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Biology subjects

Han, R.

Publications and source records attributed to Han, R..

At least 19 recordsLinked to original sources

Immune determinants of leuprolide-associated cardiovascular risk in prostate cancer

Leuprolide, a widely used androgen-deprivation therapy (ADT) for prostate cancer (PC), has been associated with increased cardiovascular events (CVE), although the underlying mechanisms remain unclear. Through integrated spatial transcriptomic analyses of murine heart and immune-stromal profiling in patient blood, we identified immune programs linked to leuprolide-associated CVE risk. Spatial analyses revealed the distinct organization of lymphoid (T+B cells) aggregates and inflammatory macrophages in the plaque following leuprolide exposure that accompanied by ventricular hypertrophy, relative to normal vasculature. Parallel profiling of circulatory soluble and cellular components in patients demonstrated CD8+T cell enriched pattern in ~44% of patients, including memory and type 1 cytotoxic subsets that linked to treatment-induced CVE, such as ventricular dysfunctions, but no contribution of adipocytokines. These translational findings highlight the stratification of leuprolide-associated CVE risk in PC patients based on circulating T cell profiling and could guide the risk mitigation with alternative ADT agents.

immunology↗

CryoMV: Structure-Prior-Guided Modeling and Real-Particle Validation of Continuous Conformational Transitions in Cryo-EM

Continuous protein conformations are essential for understanding fundamental biological processes and supporting drug discovery. Although cryo-EM can resolve individual states at high resolution, recovering continuous heterogeneity from 2D particle images remains challenging. High noise, motion blur, and limited structural priors make it difficult to accurately generate and validate high-resolution continuous conformations using raw particle data. Here, we introduce cryoMV, a framework that integrates structure-prior-guided modeling with real-particle validation for continuous conformational transitions. CryoMV uses reference density maps to establish structural anchors and motion priors, models candidate transition paths between selected conformations, and transfers the learned representation to raw 2D cryo-EM particle images. Each candidate conformation is subsequently evaluated using the estimated particle poses and contrast transfer functions. Supported conformations are reconstructed through raw particle back-projection and assessed using canonical half-maps and Fourier shell correlation. On EMPIAR-10516 and EMPIAR-10345, cryoMV achieves excellent performance in terms of robustness, verifiability, and reconstruction resolution. By incorporating structure-prior modeling and evidence from the raw particles, cryoMV offers an explicit mechanism for assessing whether generated conformations are supported by experimental data and provides a practical approach to reducing model-induced artifacts in continuous cryo-EM heterogeneity analysis.

bioinformatics↗

CryoForge: A Self-Correcting Agent for Cryo-EM Model Building That Learns When to Act and When to Stop

Automated atomic model building has accelerated cryo-EM structure determination, but different builders leave distinct residual error profiles requiring expert inspection. The post-building challenge is to decide which local interpretations are sufficiently supported by experimental evidence to be retained, corrected or rejected. Here we introduce CryoForge, an evidence-gated post-builder agent that separates repair proposal from repair acceptance. Rule and learning-based components identify candidate regions and prioritize legal actions, whereas an independent evidence gate evaluates each edit using map and half-map support, stereochemistry, connectivity and local structural context. Supported edits are retained; unsupported or conflicting modifications are rejected, rolled back, stopped or escalated for expert review. Across a resolution-stratified benchmark, 84.9% of 26,153 released trajectories yielded standard validated improvements and 3.7% yielded low-confidence partial improvements, with no quality-degrading edit retained in the final promoted models. Relative to rule-only control, learned prioritization reduced non-improving candidates and harmful actions while preserving global structural stability. External evaluations using an alternative initializer, same-team automated/manual-assisted challenge submissions and three recently released complex assemblies showed that CryoForge adapts to distinct residual error phenotypes and performs bounded, evidence-supported correction without uncontrolled remodeling. CryoForge provides a builder-independent, scalable and auditable correction layer between automated model generation and expert structural interpretation.

bioinformatics↗

Salicylic acid mediates graft incompatibility by repressing auxin-dependent vascular reconnection in tomato

Graft incompatibility limits the combination of scions and rootstocks, yet the signals that block vascular reconnection remain poorly understood. Using incompatible tomato-pepper (Solanum lycopersicum-Capsicum annuum) grafts, we found that salicylic acid (SA) overaccumulates at the graft junction, predominantly in the rootstock, while incompatible scions exhibit enhanced pattern-triggered immunity. SA-deficient nahG-expressing tomato failed to rescue incompatibility and instead showed severely impaired self-graft healing, indicating that successful tissue reunion requires an optimal, rather than minimal, SA response. Defense-associated genes remained activated in failed grafts regardless of SA accumulation, placing SA downstream of incompatibility determination. Exogenous SA application phenocopied incompatibility, blocking xylem reconnection, inducing cell death, and suppressing auxin signaling. Incompatible grafts similarly displayed reduced auxin accumulation and response at the graft junction. Exogenous auxin partially rescued xylem reconnection in incompatible grafts but failed to activate cambial regulator genes or fully restore compatibility. We propose that graft compatibility depends on SA-auxin homeostasis, where moderate SA supports wound-associated defense and regeneration, whereas excessive SA suppresses the auxin-dependent program required for xylem differentiation. These findings identify SA as a dose-dependent regulator of graft healing in tomato and link excessive immune activation to failed vascular regeneration.

plant biology↗

Quantum transduction from electron spin state to a signaling state in a wild-type LOV photoreceptor

1Whether coherent spin dynamics can control biological regulation remains an open question. Here we show that the electron spin state in the wild-type Avena sativa phototropin 1 Light-Oxygen-Voltage domain 2 (AsLOV2) modulates FMN-cysteine photoadduct formation, the covalent bond that defines its signaling state. Although AsLOV2 was thought magnetically inactive, we observe a magnetic field effect (MFE) on its fluorescence, emerging above ~100 mT and strengthening to 1300 mT. The MFE establishes a spin-correlated radical pair on the photoadduct pathway, one rendered inaccessible to direct spectroscopy by the same strong coupling that sets the high-field onset. It arises from g-factor asymmetry within the closely spaced FMN-cysteine radical pair overcoming its dipolar coupling to drive coherent singlet-triplet interconversion. We furthermore observe an MFE in UV-Vis absorption that, unlike fluorescence, shows the field modulates productive bond formation itself. LOV domains are ubiquitous biological regulators, suggesting that quantum transduction relying on radical pairs as molecular qubits may be a general property among natural and engineered photoreceptors.

biophysics↗

WattmaMod enables high-resolution and extensible RNA modification profiling for nanopore direct RNA sequencing

Nanopore direct RNA sequencing enables direct profiling of RNA modifications on native transcripts, but accurate multi-modification detection remains limited by non-stationary signals and heterogeneity across chemistries. Here, we develop WattmaMod, a deep learning framework for multi-modification detection from nanopore direct RNA sequencing data. It combines self-supervised pretraining, supervised contrastive fine-tuning, and low-label incremental adaptation to improve representation learning and support efficient extension to low-resource modification types. The framework further incorporates wavelet-guided multi-scale encoding and dynamic cross-attention fusion to model raw signals and event-level features. Results show that WattmaMod achieves robust detection of multiple RNA modifications, including m6A, m5C, m1A, A-to-I, m7G, hm5C, m1{Psi}, f5C, ac4C, m5U and {Psi}. It also extends efficiently to low-resource modification types with minimal labeled data, generalizes across sequencing chemistries and species, and predicts potential higher-order local organization among distinct RNA modifications. WattmaMod thus provides a scalable framework for high-resolution epitranscriptome profiling and expands RNA modification analysis beyond single-site prediction to coordinated multi-modification characterization.

bioinformatics↗

Evolution of a core ribosomal innovation in octopus

Much of biology focuses on how genetic changes mediate new functions, but less attention is given to adaptations in other steps of the central dogma. Octopuses exhibit complex nervous systems and sophisticated behaviors that rival vertebrates, but via an entirely divergent evolutionary history. Here, we serendipitously discovered that octopus ribosomes contain a structural break in the core ribosomal RNA that is unique among all animals. This break site enhances translation fidelity to reduce miscoding and subsequent protein aggregation, even when engineered into evolutionarily distant bacterial ribosomes. Furthermore, high fidelity translation by octopus ribosomes supports proteomic stability during extensive RNA editing observed in cephalopods, suggesting synergy between distinct non-canonical modes of gene regulation. This adaptation emerged in recently derived octopuses with expanded nervous systems, thereby revealing a mechanism that could broadly support the evolution of novel organismal traits.

biochemistry↗

CryoDiff: An uncertainty-aware diffusion model for Cryo-EM map enhancement

Cryogenic electron microscopy (cryo-EM) enables high-resolution structural determination of large macromolecular complexes. However, the interpretability of cryo-EM maps is often hindered by substantial background noise and signal attenuation, which obscure structural details. Although existing post-processing methods can partially mitigate these artifacts, they typically suffer from over-smoothing and lack reliable confidence estimation. Here, we present CryoDiff, an uncertainty-aware diffusion model for cryo-EM map enhancement. CryoDiff employs a multi-step diffusion process to progressively denoise and restore high-resolution structural features. Importantly, CryoDiff incorporates a voxel-wise confidence metric derived from Monte Carlo sampling. It unifies map enhancement and voxel-level uncertainty estimation within a diffusion-based generative framework, representing the first approach to achieve such joint modeling for cryo-EM map enhancement. In comprehensive experiments, CryoDiff markedly out-performs existing methods in both map-model correlation and map interpretability, improving the average FSC0.5 metric by 0.356 [A] over state-of-the-art approaches. When applied to de novo model building with ModelAngelo, CryoDiff further increases model completeness by 5.5%, exceeding the gains achieved by competing method.

bioinformatics↗

Benthic diatoms navigate shear flows via hydrodynamic rolling and active gliding

Navigating fluid flow is a fundamental challenge for microbial life across diverse aquatic environments. While rheotaxis in swimming microorganisms has been extensively studied, it remains unresolved whether near-bed shear merely perturbs gliding motility or instead provides directional cues for active navigation on surfaces. Here we show that the benthic diatom Navicula cryptocephala utilises a purely mechanical strategy to achieve downstream rheotaxis and anisotropic spreading on submerged surfaces. Single-cell ellipsoidal tracking reveals a direction-dependent angular response that reorients gliding cells towards the downstream direction. Using interference reflection microscopy, we further reveal that shear induces rolling of obliquely gliding cells, laterally shifting the cell-substrate contact site. This shift renders raphe-based propulsion non-collinear with substrate friction, generating a downstream-restoring yaw torque. Crucially, our results rule out alternative explanations based on longitudinal shifts of the raphe contact site or direct hydrodynamic yaw torque. A minimal stochastic model confirms that this mechanical reorientation alone is sufficient to reproduce the observed drift and diffusion patterns, without invoking either orientation-dependent switching between motility states or orientation-dependent dwell times of those states. Our findings uncover a mechanism by which ambient shear is converted into directional guidance for active surface motility, providing new insights into microbial transport, retention, and resilience on submerged surfaces.

biophysics↗

In vitro-prepared A30P alpha-synuclein fibrils adopt the conserved and disease-relevant Greek key fold

The pathological hallmark of Parkinson Disease (PD) is the formation of the protein alpha-synuclein (Asyn) into {beta}-sheet rich, self-templating fibrils in the brain. Since the first atomic structure of wild-type Asyn fibrils was determined nearly a decade ago, several other in vitro structures of hereditary mutant fibrils and structures derived from post-mortem diseased patient tissue have been determined by solid-state nuclear magnetic resonance (SSNMR) spectroscopy and cryo-electron microscopy. These structures have not only expanded the library of structures available for computational modeling of drug binding and therapeutics development but have also given unprecedented insight into the disease specificity and structural polymorphism of Asyn fibrils. Here, we report the high-resolution SSNMR structure of the A30P hereditary mutant Asyn fibril, associated with early-onset PD. Our structural model is calculated using several thousand distance restraints derived from one sample, primarily sourced through 3D 13C-13C-13C correlation experiments. The structure adopts a Greek key topology yet does not include the P30 mutation site within the fibril core. We also introduce a comprehensive method for the rapid comparison of SSNMR spectra between Asyn polymorphs of known structure and validate the A30P fold. Lastly, we find that the structure is highly similar to many other experimental structures of both in vitro and ex vivo Asyn fibrils, including those with other hereditary point mutations, suggesting a conserved accessible fold.

biophysics↗

SpecLig: Energy-Guided Hierarchical Model for Target-Specific 3D Ligand Design

Structure-based generative models often optimize single-target affinity with ignorance of specificity, resulting in the generation of high-affinity candidates that exhibit promiscuous binding across unrelated targets. This decoupling of affinity and specificity not only compromises therapeutic efficacy but also elevates off-target risks that constrain translational potential. Therefore, we introduce SpecLig, a unified structure-based framework that jointly generates small molecules and peptides with improved target affinity and specificity. SpecLig represents a complex as a block-based graph, combining a hierarchical SE(3)-equivariant variational autoencoder with an energy-guided geometric latent-diffusion model. Chemical priors derived from block-block contact statistics are explicitly incorporated, biasing generation towards pocket-complementary fragment combinations. We benchmark SpecLig on peptide and small-molecule tasks using standard public datasets and propose precision/breadth testing paradigms to quantify specificity. Across multiple evaluations, ligand candidates generated by SpecLig usually bind to the target pocket with high specificity and affinity while maintaining competitive advantages in other attributes. Ablations indicate that both hierarchical representation and energy guidance contribute to success. Finally, we present multiple real applications that demonstrate how SpecLig improves ligands in natural complexes to mitigate potential off-target risks. SpecLig, therefore, provides a practical route to prioritize higher-specificity designs for downstream experimental validation. The codes are available at: https://github.com/CQ-zhang-2016/SpecLig.

bioinformatics↗

A Unified Single-Cell Atlas of HNSCC: Uncovering HPV and Sex Variability in the Tumor Microenvironment

Head and neck squamous cell carcinoma (HNSCC) is highly heterogeneous, with variations driven by HPV status and sex. However, existing single-cell RNA sequencing (scRNA-seq) studies are often limited in sample size and lack standardized methodologies, limiting cross-study comparisons. To address this, we integrated scRNA-seq data from 78 patients (274,911 cells) across multiple studies, creating a unified HNSCC atlas that harmonizes annotations and enables robust tumor microenvironment (TME) analyses. Using STACAS for semi-supervised integration and automated annotation tools such as Ikarus and scGate, we improved tumor and immune cell classification. Leveraging our atlas, we identified HPV- and sex-specific shifts in immune and stromal composition, with HPV+ tumors enriched in adaptive immune cells and HPV- tumors showing more stromal and myeloid populations. Preliminary sex-stratified analyses suggested distinct microenvironmental patterns, warranting further investigation. This publicly available atlas provides a comprehensive framework for reproducibly studying HNSCC biology, improving patient stratification, and may help informing personalized therapies.

cancer biology↗

Giant DNA viruses encode a hallmark translation initiation complex of eukaryotic life

In contrast to living organisms, viruses were long thought to lack protein synthesis machinery and instead depend on host factors to translate viral transcripts. Here, we discover that giant DNA viruses encode a distinct and functional IF4F translation initiation complex to drive protein synthesis, thereby blurring the line between cellular and acellular biology. During infection, eukaryotic IF4F on host ribosomes is replaced by an essential viral IF4F that regulates viral translation, virion formation, and replication plasticity during altered host states. Structural dissection of viral IF4F reveals that the mRNA cap-binding subunit mediates exclusive interactions with viral mRNAs, constituting a molecular switch from translating host to viral proteins. Thus, our study establishes that viruses express a eukaryotic translation initiation complex for protein synthesis, illuminating a series of evolutionary innovations to a core process of life.

microbiology↗

RNA Binding Proteins KhpA and KhpB Interact with Small Regulatory RNAs and Affect Global Gene Expression in Deinococcus radiodurans

Small regulatory RNAs (sRNAs) in bacteria often associate with RNA-binding proteins to gain intracellular stability and/or to enable regulatory efficiency. While much of the current knowledge about those sRNA binding proteins is derived from studies in Gram-negative organisms, the characterization of such proteins in Gram-positive species is still lagging behind. Here, we identified and characterized two sRNA binding proteins (KhpA and KhpB) in Deinococcus radiodurans, a Gram-positive bacterium that exhibits extreme resistance to radiation and other oxidative stressors. We demonstrate that KhpA and KhpB interact with key sRNAs in D. radiodurans and influence their stabilities. Although KhpA and KhpB interact with each other, they do not bind the sRNAs as a complex. Insightfully, KhpA and KhpB facilitate the interactions of the representative sRNAs PprS and Dsr9 in D. radiodurans with their respective mRNA targets, pprM and DR_1968. Through RNA-seq analysis, we further revealed that KhpA and KhpB have both overlapping and specific roles in a global gene regulation in D. radiodurans. Overall, this study expands our knowledge of posttranscriptional regulation in D. radiodurans and supports the growing consensus that KhpA and KhpB homologs constitute a new family of sRNA binding proteins in Gram-positive bacteria. IMPORTANCEThe bacterium Deinococcus radiodurans is the most radiation-resistant organism identified to date. Understanding the mechanisms of resistance of D. radiodurans is essential for leveraging this bacterium in biomedical and biomanufacturing applications. It was previously revealed that small regulatory RNAs (sRNAs) play crucial roles in the gene regulation of D. radiodurans. However, how these sRNAs are influenced by RNA binding proteins is poorly understood. Here we identified two conserved RNA binding proteins, KhpA and KhpB, as sRNA binding partners in D. radiodurans. These proteins affect the sRNA stability, sRNA-target interaction, and global gene regulation. Characterization of KhpA and KhpB will help us advance the understanding of how post-transcriptional network regulates the physiology and radioresistance of D. radiodurans.

molecular biology↗

Comprehensive analysis of metabolic reprogramming-related gene signaturesmetabolic reprogramming related gene signature for predicting ovarian cancer prognosis, immune landscape, and potential treatment options

Ovarian cancer (OV) is the most lethal gynecologic malignancy. Metabolic reprogramming is a distinctive feature of cancer and is associated with tumorigenesis and progression. It could be a potential therapeutic target for cancer treatments and a biomarker for assessing cancer prognosis. In this study, we identified metabolic reprogramming-related differentially expressed genes (MRRDEGs) in OV through differential gene expression analysis and conducted a comprehensive characterization of these MRRDEGs. Based on the MRRDEGs, we constructed an effective prognostic risk model including five model genes for OV. The risk score was a valid independent prognostic factor that could more accurately predict the survival of OV patients. It could classify OV patients into distinct risk groups with significant differences in survival. We observed significant differences between risk groups in biological pathway activity, immune cell infiltration patterns, and immunotherapy responses. Specifically, the low-risk group demonstrated superior immunotherapy response compared to the high-risk group. These findings significantly advance our understanding of the relationship between metabolic reprogramming and OV pathogenesis, progression, prognosis, and immunotherapy response, laying a foundation for developing novel biomarkers and therapeutic targets in the future and providing an important reference for the formulation of precision medicine strategies.

bioinformatics↗

Hydraulic Activation of the AsLOV2 photoreceptor

How proteins transduce light into mechanical energy remains a central question in biology. This study tests the hypothesis that blue light activation of the LOV2 (light, oxygen, voltage sensitive) domain of Avena sativa phototropin 1 (AsLOV2), gives rise to concerted water movement that induces protein conformational extensions. Using electron and nuclear magnetic resonance spectroscopy, along with molecular dynamics simulations at high pressure, we find AsLOV2 activation can be initiated by blue light or high pressure, followed by selective and concerted expulsion of low-entropy, tetrahedrally coordinated "wrap" water from the protein hydration shell. These findings suggest that interfacial water serves as constituents to reshape the proteins free energy landscape during activation. Our study highlights hydration water as an active hydraulic fluid that can drive long-range conformational changes underlying protein mechanics upon light activation and offers a new concept for engineering externally controllable protein actuators. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=70 SRC="FIGDIR/small/660617v2_ufig1.gif" ALT="Figure 1"> View larger version (25K): org.highwire.dtl.DTLVardef@1a35f9dorg.highwire.dtl.DTLVardef@da4991org.highwire.dtl.DTLVardef@113e9b2org.highwire.dtl.DTLVardef@53d9fc_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

Global profiling of the proteome and acetylome in mice with abdominal aortic aneurysms

BackgroundAbdominal Aortic Aneurysm (AAA) is a life-threatening vascular condition characterized by a progressive dilation of the abdominal aorta and a high risk of rupture. Currently, no effective pharmacological therapies are available, and treatment relies mainly on surgical intervention. The lack of drug targets is largely due to limited understanding of the molecular mechanisms underlying AAA development. This study aims to identify potential therapeutic targets by performing comprehensive proteomic and acetylomic analyses in a mouse model of AAA. MethodsWe conducted global proteomic and acetylomic profiling on abdominal aortic tissues collected from an AAA mouse model. A total of 7,858 proteins and 1,790 acetylated proteins encompassing 4,581 acetylation sites were quantified. Bioinformatics analyses were performed to investigate the regulatory networks and biological pathways associated with these proteins and post-translational modifications. ResultsIntegrated analysis revealed that histone-related proteins were significantly enriched in pathways co-regulated by the proteome and acetylome. These pathways are influenced by histone acetyltransferases and deacetylases, implicating histone acetylation in AAA-related inflammatory and immune processes. Notably, the deacetylases Sirt2 and Sirt5 were identified as potential regulators of neutrophil extracellular trap (NET) formation through suppression of histone acetylation. ConclusionsThis study provides the first comprehensive proteomic and acetylomic dataset for abdominal aortic tissues in a mouse model of AAA, substantially expanding the mouse acetylation database. The results highlight the central role of histone modifications in immune dysregulation and inflammation, and propose Sirt2 and Sirt5 as candidate therapeutic targets that may inhibit NET formation and slow AAA progression. These findings suggest new avenues for drug development targeting the sirtuin family, although further experimental validation and cross-species studies are needed to confirm translational relevance. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=145 SRC="FIGDIR/small/657536v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1c397a3org.highwire.dtl.DTLVardef@188180org.highwire.dtl.DTLVardef@de1a59org.highwire.dtl.DTLVardef@193e740_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioinformatics↗

In situ light-driven pH modulation for NMR studies

Proton exchange is a fundamental chemical event, and NMR provides the most direct readout of protonation events with site-specific resolution. Conventional approaches require manual titration of sample pH to collect a series of NMR spectra at different pH values. This requires extensive sample handling and often results in significant sample loss, leading to reduced signal or the need to prepare additional samples. Here, we introduce a novel approach to control pH in NMR samples using water soluble photoacids, which alter the pH of the solution from near neutral to acidic pH upon in situ photo-illumination. We show that the solution pH can be precisely controlled by choice of illumination wavelength and intensity and sufficient protons are released from the photoacid to achieve meaningful pH change in samples where the molecule of interest has significant buffering capacity, such as a >100 M protein sample. The pH is monitored in situ using internal standards with pH-sensitive chemical shifts. This method enables precise, calibrated, non-invasive change of sample pH within an NMR magnet, dramatically reducing the necessary sample handling. These findings highlight the potential of light-induced pH control in NMR experiments and increase the robustness and reliability of pH-dependent studies. With pH playing a key role in modulating chemical behavior in both biological and synthetic systems, the ability to study protonation states and modulate sample pH in a simple and precise manner that is compatible with high-resolution NMR studies of molecular structure and function has wide applications. Entry for the Table of ContentsIn this work, we introduce a novel approach to control pH in NMR samples using light-activated photoacids. By combining light stimuli with pH-sensitive molecules, we demonstrate the ability to precisely modulate pH without physically manipulating the sample. This method enables non-invasive pH titration in NMR studies, where pH plays a key role in protein function. Our findings highlight the potential of light-induced pH control to overcome existing limitations in NMR, providing a powerful tool for advancing protein research under controlled pH conditions. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/633412v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@1bf9839org.highwire.dtl.DTLVardef@1a2d77eorg.highwire.dtl.DTLVardef@1f1a68dorg.highwire.dtl.DTLVardef@1ed73fa_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗