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Han, M.

Publications and source records attributed to Han, M..

At least 19 recordsLinked to original sources

TMEM106B C-Terminal fragment aggregation exacerbates α-synuclein and TDP-43 proteinopathy phenotypes.

Genetic variation in the human gene encoding the lysosomal transmembrane protein 106B (TMEM106B) drives risk of neurodegenerative dementia. A C-terminal fragment of TMEM106B (TMEM CT) accumulates in lesions across neurodegenerative disease, potentially contributing to neurotoxicity and hampering efficacy of therapeutic interventions. Previously, we developed the first transgenic organism model of TMEM CT neuronal aggregation in Caenorhabditis elegans (C. elegans). We demonstrated that TMEM CT neuronal aggregation drives severe neuronal dysfunction and neuronal loss. To investigate the potential synergistic interaction of TMEM CT aggregation with other types of aggregated neurotoxic proteinopathies occurring in dementia, we assessed neuronal degeneration and pathogenic protein accumulation in bigenic C. elegans expressing TMEM CT and other key proteinopathies of neurodegeneration including a-synuclein, tau, and TAR DNA binding protein 43 (TDP-43). Our results showed strong neurotoxic synergy of TMEM106B with TDP-43 or -synuclein. However, we detected only mild synergy between TMEM106B and tau. This work provides evidence in support of TMEM CT aggregation as a significant participant in the neurodegenerative process attributed to other toxic protein aggregates. The work also highlights the importance of considering secondary proteinopathy contributions including TMEM CT aggregation when developing interventions against primary TDP-43 or -synuclein proteinopathies.

neuroscience↗

Molecular anatomy of the glomerular filtration barrier reveals topology-encoded albumin sieving

The kidney filters plasma rapidly while retaining albumin, yet where and how this selectivity is encoded within the glomerular filtration barrier remain unresolved. Here we combine cryo-electron tomography (cryo-ET) of vitrified mouse glomeruli with structure-resolved transport modelling to predict albumin passage from the native three-dimensional architecture of the barrier. Among the three barrier layers, endothelial fenestrae and the flexible Nephrin-Neph1 slit-diaphragm lattice are substantially permeable to albumin. The glomerular basement membrane (GBM) instead provides the dominant restriction through steric exclusion governed by void-network topology. In local GBM reconstructions, water traverses broadly connected void space, whereas narrow throats exclude albumin, leaving few accessible paths. To scale this mechanism to the tissue level, we combine structural statistics from local cryo-ET volumes with mesoscale measurements of GBM heterogeneity to generate representative ensembles. Integrating these ensembles with other layers predicts whole-barrier albumin sieving in close agreement with an independent measurement. The topology-driven mechanism also explains early filtration failure in Alport syndrome mice, in which collagen-IV disruption remodels the GBM network and opens albumin-accessible paths while cellular interfaces remain preserved. These findings identify the structural origin of glomerular albumin selectivity and establish a quantitative route from locally resolved architecture to tissue-scale physiology.

physiology↗

spatiAlytica: Viewer-Grounded Multimodal Agentic System for Interactive Spatial Omics Analysis

Spatial transcriptomics and proteomics map tissue architecture and cellular interactions, but analysis remains limited by programming demands and text-centered AI agents that lack viewer grounding and cross-turn context. We present spatiAlytica, a viewer-centric multimodal interactive agentic system embedded in the Napari viewer that enables non-programmer biologists to perform iterative, hypothesis-driven spatial omics analysis via natural language. spatiAlytica couples viewer-state serialization, agentic memory, biological concept-to-data-field mapping, code generation and debugging, Spatial VQA, and grounded interpretation to support an exploratory analysis and interpretive reasoning workflow. We introduce spatiAlyticaBench, a comprehensive benchmark spanning 222 single-turn spatial analytical coding questions, 178 multi-turn sequential workflow questions, and 7,350 image-grounded reasoning questions. spatiAlytica outperformed strong agentic baselines, while using less time and tokens. Case studies across Kaposis sarcoma, colorectal cancer, and ovarian cancer recapitulated known spatial patterns and uncovered progressive CD8 T-cell dysfunction during KS progression.

bioinformatics↗

Lipids Regulate Export of Lysosomal Enzymes from the Endoplasmic Reticulum

Lysosomal enzymes are synthesized in the Endoplasmic Reticulum (ER) and transported to lysosomes to execute their functions. Deficiencies in lysosomal enzymes or components of the lysosomal transport machinery result in lysosomal storage disorders. While mannose-6-phosphate mediated lysosomal enzymes sorting in the Golgi has been extensively characterized, the mechanisms governing their export from the ER remain elusive. Here, we show that de novo lipogenesis, a metabolic pathway responsible for fatty acid synthesis, regulates lysosomal enzyme transport. Inhibition of de novo lipogenesis leads to the retention of lysosomal enzymes within the ER. Mechanistically, fatty acid derived from de novo lipogenesis is used for Arf1 myristoylation. Myristoylated Arf1 promotes retrograde vesicle trafficking from the Golgi to the ER, thereby maintaining the homeostatic bidirectional flux required for efficient ER export of lysosomal enzymes. Our findings uncover a critical functional link between lipid metabolism and lysosomal enzyme trafficking.

cell biology↗

FlyPredictome: A structural atlas of predicted protein-protein interactions in Drosophila

Protein-protein interactions (PPIs) are fundamental to cellular function. Yet most Drosophila PPIs remain structurally uncharacterized despite the wealth of genetic and biochemical data available for this organism. Here we present FlyPredictome, a structural interactome based on 1.5 million pairwise AlphaFold-Multimer predictions. Using a local confidence metric performing robustly on interactions involving flexible and disordered proteins, we systematically assess experimentally reported Drosophila PPIs and predict direct binding interfaces at residue-level resolution. Testing their functional relevance, we find that phenotype-associated missense mutations are enriched at predicted interaction interfaces. Building on these predictions, we construct an evidence-supported PPI network, revealing modular organization from signaling pathways to individual protein complexes. We further predict higher-order complexes for nearly 400 of these modules with AlphaFold3, matching available cryo-EM structures and extending to unresolved assemblies. Fly-Predictome is available as an open, interactive database that maps interactions to residue-level binding surfaces, providing a structural foundation for interaction discovery in Drosophila.

bioinformatics↗

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

Real-time functional connectivity-based neurofeedback of the DLPFC-amygdala pathway during threat-exposure attenuates anxiety

BackgroundAdaptive regulation of negative emotion is vital for mental health and dysregulations in this domain contribute to the major mental disorders, including anxiety and depression. On the neural level, efficient emotion regulation has been linked to functional communication between the dorsolateral prefrontal cortex (DLPFC) and the amygdala. Gaining voluntary control over this pathway may present an effective strategy for potentiating emotion regulation. ObjectiveAgainst this background, we developed a novel connectivity-based real-time fMRI (rt-fMRI) neurofeedback (NF) training that enables individuals to gain volitional control over the DLPFC-amygdala pathway during exposure to threatening stimuli. MethodsThe study employed a pre-registered, randomized, sham-controlled design with the experimental group (n = 22) receiving real-time NF information on connectivity between the right DLPFC and the amygdala during threat exposure and the sham control group (n = 23) receiving connectivity NF from a circuit not related to emotion regulation. The ability to maintain regulatory control in the absence of feedback was assessed after four NF runs. Primary outcomes included functional connectivity of the target pathway, as well as anxiety scores. ResultsThe results demonstrate that successful acquisition of self-regulation of the rDLPFC-amygdala top-down regulatory circuit in the experimental NF group facilitated attenuation of anxiety. ConclusionIn summary, our findings suggest that real-time fMRI neurofeedback (rtfMRI-NF) allows to volitionally enhance rDLPFC-amygdala connectivity, and in turn reduces negative emotional states, rendering the training a promising neurotechnology intervention for mental disorders.

neuroscience↗

Retroreflective beam multiplexing enables high-throughput two-photon voltage imaging in vivo

Voltage imaging demands technical innovations to realize its full potential in neuroscience. Although two-photon microscopy is widely used in brain research, its imaging speed is insufficient for high-throughput voltage recordings. To overcome this limitation, we developed an all-optical beam multiplexing engine via retroreflection from two near-parallel mirrors. This approach integrates seamlessly with standard two-photon microscopes, enabling kilohertz-frame-rate imaging across a 16-fold expanded field of view while maintaining synaptic resolution. Operating at over 220 megapixels per second, it enables submillisecond imaging of dendritic propagation of action potentials and simultaneous voltage recording from more than 200 hippocampal neurons in head-fixed, behaving mice. This advancement unlocks new possibilities for large-scale, high-speed functional studies in neuroscience.

neuroscience↗

Emergence of Individualized Functional Topography in the Neonatal Brain

The early postnatal period represents a critical phase for establishing the brains fundamental architecture. However, how individualized functional topography emerges and shapes long-term cognition remains unknown. Using multimodal neuroimaging data from 419 neonates, we map personalized functional topographies in the first weeks of life and reveal their association with 18-month neurocognitive outcomes. Unique and stable functional topographies are already present at birth, with interindividual variability organized along a conserved sensorimotor-to-association hierarchy. These individualized maps encode early brain maturity and robustly predict cognitive, language, and motor outcomes at 18-month of age, with predictive features concentrated at network boundaries. This functional refinement is structurally anchored by concurrent maturation in cortical myelination and sulcal depth. Preterm birth results in distinctive topographic alterations characterized by accelerated maturation of association networks. Our work establishes a foundation for precision models of early brain development and elucidates its significance for long-term neurocognitive outcomes.

neuroscience↗

Phage display-mediated immuno-PCR to detect low-abundance secreted proteins in Drosophila

Circulating hormones, that mediate communications across organs to maintain physiological balance, are commonly detected and quantified using enzyme-linked immunosorbent assays (ELISAs). However, while ELISA is well-suited for organisms where sample blood can be readily obtained, its application is considerably more challenging in smaller organisms, particularly Drosophila, which has gained widespread use in recent years for physiological studies. Here, we present sensitive phage display-mediated immuno-PCR (PD-iPCR) to detect Drosophila hemolymph proteins via two approaches: 1) by identifying high-affinity nanobodies through phage-display library screening and subsequent affinity maturation and 2) by generating a knock-in fly line producing secreted proteins tagged with tandem NanoTags composed of VHH05 and 127D01. Using these approaches, we successfully established PD-iPCR to detect insulin-binding ImpL2 protein in fly hemolymph. Notably, the tandem NanoTag-based sandwich PD-iPCR enabled highly sensitive detection of tagged antigens, allowing us to quantify elevated ImpL2 levels in the hemolymph of starved flies and those bearing Yki-induced gut tumors. Collectively, our results demonstrate that PD-iPCR enables detection of endogenous, low-abundance circulating hormones in Drosophila, providing a powerful tool for studying interorgan communication. Significance statementHormones and other secreted factors orchestrate organism-wide physiology, yet their routine quantification in Drosophila has been limited by the limited volume of hemolymph available for assays like enzyme-linked immunosorbent assay (ELISA). Here, we present phage display-mediated immuno-PCR (PD-iPCR) as a novel sensitive platform for quantifying secreted proteins in flies in vivo. Using ImpL2 as an example, we successfully detected nanomolar level of circulating ImpL2 and monitored its physiological changes during starvation and tumorigenesis using PD-iPCR. This approach can be readily expanded to multiplexed quantification of secreted proteins in vivo by leveraging the multiple available nanobodies and the vast collection of epitope-tagged Drosophila lines. This work opens the door to systematic endocrine phenotyping across developmental stages and diverse physiological conditions.

genetics↗

GABA-GABA_A Receptor Signaling Orchestrates Invasion and Metastasis in Triple Negative Breast Cancer

Cancer is a leading cause of death globally, with the majority of cancer-related deaths resulting from cancer metastasis -the process by which cancer cells disseminate to distant sites. To metastasize, cancer cells acquire traits in support of diverse cellular processes that enable dissemination, survival, and colonization. Tumor cell dissemination requires invasion at local and distant sites and this process can be influenced by intrinsic and extrinsic factors. Here, we investigate the role of the neurotransmitter gamma-aminobutyric acid (GABA) in triple-negative breast cancer (TNBC) invasion and metastasis. TNBC cells increased invasion in response to GABA and this was found to be mediated through the GABAA receptor family. TNBC cell lines were found to be responsive to exogenous GABA and also produced endogenous GABA. Pharmacological inhibition of GABAA receptors reduced TNBC invasion and cancer cell dissemination and resulted in inhibition of GSK3 activity. TNBC cell lines were found to express the GABRE subunit and loss of GABRE impaired GABA-mediated invasion and tumor cell dissemination. These findings support a role for GABA signaling through GABAA receptors in mediating TNBC progression.

cancer biology↗

Field evaluation of non-invasive sampling for monitoring nine swine pathogens in the Republic of Korea

BackgroundNon-invasive sampling methods, such as swine oral fluid (OF) and fecal boot (FB) sampling, have gained attention due to their animal welfare considerations, ease of collection, and cost effectiveness. However, comparative data regarding non-invasive and standard sampling methods remain limited, particularly in the Republic of Korea, where research on OF and FB sampling is sparse. Therefore, we investigated representative pig pathogens, including six porcine respiratory pathogens and three gastrointestinal pathogens, using OF and FB samples for pathogen surveillance across commercial farms in the Republic of Korea. MethodsThe results from targeted polymerase chain reaction (PCR) assays for major respiratory and gastrointestinal pathogens obtained using OF and FB samples were compared with those obtained from standard samples. Non-invasive samples included 30 OF ropes and 30 FBs collected from nine farms, and 360 standard samples (blood, fecal, oral, and nasal swabs) were also collected. PCR assays for the nine pathogens were conducted, and the results from OF, FB, and combined OF+FB were compared with those from standard samples at the pen level. ResultsOF sampling showed superior test concordance with respiratory pathogens than gastrointestinal pathogens, and FB sampling demonstrated superior detection of gastrointestinal pathogens compared with OF sampling. Additionally, the combination of OF+FB sampling improved the detection concordance for all nine target pathogens investigated. ConclusionsWe demonstrated the feasibility and potential applicability of OF and FB sampling under field conditions in Korean pig farms. Therefore, this study supports OF and FB sampling as useful tools for swine pathogen monitoring in both research and practical field applications.

microbiology↗

A Super-Resolution Spatial Atlas of SARS-CoV-2 Infection in Human Cells

Coronaviral replication depends on double-membrane vesicles (DMVs), yet where polyprotein processing occurs and how replication organelles mature remain unresolved. We built a multi{-}color super-resolution atlas of SARS-CoV-2 RNA, non-structural and structural proteins in infected human cells, combining 3D single-molecule localization with radial and angular pair-correlation analysis. The atlas uncovers fundamental spatial principles. First, nsp5 (3CLpro) localizes within the DMV lumen near pores, with nsp7-nsp16 positioned interior to nsp4, supporting a protease-dependent maturation model in which nsp5 action permits membrane closure and subsequently completes intravesicular polyprotein processing to activate replication complexes. Second, we identify dsRNA connectors bridging DMVs and non-canonical, nsp3/4-lacking dsRNA granules decorated with replicase components, consistent with a condensate-mediated route for trafficking replication intermediates. Third, mapping structural proteins reveals M- and S-positive virion assembly intermediates along the secretory route, while premature intracellular S1 shedding captures the baseline instability of the original virus isolate prior to evolutionary adaptation. Finally, the antiviral nirmatrelvir induces multilayered bodies of uncleaved polyproteins (nsp4-5-10-16) that persist after washout and precede rapid rebound, suggesting a drug-induced reservoir state. Beyond mapping the viral architecture, this atlas resolves the spatial context of proteolysis and organelle remodeling, providing a framework for pan-coronaviral mechanisms and antiviral design.

microbiology↗

Targeting FSP1 triggers ferroptosis in lung cancer

Pre-clinical and clinical studies have demonstrated how dietary antioxidants or mutations activating antioxidant metabolism promote cancer, highlighting a central role oxidative stress in tumorigenesis. However, it is unclear if oxidative stress ultimately increases to a point of cell death. Emerging evidence indicates that cancer cells are susceptible to ferroptosis, a form of cell death triggered by uncontrolled lipid peroxidation1-3. Despite broad enthusiasm about harnessing ferroptosis as a novel anti-cancer strategy, whether ferroptosis is a barrier to tumorigenesis and if it can be leveraged therapeutically remains unknown4,5. Using genetically-engineered mouse models (GEMMs) of lung adenocarcinoma (LUAD), we performed tumor specific loss-of-function studies of the two key ferroptosis suppressors, glutathione peroxidase 4 (Gpx4)6,7 and ferroptosis suppressor protein 1 (Fsp1)8,9, and observed increased lipid peroxidation and robust suppression of tumorigenesis, suggesting that lung tumors are highly sensitive to ferroptosis. Furthermore, across multiple pre-clinical models, we found that FSP1 was required for ferroptosis protection in vivo, but not in vitro, underscoring a heightened need to buffer lipid peroxidation under physiological conditions. Lipidomic analyses revealed that Fsp1-knockout (Fsp1KO) tumors had an accumulation of lipid peroxides, and inhibition of ferroptosis with genetic, dietary, or pharmacological approaches effectively restored the growth of Fsp1KO tumors in vivo. Unlike GPX4, FSP1 expression was prognostic for disease progression and poorer survival in LUAD patients, highlighting its potential as a viable therapeutic target. To this end, we demonstrated that pharmacologic inhibition of FSP1 had significant therapeutic benefit in pre-clinical lung cancer models. Our studies highlight the importance of ferroptosis suppression in vivo and pave the way for FSP1 inhibition as a therapeutic strategy in lung cancer patients.

cancer biology↗

The clinical drug candidate anle138b binds predominantly to the central cavity in lipidic Aβ fibrils and modulates fibril formation.

Alzheimers disease is a specific neurodegenerative disorder, distinct from normal aging, with a growing unmet medical need. It is characterized by the accumulation of amyloid plaques in the brain, primarily consisting of amyloid beta (A{beta}) fibrils. Therapeutic antibodies can slow down the disease, but are associated with potential severe side effects, motivating the development of small molecules to halt disease progression. This study investigates the interaction between the clinical drug candidate small molecule anle138b and lipidic A{beta}40 fibrils of type 1 (L1). L1 fibrils were previously shown to closely resemble fibrils from Alzheimers patients18. Using high-resolution structural biology techniques, including cryo-electron microscopy (cryo-EM), nuclear magnetic resonance (NMR) spectroscopy enhanced by dynamic nuclear polarization (DNP), and molecular dynamics (MD) simulations, we find that anle138b selectively binds to a cavity within the fibril. This structural insight provides a deeper understanding of a potential drug-binding mechanism at the atomic level and may inform the development of novel therapies and diagnostic approaches. In addition, anle138b reduces fibril formation in the presence of lipids by approximately 75%. This may suggest a mechanistic connection to its previously reported activity in animal models of Alzheimers disease15.

biochemistry↗

BioMedTools: a language model-powered community for biomedical computational tools

A large number of biomedical computational tools have spawned several tool registries. However, in the face of the rapid growth in the number of tools, existing tool registries, which are manually curated or community-driven, are difficult to keep up to date, resulting in inadequate tool repository data. In this paper, we show that language models (LMs) can aid in building a community of tools. We introduce BioMedTools (https://biomed.tools), a community of biomedical computational tools that mainly implements LM-based tool identification and a chat assistant. Compared with existing tool registries, BioMedTools achieves excellence in terms of the number of tools, frequency of data updates, and functionality. Meanwhile, the Model Context Protocol (MCP) servers hub in BioMedTools may promote the building of agents in the biomedical field. BioMedTools enables the efficient collection of tools and enhances their findability and accessibility.

bioinformatics↗

Perturbing RNA localization for functional study in neurons

Spatial RNA organization plays a pivotal role in diverse cellular processes and diseases, but the functional implications of spatial RNA localization remain underexplored. We present CRISPR-mediated transcriptome organization (CRISPR-TO) that harnesses RNA-guided, nuclease-dead dCas13 for programmable control of RNA localization in live cells. CRISPR-TO enables targeted localization of RNAs to diverse subcellular compartments, including p-bodies, stress granules, telomeres, and nuclear stress bodies, across cell types. In primary cortical neurons, we demonstrate that repositioned mRNAs undergo local translation along neurites and at neurite tips and co-transport with ribosomes, with {beta}-actin mRNA localization enhancing the formation of dynamic filopodial protrusions and inhibiting axonal regeneration. Furthermore, CRISPR-TO-enabled parallel screening in primary neurons identifies Stmn2 mRNA localization as a driver of neurite outgrowth. By enabling large-scale perturbation of the spatial transcriptome, CRISPR-TO bridges a critical gap left by current sequencing and imaging technologies, offering a versatile platform for high-throughput functional interrogation of RNA localization in living cells and organisms.

bioengineering↗

Lipid metabolism of hepatocyte-like cells supports intestinal tumor growth by promoting tracheogenesis

Tumors reprogram lipid metabolism in distant tissues to support their growth. In adult Drosophila, gut tumors secrete the PDGF/VEGF-like factor Pvf1, which activates the TORC1-Hnf4 pathway in hepatocyte-like oenocytes. This drives production of very long-chain fatty acids and wax esters essential for tracheal growth around the tumor. Blocking Hnf4 or the elongase mElo in oenocytes strongly suppresses tracheogenesis, tumor progression, and cachexia-like organ wasting, while extending host lifespan. The same pathway also controls tracheal development in healthy flies. Lipoprotein receptor LpR2 depletion in oenocytes rescues the observed tumor induced tracheal tracheal remodeling. This tumor-host interaction is conserved: VEGF-A induces lipid metabolism genes in human hepatocytes, and lung tumor-bearing mice show elevated hepatic Hnf4 and Elovl7. The study reveals a non-autonomous role of the TORC1-Hnf4 axis in lipid-mediated tumor progression and identifies potential therapeutic targets for cancer-associated metabolic dysfunction.

cell biology↗