Biology subjects

Hao, Y.

Publications and source records attributed to Hao, Y..

At least 19 recordsLinked to original sources

bioRxiv2026

Spatiotemporal AI modeling of gene regulation and variant effects in the developing human brain

Understanding how genetic variation shapes gene regulation in the developing human brain remains a central challenge in neuroscience, particularly in transient cell types and developmental stages where data are limited. We present Seal, an interpretable AI transfer learning framework for genome-based modeling of gene expression and variant effects with spatiotemporal resolution across 26 brain regions, 30 cell types, and seven developmental stages. Seal predictions enable characterization of both germline and somatic brain variants, and provide mechanistic interpretation by linking sequence variants to transcriptional regulators in spatiotemporal context. Applying Seal to genome-wide association studies, we identify cell types and developmental windows relevant to neuropsychiatric disease risk, revealing shared and distinct regulatory architectures across six neuropsychiatric conditions that align with clinical trajectories. In the Simons Simplex Collection autism cohort whole genome data, Seal uncovers a significant burden of de novo regulatory variants in transient fetal excitatory neurons, revealing a cell-type and developmentally specific regulatory burden. By connecting genetic variation to spatiotemporal regulatory programs, Seal offers a general framework for uncovering mechanisms of human brain development and disease.

genomics↗

bioRxiv2026

A long-term organotypic slice culture model of patient high-grade glioma preserving tumor heterogeneity and architecture, and specificity of CAR T cell targeting

ABSTRACT Background: High grade glioma (HGG), encompassing IDH-wildtype glioblastoma (CNS WHO grade 4), diffuse midline glioma (CNS WHO grade 4), oligodendroglioma (IDH-mutant and 1p/19q-codeleted) CNS WHO grade 3, together with IDH-mutant astrocytoma of CNS grade 3 and grade 4, represents the most lethal group of adult diffuse gliomas. Despite significant efforts, obtaining improvements in patient survival has been limited, in part, by difficulties in comprehensive ex vivo modeling of the complexities of HGG. Although organotypic slice cultures and other platforms have shown promise, existing models often fail to capture the intrinsic cellular heterogeneity, microenvironment, and architecture of HGG, restricting investigations into their fundamental biology as well as design of novel therapeutics. Methods: We developed a patient-derived HGG organotypic slice culture (GOSC) platform demonstrating long-term preservation of intrinsic tumor characteristics. Vibratome-sectioned slices were cultured in defined medium under conditions approximating those in situ: reduced oxygen (4%), low glucose (2.5 mM), and no added growth factors. The characteristics of GOSCs after 28 days in culture, including expression of immunotherapy targets, were compared to parental tumors using histological staining, immunofluorescence, multiplexed PhenoCycler (CODEX) imaging, bulk RNA-seq expression profiling, and CAR T cell killing assays. Results: GOSCs preserved the histopathology, cell heterogeneity, tumor microenvironment, and tissue architecture of their parental tumors throughout at least 28 days in culture. Importantly, GOSCs retained parental patterns of immunotherapy target expression, and CAR T cells co-cultured with GOSCs demonstrated target-specific killing consistent with parental tumors. Conclusions: This ex vivo GOSC platform offers long-term preservation of the cellular and structural properties of parental HGG tumors, thereby providing a robust tool for extended preclinical studies, and facilitating development and evaluation of advanced tumor-targeting strategies.

cancer biology↗

bioRxiv2026

Profiling of Aggregated Amyloid β42-induced Proteomic Alterations in KOLF2.1J Induced Pluripotent Stem Cell-derived Neurons

Amyloid[beta]; (A[beta];) plaques are a hallmark of Alzheimer[prime]s disease (AD). A human cellular neuronal model that recaptures A[beta];-induced pathology is critical for advancing AD research. However, comprehensive proteomic profiling of A[beta];-induced cellular model remains elusive. In this study, we investigated the proteomic changes in induced pluripotent stem cell (iPSC)-derived neurons (iNs) exposed to synthetic A[beta]; (1-42) peptides (A[beta];42A) to improve our understanding of the cellular responses of A[beta]; aggregates and to establish a human-related platform for AD research. A[beta];42A formed extracellular aggregates around neuronal soma and neurites, impaired neurite outgrowth, and induced the expression of multiple AD-associated genes, such as APOE, BACE1, ADAM10. To define the molecular landscape of A[beta];-induced neuronal dysfunction, we performed proteomic analyses of whole-cell lysates as well as soma- and neurite-enriched fractions. Proteomic profiling revealed extensive gene alterations in pathways associated with synaptic function, neuronal maintenance, and AD pathogenesis, such as the upregulation of APOE. Importantly, the A[beta];42A-iNs system recapitulated molecular signatures observed in AD brain tissue and cerebrospinal fluid. Representative protein changes, including APOE upregulation and its colocalization with A[beta]; aggregates, were further validated in postmortem human AD brain tissue. Together, these findings manifest that the A[beta];42A-iNs system reproduces multiple cellular and molecular features of AD and exhibits strongly consensus with clinical observations. It provides a valuable platform for investigating A[beta];-driven neurodegeneration and for the discovery of therapeutic targets for AD.

neuroscience↗

bioRxiv2026

A Test for Confounding in Coupling of Multimodal Neuroimaging Data

Multimodal neuroimaging studies often involve comparisons between brain maps. Recently, statistical methods have been proposed to quantify and assess spatial correspondence between two modalities. The simple permutation-based inter-modal correspondence (SPICE) test evaluates whether within-subject correspondence exceeds chance, where the null distribution is constructed by permuting subject labels for one modality. Despite its easy implementation and minimal spatial assumptions, the critical assumption underlying permutation analysis, that subjects are exchangeable under the null, may be violated when covariates such as age, sex, or disease status systematically alter brain map distributions. This violation can produce results analogous to Simpson's paradox, where apparent population-level correspondence reflects between-group differences rather than genuine within-subject coupling. We propose a formal U-statistic-based test for such covariate effects, enabling both diagnostic evaluation of assumption violations and scientific discovery. Using synthetic and semi-synthetic neuroimaging data, we demonstrate well-controlled Type I error and high statistical power. We apply our method to test for confounding effects due to age and sex using real data from two pairs of imaging modalities in the Philadelphia Neurodevelopmental Cohort. Our framework increases the rigor and interpretability of intermodal coupling analyses, with broad implications for neuroimaging studies in heterogeneous populations, especially in developmental, aging, and disease-focused research.

neuroscience↗

bioRxiv2026

ProtPipe2: Multi-Platform Downstream Proteomics Analysis Tool

Proteomics studies increasingly use different technologies, including mass spectrometry, the antibody-based Olink platform, and the aptamer-based SomaScan platform. However, downstream analysis often depends on platform-specific scripts or point-and-click tools, limits flexibility and makes analyses difficult to reuse across platforms. We developed ProtPipe2, a downstream proteomics analysis framework for mass spectrometry, Olink, and SomaScan data that is available as both an R package and an interactive web application. ProtPipe2 supports quality control, preprocessing, imputation, batch correction, statistical analysis, visualization, pathway analysis, and result export. ProtPipe2 expands the original Protpipe workflow to additional proteomics platforms and provides reusable R functions for imputation, batch correction, and other downstream analyses. Its redesigned web application provides user-controlled methods and parameters through the same R-based workflow. Case studies across mass spectrometry, Olink, and SomaScan datasets demonstrated a consistent downstream analysis workflow across platforms. By supporting three proteomics platforms through both graphical and scripted workflows, ProtPipe2 makes downstream analysis easier to perform, repeat, and review. ProtPipe2 is freely available at https://nih-card.github.io/ProtPipe2/.

bioinformatics↗

bioRxiv2026

The neural geometry of surprise: Graded boundary breakthroughs in the human brain

How whole-brain neural states reorganize when events violate observers' predictions remains unclear. Using naturalistic magic-viewing fMRI, we show that more surprising events carry the whole-brain neural state progressively farther beyond the range occupied during non-surprise viewing. This graded departure is accompanied by coordinated reconfiguration across sensory and association systems rather than uniform response amplification. We call this phenomenon a boundary breakthrough. To quantify its depth, we used non-surprise brain states to define a reference range along the surprise-related transition direction. Boundary exceedance (E_BB) expresses the depth beyond this range in bits; each additional bit means that a reference state is half as likely to reach at least that far. On this scale, depth increased with independently rated surprise intensity, specifically in the breakthrough state and not in the paired reference state. Peri-event trajectories showed that the event deepened an excursion already under way. Exploratory analyses linked exceedance to one-week recognition memory in a surprise-dependent manner. Together, these findings identify a graded systems-level relationship between surprise intensity and the departure of the whole-brain neural state from its non-surprise reference range.

neuroscience↗

bioRxiv2026

Retinal degeneration in a mouse model of CRB1 disease rescued by the photoreceptor-specific CRB1-B isoform

Many genes involved in inherited diseases produce alternate mRNA isoforms that remain poorly characterized. Functional assessment of these isoforms could therefore unlock new insights into disease pathobiology or treatment. Here we investigated the function of the newly discovered B isoform of CRB1, a gene implicated in inherited retinal degenerations. CRB1-B is the most abundant retinal isoform, and differs from the canonical CRB1-A isoform in several important ways. Crucially, CRB1-B is the only isoform expressed by photoreceptors -- the cells vulnerable to degeneration. Using a mouse model of CRB1-associated degeneration with degraded visual acuity, we find that restoring CRB1-B to photoreceptors prevents degeneration and completely rescues visual function, despite the absence of other isoforms. The therapeutic mechanism involves preservation of adherens junctions between photoreceptors and supporting glia: We establish that progressive loss of these junctions is a key pathobiological mechanism underlying photoreceptor death, and that junction loss is prevented by restoring photoreceptor expression of CRB1-B. Our findings nominate CRB1-B replacement as a promising gene therapy strategy. More broadly, they suggest that exploring disease gene isoform diversity offers an untapped opportunity to devise novel therapeutics.

neuroscience↗

bioRxiv2026

A longevity-associated ubiquitin E3 ligase UBE3C governs lamin B1 homeostasis through selective autophagy and delay senescence

Nuclear lamina integrity is fundamental to cellular homeostasis across the lifespan 1, and its progressive deterioration is closely linked to human aging 2. Yet, the regulatory mechanism that govern this decline and how they might be counteracted in long-lived individuals remain poorly defined. Here, by combining whole-exome sequencing of Ashkenazi Jewish centenarians with GTEx transcriptomes, we identify ubiquitin E3 ligase UBE3C strongly associated with exceptional longevity and progressively declines with age across human tissues. UBE3C knockdown triggers premature senescence and destabilizes key nuclear lamina components Lamin B1 (LMNB1) and Lamin B receptor (LBR), while the longevity-associated UBE3C variant delays senescence and preserves LMNB1/LBR expression. Mechanistically, UBE3C interacts directly with LMNB1/LBR and modulates their abundance via selective autophagy. Notably, we uncover the ER- resident autophagy trigger CKAP4 3 bridges UBE3C and LMNB1. UBE3C loss enhances LMNB1-CKAP4 binding, linking nuclear lamina turnover to autophagy. Together, our findings establish UBE3C as a central guardian of nuclear lamina maintenance during senescence and offering novel insights into interventions against age-related nuclear lamina deterioration.

cell biology↗

bioRxiv2026

A multimodal interrogation of Broca's area in the pediatric and adult human brain

Language is a defining trait of our species, and disruptions in language acquisition can have profound consequences to the individuals affected. Uncovering the neurodevelopmental basis of this complex trait requires detailed molecular and cellular insights into the neocortical areas that support linguistic abilities. Here we performed joint gene expression and chromatin accessibility profiling at single-nucleus resolution (10x Genomics Single cell Multiome) and spatial transcriptomic profiling (Xenium high-plex in situ spatial transcriptomics) of Brocas area alongside adjacent motor cortical areas. We profiled individuals from different ancestries (European and African) and developmental stages (infancy, childhood, adolescence, and adulthood). We provide a high-resolution dissection of the cellular and molecular architecture of Brocas and motor cortical areas across early life stages and anchor the trajectories to the cellular states found in the adult human brain. We identify distinct area- and stage-specific cellular signatures, including a prominent role of glia populations and interneuron subtypes contributing to cytoarchitectonic specializations. Using longitudinal single cell spatial transcriptomic profiling, we orthogonally validate our consensus cell taxonomy and spatially resolve layer enrichment of neuronal and astrocyte subtypes that distinguish Brocas area and motor cortex. We also uncover cell type-specific molecular signatures that distinguish cell developmental trajectories in these cortical areas, including an early molecular code established by differential expression of cadherin genes that might contribute to area-specific intercellular communication. We also identify cell type-specific vulnerabilities to language- related neurodevelopmental and neuropsychiatric disorders, with selective susceptibility of particular somatostatin-positive interneuron subtypes to ASD/ADHD. Finally, evolutionary analysis of differentially accessible regions between Brocas area and motor cortex suggests that genetic mutations that might have contributed to the emergence of linguistic abilities accumulated over the course of million years following the divergence of human and chimpanzee lineages. Together, our study provides a comprehensive molecular, cellular and spatial definition of Brocas area and motor cortex, laying the groundwork for investigations into unique aspects of human cognition and related neurodevelopmental and neuropsychiatric disorders.

neuroscience↗

bioRxiv2026

LARP4 is a B cell-specific metabolic checkpoint for plasma cell differentiation and a therapeutic target in systemic lupus erythematosus

RNA-binding protein LARP4 plays an important role in T cell activation and differentiation, but its role in B cell biology and the pathogenesis of systemic lupus erythematosus (SLE) remains unclear. This study found that LARP4 was specifically highly expressed in B cells of SLE patients and was positively correlated with disease activity. By constructing T cell-specific and B cell-specific conditional knockout mice, we found that deletion of LARP4 in B cells, but not in T cells, significantly alleviated pristane-induced and Bm12-induced lupus nephritis. Further analysis showed that LARP4 deletion selectively inhibited B cell differentiation into plasma cells, but did not affect germinal center B cell formation. Integrated transcriptomic and metabolomics analyses revealed that this effect is due to reduced phosphatidic acid synthesis and decreased mTORC1 activity caused by mitochondrial oxidative phosphorylation dysfunction. Furthermore, we used LIPEP, a LARP4 inhibitory peptide that effectively mimicked the therapeutic effects of LARP4 gene knockout in the MRL/lpr spontaneous lupus model and outperformed cyclophosphamide in reducing glomerular immune complex deposition and improving extrarenal dermatitis. These results indicates that LARP4 is a key metabolic checkpoint regulating B cell differentiation into Plasma cells and suggest that it may be a potential therapeutic target for SLE.

immunology↗

bioRxiv2026

Haplotypes variations of yellow stripe like (TaYSL) genes are associated with grain iron and zinc contents in wheat (Triticum aestivum L.)

The availability of pangenome and resequencing of wheat collections have facilitated the discovery of gene-trait associations in wheat. Yellow stripe-like (YSL) proteins play a key role in the uptake and translocation of metals and yet have not been fully identified and analyzed at the genome-wide level in wheat. In this study, 26 TaYSL genes were identified and divided into four distinct clades, each clade sharing similar domains and motif compositions. Most genes were upregulated under iron deficiency, whereas homoeologs of TaYSL1 were downregulated. Both SNP-based and haplotype-based association studies were used to dissect the role of TaYSLs underpinning grain iron contents (GFeC) and zinc contents (GZnC) in wheat. TaYSL6-2B and TaYSL16-1A haplotypes showed strong association with GFeC, and TaYSL14-6A showed strong association with GZnC in multiple field trials. The distribution of favorable haplotypes in global wheat collection of [~]3000 accessions showed that majority of haplotypes were more prevalent in landraces and winter wheat compared to modern cultivars and spring types, indicating their potential for use in breeding. The combination of favorable haplotypes of three YSL genes associated with GFeC and GZnC were very rare, and most of the wheat accessions has single or double favorable haplotypes. These findings provide the first comprehensive characterization of the TaYSL gene family in wheat and identify significant SNPs and elite haplotypes that can be utilized for genetic improvement and biofortification.

plant biology↗

bioRxiv2026

DesignMaster: A Multi-Conditional Diffusion Framework for Rational PROTAC Design

MotivationProteolysis-targeting chimeras (PROTACs) enable targeted protein degradation through ternary complex formation with E3 ubiquitin ligase. However, the rational design of PROTACs remains highly challenging due to limited structure-activity relationship data and the vast conformational diversity of linkers. Existing computational approaches can be broadly divided into structure-based ternary modelling methods and fragment-based linker generation models. Although these approaches have advanced PROTAC design, they typically neglect key physicochemical constraints and linker-length control during the generation process, causing the generated PROTACs to lack balanced structural properties required for effective ternary complex formation with drug-like characteristics. ResultsTo address these limitations, we propose DesignMaster, a diffusion-based generative framework that explicitly incorporates linker length and physicochemical properties as controllable conditioning signals. DesignMaster employs an E(3)-equivariant graph Transformer with a gated multi-condition fusion module to inject linker length and physicochemical constraints throughout the diffusion process, enabling fine-grained and constraint-aware molecular generation. Experiments on PROTAC-DB 2.0 and 3.0 demonstrate that DesignMaster outperforms state-of-the-art baselines, with a 3.2% improvement in validity and a 34.4% improvement in recovery. The Case study shows DesignMaster achieves a 51.78% reduction in RMSD when predicting the linker of PROTAC BCPyr targeting 6W7O, highlighting its potential for practical structure-guided PROTAC design. AvailabilityThe source code and datasets are available at https://github.com/ABILiLab/DesignMaster.

bioinformatics↗

bioRxiv2026

Autoantibodies Drive Fc Gamma Receptor-Dependent Colon Inflammation During Immune Checkpoint Blockade

Immune checkpoint inhibitor (ICI)-associated colitis limits effective cancer immunotherapy, yet host determinants of severe toxicity remain undefined. We investigated whether humoral immunity is associated with subsequent severe immune-related colitis (irC). In melanoma patients, baseline serum autoantibody (AAb) profiling identified a composite antigen signature - a signature-level association rather than validated functional specificities - associated with severe irC, marked by retained reactivity to tumor-associated antigens and relative depletion of antibodies recognizing immune- and mucosal-regulatory proteins. To assess functional relevance, we transferred polyclonal IgG from severe- or non-severe-irC patients into wild-type or humanized Fc{gamma} receptor (hFc{gamma}R) mice treated with anti-PD-1 or anti-CTLA-4. IgG alone did not induce inflammation; however, severe-irC IgG amplified checkpoint-driven colonic inflammation in hFc{gamma}R mice, but not in wild-type mice, with checkpoint-specific remodeling of myeloid, lymphoid, and innate lymphoid compartments. These findings suggest that pretreatment humoral immunity conditions susceptibility to irC via the IgG-Fc{gamma}R axis.

cancer biology↗

bioRxiv2026

Iron-deficiency in the tumor microenvironment reprograms tumor-immune interactions in a sex biased manner

BackgroundGlioblastoma (GBM) is a sex-biased disease characterized by higher incidence and poorer survival in males. These sex differences are primarily driven by metabolic and immune signatures, with iron metabolism playing a major role. While iron is essential for tumor cell proliferation, it is also critical for T cell recruitment and function within the tumor microenvironment (TME). Clinical data indicates that iron deficiency impacts GBM survival in a sex-biased manner; however, the underlying mechanisms remain unexplored. MethodsWe employed a FTH1 heterozygous knockdown mouse model to induce tumor iron deficiency in GBM-bearing mice. TME dynamics were interrogated using flow cytometry and spatial transcriptomics (10X Xenium) to analyze immune infiltration, localization, and ligand-receptor signaling between GBM and immune cells. ResultsFTH1 knockdown resulted in iron deficiency in the GBM TME. Iron deficiency altered the TME dynamics in a sex biased manner. FTH1 knockdown in females caused an anti-inflammatory, cytokine deficient TME which failed to recruit CD4 and CD8 T cells. In males, FTH1 knockdown caused a proinflammatory environment by activating the innate immune response. Additionally, FTH1 knockdown increased the density of TAMs in the immediate surrounding of GBM cells in a sex biased manner. ConclusionThese results demonstrate that tumor iron plays a sex-biased role in immune infiltration and anti-tumor immunity.

cancer biology↗

bioRxiv2026

SpatialDataAgent: Autonomous Spatial Omics Data Curation at Decade Scale

Fragmented metadata in spatial omics archives has rendered large volumes of multimodal molecular-histological data inaccessible as dark data. Here, we introduce SpatialDataAgent, an agentic workflow for autonomous spatial omics data curation, combining schema-constrained evidence evaluation with a self-refining standardization agent. Applied to a decade of GEO records, SpatialDataAgent identified 769 paired H&E-spatial transcriptomics (ST) datasets, representing a 6.4-fold scale expansion over existing manually curated baselines. Within the benchmarking window, the framework achieved a 141% increase in high-confidence Class A paired datasets. We further assembled a recent high-confidence subset into HESRT, a standardized datalake containing 29.2 million spots/cells, establishing a blueprint for evidence-grounded autonomous curation of multimodal biomedical archives.

bioinformatics↗

bioRxiv2026

Telomere Dysfunction in Human Astrocytes Drives Acrocentric Chromosome Instability and Nucleolar Reorganization

Loss of p53 and Rb enables continued cell division despite progressive telomere erosion, ultimately triggering telomere crisis. While recent work has clarified mechanisms of chromatin bridge resolution, the longitudinal dynamics of structural damage through crisis remain incompletely understood. We transduced normal human astrocyte (NHA) cells with HPV18 E6/E7 and tracked them across extended population doublings. NHA E6/E7 cells showed progressive telomere shortening, anaphase bridges, and a growth plateau consistent with crisis. Multicolor FISH revealed subclonal chromosomal abnormalities largely invisible to short-read sequencing, with acrocentric chromosomes disproportionately affected: chromosome 13 was abnormal in over 92% of metaphases, and chromosomes 21 and 22 were similarly enriched. Translocations involving chromosome 13 were transient, replaced at later passages, while numerical aberrations persisted. Immunofluorescence revealed compact spherical nucleoli replaced by dispersed necklace-like structures, indicating a large-scale reorganization of nucleolar structure in response to telomere dysfunction. To determine whether these changes reflected altered chromosomal organization in the nucleus, we performed Hi-C and deployed KaryoScope, our alignment-free k-mer-based approach that recovers trans-chromosomal signal from repetitive acrocentric short arms. Inter-chromosomal contacts among nucleolar organizing region-bearing acrocentric chromosomes were markedly and persistently depleted in E6/E7 cells. Together, cytogenetic, imaging, and chromatin-contact data identify the nucleolus as a structural nexus linking telomere dysfunction to large-scale genomic rearrangement.

cancer biology↗

bioRxiv2026

Nascent protein retention at polysomes reduces kinetic barriers to self-assembly

Living proteomes are necessarily far from equilibrium. It is paradoxical, then, that reducing the translation of new proteins -- which should promote equilibration -- instead prolongs life. We investigated the impact of translational flux to nucleation barriers that preserve the solubility of proteins destined to form amyloids or other assemblies. By manipulating translation initiation rates directly or indirectly, across yeast and human cells, and across a variety of supersaturable proteins, we find that accelerating translation initiation broadly accelerates nucleation irrespective of their global concentrations. We showed that this effect was confined to polysomes and was enhanced by N-terminal placement or other features that retained the nascent aggregating domain at polysomes. Finally, we show that intrinsically disordered regions with high tendencies to self-associate are specifically positioned to do so co-translationally, providing evidence that cotranslational nucleation has shaped proteome evolution.

cell biology↗

bioRxiv2026

Structure-aware geometric graph learning for modeling protease-substrate specificity at scale

Protease-substrate specificity is central to cellular regulation and disease pathogenesis, and accurately modeling its structural determinants remains challenging. Substrate recognition is governed by spatial constraints and higher-order relationships that extend beyond local sequence motifs. Most computational approaches rely predominantly on motif-centric or sequence-based representations, limiting their ability to capture the geometric and relational structure underlying enzymatic specificity. Here, we introduce OmniCleave, a structure-aware geometric graph learning framework for modeling protease-substrate specificity at scale. OmniCleave is trained on 57,278 structure-informed protease-substrate pairs derived from 9,651 substrates spanning over 100 proteases across six distinct families. The framework integrates multi-scale structural graphs with higher-order protease relational topology, explicitly encoding spatial context and inter-protease dependencies within a unified geometric representation. This formulation moves beyond local pattern recognition and enables transferable modelling across six protease families. Across large-scale benchmarks, the framework consistently outperforms existing approaches and reveals interpretable geometric determinants underlying substrate recognition. Experimental validation confirms three novel caspase-3 substrates and 21 cleavage sites predicted by OmniCleave, supporting the biological relevance of the learned representations. Together, OmniCleave provides a scalable geometric framework for modeling protease-substrate specificity, with practical utility for systematic analysis of protease biology.

bioinformatics↗