHV3-53 antibody abundance drives divergent SARS-CoV-2 immune imprinting

The mechanisms driving divergent SARS-CoV-2 immune imprinting in populations with distinct SARS-CoV-2 exposure histories remain unclear. However, conventional wild-type mouse models fail to recapitulate severe imprinting, even after potent ancestral-strain mRNA immunization, hindering imprinting-related mechanistic investigation and vaccine evaluation. Here, we surprisingly found that V(D)J-humanized mice could faithfully recapitulate human severe imprinting phenotypes. Comprehensive antibody repertoire analysis and deep mutational scanning-based epitope mapping of 583 monoclonal antibodies from these models revealed that the pre-existing IGHV3-53/66 antibody abundance determine imprinting severity through antibody-mediated masking of Omicron-specific epitopes. Both passive IGHV3-53/66 antibody transfer and IGHV3-53 knock-in were sufficient to induce severe imprinting in wild-type mice. Together, these findings demonstrate that the V(D)J germline repertoire--even a single germline-encoded antibody response--can profoundly shape humoral imprinting severity. Accordingly, we established an IGHV3-53 knock-in mouse model that accurately recapitulates the human antibody landscape, providing a valuable tool for guiding future COVID-19 vaccine updates.

immunology↗

bioRxiv2025

Metabolic dysfunction related to specific genetic variant sites of methylmalonic acidemia

Methylmalonic acidemia (MMA) is a genetic metabolic disease, with mut (mut-MMA, caused by MMUT gene variation) and cblC (cblC-MMA, caused by MMACHC gene variation) being the predominant subtypes. MMA patients carrying c.729_730insTT and c.609G>A exhibit severe clinical manifestations and have poorer outcomes. Little information is known on the potential mechanism. The metabotypes of MMA patients carrying c.729_730insTT and c.609G>A were profiled. The potential effect of genetic variation sites on the metabolism were explored. Leveraging the gene variation spectrum and the targeted metabolomics, propionic acid, indolelactic acid, myristoleic acid, tetradecenoic acid, tridecanoic acid, and oxoadipic acid showed strong enrichment in c.729_730insTT carrying mut-MMA patients. Whereas mutation c.609G>A caused adipic acid, pimelic acid, fructose, AMP, hexanylcarnitine, and methionine significnatly altered in cblC-MMA patients. Furthermore, the metabolomic profiles were obviously different in c.729_730insTT and non-c.729_730insTT carrying mut-MMA patients after treatment. Different metabolic alterations in cblC-MMA patients carrying c.609G > A and non-c.609G > A under treatment were also observed. Our findings provide unique insights into the metabolic basis of MMA specific subtypes and its implications across different variants.

molecular biology↗

bioRxiv2025

Synchronized Latency Reversal and Immune Clearance by a Multifunctional Fusion Protein Enables HIV-1 Reservoir Reduction

Strategies that concurrently reactivate latent reservoirs and enhance immune-mediated clearance hold significant promise for achieving an HIV cure. Here, we developed hyperIL-15xsCD4-Fc (15xsCD4-Fc), a fusion protein that integrates latency reactivation, targeted immune engagement, and effector-mediated killing into a single molecule. This agent not only potently reverses HIV-1 latency in CD4+ T cells from people living with HIV-1 (PLWH) through coordinated IL-15 receptor signaling and sCD4-mediated HIV-1 envelope (Env) engagement, but also enhances antigen-specific CD8+ T cell response in PBMCs derived from PLWH. Furthermore, 15xsCD4-Fc enables Env-specific elimination of reactivated latently infected cells by NK cells while preventing off-target cytotoxicity. In PBMCs from PLWH, 15xsCD4-Fc reduced replication-competent HIV-1 DNA by 93.8%. In antiretroviral treated HIV-1-infected humanized mice, the molecule demonstrated both safety and efficacy in diminishing viral reservoir in lymphoid organs. This spatiotemporally coupled approach to reservoir exposure and immune recognition establishes a clinically viable strategy for clearing the HIV-1 reservoir. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/693434v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@8f8f0org.highwire.dtl.DTLVardef@10f63f7org.highwire.dtl.DTLVardef@16c1de2org.highwire.dtl.DTLVardef@11e1787_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

AAV vectors with enhancer-controlled ITR promoters

Adeno-associated virus (AAV) is limited by its packaging capacity and the unwanted promoter activity of inverted terminal repeats (ITRs). Here we utilized mini-enhancers to regulate ITR promoters and drive AAV cargo expression in the absence of the canonical promoters, which not only solved the ITR issue but also released more payload for the cargo. As an example, this new design successfully enabled robust, tissue-specific SpCas9 gene editing via a single AAV, which otherwise requires a dual-AAV system due to the large size of SpCas9.

bioengineering↗

bioRxiv2025

Protein-protein interactions drive differences in the spatiotemporal dynamics of transcription factors NANOG and SOX2 in naïve pluripotent cells

Maintenance of naive pluripotency requires core transcription factors (TFs) like SOX2 and auxiliary TFs like NANOG, yet molecular mechanisms governing their intra-nuclear dynamics and DNA binding interactions remain unclear. Here, using high-density 3D single-molecule light-field microscopy combined with novel spatiotemporal analysis pipelines, we track SOX2 and NANOG dynamics in live cells. Despite lower protein abundance, NANOG displays a similar chromatin-bound fraction to SOX2. This arises partially because, while both TFs undergo frequent transient non-specific binding interactions ([~]0.5-0.7s), NANOG exhibits more stable specific binding ([~]25s vs [~]16s). Both TFs also assemble into phase-separated domains of [~]400 nm containing both freely diffusing and chromatin-bound proteins, which further influences their dynamics. Strikingly, NANOGs protein-protein interaction domain markedly increases chromatin residence time (>5-fold) and the size of these phase-separated domains. Our work uncovers how NANOG and SOX2 stabilise gene regulatory networks that maintain naive pluripotency while providing quantitative pipelines for dissecting spatiotemporal TF dynamics.

cell biology↗