Biology subjects

Yang, R.

Publications and source records attributed to Yang, R..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Distinct EBV-Associated Phenotypes Due to a Novel Homozygous Missense Variant in CD27.

Biallelic deficiencies of CD27 and its ligand CD70 underlie selective susceptibility to Epstein-Barr virus (EBV) infection and its acute and chronic complications, underscoring their non-redundant roles in anti-EBV immunity. To date, 16 pathogenic CD27 variants have been reported. Here, we describe three patients from two unrelated families, homozygous for a novel loss-of-function (LOF) CD27 variant, resulting in substitution of serine 70 with proline (S70P). All three patients presented with EBV viremia and lymphoproliferative disease, with variable immune dysregulation or recurrent otosinopulmonary infections. One patient developed EBV-associated Hodgkin lymphoma. Functional studies demonstrated that the S70P variant impaired surface expression of CD27 and abolished CD70 binding, rendering complete LOF. Together, S70P represents a novel pathogenic CD27 variant causing autosomal recessive (AR) CD27 deficiency, characterized by a unified susceptibility to EBV yet variable clinical manifestations, ranging from chronic viremia to malignancy.

immunology↗

bioRxiv2025

Single-cell transcriptomic atlas reveals that vascular tissues orchestrate cell fate transitions to initiate adventitious root formation in tomato

O_LIAdventitious root (AR) formation enables vegetative propagation critical for agriculture, conservation, and breeding, yet the cellular basis of AR competence in crop species remains poorly characterized. Most mechanistic studies rely on Arabidopsis, which exhibits constrained AR capacity compared to species dependent on clonal propagation. C_LIO_LIWe constructed a single-cell transcriptomic atlas of tomato (Solanum lycopersicum) AR development comprising 7,920 cells across 12 cell types. Regulatory networks were inferred using hdWGCNA and MINI-EX, validated by RNA in situ hybridization and qPCR. Cross-dataset integration with shoot-borne root initiation data enabled developmental staging, while SATURN-based integration of 118,730 vascular cells from eight species permitted evolutionary comparison. C_LIO_LICytoTRACE analysis revealed that vascular tissues--root stele and phloem--possess the highest developmental potential, supporting a model of latent stem cell-like identity rather than dedifferentiation-based reprogramming. Network analysis identified LEA3 as a central hub gene constitutively expressed throughout AR development, regulated by the DOF transcription factor DOF11. Cross-species integration demonstrated that tomato AR-initiating cells share transcriptomic similarity with woody dicots (Liriodendron, r = 0.46; Eucalyptus, r = 0.42) but not Arabidopsis (r = -0.02), with LEA3-containing macrogene weights highest in basal angiosperms and woody species. C_LIO_LIOur findings establish the DOF11-LEA3 axis as a conserved vascular identity module and suggest that AR competence represents an ancestral program retained in species with active cambial dynamics. These results reframe Arabidopsis as a derived rather than representative model for AR biology and identify molecular targets for enhancing vegetative propagation. C_LI

plant biology↗

bioRxiv2025

TRAF6 coiled-coil domain mediates its trimerization

Tumor necrosis factor receptor-associated factor 6 (TRAF6) is an adaptor protein that plays a critical role in innate immune signaling. TRAF6 consists of an N-terminal RING domain, five zinc fingers, a coiled-coil domain, and a C-terminal TRAF domain. Although structural and oligomeric information for coiled-coiled domains in TRAF2-5 is known, information on TRAF6s coiled-coiled domain is relatively unknown. Here, we characterized the oligomeric state of the human TRAF6 domain (residues 288-348) using size-exclusion chromatography (SEC) and size-exclusion chromatography coupled multi-angle light scattering (SEC-MALS). Both His-tagged and tagless proteins displayed molecular masses consistent with a trimer. Coiled-coil computational tools identified a heptad repeat pattern that supported the trimeric findings. AlphaFold-Multimer modelling further showed a symmetric, trimeric coiled-coiled domain with a conserved hydrophobic core. These results provide experimental support for TRAF6 coiled-coiled domain trimerization and help establish a structural framework for understanding how TRAF6 assembles into higher-order structures.

biochemistry↗

bioRxiv2025

De novo design of protein binders that target DELE1 to inhibit the mitochondrial stress response

Mitochondrial stress activates the integrated stress response (ISR) through the mitochondrial protein DELE1, which relays stress signals to the cytosolic kinase HRI to induce ATF4. Dysregulation of DELE1-mediated signaling has been implicated in pathological conditions, yet molecular strategies to modulate DELE1 remain unavailable. Here, we report de novo designed proteins that bind DELE1, block its oligomerization, and inhibit DELE1-mediated ISR activation. Several designs form stable complexes with DELE1 and disrupt its oligomerization in vitro while preserving DELE1s ability to bind HRI. In cells, these designs suppress ATF4 induction during mitochondrial stress and impair the recovery of elongated mitochondrial morphology following transient insult. Crystal structure of a representative binder, together with structural modeling and targeted mutagenesis, confirm that the designed proteins engage a critical interface required for DELE1 oligomerization. These findings establish DELE1 as a druggable target and demonstrate that de novo designed proteins offer precise tools to modulate this pathway, providing a foundation for future therapeutic exploration. SIGNIFICANCEMitochondrial stress activates the integrated stress response through the signaling protein DELE1, but no molecular tools have been available to directly target DELE1 and selectively modulate this pathway. We developed de novo designed protein binders that recognize a critical oligomerization interface in DELE1, disrupt its assembly, and suppress mitochondrial stress-induced ISR activation in cells. These binders also impair recovery of mitochondrial network morphology following transient stress, linking DELE1 assembly to adaptive remodeling. Our study establishes DELE1 as a tractable and druggable target in mitochondrial stress signaling and demonstrates that de novo protein design can generate precise modulators of intracellular stress-response pathways.

biochemistry↗

bioRxiv2025

A neuron type-specific microexon in Ank3/ankyrin-G modulates calcium activity and neuronal excitability

Recent studies have revealed many alternative exons differentially spliced across diverse neuron types in the mammalian brain, but their links to neuronal physiology remain unclear. Here we characterize a deeply conserved microexon E35a in Ank3 encoding ankyrin-G (AnkG), a multifaceted adaptor protein best known as a master organizer of the axon initial segment (AIS) and as a leading genetic risk factor for bipolar disorder. E35a is predominantly skipped in cortical glutamatergic neurons but included in cortical GABAergic neurons and cerebellar neurons, which is dictated by multiple neuronal splicing factors. In E35a-deletion mice we generated, interneurons show increased excitability and somatic Ca2+ activity, without disruption in AIS. Biochemical analyses suggest that E35a inclusion facilitates AnkG interaction with a protein complex involving inositol trisphosphate receptors (InsP3Rs) important for intracellular Ca2+ signaling. Alternative splicing therefore allows AnkG to modulate neuron type-specific excitability in addition to its ubiquitous pan-neuronal role in organizing the AIS.

neuroscience↗

bioRxiv2025

Signaling induced biophysical disruption of repressed chromatin domains drives immune cell fate

Cell fate transitions require signal-induced chromatin derepression, yet mechanisms governing transitions from repressed to active chromatin states are poorly understood. We discover, at fate-defining genes across immune cell types, a signal-induced histone code, and describe domains of H3 serine 28 phosphorylation (H3S28ph) spanning architectural features, often coincident with repressive H3 lysine 27 trimethylation (H3K27me3). Employing biophysical, single cell, and functional approaches to study signal-induced cell differentiation in the immune system, we uncover epigenomic transitions and cell fate choices precipitated by histone phosphorylation (H3ph). Mechanistically, H3ph overrides Polycomb Repressive Complex 2 (PRC2) chromatin repression, biophysically disrupts polynucleosome compaction, and promotes loss of H3K27me3, while increasing activating H3K27 acetylation and H3K36 dimethylation to drive domain interactivity and stabilize transcription. We demonstrate the activity of H3ph in several cell fate transitions and illuminate biophysical mechanisms enabling rapid signal-activated chromatin derepression, processes with general relevance for cellular differentiation and activation.

immunology↗

bioRxiv2025

Dordaviprone/ONC201 Activation of the ClpP Mitochondrial Protease Inhibits the Growth of KRAS-Mutant Pancreatic Cancer and Overcomes RAS Inhibitor Resistance

Pancreatic ductal adenocarcinoma (PDAC) is characterized by KRAS-driven oncogenic signaling and tumor growth. Blockade of the KRAS ERK-MAPK pathway via small molecule direct RAS inhibitors has shown clinical promise, but intrinsic and acquired resistance limit the efficacy of these inhibitors as single agents. To identify potential combination strategies, we first assessed the ability of dordaviprone/ONC201, an FDA-approved agent, to inhibit PDAC cell and organoid growth. We observed that ONC201 reduced the growth of a broad panel of KRAS-mutant PDAC cell lines, and that the expression of mitochondrial protease ClpP was required for this efficacy. Mechanistically, we observed that treatment with ONC201 led to inhibition of mitochondrial respiration, causing a compensatory increase in glycolysis. Furthermore, ONC201 caused ClpP-dependent activation of PI3K-AKT-mTOR signaling and concurrent PI3K and mTOR inhibition further enhanced ONC201 growth suppression. ONC201 demonstrated an additive effect when combined with a RAS(ON) multi-selective inhibitor RMC-7977 in PDAC cells and organoids. Finally, PDAC cell lines with acquired resistance to RMC-7977 or KEAP1 loss-driven resistance retained sensitivity to ONC201. We propose that concurrent treatment with ONC201 may delay onset of resistance to RAS inhibitor therapy. Statement of SignificanceClpP activation by dordaviprone/ONC201 suppressed PDAC cell growth and overcame resistance to the RAS(ON) multi-selective inhibitor RMC-7977, providing support for investigating this combination as a potential combination treatment for KRAS-mutant pancreatic cancer.

cancer biology↗

bioRxiv2025

Structural atlas of Pakpunavirus P7-1 reveals determinants of virion stability and genome ejection

Bacteriophages of the Pakpunavirus genus exhibit broad host range and potent bacteriolytic activity, making them promising candidates for clinical use. Here, we present a structural atlas of the therapeutic phage Pakpunavirus P7-1, a component of a phage cocktail targeting Pseudomonas aeruginosa that has undergone Phase 1/2 clinical trials. We determined the near-atomic structure of the extended virion and obtained a medium-resolution reconstruction of the contracted tail. Atomic models were built for 20 structural proteins comprising the icosahedral capsid, neck, contractile tail, and baseplate. We identified six upward-pointing Short Tail Fibers that stabilize the extended sheath and six highly flexible Long Tail Fibers likely involved in host recognition. Ordered fragments of the Tape Measure Protein revealed six copies inside the tail tube, forming a 3-helix cork at the tail tip. Sheath contraction repositions the baseplate, projecting all twelve tail fibers outward, yet contraction alone is insufficient to trigger genome ejection.

biochemistry↗

bioRxiv2025

Global Mapping of circRNA-Target RNA Interactions Reveals P-Body-Mediated Translational Repression

Circular RNAs (circRNAs) are primarily produced through pre-mRNA back-splicing, yet their target repertoire and functional mechanisms remain elusive. Here, we present circTargetMap, a computational framework for globally mapping circRNA targets using RNA-RNA interactomes obtained via RNA in situ conformation sequencing (RIC-seq) in the hippocampus and ten human cell lines. This approach identified 117,163 high-confidence circRNA-target RNA interactions, with 83% of target mRNAs bound by multiple circRNAs. Functionally, CDR1as and circRMST repress target mRNA translation by sequestering them into processing bodies (P-bodies)--membraneless granules--through sequence-specific base-pairing, probably independent of AGO2, DICER, and miRNAs. To directly capture granule-associated interactions, we developed granule RIC-seq (GRIC-seq) method, revealing the broad role of circRNA-target RNA interactions in translational repression. Moreover, pathogenic variants are significantly enriched around circRNA-target RNA interaction sites, suggesting potential roles in disease. Our study provides valuable resources for circRNA functional exploration and a framework for investigating RNA-RNA interactions within membraneless organelles.

molecular biology↗

bioRxiv2025

Yuanyang allele pairs enable engineered obligate co-inheritance for population replacement and suppression

Mendels law of segregation, which dictates independent assortment of alleles, is a cornerstone of genetics. Here, we present the Yuanyang allele pair (YYAP), an engineered underdominance gene drive system that enforces obligate co-dependency between homologous alleles via synthetic toxin-antitoxin circuits. This design produces a striking deviation from classical Mendelian segregation: YYAP alleles cannot segregate independently, reshaping inheritance outcomes without altering the physical mechanics of meiosis. In Drosophila melanogaster, optimized YYAP strain K711 exhibits >99% hemizygous lethality when crossed with wild type, while maintaining stable transmission and high fitness in transheterozygotes. Cage experiments demonstrate efficient population replacement, positioning YYAP as a confined, resistance-proof alternative to CRISPR homing gene drives. Release of only males represents a self-limiting suppression strategy that was also successful in cage experiments. By imposing a near-complete postzygotic incompatibility, YYAP establishes a programmable framework that not only supports pest management, but also enables modeling of reproductive isolation and allelic co-dependency, thereby creating opportunities to explore speciation and broader synthetic inheritance systems in ecology and evolution.

molecular biology↗

bioRxiv2025

Structural and Functional Insights into HBx-Smc6 Targeting for HBV Inhibition

The hepatitis B virus (HBV) X protein (HBx) is a multifunctional regulator essential for HBV replication and HBV-associated hepatocarcinogenesis. Despite its central role, the molecular basis of HBx function has remained elusive. Here, we present the first cryo-electron microscopy structure of the human HBx-CRL4-Smc5/6 complex at 3.1 [A] resolution. In this reconstituted ten-subunit assembly, HBx adopts a Zn2 {square}-stabilized Y-shaped architecture that simultaneously engages the DDB1 and the Smc6 subunit. A composite helix-turn-helix (HTH) pocket in HBx accommodates a conserved "Leucine Key" motif (LRCKL) on Smc6, forming a critical interface essential for complex stability and function. Molecular docking and biochemical validation reveal that the compound Tranilast binds this HTH pocket, disrupts the HBx-Smc6 interaction, and suppresses HBV replication. These findings define the structural mechanism by which HBx counteracts host restriction and establish the HBx-Smc6 interface as a previously unrecognized and druggable target for antiviral intervention.

cell biology↗

bioRxiv2025

Dynamic epigenetic and transcriptional regulatory network in pepper fruit development and ripening

Pepper (Capsicum) is among the most widely cultivated and consumed vegetable crops worldwide. Although extensive studies in model fruit crops such as tomato have provided insights into the genetic and epigenetic regulation of fruit development and ripening, comparable knowledge in pepper remains limited. Here, we employ a multi- omics approach to investigate transcriptome and epigenome dynamics during pepper fruit pericarp development and ripening. Our analyses reveal coordinated changes in chromatin accessibility and histone modifications accompanying transcriptome reprogramming, with changes in H3K27ac closely associated with chromatin accessibility dynamics, and H3K27me3 dynamics potentially contributing to the transition from fruit growth to ripening. Moreover, construction of the transcriptional regulatory network underlying pepper fruit development and ripening suggests that several ripening regulators identified in the climacteric tomato may also play critical roles in governing ripening in the non-climacteric pepper. During ripening, DNA methylation, particularly in the CG and CHG contexts, undergoes global demethylation, especially at promoter regions, which is accompanied by increased chromatin accessibility and likely enhances transcription factor binding activity. We further demonstrate transcriptional and epigenetic regulation of carotenoid and ascorbic acid (vitamin C) biosynthesis pathways. Collectively, this study provides a comprehensive resource for mechanistic dissection and comparative analysis of fruit development and ripening, with practical implications for improving key fruit traits.

plant biology↗

bioRxiv2025

Normative models of individualized functional brain networks reveal language network expansion in autism

Autism spectrum disorder is a highly heterogeneous neurodevelopmental disorder, hindering mechanistic insights and the identification of biomarkers for clinical diagnosis. Recently, precision functional mapping has been developed to identify abnormalities in brain network topologies associated with various psychiatric disorders, yet its application in autism remains limited. Here, we utilized precision functional mapping and a large, multisite neuroimaging dataset (N = 1,182) to construct individualized functional networks in individuals with autism. We developed normative models using network surface area from healthy controls (n = 628) to characterize typical brain network organization across age, allowing for the quantification of individual-specific deviations in individuals with autism (n = 554). We found widespread and heterogeneous deviations from the normative model, with the language network emerging as the most significantly altered region, thereby emerging as an epicenter of functional disruption in autism. Individuals with autism were clustered into three subtypes involving distinct functional network topologies, associated with behavioral profiles marked by impairments in perception, language processing, or socio-emotional functioning. We further linked these atypical brain features to cortical gene expression patterns, revealing enriched pathways related to neurodevelopment, language, and signaling processes. Together, these findings reveal autism-specific deviations in individualized functional brain networks, offering potential clinical relevance for understanding and stratifying autism.

neuroscience↗

bioRxiv2025

Transcriptomic Signature and PROTAC Strategy Revealed Histone Lysine Demethylase as a Target of Anticancer Activity of Deferiprone.

Deferiprone (DFP) is an iron chelator approved for treating iron overload in thalassemia patients. Recent observations have suggested that DFP has promising anticancer activities ascribed to several mechanisms including reduction of the intracellular free labile iron and zinc ion pools and inhibition of the activities of other intracellular targets, including ribonucleotide reductase (RNR). We previously reported that DFP inhibits the demethylase activities of several Fe(II)/- ketoglutarate dependent histone lysine demethylases (KDMs) at much lower concentrations at which it inhibits RNR activities and/or reduces the labile intracellular iron and zinc ion pools. In this study, we used RNA sequencing (RNA seq) and PROTACs strategies to validate and quantify the contribution of intracellular KDM inhibition to the antiproliferative activities of DFP. We report herein that DFP elicited gene expression signature that is largely similar to that of JIB-04, an established KDM inhibitor (KDMi), in two breast cancer (BCa) cells (MCF-7 and MDA-MD-231). Importantly, RNA seq revealed that DFP and JIB-04 downregulated the expression of hypoxia-inducible factor 1 (HIF-1), an oncogene whose expression is commonly modulated through histone demethylation mediated by KDMs and degraded by several KDMi. Moreover, DFP-derived PROTACs elicited enhanced cancer cell selective antiproliferative activities and intracellular on-target effects, downregulating several KDMs implicated in the etiology of BCa cells, including a strong degradation of KDMs 2A, 3A and 5B, and a moderate degradation of KDMs 4A-C, 5C, 6B. Collectively, our data supports KDM inhibition as a key mechanism of anticancer activity of DFP and identifies PROTAC is a viable strategy to obtain novel DFP analogs with improved potency and therapeutic index.

cancer biology↗

bioRxiv2025

CRlSPR/Cas9 screening revealed BlRC6-AS1/BlRC6 mediates abiraterone resistance via NHEJ pathway-dependent A20 degradation in prostate cancer

Abiraterone acetate serves as the first-line therapeutic agent for prostate cancer (PCa) treatment. However, drug resistance frequently emerges. Employing a genome-wide CRISPR/Cas9 library screening strategy, we identified 523 long non-coding RNAs (lncRNAs) and 2183 protein-coding genes associated with abiraterone resistance. Notably, a pair of sense-antisense genes, BIRC6-AS1/BIRC6, was demonstrated to be a pivotal driver for abiraterone resistance. BIRC6-AS1 depletion led to a reduction in both the mRNA and protein levels of BIRC6. Moreover, depletion of either BIRC6-AS1 or BIRC6 enhanced the chemosensitivity of PCa cells to abiraterone both in vitro and in vivo settings. Further investigation revealed that BIRC6-AS1 stabilized the mRNA of BIRC6 through interaction with ILF2. Diminishing either BIRC6-AS1 or BIRC6 predominantly suppressed non-homologous end joining (NHEJ) repair activity, resulting in the disassembly of 53BP1 foci at DNA damage sites and an increased accumulation of DNA damage in PCa cells induced by abiraterone. Mechanistically, BIRC6 interacted with A20 and facilitated the K48-linked ubiquitination and subsequent degradation of A20 at the K337 residue. Additionally, A20 knockdown effectively reversed the abiraterone sensitivity induced by BIRC6-AS1 depletion. Collectively, we conducted a comprehensive screen to identify lncRNAs and protein-coding genes associated with abiraterone resistance and proposed that targeting BIRC6-AS1/BIRC6 axis represents a promising strategy to overcome abiraterone resistance in prostate cancer.

molecular biology↗

bioRxiv2025

Assembly of the complete horse genome reveals variants associated with reproduction and temperamental traits

A high-quality horse genome assembly is crucial for genetic analysis of equine. Benefiting from long-read sequencing techniques and trio-binning strategy, we assembled a complete telomere-to-telomere horse genome (T2T-horse 1.0) with a size of 2.80 Gb and a base accuracy of more than 99.9999%, comprising a 34.11-Mb entire Y chromosome. T2T-horse 1.0 filled the gaps and corrected errors in previous assemblies, and added 180.30 Mb of previously unresolved regions and 77 new genes compared with the previous reference genome TB-T2T. We identified five types of centromeric satellites and revealed the features of the horse centromeric regions. We characterized the structure of the Y chromosome, and determined the borders of PAR transposed region, and annotated 59 novel genes on Y chromosome of T2T-horse 1.0. Using SNPs in the X-degenerate region of the Y chromosome of T2T-horse 1.0, we performed selection signatures analysis between indigenous horses and horses from intensively selected breeds, and detected the selected genes ARSF and NLGN4Y, which are closely associated with reproduction and temperamental traits, respectively.

genomics↗

bioRxiv2025

Mating-Type Imputation (MTI) provides an efficient tool for the mating-type inference of tetrapolar fungi

Mating-type identification is fundamental for the genetic diversity and genetic breeding study in fungi, especially for tetrapolar basidiomycetes, whose mating-types are determined by two multiallelic loci A and B. Traditional mating-type identification of monokaryons relies on manual inference based on their hybridization experiments; however, the process is rather complex, time-consuming and error-prone for large-scale hybridization experiments. In this study, we developed the Mating-Type Imputation (MTI) software for automatic, rapid and accurate monokaryon mating-type inference for tetrapolar fungi using a combinatorial pruning traversal algorithm. Taking the compatibility matrix from 435 hybridization experiments of 30 Flammulina velutipes monokaryons as an example, MTI takes a few minutes to infer the accurate mating-types of all monokaryons, which might take several days for manual inference by experienced investigators. Furthermore, MTI enables us to investigate how false-positives and false-negatives influence mating-type inference results. Using simulated compatibility matrix, we found that MTI could accurately detect potential false-negatives in compatibility and successfully infer the true mating-type combination with limited false-negatives, but the tool could be misled by any false-positives to result in a wrong mating-type combination, indicating that false-positives records in hybridization experiments should be strictly obviated for mating-type inferences. In summary, MTI provides an efficient tool for mating-type inference of tetrapolar fungi, offering technical support for the research paradigm in mating-type studies of edible and medicinal fungi and holding significant theoretical value and broad application prospects in the fields of fungal genetic diversity and breeding studies.

genetics↗

bioRxiv2025

Remodeling of the immune-metabolic landscape triggered by long-term high-altitude exposure

Growing evidence indicates that immunological and metabolic outcomes are key mediators of long-term high-altitude exposure (LTHAE) adaption, but the underlying mechanisms remain poorly understood. This study employs plasma metabolomics and peripheral blood single-cell transcriptomic sequencing to analyze the metabolic and immune dynamic regulation in 46 young male lowlanders following a 90-day adaptation period at high altitude. Single-cell analysis shows a pattern of "innate immune activation and adaptive immune suppression" under LTHAE, characterized by facilitated maturation of neutrophils, enhanced cytotoxicity of CD56dim NK cells, and increased immune responsiveness of cDC2 and pDC, while inhibited maturation of plasmablasts and suppressed immune responsiveness of CD8{square}TEM and CD4+ T cells. Plasma metabolic analysis reveals significant alterations, involving enhanced steroid hormone synthesis, unsaturated fatty acid and amino acid metabolism under LTHAE, which in turn are associated with immune remodeling. Moreover, transcriptomic-metabolic integration analysis indicates the molecular mechanisms of enhanced aerobic oxidation efficiency under LTHAE. Collectively, these findings provide integrated insights into immune-metabolic landscape remodeling and suggest potential mutual regulatory relationship between immune and metabolic state following LTHAE, offering a molecular foundation for high-altitude adaptation research.

genomics↗