Biology subjects

Han, H.

Publications and source records attributed to Han, H..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Rare centenarian SIRT6 coding variants elevate SIRT6 protein levels and resist cellular senescence

Centenarians provide valuable insights into the biological mechanisms underlying human longevity and potential gerotherapeutic targets. We previously identified two linked missense variants in SIRT6 that are enriched in Ashkenazi Jewish centenarians. To investigate their functional impact in physiologically relevant cellular contexts, we generated human embryonic stem cells carrying these variants through precise genomic knock-in and differentiated them into somatic lineages. Functional characterization revealed that the centenarian variants endogenously elevated SIRT6 protein levels through weakened interaction with vimentin, and altered SIRT6 enzymatic activities including enhanced mono-ADP-ribosyl transferase activity and reduced deacetylase activity. These variants delayed replicative and progerin-induced cellular senescence, preserving genome stability through maintenance of DNA repair pathways and suppression of transposable element derepression. Moreover, pharmacologically mimicking the centenarian variants using SIRT6 activator Fucoidan-FV partially ameliorated premature aging-associated molecular defects in progeria fibroblasts. Together, our findings demonstrate that rare centenarian variants exert multifaceted effects on SIRT6 and enhance cellular resilience, providing insights for developing geroprotective therapies informed by genetic discoveries in exceptionally long-lived individuals.

cell biology↗

bioRxiv2025

Epigenetic CRISPR Screening of 9p21.3 Non-Coding Regions identifies Cis-Regulatory Elements of P16INK4a and P15INK4b Controlling Cellular Senescence

Cellular senescence is a hallmark of aging and a promising target for extending human healthspan. Senescence is often accompanied by upregulation of the key senescence marker gene CDKN2A, yet the mechanism underlying its transcriptional activation remains unclear due to complex cis-regulations within the 9p21.3 locus. Here, we performed complementary CRISPR activation and interference screens in human mesenchymal stromal cells (MSCs) to systematically map non-coding cis-regulatory elements (CREs) at this locus that epigenetically regulate senescence. This approach revealed senescence-regulating CREs (SenReg-CREs) that bidirectionally modulate senescence through P16INK4a and P15INK4b. Notably, we identified a primate-specific short interspersed nuclear element (SINE) MIR3 embedded within the most potent distal SenReg-CRE. Deletion of this SINE:MIR3 accelerated senescence, revealing its potential insulator function in restraining CDKN2A/CDKN2B activation. Collectively, these findings reveal novel mechanisms underlying senescence-associated transcriptional activation of CDKN2A/CDKN2B and demonstrate that senescence is malleable through manipulation of regulatory element activity, highlighting the potential of epigenetically targeting these SenReg-CREs for senomorphic interventions.

genomics↗

bioRxiv2025

Breaking Free from the Acquisition Dogma for Volume Electron Microscopy

Volume electron microscopy (VEM) enables nanometer-resolution three-dimensional (3D) visualization of biological specimens via serial sectioning and imaging. Owing to precautions against additional challenges in downstream analysis, VEM datasets are often acquired unnecessarily at slow speeds and high resolutions, thereby limiting achievable imaging throughput. By systematically searching for optimal VEM acquisition conditions, we find that sufficient spatial resolution effectively counteracts high image noise in preserving 3D structural information. To further verify that denoising is more effective in restoring volumetric datasets than axial interpolation, machine learning-based methods, including a newly developed 3D context-based denoising model, were compared through various tasks on VEM datasets acquired simultaneously. Our volumetric approach not only outperforms other baseline methods in faithful feature recovery but also facilitates robust serial block-face cutting down to 20 nm by allowing fast imaging. This work provides both an optimized acquisition strategy and volumetric denoising methods as actionable guidelines for maximizing VEM throughput.

bioinformatics↗

bioRxiv2025

Scalable automated segmentation quantifies mitochondrial proteins and morphology at the nanoscale

Ultrastructural changes of mitochondria are closely associated with metabolic dysfunction, leading to a variety of human disorders. These changes can be visualized by pan-Expansion Microscopy (pan-ExM), a 3D microscopy technique requiring only standard fluorescence microscopes, at a throughput exceeding that of the current gold standard, 3D electron microscopy, by orders of magnitude. However, a lack of tools that enable the characterization and quantification of the observed ultrastructural features in the acquired 3D datasets at a comparable throughput has hindered the widespread adoption of pan-ExM for quantitative imaging. Here, we present an automated deep-learning based segmentation approach that utilizes pan-ExMs power to acquire multi-channel images and uses specific labeling as the annotation for the training of the segmentation network. This molecular annotation reduces the required manual annotation effort for mitochondria substructures to just a few hours when setting up the experiment and thereby provides access to 3D suborganellar morphology of mitochondria at an unprecedented throughput. Our approach, which we term MAPS (Mitochondrial Automated Pan-ExM Segmentation), enables for the first time to quantify mitochondrial ultrastructural morphology at scale. We demonstrate this power by characterizing the 3D mitochondrial morphology at the organelle and sub-organelle level in tens of HeLa cells under different treatments and localizing mitochondrial proteins in the sub-organellar context. To demonstrate our technology in tissue, we compare the ultrastructural morphology of mitochondria in proximal tubules of kidneys of mice exhibiting acute kidney injury (AKI) with those of untreated mice, revealing striking differences in their cristae structure. MAPS can easily be adapted to different cell and tissue types, allowing the analysis of tens of samples per day, and therefore provides a versatile tool for a comprehensive understanding of mitochondrial ultrastructural changes in many disease contexts. Requiring only standard fluorescence microscopes and computer infrastructure, MAPS is readily adoptable by any lab. HighlightsO_LIMAPS utilizes specific labeling to train a segmentation model for 3D super-resolution pan-ExM images C_LIO_LISuborganellar mitochondrial features and their changes in disease models are quantified at high throughput C_LIO_LI3D protein distributions are correlated to ultrastructural features in mitochondria C_LIO_LIRequiring only standard lab infrastructure, MAPS is readily adoptable C_LI

cell biology↗

bioRxiv2025

ASCENT: Annotation-free Self-supervised Contrastive Embeddings for 3D Neuron Tracking in Fluorescence Microscopy

Tracking individual neurons in dense 3D microscopy recordings of fast-moving, deforming organisms is a critical challenge in neuroscience. This task is often hindered by complex tissue motion and the need for laborious manual annotation. Here, we introduce ASCENT, an annotation-free computational framework that learns robust representations of neuronal identity that are invariant to tissue deformation. ASCENT trains a Neuron Embedding Transformer (NETr) through a self-supervised contrastive scheme on augmented data that mimics tissue deformations. NETr generates highly discriminative embeddings for each neuron by combining visual appearance with positional information, refined by the context of all other neurons in the frame. On a challenging benchmark C. elegans datasets, ASCENT achieves state-of-the-art tracking accuracy, surpassing supervised methods. The method is robust to image noise, highly data-efficient, and generalizes across different imaging conditions. By eliminating the annotation bottleneck, ASCENT provides a practical and scalable solution for the robust analysis of whole-brain neural dynamics in behaving animals.

bioengineering↗

bioRxiv2025

De Novo design of a potent Wnt Surrogate specific for the frizzled7 subtype members

In humans, 19 Wnt ligands interact with 10 Frizzled (Fzd) receptors and the co-receptors LRP5/6 to initiate signaling. Wnts and Fzds are highly promiscuous, making it challenging to dissect the specific outcomes of individual Wnt-Fzd interactions. Developing Wnt surrogates with specificity for individual Fzd subtypes could be pivotal. We present a modular, potent, and Fzd7-specific Wnt surrogate that consists of three de novo designed modules, a Fzd7 binder, an LRP6 binder and a homodimeric protein. The Fzd7-specific module was designed by targeting two less conserved surface patches on the cysteine-rich domain (CRD) of Fzds to achieve both selectivity and affinity. It exhibits a strong binding affinity (KD < 2.3 nM) for the very closely related Fzd7 subtype members (Fzd7, Fzd1, Fzd2) with no measurable binding to the CRDs of the other seven Fzd receptors. This Wnt surrogate induced spheroid organoid formation from intestinal stem cells at subnanomolar concentration, and promoted full hair follicle regeneration and robust hair growth in mice. These results suggest that our strategy could be extended to design modular Wnt surrogates capable of selectively activating individual Fzd receptors, providing a valuable tool kit for development and differentiation, organoid cultures and targeted regeneration.

bioengineering↗

bioRxiv2025

Agropyron cristatum genome provides a new insight for wheat improvement with wild relatives

Exploring novel genetic variation for target traits is crucial for advancing wheat breeding and genetic improvement. Since 1990, we have been transferring genes from Agropyron cristatum, a promising wild relative genetic resource featuring robust spike morphology and stress tolerance, into common wheat by distant hybridization. To efficiently harness A. cristatum genes, we de novo assembled a 25.62-Gb high-quality genome of an autotetraploid accession Z559 with 28 chromosomes, and uncovered its specific genome features and an extensive repertoire of genes associated with yield and resistance to abiotic and biotic stresses. We systematically characterized A. cristatum genome introgressions by resequencing 431 wheat-A. cristatum derivatives and cloned the gene AcGNS1, which functions in the regulation of grain number per spike in wheat. Subsequently, we developed an optimized genome-selection model for wheat-A. cristatum breeding derivatives, enabling the rapid selection of new potential varieties. These findings demonstrate a genomic breeding strategy for leveraging novel genetic resources of wild relatives and advancing wheat improvement.

genomics↗

bioRxiv2025

Multiplexed Neuromodulatory-Type-Annotated EM-Reconstruction of Larval Zebrafish

Diverse neuromodulatory systems confer functional flexibility upon the hardwired sensorimotor pathways of the brain1-6. Among these, the evolutionarily conserved locus coeruleus (LC)-norepinephrinergic (NE) system integrates and broadcasts information globally7-9. While previous studies have primarily focused on its axonal outputs and effects on neural processing, the organizational logic of its synaptic inputs, enabling it to sense global brain states and in turn shape its activity dynamics for appropriate neuromodulation10,11, remains poorly explored. To address this, we mapped the synaptic input architecture of individual LC-NE neurons by establishing Fish-X, a whole-brain microscale reconstruction of larval zebrafish with neuron-type annotations. This dataset encompasses the retina, brain and anterior spinal cord, capturing >240,000 cells and >25 million synapses. Monoaminergic (including NE, dopaminergic, and serotonergic), hypocretinergic, and glycinergic neurons were resolved by multiplexed subcellular APEX2 labeling, while glutamatergic and GABAergic identities were inferred via morphology comparison with a zebrafish mesoscopic atlas12,13. Compared with other neuronal populations, LC-NE neurons display distinct perisomatic features and high dendritic indegrees. Reconstruction of near-complete dendritic inputs to individual LC-NE neurons reveals their broad yet sparse synaptic convergence across the brain. These synaptic inputs are not randomly distributed but instead organized according to sensory/motor modality, excitatory/inhibitory identity, and synaptic strength. Individual LC-NE neurons share common inputs, a feature conserved within and across monoaminergic systems, suggesting a co-innervation mechanism for coordinated neuromodulation. Thus, our study uncovers multi-level principles governing the spatial organization of LC-NE neurons broad-yet-sparse inputs and provides a pivotal resource for deciphering the microscale architecture of neuromodulatory systems.

neuroscience↗

bioRxiv2025

Swine reporter model for preclinical evaluation and characterization of gene delivery vectors

Delivery of gene therapy vectors targeted to any somatic cell remains a key barrier for the development of genetic medicines. While rodent models provide insights into vector biodistribution and cellular tropism, their anatomical and physiological differences from humans limit their translational potential and studies in large animal models are often required. In this study, we developed a swine reporter model (SRM-1) to evaluate both viral and nonviral vector delivery in a large animal system. The SRM-1 model harbors a Cre- and CRISPR-activated tdTomato reporter at the Rosa26 locus that allows for tracing of cell-specific delivery and expression of gene therapy vectors in vivo. To evaluate this model, we administered adeno-associated virus serotype 9 (AAV9) and lipid nanoparticles (LNPs) carrying mRNA systemically and found successful in vivo reporter activation across a variety of tissues. Intracerebroventricular (ICV) administration of LNP-Cre mRNA was also performed and demonstrated localized activation in cortical brain cells. In addition to biodistribution studies, this model has utility for testing safety and clinically relevant administration methods, surgical and non-surgical, of delivery vectors. Our findings support the SRM-1 model as a valuable tool for advancing gene therapies from preclinical testing to clinical application.

genetics↗

bioRxiv2025

KLHL41 orchestrates sarcomere assembly and size to drive skeletal muscle hypertrophy in vivo

Sarcomere assembly and growth are fundamental processes essential for the development, function, and repair of skeletal muscle. However, the mechanisms underlying sarcomere formation and assembly in vivo, which are critical for the formation of functional myofibers in vertebrates, remain poorly understood. Defects in sarcomeres contribute to muscle dysfunction in numerous genetic and acquired myopathies, yet the lack of a clear understanding of specific sarcomeric defects has hindered the development of effective therapies. Nemaline myopathy (NM) is caused by mutations in genes that primarily affect sarcomere structure and function. The disease is clinically heterogeneous, with the congenital form being the most severe. Using zebrafish models of congenital forms of NM, we investigated sarcomere assembly in vivo during skeletal muscle development to identify key steps contributing to myofibril formation and muscle growth under both normal and disease conditions. Our findings demonstrate that the gene encoding the sarcomeric protein KLHL41 plays a critical role in the formation and directional organization of new sarcomeres within developing myofibrils, facilitating both radial and longitudinal muscle growth. Dysregulation of sarcomeric proteins and impaired protein turnover in the KLHL41-NM zebrafish model resulted in the development of sarcomeric defects. Moreover, we show that the interaction between the KLHL41-troponin complex is essential for muscle growth and cross-bridge regulation in developing muscle. These studies address a significant gap in the understanding of sarcomeric defects in myopathies and will help guide the development of targeted therapies aimed at rescuing these processes.

genetics↗

bioRxiv2025

ROMO1 loss in cholinergic neurons induces mitochondrial ultrastructural damage and ALS-like neuromuscular degeneration

Mitochondrial dysfunction is strongly associated with the pathogenesis of amyotrophic lateral sclerosis (ALS), a neurodegenerative disorder characterized by progressive motor neuron degeneration. However, it remains obscure whether mitochondrial abnormities are sufficient to drive ALS development. Here, we show that selective depletion of reactive oxygen species modulator 1 (ROMO1), an inner mitochondrial membrane-delimited protein, in cholinergic neurons leads to adult-onset, progressive locomotor deficits in mice that closely resemble ALS pathology. ROMO1 ablation in cholinergic neurons induces ALS-like neuromuscular degeneration, as evidenced by age-dependent motor neuron loss, axon degeneration, disrupted cholinergic transmission, neuromuscular junction denervation, and the resultant muscle atrophy. Notably, ROMO1 loss induces early and progressive mitochondrial cristae deformation in motor neurons, preceding the onset of ALS-like syndromes. Our findings support that mitochondrial impairment in vulnerable motor neurons is a sufficient contributor to ALS etiology, positioning mitochondria as a potential therapeutic target.

neuroscience↗

bioRxiv2025

Multiple FGFR1 mutations modulate tumorigenic mechanisms in glioneuronal tumors.

FGFR1 genetic alterations are associated with human diseases, including brain tumors. We reported multiple FGFR1 mutations in familial and sporadic cases of low-grade glioneuronal tumors, suggesting intrinsic mechanisms of selective pressure toward FGFR1 multiple events arising in the context of a quiet genome. To decipher the molecular mechanisms triggered by multiple FGFR1 mutations, we have mapped the proximal interactome of wild-type, single-and double-mutant FGFR1 proteins through a BioID-MS approach. Our data reveals novel oncogenic functionality for the two hotspots N546K and K656E, linked to evasion of lysosomal degradation. We identified a modulatory role played by the susceptibility variant R661P, which hampers the oncogenic potential of both hotspot mutations by rescuing receptor degradation and reducing N546K affinity for the downstream effector PLC{gamma}. The R661P variant alone abolished the self-renewal capacity of oligodendroglioma cells and showed downregulation of genes involved in neurodevelopment and neuro-glial cell fate decisions, both aspects overcome in the double mutants. This study sheds light on the oncogenic effects associated with FGFR1 alterations and their recurrence in low-mutation burden and therapy naive tumors.

cancer biology↗

bioRxiv2025

PIBE: Parallel ion beam etching of sections collected on wafer for ultra large-scale connectomics

We developed a parallel ion beam etching device that simultaneously thins hundreds of sections on a whole 4-inch wafer at 20 nm steps, enabling sub-centimeter volumetric imaging with high axial resolution. Compared with traditional volume electron microscopy, PIB preserves in-situ continuity within sections and simplifies inter-section registration. Its high axial resolution facilitates reliable neuron segmentation and tracing with reduced proofreading, providing an efficient route toward ultra-large-scale connectomics, such as whole-mouse-brain reconstruction.

neuroscience↗

bioRxiv2025

Stress Granule Formation Drives ZBP1-dependent Necroptosis in Non-obstructive Azoospermia and Aging testes

Male infertility and age-related reproductive decline remain major unmet medical challenges, with limited understanding of the underlying mechanisms. Here, we identify a stress granule-driven necroptosis pathway involving ZBP1 and RIPK3 as a central driver of non-obstructive azoospermia (NOA), a severe form of male infertility marked by loss of spermatogenesis. We show that heat stress or environmental insults activate eIF2 kinases, inducing stress granules that recruit ZBP1 and RIPK3 to form a signaling complex. This leads to RIPK3 activation, MLKL phosphorylation, and necroptotic death of spermatogonia and Sertoli cells. Genetic ablation of Zbp1 or Ripk3 protects mice from heat-induced testicular atrophy, highlighting their essential role in testicular cell death. Notably, this same necroptosis pathway is also activated in aged human testes, suggesting a shared mechanism driving both male infertility and age-related testicular degeneration.

molecular biology↗

bioRxiv2025

Reshaping epistatic network modules enhances wheat yield potential

Increasing wheat yield is a key approach to ensuring global food security and an enduring focus in crop breeding. Here, we assembled a panel of 3,030 wheat lines to dissect the genetic mechanisms of yield improvement. We conducted large-scale field trials across five ecological environments over two consecutive years to evaluate yield performance and constructed a haplotype atlas using the Wheat 660K genotype array. 234 quantitative trait loci (QTLs) and 522 haplotype blocks (HBs) were identified for 14 traits through genome-wide association studies (GWAS), including 10 QTLs and 35 HBs associated with grain yield. Genomic analysis revealed that wheat yield improvement is primarily driven by changes in the epistatic network rather than the introduction of new haplotype segments. SNPs or HBs explain 53.3%-62.9% of the phenotypic variation in yield, whereas epistasis explains 70.4%, highlighting the role of epistasis in yield improvement. Moreover, yield improvement is significantly correlated with the accumulation of favorable epistatic modules. Pedigree-based analysis revealed that the modules remained relatively stable under the pressure of breeding selection, while new favorable modules were also created during hybrid breeding, highlighting that crop design breeding should be based on genetic modules. This study provides insights into genetic mechanism of wheat yield improvement and guidance for designing future wheat in the era of artificial intelligence.

genetics↗

bioRxiv2025

Discovery of a VHL molecular glue degrader of GEMIN3 by Picowell RNA-seq

Targeted protein degradation (TPD) is an emerging therapeutic modality in which small molecules are used to recruit targets to the natural protein degradation machinery of the cell. Molecular glue degraders (MGD) are monovalent small molecules that accomplish this by redirecting E3 ubiquitin ligases to target proteins, offering the potential to degrade previously unliganded and "undruggable" proteins in cancer, neurodegenerative, and other diseases. While attractive due to their drug-like properties, MGDs are exceptionally hard to discover and have largely been identified serendipitously. The Von Hippel-Lindau (VHL) E3 ligase is the second most widely used effector for TPD, though current VHL-based degraders are primarily large heterobifunctional PROTACs (proteolysis-targeting chimeras) designed using target-based ligands. Here, we have instead pursued target-agnostic discovery of VHL MGDs leveraging proprietary ultra-miniaturized microfluidics devices (Picowells) to facilitate unbiased RNA-seq screening of a biased E3-focused library. This resulted in dGEM3, a novel VHL molecular glue that targets the survival of motor neuron (SMN) complex member GEMIN3 for degradation. Through a combination of cellular, biochemical, and biophysical assays, we have characterized the GEMIN3 degron within its helicase ATP-binding domain, and how the kinetics of ternary complex formation impact degradation. These findings provide insights on the re-programmability of VHL for novel targets using drug-like molecular glues.

biochemistry↗

bioRxiv2025

A cardiac microphysiological system for screening lipid nanoparticle/mRNA complexes predicts in vivo efficacy for heart transfection

Lipid nanoparticle (LNP)/mRNA complexes have tremendous potential for treating cardiac diseases but lack the transfection efficiency required for successful heart therapeutics. A challenge preventing the development of cardiac LNPs is the lack of in vitro screening platforms that maximize transfection and predict efficacy. Here, we demonstrate that a phenotypic cardiac microphysiological system (MPS), constructed from a human induced pluripotent stem cell cardiomyocytes (hiPSC-CM) Cre-reporter line, can identify LNP/mRNA complexes that diffuse efficiently within 3D cardiac micromuscles and transfect cardiomyocytes with high efficiency. Successful LNP formulations contained an acid-degradable PEG (ADP)-lipid, where ADP-LNPs containing 10% PEG had enhanced diffusion and gene editing efficiency in the cardiac MPS. The in vivo delivery of LNP/mRNA complexes, including luciferase and CRE mRNA, into Ai6 mice confirmed the cardiac MPS screening outcomes. It revealed that ADP-LNPs achieved notably superior transfection in the heart with reduced off-target liver uptake compared to a standard LNP formulation. The cardiac MPS showed strong LNP transfection in vitro and pinpointed a promising formulation for in vivo mRNA delivery to the heart.

bioengineering↗

bioRxiv2025

Ambient temperature structural studies of Penicillin-binding Protein 2a of Methicillin-Resistant Staphylococcus aureus with XFELs and synchrotrons

Penicillin-binding protein 2a (PBP2a) is a transpeptidase responsible for the {beta}-lactam resistance in methicillin-resistant Staphylococcus aureus (MRSA), posing significant challenges to antibiotic therapy. PBP2as unique structural features, including its highly flexible active site and allosteric regulation, enable it to maintain catalytic activity even in the presence of {beta}-lactam antibiotics. Despite extensive characterization using cryogenic crystallography, key questions remain about its dynamic properties and conformational changes under near-physiological conditions. Room-temperature crystallography methods, particularly serial femtosecond X-ray crystallography (SFX) at XFELs, provide a powerful approach to capture these dynamics. Unlike cryogenic conditions that can constrain protein flexibility, SFX enables the study of conformational variability and interaction networks closer to physiological states. Here, we present the first room-temperature structures of PBP2a obtained using SFX to uncover insights into the enzymes flexibility, allosteric communication, and catalytic mechanisms. These findings are built upon optimized large-scale production and crystallization protocols for PBP2a, ensuring high-quality microcrystals suitable for SFX data collection. The room-temperature structures reveal novel interaction patterns, including unique salt bridge networks and dynamic structural elements absent in cryogenic studies. Furthermore, comparative analyses highlight how environmental conditions influence the conformational states of PBP2a, providing new perspectives on its resistance mechanisms. By integrating structural data from EuXFEL and LCLS, this study not only enhances our understanding of PBP2as functional dynamics but also underscores the value of room-temperature crystallography in studying antibiotic resistance. These insights could guide the design of next-generation {beta}-lactam antibiotics capable of overcoming PBP2a-mediated resistance.

biochemistry↗