Biology subjects

Yu, D.

Publications and source records attributed to Yu, D..

At least 37 records · Page 2Linked to original sources

bioRxiv2026

CORe Designer: a CRISPR design tool for proteome engineering

Precision proteome engineering requires tools that leverage CRISPR technologies, yet most current design platforms remain gene-centric. To bridge this gap, we introduce CORe Designer. Featuring an intuitive graphical user interface, CORe Designer enables researchers to design guide RNAs and homology-directed repair templates in a protein-centric manner. By automating these workflows, CORe Designer enables the design of targeted mutagenesis experiments for precision proteome engineering to be completed in minutes.

bioengineering↗

bioRxiv2026

PXN Unlocks the Power of Public Gene Expression Data Through Cross-Technology Integration

The immense value of public gene expression repositories is constrained by the lack of compatibility among datasets generated from diverse experimental technologies. Differences in measurement scales, probe chemistries, and signal distributions create systematic discrepancies across platforms and laboratories. These inconsistencies make large-scale integrative analysis nearly impossible, even though such studies could achieve great statistical power and improved reproducibility. We introduce PXN, a probabilistic machine learning framework that captures a unified representation of biological signal across multiple gene expression technologies. Once trained, PXN can seamlessly translate data between multiple platforms, preserving informative biological variation while removing technology-specific biases. In benchmarking studies, PXN consistently outperforms existing normalization methods in cross-platform accuracy and substantially enhances the power of differential expression analysis. Importantly, we show that PXN is powerful enough to bridge even the most challenging technological divide--between microarray and RNA-seq. This capability provides a scalable route for integrating legacy microarray data with modern RNA-seq studies. By enabling direct comparison and integration of heterogeneous datasets, PXN unlocks the full potential of public repositories for future biological discovery and therapeutic innovation.

bioinformatics↗

bioRxiv2026

AEGIS reveals epitope- and clone-resolved convergence of CNS B and T cell autoreactivity in ROHHAD

Autoimmune diseases arise when B and T lymphocytes lose tolerance to self. Yet in most disorders, the underlying molecular determinants, including autoantibodies, epitopes and lymphocyte clones that drive tissue injury remain undefined. Rapid-onset obesity with hypothalamic dysfunction, hypoventilation and autonomic dysregulation (ROHHAD) is a rare and often fatal pediatric neuroendocrine syndrome with strong evidence of antigen-driven paraneoplastic autoimmunity, including association with the intracellular autoantigen ZSCAN1. However, the effector immune circuit and the epitope-level determinants operating within the hypothalamus and brainstem have remained unknown. To address this challenge in ROHHAD and more broadly in autoimmune disease, we developed the Autoimmune Epitope and immunoGlobulin/Immune-receptor identification System (AEGIS), an integrated framework that links immune repertoires to their cognate self-epitopes. AEGIS combines B cell and T cell receptor profiling from sites of tissue injury with high-resolution epitope mapping, direct sequencing of antigen-specific autoantibodies, in silico antibody-antigen folding, selection, and T cell antigen discovery. Applied to a deeply phenotyped child with ROHHAD, AEGIS revealed a compartmentalized, clonally restricted immune response in which brain-deposited IgG and expanded cerebrospinal fluid B cell and CD4 T cell clonotypes converged on shared ZSCAN1 epitopes, resolved to minimal determinants and peptide-MHC ligands. These findings provide a clone- and epitope-linked mechanistic map of ROHHAD autoimmunity and establish a generalizable framework for identifying candidate pathogenic clones and antigens across diverse autoimmune diseases.

immunology↗

bioRxiv2026

Engineering age-adaptive mRNA lipid nanoparticle cancer vaccines via reprogramming systemic gene expression

Lipid nanoparticle (LNP)-based mRNA vaccines have transformed cancer immunotherapy, yet their efficacy in older individuals, who represent the majority of cancer patients, remains poorly understood. Here, we uncover a critical and previously underappreciated barrier to mRNA LNP cancer vaccine performance in aged hosts: impaired systemic transgene expression. Using the SM-102 mRNA LNPs as a benchmark formulation, we show that while local immune activation and antigen presentation at the injection site and draining lymph nodes remain largely intact with age, transgene expression in peripheral organs, including the liver, lungs, and spleen, is markedly reduced. This deficit limits the magnitude and durability of CD8 and CD4 T cell responses and substantially compromises tumour control. Transcriptomic profiling further reveals that attenuated transgene expression parallels broad attenuation of antigen processing, presentation, and activation pathways in immune cells from aged animals, implicating impaired systemic mRNA translation as a central driver of the downstream immune defects and antitumour efficacy loss. Building on these insights, we identify a rationally selected LNP formulation that reestablishes distal antigen expression across age groups as an engineering strategy to revive T cell immunity, achieving full rescue of therapeutic efficacy in aged mice without additional intervention. Together, these findings establish systemic mRNA translation as a tuneable lever of vaccine performance and highlight that optimizing LNP formulations to sustain systemic transgene expression across age groups may enable next-generation, age-adaptive mRNA vaccines for cancer and other diseases of aging.

bioengineering↗

bioRxiv2026

The world's first cloned golden wild yak via interspecific SCNT: 4800m donor origin and 4200m vitrified blastocyst transfer

Primarily inhabiting the harsh, high-altitude environment of the Qiangtang National Nature Reserve exceeding 5,000 meters above the sea (m.a.s.l.), the golden wild yak is critically endangered, with fewer than 300 individuals remaining in the world, a situation exacerbated by the significant challenges of conducting research and conservation of their genetic resources. Somatic cell nuclear transfer (SCNT) can be an effective method for their preservation, but facing several obstacles in this context, including the hypoxic stress at high altitude that impairs embryonic development due to in vitro manipulation, and constraints of long-distance embryo transport. In the present study, the ear tissue was collected from a childhood male golden wild yak at Xizang Geye Wildlife Rescue Station (4800 m.a.s.l.) and send to Institute of Animal Science at Beijing to derive fibroblast cells. Using fibroblast cells of the golden wild yak as nuclear donors, and bovine oocytes from a local slaughterhouse at Beijing as recipients, the interspecific SCNT (iSCNT) embryos were generated and in vitro developed to blastocysts. To maintain the embryonic viability after long-distance transportation from Beijing to Xizang, iSCNT blastocysts were subjected to cryopreservation by vitrification method. Thawing of vitrified iSCNT blastocysts were completed at Xizang Dangxiong Yak Breeding Innovation Base (4200 m.a.s.l.), and transferred into the uterine horn of domestic yaks. 257 days after blastocyst transfer, a cloned golden wild yak was successfully harvested on January 10, 2026. This work demonstrates, for the first time, that interspecies somatic cell nuclear transfer can successfully produce a cloned offspring under extreme conditions, spanning 4800 m.a.s.l. donor origin, long-distance vitrified embryo transportation, and high-altitude blastocyst transfer at 4200 m.a.s.l., establishing a viable strategy for conserving critically endangered high-altitude species.

genetics↗

bioRxiv2026

Structure-guided discovery and engineering of miniature CRISPR-Cas12m for epigenome editing

CRISPR-based epigenome editing represents a programmable strategy to precisely modulate gene expression, holding immense promise for therapeutic applications. However, the large size of the dCas proteins substantially impedes the delivery via adeno-associated virus (AAV) vectors. Here, through iterative bioinformatics analysis, structure-guided predictions, and functional assays, we identified and characterized PmCas12m, a novel miniature subtype V-M CRISPR-Cas12m. PmCas12m exhibited flexible 5-YTN-3 PAM-dependent recognition and robust double-stranded DNA binding properties, while lacking DNA cleavage activity, thus positioning it as an ideal tool for epigenome editing. Cryogenic electron microscopy (cryo-EM) structures of PmCas12m unveiled its unique molecular mechanism of DNA binding facilitating interference. Guided by these structural insights, we employed deep mutational scanning (DMS) and protein engineering to develop xCas12m, a hypercompact variant with highly potent and specific epigenome editing capabilities in human cells. We further constructed the xCas12m-CRISPRoff platform in a single AAV vector, which achieved durable epigenetic silencing and effective inhibition of hepatitis B virus (HBV) infection in a mouse model. Collectively, these findings establish xCas12m as a versatile epigenome editing platform with transformative potential for treating diseases, paving the way for clinical translation of epigenetic therapies.

bioengineering↗

bioRxiv2026

Development of hybrid alphavirus-influenza A, B, and D pseudovirions for rapid quantification of neutralization antibodies and antiviral drugs

The emergence and spread of highly pathogenic avian influenza H5N1 subtypes have raised global concerns due to their ability to cross species barriers and occasional spillover to humans. The viruses primarily infect wild birds and poultry, which have caused significant, sporadic outbreaks in mammals including dairy cattle. Influenza D virus is a recently identified influenza virus that mainly affects cattle with frequent spillover to other species such as swine. Despite the availability of poultry vaccines, there are no H5N1 and Influenza D vaccines for cattle or other potentially affected livestock. Given a history of frequent influenza pandemics originating from avian and mammalian hosts, there is an urgent need for enhanced surveillance, biosecurity, and the development of antivirals and vaccines. Here we describe the development of a novel hybrid alphavirus-influenza pseudovirion (Ha-IV), which is a non-replicating influenza virus-like particle composed of viral structural proteins and an RNA genome derived from a fast-expressing alphaviral vector. As a proof-of-concept, we assembled Ha-IV pseudoviruses based on influenza D and influenza A and B subtypes, and demonstrated their infectivity. In addition, we validated an influenza A pseudovirus based on the H5N1 clade 2.3.4.4b strain, A/Texas/37/2024, for rapid quantification of neutralization antibodies within 4 to 18 hours. Furthermore, we used the pseudovirus to quantify infected cow sera and performed a correlation study with the classic hemagglutinin inhibition assay (HIA). We demonstrate that the Ha-IAV pseudovirus-based assay is consistent with HIA in identifying protective antibody responses. Our results demonstrate that this new Ha-IV pseudovirus provides a rapid tool for quantifying the infectivity of emerging HA mutants and for assessing neutralizing antibody responses.

microbiology↗

bioRxiv2026

Subcellular proteomic profiling of human skeletal muscle reveals exercise-induced coordinated and compartment-specific protein remodeling

Exercise training induces extensive protein modifications in skeletal muscle, yet how acute exercise and training-induced molecular responses are spatially coordinated across muscle subcellular compartments remains unclear. Using subcellular fractionation combined with data-independent acquisition mass spectrometry, we profiled skeletal muscle mitochondrial, nuclear, and cytosolic proteomes in response to an acute bout of intense cycling (pre-, mid-, post- and 3 h post-exercise) and after eight weeks of endurance training in 40 healthy adults (20 males and 20 females). Acute exercise triggered coordinated, compartment-specific proteomic remodelling, including reductions in protein translation and import machinery concomitant with increased redox-related proteins. Notably, acute exercise increased markers of ribosomal translation within the mitochondrial fraction, revealing ribosomal scaffold protein RACK1 as a potential regulator of subcellular translational control under contractile stress (confirmed by targeted immunoblotting). The nuclear proteome displayed transient remodelling of RNA-processing and chromatin-associated proteins, while cytosolic changes were modest. Endurance training induced robust proteomic remodelling across all compartments, including increased markers of mitochondrial oxidative metabolism and proteostasis. While there were sex differences at baseline, subcellular proteomic responses were largely conserved between sexes. We provide the first comprehensive, time-course subcellular characterisation of the skeletal muscle proteome, revealing regulation of translational machinery underlying the acute exercise response.

physiology↗

bioRxiv2026

Integrative Multi-Omics Analysis Identifies a Functional Enhancer Driving Tumorigenesis in Head and Neck Squamous Cell Carcinoma

Enhancer is a critical epigenetic feature in head and neck squamous cell carcinoma (HNSCC), yet the functional roles of individual enhancers remain poorly understood. Here, we conducted an integrative multi-omics analysis based on publicly available ATAC-seq, H3K27ac ChIP-seq, transcriptomic profiling, and genetic association datasets to systematically map HNSCC-associated enhancers and their target genes. Integrating ATAC-seq and H3K27ac ChIP-seq, we identified 20,362 enhancers and 18,040 enhancer-associated genes, highlighting widespread regulatory complexity. Functional characterization of the TERT-associated enhancer GH05J001312 (GRCh38/hg38: chr5:1312099-1317743) revealed strong transcriptional activity in HNSCC. CRISPR-mediated deletion of a core sequence significantly reduced TERT expression, impaired cellular proliferation in vitro, and suppressed tumor growth in vivo, confirming its role as a key cis-regulatory element. RNA-seq analysis of enhancer-edited cells uncovered 742 differentially expressed genes enriched in cancer-related pathways, including MAPK and IL-17 signaling, indicating a broad transcriptional impact. Collectively, our findings establish GH05J001312 as a functional enhancer driving oncogenic programs in HNSCC and suggest enhancer-targeted strategies as a potential therapeutic avenue.

cancer biology↗

bioRxiv2026

Therapeutic interleukin-2 rewires skeletal-immune circuits to reverse postmenopausal bone loss

Postmenopausal osteoporosis results from excessive osteoclast activity, but the immune circuits that limit osteoclastogenesis in the bone marrow remain poorly understood. Here, we tested a clinically accessible immunotherapy low-dose interleukin-2 (IL-2) as a therapeutic intervention in mice with established ovariectomy-induced bone loss, integrating microcomputed tomography imaging, single-cell transcriptomics, genetic perturbation, and human monocyte-osteoclast assays. Therapeutic administration of IL-2 reversed trabecular bone loss, expanded CXCR3 regulatory T cells in bone marrow, and promoted IL-10- and CGRP-producing ILC2s that were required for protection. IL-2 also acted directly on the osteoclast lineage, suppressing mouse and human osteoclastogenesis through activation of a STAT1-IRF1-dependent IFN program in RANKL-stimulated monocytes. Together, these data define an IL-2-responsive skeletal-immune network that can be therapeutically engaged to suppress osteoclastogenesis, which opens new avenues for cytokine-based immunotherapies in postmenopausal osteoporosis and related bone disorders.

immunology↗

bioRxiv2026

resolveS: An ultra-fast, memory-efficient and reference-free tool for RNA-seq Strandedness Detection

Accurate specification of RNA-seq library strandedness is essential for read counting, transcript assembly and antisense transcription analysis, yet this information is frequently missing from public metadata. We present resolveS, a fast and lightweight method that infers strandedness from alignments to a compact universal rRNA database, avoiding the need for organism-specific reference genomes and annotations. Across benchmark datasets, resolveS provides robust strandedness calls while maintaining very low runtime and memory usage, making it suitable for both routine quality control and large-scale reanalysis of public RNA-seq data.

bioinformatics↗

bioRxiv2025

Sensitizing tumor response to topoisomerase I antibody drug conjugate by selective CDK7 inhibition

This study investigates the transcriptional impact of Q901, a highly selective CDK7 inhibitor in clinical development. Q901 primarily disrupted MYC and E2F-dependent transcription program, downregulating cell cycle control and DNA damage repair pathways. CDK7 binding at the promoter-proximal regions was dramatically stabilized by Q901, leading to reduced occupancy of MYC, E2F, and RNA Polymerase II (RNAPII). These findings offered a novel therapeutic strategy to enhance cancer susceptibility to TOP1-DNA protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors. Resistance to TOP1 inhibitors arises through activation of DNA repair pathway when elongating RNAPII encounters TOP1-DPCs. By suppressing RNAPII transition from initiation to elongation and DNA repair pathways, Q901 stabilizes TOP1-DPCs and sensitizes tumor to TOP1 inhibitors. Preclinical studies demonstrated enhanced tumor suppression when combining Q901 with TOP1 inhibitor-based antibody-drug conjugates (TOP1i-ADCs), highlighting its potential as a therapeutic option for cancers resistant to TOP1i-ADC therapy. TeaserOvercoming ADC cross-resistance through combination approach.

cancer biology↗

bioRxiv2025

Distinct patterns of de novo coding variants contribute to Tourette Syndrome etiology

Tourette syndrome (TS) is a highly heritable childhood-onset neuropsychiatric disorder characterized by persistent motor and vocal tics. While both common and rare variants contribute to TS susceptibility, the role of rare de novo mutations (DNMs) remains incompletely characterized. Here, we report findings from the largest TS whole-exome sequencing study to date, analyzing 1,466 TS trios alongside 6,714 autism spectrum disorder (ASD) trios and 5,880 unaffected sibling controls from the Simons Simplex Collection (SSC) and SPARK cohorts. Leveraging a trio-based design across these cohorts enabled calibrated assessment of DNM burden while controlling for background mutation rates. We observed a significant exome-wide enrichment of protein-truncating DNMs in TS probands, particularly within genes intolerant to loss-of-function variation (pLI [≥] 0.9), with little contribution from damaging missense variants. Notably, TS probands did not exhibit enrichment in previously implicated ASD or developmental delay (DD) genes, but elsewhere in the genome, suggesting a distinct rare variant architecture. Using a Bayesian statistical framework that integrates both de novo and rare inherited coding variants, we identified three candidate TS risk genes with FDR [≤] 0.05: PPP5C, EXOC1, and GXYLT1. Literature shows that they have prior links to neurodevelopmental and psychiatric disorders. These findings reveal a rare variant burden in TS that is genetically distinguishable from ASD, underscore the importance of loss-of-function mutations in TS risk, and nominate novel candidate genes for future functional investigation.

neuroscience↗

bioRxiv2025

Ethylene receptors are functionally conserved in calcium permeability across the green lineage

The gaseous hormone ethylene plays a key role in regulating plant growth and stress responses. Although Ca{superscript 2} has long been implicated in ethylene signaling, the identity of molecules controlling Ca{superscript 2} permeability involved has remained elusive. Here we show that Arabidopsis ethylene receptors ETR1 and ERS1 are Ca2+ permeable, and that ETR1 mediates ethylene-induced cytosolic Ca2+ increase and regulates hypocotyl elongation. Homologs of ETR1 from eight land plant and algal species also exhibit Ca{superscript 2} permeability, suggesting an evolutionarily conserved function. We further demonstrate ethylene enhances the Ca2+ permeability of ETR1 and its homologue from the charophyte Klebsormidium flaccidum. These findings uncover a previously unrecognized but conserved role of ethylene receptors in Ca{superscript 2} permeability regulation in the green lineage, with broad implications for Ca{superscript 2} signaling in plant development and environmental adaptation.

plant biology↗

bioRxiv2025

HypoAD: volumetric and single-cell analysis reveals changes in the human hypothalamus in aging and Alzheimer's disease

Alterations in metabolism, stress response, sleep, circadian rhythms, and neuroendocrine processes are key features of aging and neurodegeneration. These fundamental processes are regulated by the hypothalamus, yet how its functionally distinct subregions and cell types change during human aging and Alzheimers Disease (AD) remains largely unexplored. Here, we present HypoAD, a comprehensive atlas of the human hypothalamus in aging and AD, integrating high-resolution MRI from 202 individuals with single-nucleus RNA-seq (snRNA-seq) of 614,403 nuclei from young, AD, and age-matched non-dementia controls. Our analysis reveals that hypothalamic subregions governing metabolism, stress, and circadian rhythms are particularly vulnerable, exhibiting significant changes in both volumes and gene expression during aging and AD. At the molecular level, machine learning models identified the inflammatory response and regulators of circadian rhythms as key cellular predictors of AD. These signatures were reflected in specific cell types: microglia transitioned to a pro-inflammatory state, while inhibitory neurons within sleep-and circadian-regulating hypothalamic subregions showed the most profound transcriptional alterations, including disruptions in ligand-receptor interactions and G-protein-coupled receptor signaling. Together, HypoAD provides a high-resolution volumetric map and a comprehensive transcriptomic atlas of the human hypothalamus in aging and AD, linking lifestyle and behavioral changes to their underlying volumetric and molecular pathways. Additionally, HypoAD provides a framework to investigate hypothalamic dysfunction and establishes a roadmap for targeted interventions aimed at mitigating physiological disruptions to potentially slow disease progression.

neuroscience↗

bioRxiv2025

Crosslinking of Lipid Nanoparticles Enhances the Delivery Efficiency and Efficacy of mRNA Vaccines

Lipid nanoparticles (LNPs) have enabled the effective delivery of RNA therapeutics and mRNA vaccines. However, their broader applications are limited by the suboptimal stability and endosomal escape efficiency. Here, we present an easy-to-adopt post-assembly crosslinking approach to enhance the structural and functional stability of mRNA LNPs. By leveraging a series of cholesterol derivatives and crosslinking methods, we induce crosslinks of the lipid components following mRNA LNP assembly to form the crosslinked LNPs (cLNPs). We systematically evaluated crosslinking parameters and identified optimal conditions that enhance both the physical stability and transfection efficiency of cLNPs. Our findings demonstrate that cLNPs exhibit improved structural integrity under storage and lyophilization conditions, as well as increased extracellular stability and endosomal escape efficiency, resulting in improved performance of mRNA LNPs both in vitro and in vivo. This crosslinking strategy represents a critical advance in LNP engineering, enabling more resilient LNPs and broadening the applicability of LNP-based therapies for gene therapy and vaccine delivery. Our work lays the foundation for developing next-generation LNPs with superior stability and delivery efficiency, broadening the impact of RNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

Versatile HIV Rev-dependent reporter cell system for stringent and sensitive quantification of viral reservoirs, neutralizing antibodies, and restriction factors

Detecting and measuring HIV reservoirs, neutralizing antibodies, and restriction factors are important for HIV cure research and the development of new therapeutics and vaccines. Here we describe the development and validation of several HIV Rev-dependent indicator cell lines for these purposes. These reporter cells come from different T-lymphoblast cell lines, including MOLT-4-R5, SupT1-R5, CEM-SS, A3R5, and from the adherent TZM cell platform based on HeLa clone JC53. These cells express CD4, CXCR4, and various levels of CCR5. We compared these cell lines for responsiveness to both X4 and R5-tropic viruses, and confirmed that reporter expression in these cells is not affected by stimulation from mitogens but is responsive to HIV Tat and Rev, reducing non-specific reporter induction from the leaky LTR promoter. To validate the sensitivity of the Rev-dependent reporter cell systems, we conducted a viral dilution assay with three primary HIV-1 clade C swarms from an adult in Malawi. We also validated the systems for quantifying antibody neutralization and screening restriction factors; these systems are also sensitive for viral outgrowth assays for quantifying viral reservoirs in clinical and basic research settings. Given that the systems can measure HIV accurately in complex environments with mitogens or other substances, they can be used for versatile applications, such as quantifying latent reservoirs, testing inhibitory compounds, conducting neutralizing antibody assays, and identifying new restriction factors.

microbiology↗

bioRxiv2025

A clade 2.3.4.4b H5N1 virus vaccine that elicits cross-protective antibodies against conserved domains of H5 and N1 glycoproteins

The continuous evolution and widespread dissemination of highly pathogenic avian influenza (HPAI) H5N1 viruses, particularly clade 2.3.4.4b, pose critical challenges to global pandemic preparedness. In this study, we assessed a low-dose inactivated split virus vaccine derived from clade 2.3.4.4b H5N1, formulated with an Alum/CpG adjuvant, using a preclinical mouse model. This vaccine induced potent humoral and cellular immune responses, generating high titers of cross-reactive antibodies targeting both hemagglutinin (HA) and neuraminidase (NA) glycoproteins across homologous and heterologous H5 clades. The Alum/CpG adjuvant enabled significant antigen dose-sparing while promoting a balanced Th1/Th2 immune profile. Functional analyses demonstrated strong virus neutralization, neuraminidase inhibition, and potent antibody-dependent cellular cytotoxicity activity. Additionally, the vaccine elicited robust antigen-specific CD4+ and CD8+ T cell responses and effectively controlled viral replication in the lungs, accompanied by reduced lung inflammation. Importantly, vaccinated mice were fully protected against lethal challenges with both the homologous clade 2.3.4.4b and heterologous clade 1 H5N1 viruses, despite low hemagglutination inhibition titers. Electron microscopy polyclonal epitope mapping revealed serum antibodies targeting multiple epitopes on homologous HA and NA, with some cross-reacting to conserved epitopes on heterologous proteins, underscoring broad immune recognition. Collectively, these results highlight the potential of this vaccine candidate to provide broad, multifunctional, and durable immunity against both current and emerging H5N1 threats, supporting its further development for pandemic preparedness.

microbiology↗