Biology subjects

Han, S.

Publications and source records attributed to Han, S..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

Insight into the scaffolding function of USP18 from a high resolution cryo-EM structure of STAT2-USP18-ISG15 ternary complex

USP18 is a primary negative regulator of the type I interferon (IFN-I) signaling which regulates hundreds of IFN-stimulated genes for viral protection and anti-cancer immunity. USP18 plays dual roles in the IFN-I signaling: 1) deubiquitinase enzymatic function which cleaves ISG15 from its substrates and 2) scaffolding function through forming a complex with STAT2 to suppress IFN-I signaling. Targeting the scaffolding function of USP18, instead of its enzyme activity, is crucial for reducing cancer cell fitness and boosting anti-tumor immunity. However, the molecular basis of USP18s scaffolding function remains unclear due to the lack of structural information. Here, using a fusion tag strategy, we captured the transient USP18-STAT2 complex and determined a ternary complex structure of STAT2-USP18-ISG15 at 3.05 [A] resolution by cryogenic electron microscopy (cryo-EM) that delineated detailed USP18-STAT2 interactions. Remarkably, the ternary complex impairs USP18s enzymatic function by STAT2-mediated disruption of its catalytic triad. Structural analysis and mutagenesis identify specific USP18 point mutations, facilitating further investigation into the role of USP18 in IFN-I signaling. Taken together, our findings suggest that USP18s scaffolding function could present an untapped opportunity for cancer therapy.

molecular biology↗

bioRxiv2026

Stromal estrogen signaling regulates fallopian tube homeostasis and cancer initiation via inflammatory pathways

Lifetime estrogen exposure is a major risk factor for ovarian cancer, which can originate from fallopian tube epithelial (FTE) cells. Here we report that estrogen receptor (ER) signaling in fallopian tube (FT) stromal cells plays a critical developmental role in maintaining epithelial homeostasis by promoting FTE proliferation and ciliated differentiation. Stromal ER regulates expression of inflammatory cytokines, growth factors, and extracellular matrix components, creating a differentiation-supportive, tumor-suppressive niche that coordinates epithelial regeneration during hormonal cycles. Excessive or prolonged estrogen exposure, however, shifts this niche toward a tumor-promoting state by inducing inflammation and activating stemness-associated pathways, including JAK/STAT, in FTE cells. This effect is exacerbated in genetically altered FTE cells lacking key tumor suppressors, which resist differentiation while remaining responsive to stromal proliferation signals. These findings reveal how stromal ER signaling integrates hormonal cues, inflammation, aging, and genetic susceptibility to influence early events in FT carcinogenesis. In BriefEstrogen receptor signaling in fallopian tube stromal cells maintains epithelial homeostasis by promoting proliferation and ciliated differentiation. Excessive estrogen shifts this niche toward inflammation and stemness, cooperating with genetic susceptibility to drive early fallopian tube carcinogenesis. O_FIG O_LINKSMALLFIG WIDTH=190 HEIGHT=200 SRC="FIGDIR/small/700864v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@113b543org.highwire.dtl.DTLVardef@e1465corg.highwire.dtl.DTLVardef@1d279dcorg.highwire.dtl.DTLVardef@13e782c_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIStromal ER signaling maintains fallopian tube epithelial (FTE) cell homeostasis C_LIO_LIStromal ER promotes proliferation and ciliated differentiation of FTE cells C_LIO_LIExcess estrogen shifts this stromal niche toward tumor promotion via inflammation C_LIO_LIDifferentiation-resistant mutant FTE cells respond to stromal proliferation signals C_LI

cancer biology↗

bioRxiv2026

Targeted Chromosomal Sequencing of Wild Bonobos Identifies a Genetically Distinct Subpopulation East of the Lomami River

Bonobos (Pan paniscus), an endangered species, have for decades been genetically understudied, partly due to difficulties in obtaining high-quality samples. The study of their genome is important not only for understanding their evolution, but also for improving conservation efforts, including population management, diversity and inbreeding assessment, and tracking rescued individuals to combat illegal wildlife trafficking. Here, we use chromosome 21 target capture data from 156 non-invasively collected faecal samples from wild bonobos to perform a comprehensive analysis of their population structure. We confirm the existence of three previously suggested subpopulations identified here as Western, Central and Eastern bonobos which are defined by natural barriers of gene flow such as the Lomami River. By estimating levels of inbreeding, diversity and differentiation, we find support for isolation of mainly Western and Eastern populations and add information on the dispersal routes of their ancestors. We infer split times and separation of these populations and apply a genetic framework to geolocalize samples of unknown origin, showing that locations of their potential origin can be estimated with a precision of up to a median of [~]50 km. Our study provides valuable insight into the evolution and population structure of bonobos and reveals how rivers act as strong barriers between populations. It also offers resources for conservation efforts and highlights the need to monitor bonobo populations more closely, in particular isolated ones. ImpactBonobos have been difficult to study genetically due to their remote forest habitat and endangered status. Here we used non-invasive sampling and chromosome 21 target capture sequencing to perform the most detailed analysis to date of their population structure. We find three main subpopulations and genetic differentiation influenced by river barriers, especially with populations found on the Eastern side of the Lomami river. This data will be useful for identifying the geographic origin of confiscated samples and thus aid bonobo conservation efforts.

bioinformatics↗

bioRxiv2026

NORAD orchestrates KLC1-mediated SFPQ transport via liquid-liquid phase separation

Neuronal function requires precise long-distance axonal transport mediated by molecular motors and RNA-binding proteins like SFPQ, though regulatory mechanisms remain poorly defined. We identify long non-coding RNA NORAD as a master regulator of this process through liquid-liquid phase separation (LLPS). While SFPQ and kinesin-1 mediate cargo delivery, the specific RNA coordinating their interaction was unknown. We demonstrate NORAD directly binds kinesin light chain 1 (KLC1) and promotes SFPQ condensation into dynamic LLPS droplets, enabling efficient transport. CRISPR-assisted mapping and functional assays show NORAD depletion disrupts granule dynamics, impairs neuroprotective mRNA localization, and induces axonal degeneration. In vitro reconstitution confirms NORAD-KLC1 synergy enhances SFPQ phase separation, and neuron-specific knockout mice exhibit motor deficits with reduced neuronal density. These findings establish the first evidence of lncRNA NORAD-mediated LLPS in axonal transport, revealing a new paradigm for RNA-guided neuronal maintenance.

molecular biology↗

bioRxiv2025

APOE E4 Alzheimer's Risk Converges on an Oligodendrocyte Subtype in the Human Entorhinal Cortex

The entorhinal cortex (ERC) is implicated in early progression of Alzheimers disease (AD). Here we investigated the impact of established biological risk factors for AD, including APOE genotype (E2 versus E4 alleles), sex, and ancestry, on gene expression in the human ERC. We generated paired spatially-resolved transcriptomics (SRT) and single-nucleus RNA sequencing data (snRNA-seq) in postmortem human ERC tissue from middle aged brain donors with no history of AD. APOE-dependent changes in gene expression predominantly mapped to a transcriptionally-defined oligodendrocyte subtype, which varied substantially with ancestry, and suggested differences in oligodendrocyte differentiation and myelination. Integration of SRT and snRNA-seq data identified a common gene expression signature associated with APOE genotype, which we localized to the same oligodendrocyte subtype and a white matter spatial domain. This suggests that AD risk in ERC may be associated with disrupted oligodendrocyte function, potentially contributing to future neurodegeneration. Lay SummaryAlzheimers disease (AD) is a neurodegenerative disorder that accounts for 60-80% dementia cases. Apolipoprotein E (APOE) genotype is the strongest genetic risk factor for AD, and the entorhinal cortex (ERC) is a brain region implicated in its earliest progression. Our study investigated how APOE genotype impacts gene expression in the ERC. We identified genotype-dependent effects on oligodendrocytes with different transcriptional profiles related to maturation that may help explain how APOE genotype mediates its effects on AD risk.

neuroscience↗

bioRxiv2025

Colorectal cancer relies on an immunosuppressive cellular topography and genomic adaptations for establishing brain metastases

Colorectal cancer (CRC) brain metastases have a poor prognosis and limited treatment options, including resistance to radiation therapy. Little is known about the molecular and cellular mechanisms that enable CRC tumor cells to adapt to the brain and establish a supportive tumor microenvironment. To address this gap we used spatial transcriptomics to analyze 51 CRC brain metastases. A subset had matched primary colon tumors and longitudinally paired metastatic resections before and after radiation treatment. We identified the critical spatial cellular features of the tumor epithelium and the surrounding tumor microenvironment that support metastatic growth in the brain. CRC brain metastases developed a stromal microenvironment with abundant fibroblasts and tumor-associated macrophages. A fibroblast-macrophage cellular neighborhood promoted angiogenesis, extracellular matrix remodeling, and immune suppression. Tumor cells showed local adaptations. In endothelial-rich regions, they were proliferative whereas in macrophage-rich regions, they were more differentiated and immune evasive. Compared with paired primary tumors, CRC brain metastases showed increased chromosomal instability, with activation of RNA-processing, stress response, and junctional remodeling pathways. After radiation treatment, resistant clones had increased epithelial-mesenchymal transition, while the immunosuppressive stroma remained intact. We identified tumor-derived MIF, GDF15, PRSS3 and SEMA3C ligands and macrophage-derived SPP1 that have the potential to affect multiple cell types in the metastatic niche. These ligand-receptor interactions drive angiogenesis, stromal activation and immune suppression. In a macrophage-tumor-fibroblast co-culture model, knockout of SPP1 in macrophages led to reduced expression of lipid-metabolism related genes and disrupted tumor-promoting interactions. Together, these results indicate that CRC growth in the brain is sustained by a specific cellular organization with immunosuppressive multicellular interactions.

cancer biology↗

bioRxiv2025

DEER of Singly Labelled Proteins to Evaluate Supramolecular Packing of Amyloid Fibrils

1The formation of protein amyloid fibrils in the brain is a hallmark of various neurodegenerative diseases, including Alzheimer diseases and Parkinson diseases. Amyloid fibrils are highly ordered aggregates in which proteins folded in two-dimensional layers stack along one axis to form elongated linear assemblies. The specific conformations adopted by the proteins within each layer of the amyloid correlates with the pathology. Furthermore, their spreading and templating competency relies on strict in register packing of the folded proteins along the fibril growing axis. There is a need for tools to characterize not only the protein fold across the fibril cross section but also the spatial ordering of the proteins stacked along the amyloid fibril axis. We present an approach based on double electron electron resonance spectroscopy (DEER) using singly labelled tau protein assembled in amyloid fibrils that can deliver an apparent dimensionality of the supramolecular organization of tau fibrils. The parameters of the DEER background function can be used to assess the amyloid core location and packing order, and track time-resolved formation of aggregation intermediates. Showcasing the method on tau, we demonstrate that heparin-induced tau fibrils are mispacked while seeded aggregation can template amyloid fibrils with a higher packing order. This study benchmarks a new method that will provide critical structural insights into amyloid assemblies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/687719v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@8c42c9org.highwire.dtl.DTLVardef@74b0f8org.highwire.dtl.DTLVardef@10e8095org.highwire.dtl.DTLVardef@11bc727_HPS_FORMAT_FIGEXP M_FIG DEER-derived dimensionality parameter differentiates between spin-labelled tau protein in solution, in perfectly aligned fibril or in imperfectly aligned fibril (fibril structure edited from PDB 6qjh). C_FIG

biophysics↗

bioRxiv2025

Impact of Alzheimer's disease risk factors and local neuromelanin content on the transcriptomic landscape of the human locus coeruleus

The locus coeruleus (LC) is a small noradrenergic nucleus in the dorsal pons that sends projections across the brain regulating sleep, arousal, attention, stress responses, and some forms of cognition. LC neurons show pathology in the earliest stages of Alzheimers disease (AD), including age-related accumulation of hyperphosphorylated tau (pTau) and accelerated loss of neuromelanin (NM) pigmentation. NM-sensitive neuroimaging of the LC predicts previous cognitive decline, clinical severity, and future AD progression. While these findings suggest that the LC plays an etiologic role in AD, the molecular landscape of the LC prior to clinical manifestation of sporadic AD remains largely uncharacterized. This information is critical for developing interventions that preserve LC integrity and function. We performed spatially-resolved transcriptomics on 85 sections of human postmortem LC from N=33 neurotypical middle-aged donors, balanced for epidemiologic AD risk factors including sex, African or European ancestry, and APOE genotype (carriers of the E4/risk or E2/protective alleles). Comparing across APOE genotypes, we find astrocytic gene expression differences proximal to LC neurons. Associating NM content with local gene expression, we show that higher overall APOE gene expression correlates with reduced NM content and an enrichment of NM-associated genes in aging pathways. Unexpectedly, we find enriched LC expression of cholesterol synthesis genes, alongside evidence for lipid synthesis gene regulatory network activity in NM-containing LC specifically, revealing a potential intersection between intrinsic lipid metabolism in LC neurons, NM, and the role of APOE-mediated lipid biology in AD. Together, these data illuminate the molecular features of the human LC at spatial resolution with unprecedented sampling depth, revealing how AD risk factors and NM content influence resilience and susceptibility of this critical brain nucleus to pathology accumulation and degeneration.

neuroscience↗

bioRxiv2025

Human gut Bifidobacteria strains promote longevity via shared and divergent mechanisms

Human gut Bifidobacteria are abundant during infancy and have been reported to be enriched in some exceptionally long-lived populations, yet whether their beneficial effects on lifespan and healthspan are broadly shared across the genus or restricted to specific strains remains unclear. Using an anaerobic bacteria-Caenorhabditis elegans platform with heat-killed diets, we systematically compared 11 human gut Bifidobacteria strains representing nine species. B. infantis ATCC 15697, B. longum NCC 2705, and B. breve DSMZ 20213 produced the largest lifespan extensions and improved multiple measures of physiological resilience, whereas the other strains produced smaller, neutral, or detrimental effects. Genetic analyses showed that these three strains required different combinations of conserved cytoprotective regulators, yet all depended on NHR-49, a lipid-regulating nuclear receptor functionally related to mammalian PPAR, for full lifespan extension. Consistent with this shared requirement, further analyses showed that B. infantis and B. longum also required FAT-7, an NHR-49-regulated delta-9 fatty acid desaturase, for full lifespan extension and oxidative stress protection. Untargeted lipidomics identified distinct but partially overlapping phosphatidylethanolamine, diacylglycerol, and triacylglycerol species that were enriched by these diets and reduced by fat-7 RNAi. Bulk lipid extracts from either strain enhanced oxidative stress resistance when added to a standard E. coli diet, providing functional evidence that bacterial lipids contribute to protection. Together, these findings support a strain-selective model. Related commensal strains differ in their physiological effects and cytoprotective pathway requirements but share dependence on host lipid regulation. The findings also identify gut bacteria-host lipid interactions as a mechanistic axis linking microbial products to stress resilience and longevity. Author summaryGut bacteria are increasingly linked to healthy aging, but which strains are beneficial and how they act on the host remain poorly understood. Human gut Bifidobacteria are common members of the infant gut microbiome and have been reported to be enriched in some exceptionally long-lived populations. Using Caenorhabditis elegans and controlled, heat-killed bacterial diets, we compared 11 human gut Bifidobacteria strains representing nine species. B. infantis, B. longum, and B. breve produced the largest lifespan benefits and improved physiological resilience, whereas the remaining strains produced smaller, neutral, or detrimental effects, showing that these benefits are highly strain-selective. Genetic experiments revealed that the three selected strains required different combinations of conserved stress response regulators. Despite these differences, all depended on NHR-49, a regulator of host lipid metabolism functionally related to mammalian PPAR, for full lifespan extension. Consistent with this shared requirement, B. infantis and B. longum also required FAT-7, an NHR-49-regulated fatty acid desaturase, for lifespan extension and protection from oxidative stress. Lipidomic profiling showed that the two strains reshaped host complex lipid composition in partially overlapping ways, with many changes reduced when fat-7 expression was lowered. Lipid extracts from either strain were also sufficient to improve oxidative stress resistance when added to a standard diet, providing functional evidence that bacterial lipids contribute to protection. Together, these findings identify gut bacteria-host lipid interactions as a mechanistic axis linking strain-specific bacterial effects to stress resilience and longevity.

microbiology↗

bioRxiv2025

DeepCEF: A Deep Causal Estimation Framework for Complex Biological Systems Integrating Local Scores, Independence Tests, and Relation Attributes

Causal relationship identification is a fundamental and complex research challenge that spans multiple disciplines, including biology, epidemiology, economics, and philosophy. Various scoring techniques and independence tests, such as local scores (e.g., Degenerate Gaussian (DG) and Bayesian Information Criterion (BIC)) and independence tests (e.g., Fishers Z), have been employed in causality estimation. However, these local scores often excel in specific data types or application areas but falter in others, limiting their ability to capture the complexity and heterogeneity of underlying causal mechanisms. For instance, a method may perform well on linear relationships or continuous variables but struggle with discrete variables or non-linear relationships. Real-world observational datasets, particularly those generated in complex biological systems, often contain diverse data types and relationships, making it essential to develop a more comprehensive approach. To address this challenge, we propose a novel causal estimation framework that leverages the powerful classification capabilities of deep neural networks (DNNs) to identify causal patterns in pairwise relationships. Our framework integrates multiple local causality estimation scores, independence tests, and variable attributes, allowing it to capture a wide range of causal mechanisms. To ensure the frameworks robustness and generalizability, we incorporate a diverse range of simulation data and 10 curated real-world datasets into the training procedure. Furthermore, our framework is designed to be extensible, enabling users to easily integrate their own data and additional scores and tests. Our validation results demonstrate that our framework outperforms existing methods in terms of estimation accuracy and precision on both simulation data and real-world biological datasets. By providing a more comprehensive and adaptable approach to causal relationship identification, our framework has the potential to advance research in various fields and improve our understanding of complex biological systems.

bioinformatics↗

bioRxiv2025

Development of a High-Throughput Screening Method for Anti-NNV Drugs

Nervous necrosis virus (NNV) is an infectious pathogen, characterized by rapid infection and high mortality, commonly encountered in the aquaculture industry. Therefore, there is an urgent need to develop effective antiviral drugs against NNV, which is crucial for targeted treatment strategies, pathogen control, and loss reduction. Screening of effective antiviral active compounds, namely drug precursors, is key to developing highly efficient drugs against NNV. Reverse transcription-quantitative real-time PCR (RT-qPCR) is widely applied to screen and evaluate various substances to prevent and control virus infection. However, RT-qPCR is a cumbersome procedure and not suitable for high-throughput rapid screening. The aptamer TNA1c, which specifically binds to NNV-infected cells, was used to construct a target-driven activatable aptamer probe (TAA). Then, the TAA probe was applied to establish a high-throughput screening (TAA-HTS) method for efficient evaluation of substances against NNV infection. TAA-HTS technology achieved rapid, sensitive, and specific screening of bioactive substances with significant anti-NNV effects. As compared to commonly used analytical methods, such as RT-qPCR, TAA-HTS has the advantages of easy operation and high sensitivity and specificity. The findings of this study provide data support and a theoretical basis for the development of effective antivirus preparations. IMPORTANCEIn this study, a target-driven activatable aptamer probe was employed to establish a high-throughput screening method for anti-NNV drugs. This method enables rapid, sensitive, and specific screening of anti-NNV compounds while reducing background interference. Although RT-qPCR is currently the most widely used technique for antiviral drug screening and validation, the screening approach developed in this study significantly shortens screening time while achieving results consistent with those of RT-qPCR. This demonstrates that the screening method presented here has the potential to become a universal strategy for future drug screening against viral diseases. Moreover, this study not only provides a novel technical solution for NNV control but also demonstrates the potential of aptamer-based probes in high-throughput antiviral screening, serving as a model for combating viral pathogens in aquaculture and other fields.

pathology↗

bioRxiv2025

Neural basis of social-categorization function of language

Languages provide social-category markers that tag people as one or another social group. How does the brain sort words into different language categories as a basis of the social-categorization function of language? We addressed this issue by testing neural categorization of visual words of different writing systems in nine studies using electroencephalography, magnetoencephalography, and a repetition suppression paradigm. We showed that a neural network, including the anterior temporal, insular, orbital frontal, and ventral occipito-temporal cortices in both hemispheres, was engaged in computations of correlation distances between two words to represent intra-language similarity and inter-language difference during categorization of visual words of alphabetic and non-alphabetic languages. These processes occurred as early as 150 ms post-stimulus, recruited within-hemisphere functional connections, operated independently of words semantic meanings and pronunciations, and exhibited consistently across individuals with diverse language backgrounds. These findings highlight the neural mechanisms of language-based spontaneous neural categorization of visual words as a basis of the social-categorization function of language.

neuroscience↗

bioRxiv2025

Nanoscopy Reveals Heparan Sulfate Clusters as Docking Sites for SARS-CoV-2 Attachment and Entry

Virus entry is thought to involve binding a unique receptor for cell attachment and cytosolic entry. For SARS-CoV-2 underlying the COVID-19 pandemic, angiotensin-converting enzyme 2 (ACE2) is widely considered the receptor for cell-surface attachment and cytosolic entry. Using advanced light microscopy to resolve individual virions and receptors, we found instead that heparan sulfate (HS), not ACE2, mediates SARS-CoV-2 cell-surface attachment and subsequent endocytosis. ACE2 functions only downstream of HS to enable viral genome expression. Instead of binding single HS molecules that electrostatically interact with viral surface proteins weakly, SARS-CoV-2 binds clusters of [~]6-137 HS molecules projecting 60-410 nm above the plasma membrane. These tall, HS-rich clusters, present at about one per 6 m{superscript 2}, act as docking sites for viral attachment. Blocking HS binding with the clinically used HS-binding agent pixantrone strongly inhibited an authentic pathogen, the SARS-CoV-2 Omicron JN.1 subvariant, from attaching to and infecting human airway cells. This work establishes a revised entry paradigm in which HS clusters mediate SARS-CoV-2 attachment and endocytosis, with ACE2 acting downstream, thereby identifying HS interactions as a key anti-COVID-19 strategy. This paradigm and its therapeutic implications may apply broadly beyond COVID-19 because, analogous to SARS-CoV-2, HS binds many other viruses but is only considered an attachment regulator. Statement of SignificanceViral entry, a crucial antiviral target, is typically thought to involve binding its unique receptor for the cell surface attachment and subsequent entry. We examined this concept with advanced microscopies to resolve individual receptors and SARS-CoV-2 virions responsible for the COVID-19 pandemic. We discovered two receptors for viral entry: heparan sulfate, a polysaccharide that may bind many viruses, mediates viral attachment and subsequent endocytosis, whereas angiotensin-converting enzyme 2 (ACE2), the generally assumed SARS-CoV-2 receptor, acts only downstream to facilitate viral infection. This model suggests perturbation of HS binding as a more effective anti-COVID-19 strategy than previously recognized. It may apply broadly beyond COVID-19 because, analogous to SARS-CoV-2, HS binds many other viruses but is only considered an attachment regulator.

microbiology↗

bioRxiv2025

Spatiomolecular mapping reveals anatomical organization of heterogeneous cell types in the human nucleus accumbens

The nucleus accumbens (NAc) is a key component of the mesolimbic dopamine system that critically regulates many behaviors related to reward and motivation. The NAc is implicated in several neuropsychiatric disorders, including major depressive disorder, schizophrenia, and substance use disorders. Rodent studies have identified spatial organization of heterogeneous medium spiny neuron (MSN) subtypes across the NAc core and shell, but the extent to which this cellular diversity and spatial organization is conserved in the human brain remains unclear. Here, we generated a spatiomolecular atlas of NAc cell types and spatial domains by integrating spatial transcriptomics and single-nucleus RNA sequencing data from postmortem NAc tissue from 10 neurotypical adult donors. We identified 20 transcriptionally unique cell populations and 8 spatial domains, including specialized D1 islands composed of distinct dopamine receptor 1 (DRD1) MSN subtypes, which were enriched for OPRM1. In contrast to a discrete core vs. shell division, we observed continuous spatial gradients of gene expression across MSN domains, suggesting a more complex organization of DRD1 and DRD2 MSNs. Cross-species comparisons demonstrated conservation of MSN subtypes and spatial features between human, rodent, and nonhuman primate NAc. Genetic enrichment analysis with stratified linkage disequilibrium score regression revealed specific spatial domains associated with risk for psychiatric and addiction-related traits. To investigate this further, we spatially mapped ligand-receptor interactions involving neuropsychiatric risk genes. Finally, we leveraged existing rodent NAc data to identify drug-responsive transcriptional programs and predict their spatial distribution in the human NAc. Collectively, we provide a spatiomolecular framework for understanding the human NAc and its relevance to neuropsychiatric disease.

neuroscience↗

bioRxiv2025

Therapeutic Salmonella induces long-term protective trained immunity in NK cells against cancer metastasis

Trained immunity, a form of innate immune memory initially recognized in pathogen defense, has recently been reported to aid in combating cancer. Although trained immunity has been well-characterized in myeloid lineage cells, its presence in innate lymphoid cells, particularly natural killer (NK) cells, remains largely unexplored. Here, we report that a single dose of Salmonella YB1, an attenuated candidate anticancer vaccine strain, provides long-lasting protection against cancer metastasis in mice by inducing trained natural killer (NK) cells. Functional assays coupled with multiomics analysis revealed that Salmonella-trained NK (stNK) cells establish an enduring reprogrammed epigenome characterized by enhanced pro-survival signaling and immune effector functions, resulting in more potent IFN-{gamma} release and cytotoxicity upon secondary stimulation. We further revealed that IL-12 and IL-18 are essential but insufficient for this NK cell training effect. Crucially, stNK cells far outperform the common immune checkpoint therapies, including PD-1 and TIGIT blockade, in suppressing metastasis, underscoring the unique immunological mechanisms in combating metastasis. These findings uncover a novel long-term anti-metastatic function of trained immunity in NK cells, highlighting its potential as an effective antitumor strategy.

immunology↗

bioRxiv2025

Genomic Landscapes of Natural Selection in Great Apes

BackgroundGreat apes are a primate clade with unique biological features. The different species and subspecies have adapted to their respective habitats and followed various evolutionary trajectories influencing their diversity. Hence, studying patterns of natural selection across this clade is an important aspect in understanding their biology. ResultsWe analyzed a curated panel of genomic diversity for bonobos, chimpanzees, eastern and western gorillas, and Bornean and Sumatran orangutans to explore their selection landscapes. A genome-wide screen was conducted for recent positive and long-term balancing selection, revealing candidate loci potentially related to sensory and immune systems, environmental pressures such as diet or altitude, and reproductive strategies in these species. In addition, the distribution of fitness effects (DFE) was determined, along with the correlations of DFEs across lineages. ConclusionsWe interpret the potential biological meaning of the landscapes of recent positive and long-term balancing selection in our closest living relatives, revealing novel lineage-specific candidate genes and gene categories, as well as recurrent targets across lineages. Our investigation of the deleterious DFE indicates that most non-synonymous mutations fall into either the nearly neutral or strongly deleterious categories, with high correlations between closely related lineages.

evolutionary biology↗

bioRxiv2025

Conformational dynamics underlying slow inactivation in voltage-gated sodium channels

Voltage-gated sodium (Nav) channels initiate and propagate action potentials in many excitable cells. Upon repetitive activation, the conductance of Nav channels gradually decreases on a timescale ranging from seconds to minutes, a phenomenon known as slow inactivation, which is crucial for regulating the excitability of many cells. Many studies indicated that slow inactivation is associated with conformational changes at the selectivity filter, but the underlying mechanisms remain unclear. By examining the conformational dynamics of a prokaryotic NavAb channel using single-molecule FRET (smFRET), our work revealed the transitions of its selectivity filter among three distinct conformational states and showed that activating voltages enriched the high-FRET conformations, potentially associated with slow inactivation. We further identified L176 in the selectivity filter P1 helix and T206 in the pore-forming S6 helix as residues coupling the primary and slow inactivation gates by showing that the additional L176F mutation stabilizes the S6 C-terminal deletion opening mutant in the closed state. Consistently, our smFRET results also indicated that the high FRET conformation of the selectivity filter was markedly attenuated in the S6 C-terminal deletion opening mutant, but reverted by the L176F mutation. Open-pore blocker lidocaine has been shown to prevent eukaryotic Nav channels from entering the slow inactivation state. Moreover, our smFRET studies showed that it diminished the high FRET conformation of the NavAb selectivity filter in a dose-dependent manner, while the L176F mutation, again, markedly reversed the lidocaine effects. Collectively, our studies suggested that slow inactivation in the NavAb channel results from the collapse of the selectivity filter pore, as revealed by the high FRET conformation in our smFRET measurements. The L176 in the selectivity filter and T206 in the pore-forming S6 helix coordinate conformational changes of the slow inactivation gate at the selectivity filter and the primary gate at the helix bundle crossing, providing the structural basis for slow inactivation in prokaryotic voltage-gated sodium channels.

biophysics↗

bioRxiv2025

Single-molecule localization microscopy reveals the molecular organization of endogenous membrane receptors

Super-resolution microscopy in combination with genetic labeling methods allows imaging of single proteins in cells. However, visualizing endogenous proteins on primary cells remains challenging due to the use of sterically demanding antibodies for labeling. Here, we demonstrate how immunolabeling conditions and antibody crosslinking influence the quantification and identification of membrane receptor stoichiometry on cells using single-molecule localization microscopy. We developed an optimized immunolabeling and analysis protocol and demonstrate the performance of the approach by resolving the molecular organization of endogenous CD45, CD69, and CD38 on Jurkat T cells. To demonstrate the usefulness of the method for immunotherapy applications we investigated the interaction of primary multiple myeloma cells with the therapeutic monoclonal antibodies (mAbs) daratumumab and isatuximab, and a polyclonal anti-CD38 antibody. Our approach might lay the foundation for improved personalized diagnostics and treatment with therapeutic antibodies. One-Sentence SummarySingle-molecule localization microcopy quantifies the expression and resolves the stoichiometry of endogenous membrane receptors

biophysics↗