Biology subjects

Lin, Y.-H.

Publications and source records attributed to Lin, Y.-H..

At least 19 recordsLinked to original sources

bioRxiv2026

A habenula-enriched GPCR, GPR151, regulates behavioral sensitivity to inflammation

BackgroundInflammation-associated depression is a subtype of major depressive disorder that is often resistant to conventional pharmacotherapies, which act in a regionally non-specific manner and therefore also produce unwanted side effects. Here we test GPR151, an orphan GPCR associated with inflammation and highly expressed in the habenula--a region linked to negative valence and depression--as a therapeutic target for inflammation-associated depression. MethodsWe integrated mouse and human habenular expression analyses with genetic loss-of-function and adult habenular re-expression approaches in mice. Gpr151 knockout mice and littermate controls were exposed to lipopolysaccharide (LPS) inflammatory challenge and assessed for stress coping and motivated behavior, body weight loss, and peripheral immune activation. To test whether adult habenular GPR151 expression is sufficient to restore inflammation-associated behavioral vulnerability, GPR151 was re-expressed in the habenula of knockout mice. ResultsGPR151 was exceptionally enriched in the habenula and showed conserved topographic organization and similar expression relationships with habenular marker genes in mice and humans. Following LPS challenge, male Gpr151 knockout mice showed reduced passive coping despite body weight loss and immune activation comparable to littermate controls. Adult habenular GPR151 re-expression increased LPS-induced amotivation in male knockout mice without increasing LPS-induced weight loss or immune activation. Female Gpr151 knockout mice also showed reduced passive coping after LPS challenge; however, habenular GPR151 re-expression was insufficient to increase LPS-induced amotivation in females. ConclusionsThese findings identify GPR151 as a conserved, regionally enriched regulator of behavioral sensitivity to inflammatory challenge and support GPR151 as a candidate therapeutic target for inflammation-associated depression.

neuroscience↗

bioRxiv2026

Evolutionary rise of a synaptic mechanism for creating and diversifying key reinforcement signals

Most neurons release either excitatory or inhibitory neurotransmitters. However, multiple inputs to the lateral habenula (LHb) co-transmit glutamate and GABA, transmitters with opposing effects on LHb output. Although the LHb has an established role in reinforcement learning, the adaptive significance of glutamate/GABA co-release remains unclear. Using experimentally informed simulations, we show that GABA co-release is sufficient to produce temporal difference (TD)-like transformations of input activity, computations commonly used for reinforcement learning and behavioral optimization. Heterogeneous GABA-to-glutamate ratios, like those found among LHb neurons ex vivo, produce diverse TD-like computations linked to higher-order decision-making. Single-cell RNA-sequencing analysis and machine-learning image analysis further indicate that glutamate/GABA co-release expanded across vertebrate evolution, from fish to mice, rats, and monkeys. Evolutionary expansion of glutamate/GABA co-release may have supported increasingly sophisticated learning and decision-making that contribute to intelligent behavior.

neuroscience↗

bioRxiv2026

Multi-Omics Characterization of Plasma and Urine Extracellular Vesicles Identifies Non-Invasive Biomarkers for IgA Nephropathy

BackgroundIgA nephropathy (IgAN) is increasingly recognized as a systemic immune-mediated disease characterized by aberrant IgA1 glycosylation, circulating immune complex formation, complement activation, and emerging metabolic perturbations. However, clinical diagnosis still relies on invasive renal biopsy, and non-invasive biomarkers capable of capturing both systemic immune activation and kidney-specific alterations remain lacking. Extracellular vesicles (EVs), as biologically active carriers of proteins and metabolites, provide a unique opportunity to interrogate compartment-specific molecular signatures underlying IgAN pathophysiology. MethodsWe performed an integrated, untargeted multi-omics analysis of plasma- and urine-derived EVs from 60 individuals (24 IgAN, 21 chronic kidney disease [CKD], and 15 controls). Differentially expressed proteins (DEPs) and metabolite features (DEFs) discriminating IgAN from CKD and controls were identified using Venn diagram analysis, followed by pathway enrichment and receiver operating characteristic (ROC) evaluation. ResultsVenn analysis identified 22 and 3 candidate DEPs in plasma EVs (pEVs) and urinary EVs (uEVs), respectively, revealing broader systemic proteomic alterations relative to renal EV cargo. Notably, complement and coagulation regulators, including C4b-binding protein alpha chain (C4BPA) and vitamin K-dependent protein S (PROS1), demonstrated strong discriminatory performance between IgAN and CKD (AUC = 0.826 and 0.795), suggesting EV-associated complement-coagulation crosstalk in IgAN. Metabolomic profiling revealed 1,006 and 540 candidate DEFs in pEVs and uEVs, respectively. Enrichment analyses highlighted steroid biosynthesis and fatty acid metabolism pathways in both compartments, indicating immune-metabolic reprogramming. Three metabolite features (C27H44O, C30H50O, and C28H46O) distinguished IgAN from CKD with high accuracy (AUC = 0.942-0.877). ConclusionsThis study provides the first compartment-resolved, plasma- and urine-derived EV multi-omics landscape of IgAN. Our findings suggest that EV cargo reflects coordinated complement dysregulation and metabolic alterations, extending current understanding of IgAN beyond glomerular immune complex deposition. These EV-associated proteins and metabolites offer a mechanistically informed framework for non-invasive biomarker development and for exploring immune-metabolic pathways involved in IgAN progression.

biochemistry↗

bioRxiv2026

Nonequilibrium States Promote One-Pot Nonenzymatic Carbon Fixation in the Reverse Tricarboxylic Acid Cycle and Amino Acid Synthesis

Several metabolites within the reductive tricarboxylic acid (rTCA) cycle have been found to form prebiotically. However, how these metabolites connect to each other and form rTCA cycle remains unresolved. The rTCA cycle is an ancient route and is considered significant for the emergence of life, since it connects to the routes of amino acids and nucleobases synthesis. A major challenge to complete the rTCA cycle under prebiotic conditions is the thermodynamically unfavorable reductive carboxylation of succinate to -ketoglutarate. Here, we address this challenge by using the nature of energy: nonequilibrium conditions. By calculating the changes in free energy, {Delta}G, of succinate to -ketoglutarate, and its downstream reactions: -ketoglutarate to glutamate and -ketoglutarate to isocitrate under different nonequilibrium conditions, we find that these two-step reactions are exergonic under nonequilibrium conditions at a 10000:1 reactant-to-product ratio at 1.013 bar, pH 10 and 70{degrees}C. To prove the concept, we catalyze succinate to glutamate at a 10000:1 reactant-to-product ratio, with NH2OH and sodium dithionite. The process is catalyzed by Fe(0), Fe3O4, and artificial proto-[4Fe4S] clusters in 1M NaCl at pH 10 and 70{degrees}C under 1 atm of 13CO2 for 48 hours. This nonequilibrium condition and one-pot system successfully promote the formation of -ketoglutarate through carbon fixation with succinate and its subsequent conversion to glutamate. These findings demonstrate nonequilibrium states enable -ketoglutarate formation through succinate and CO2, and suggest that a tendency toward natural thermodynamics may serve as a driving force for autocatalysis in the origin of life. ImportanceHow life began remains open, metabolism provides a key framework for origins. We use a simple and robust energetic principle to show that non-equilibrium conditions can drive the highly endergonic carboxylation step of the reverse tricarboxylic acid (rTCA) cycle, enabling one-pot synthesis of glutamate. This is work bridges the gap between protometabolites and protometabolsim, suggesting that metabolites may have accumulated first, creating concentration gradients that drove reactions and ultimately enabled the emergence of protometabolism. These findings provide a plausible pathway from prebiotic chemistry to the emergence of metabolism.

biochemistry↗

bioRxiv2026

Mitochondrial ATP production promotes T cell differentiation and function by regulating chromatin accessibility

Immune elimination of chronic infection or cancer requires cytotoxic CD8+ T cells that adopt and maintain an effector phenotype. Cytotoxic T cell function is a bioenergetically demanding process and T cells subjected to chronic antigen exposure have compromised effector function despite high rates of glycolysis. Here we report the ability of the short-chain -hydroxy acid, D--hydroxybutyrate, to act as a signaling molecule that increases mitochondrial ATP production and drives the conversion of proliferating T cells into cytotoxic effector cells. DAHB signaling switches ATP production from glycolysis to oxidative phosphorylation supported by fatty acid oxidation, even in glucose-replete media. This conversion suppresses both AMPK phosphorylation and the integrated stress response (ISR) in activated T cells while significantly elevating the level of the phosphagen, phosphocreatine (PCr). Both the PCr bioenergetic reserve and oxidative phosphorylation were required for T cell effector differentiation. DAHB-induction of CD8-effector gene transcription was coupled to bioenergetics by enhanced ATP-dependent remodeling of chromatin accessibility at effector gene loci. DAHB enhanced CD8+ T cell antitumor activity both in vitro and in vivo, and DAHB treatment of transferred T cells led to persistent in vivo antitumor effects. Together, these findings link cellular bioenergetics to the regulation of chromatin accessibility and gene expression required to support effector function.

immunology↗

bioRxiv2026

Robust volumetric multiplex staining of centimeter-scale FFPE tissues guided by neural network-based optimization

Archived formalin-fixed, paraffin-embedded (FFPE) tissues, including brain-bank specimens, are valuable resources for disease research, but rapid cyclic immunolabeling of intact specimens remains challenging. Here, we present FIDELITY, an epoxy-free workflow that balances optical transparency, immunostaining performance, and tissue integrity for multi-cycle protein profiling in centimeter-thick FFPE specimens. Neural network-guided optimization identified an SDS-glycine formulation that integrates delipidation and epitope retrieval while preserving tissue stiffness, replacing prolonged epoxy reinforcement and subsequent high-temperature antigen retrieval with a single aqueous pretreatment. Application to human Alzheimer's disease specimens enabled volumetric imaging and quantitative analysis while retaining compatibility with conventional histopathology. Its compatibility with active electrophoretic staining further supported rapid labeling and five rounds of immunolabeling in a whole FFPE mouse brain. Two-round labeling of a human glioma specimen further demonstrated the applicability of the cyclic workflow to human pathological tissue. Together, FIDELITY provides a practical platform for large-volume, multiplexed protein profiling of intact FFPE specimens.

neuroscience↗

bioRxiv2026

A post-translational regulatory map of chronic antigen-driven human T cell dysfunction.

T cells exposed to persistent antigen in the context of chronic viral infections or cancer lose self-renewal and cytotoxic capacity. Several transcriptional, epigenetic, and metabolic drivers of this process have been identified. However, the post-transcriptional regulatory mechanisms influencing the proteome of dysfunctional T cells are not well understood. Here we present a time-resolved molecular landscape of human T cells during the development of chronic antigen-driven dysfunction. Persistent T cell receptor stimulation significantly remodeled the proteome, including changes in canonical T cell exhaustion-associated proteins and proteins related to mitochondrial function, redox homeostasis, nucleotide metabolism, and cell-cycle progression. Dysfunctional T cells displayed activation of stress response pathways that were recapitulated in vivo; targeting these pathways altered the cytotoxic capacity of T cells during persistent tumor exposure. Our comprehensive proteomic resource reveals unique post-transcriptional changes in dysfunctional T cells and lays the groundwork for novel cysteine-directed therapeutics to enhance cancer immunotherapy.

immunology↗

bioRxiv2026

Development of autotrophy in Escherichia coli through adaptive laboratory evolution

Enabling heterotrophic Escherichia coli to use CO2 as its only carbon source remains a great challenge, and previous studies approached autotrophy conversion by metabolic engineering. Although its native carbon fixation routes were identified, the potential to reach autotrophy by itself has long been overlooked. In this study, autotrophy in E. coli was developed through adaptive laboratory evolution. After 1,000 days of consecutive inorganic subculturing, missense mutations were found in isocitrate dehydrogenase icd and isocitrate dehydrogenase kinase/phosphatase aceK genes, determining the metabolic switch between the citrate cycle and the glyoxylate shunt. By transcriptomic comparison of the adapted E. coli between inorganic and organic cultivations, two CO2 fixing enzymes activated in autotrophic mode were found, including the upregulated pyruvate:ferredoxin oxidoreductase YdbK and phosphoenolpyruvate carboxykinase Pck. Connected by the upregulated phosphoenolpyruvate synthase PpsA, a carbon fixation module was constituted, which was the shared foundation of the aspartate-threonine cycle and the citrate-glyoxylate-methylcitrate cycle, and thus integrating into an autotrophic network. By comparing the 13C enrichment patterns in inorganic cultivations between the adapted and initial E. coli, the favorable direction of the autotrophic network was confirmed. IMPORTANCEThis is the first study to accomplish autotrophy in E. coli through long-term evolution alone. Besides missense mutations in icd and aceK genes, adapted E. coli also actively regulated its gene expression to respond to inorganic environment, such as directing the metabolic switch towards the glyoxylate shunt. For biomass formation, a carbon fixation module consisted of the upregulated YdbK, PpsA, and Pck produced pyruvate and oxaloacetate as precursors for two cycles. The aspartate-threonine cycle with a replenishment side loop further accumulated these precursors, and the citrate-glyoxylate-methylcitrate cycle was driven by four overexpressed enzymes to catalyze six reactions. These metabolic pathways were integrated into a novel autotrophic network, and by understanding the nature of E. coli, rational designs for its carbon fixation optimization become attainable by using compatible mechanisms.

microbiology↗

bioRxiv2026

A Streamlined Protocol for Small-scale Protoplast Generation and CRISPR/Cpf1-mediated Genome Editing in Fusarium oxysporum

Fusarium oxysporum is a significant threat to agriculture and One Health, requiring advanced molecular tools for functional genomics analyses and biological control agent development. Existing gene-editing methods are hampered by costly protoplast preparation protocols and by CRISPR/Cas9 limitations, such as restricted PAM sequences and complex guide RNA requirements. We engineered an efficient CRISPR/Cpf1 system that overcomes these issues through three main innovations: small-scale protoplast generation using novel filter columns that greatly reduces enzyme consumption while simplifying workflows, a CRISPR/Cpf1 system with flexible PAM recognition and staggered DNA cleavage to promote homologous recombination, and minimal homology arm strategies that significantly decrease cloning complexity. Extensive validation confirms successful gene targeting with molecular verification and functional analysis via standardized pathogenicity assays. This integrated platform offers affordable, accessible tools for systematic F. oxysporum research, enhancing fundamental understanding of plant-pathogen interactions and supporting high-throughput screening vital for agricultural biotechnology and biological agent development. MOTIVATIONFusarium oxysporum plays crucial roles as both a damaging plant pathogen and a model for studying host-pathogen interactions. It is well established that systematic functional genomics approaches are vital for advancing agricultural biotechnology and developing biological agents. Creating efficient gene-editing systems can help elucidate virulence mechanisms and enable rapid production of modified strains for practical use. However, current transformation methods face major challenges, such as high enzyme costs, and CRISPR/Cas9 systems are limited by PAM sequence availability and by blunt-end DNA cleavage, which hampers homologous recombination. Furthermore, complex guide RNA scaffolds complicate large-scale functional studies with traditional methods. To address these challenges, we have developed a streamlined CRISPR/Cpf1 (Cas12a) platform that combines small-scale protoplast preparation with significantly reduced enzyme use, exploiting Cpf1s unique features, such as flexible PAM recognition, staggered DNA cuts that promote recombination, improved target specificity, and simpler guide RNA design. This platform can also accelerate the development of biological agents and support high-throughput screening applications essential to the progress of agricultural biotechnology. HIGH LIGHTSO_LIReduced enzyme costs by 95% through small-scale protoplast preparation C_LIO_LICRISPR/Cpf1 system established for efficient gene editing in Fusarium oxysporum C_LIO_LIStreamlined workflow enables routine gene targeting and rapid mutant screening C_LIO_LIComplete workflow validated with EGFP-marked pathogenicity C_LI

microbiology↗

bioRxiv2025

Phosphatidylinositol Transfer Protein-1 Integrates Insulin/IGF-1 and TOR Signaling to Negatively Regulate Lifespan and Healthspan in Caenorhabditis elegans

BackgroundPhosphatidylinositol transfer protein-1 (pitp-1) is involved in phosphoinositide turnover. The role of pitp-1 in promoting healthy longevity remains unknown. Our previous work showed that the phosphoinositide turnover genes dagl-1 and dgk-5 regulates lifespan, as overexpression of dagl-1 or knockdown of dgk-5 prolongs lifespan and enhances oxidative stress resistance through TOR signaling. As pitp-1 is a key component of this pathway, we investigated its role in lifespan regulation and the underlying mechanisms, aiming to clarify whether it represents a critical regulator of healthy longevity and how it coordinates conserved signaling pathways to regulate aging. MethodsC. elegans mutants, RNAi-mediated knockdown, and transgenic overexpression were applied to assess lifespan, motility, stress resistance. Temporal and tissue-specific RNAi were applied to identify the critical time window and tissue for pitp-1-mediated lifespan regulation. TOR signaling was measured by phosphorylated S6 kinase and puromycin incorporation, and transcriptomic analysis identified affected pathways. Resultspitp-1 negatively regulates lifespan and healthspan in Caenorhabditis elegans. Genetic deletion or RNAi-mediated knockdown of pitp-1 extends lifespan, attenuates age-related motility decline, and increases oxidative stress resistance. Temporal and spatial analyses reveal that suppression of pitp-1 in neurons during early adulthood is sufficient to promote healthy longevity. Mechanistically, these beneficial effects upon pitp-1 reduction are mediated by suppressing TOR signaling. Conversely, pitp-1 overexpression shortens lifespan and impairs healthspan via TOR activation. Moreover, pitp-1 is transcriptionally repressed by DAF-16 downstream of insulin/IGF-1 signaling (IIS), and contributes to IIS-mediated lifespan extension. ConclusionThese findings identify pitp-1 as a novel regulator of healthy aging that integrates IIS and TOR pathways, providing new insights into conserved mechanisms for promoting healthy longevity.

genetics↗

bioRxiv2025

Mus Musculus papillomavirus MmuPV1 resists restriction by human APOBEC3B

The single-stranded DNA deaminase APOBEC3B (A3B) is capable of potently restricting the replication of a range of viruses including retroviruses (cDNA) and herpesviruses (genomic DNA). However, these and likely other DNA virus families have evolved host species-specific counter-defenses that are equally potent and serve to protect viral DNA from restriction. Although high-risk human papillomavirus (HPV) infection triggers A3B upregulation, potentially as part of an antiviral response, the impact of this restriction factor on papillomavirus replication and pathogenesis has yet to be assessed. To study human A3B antiviral function in the absence of a species-specific counter-defense, here we ask whether human A3B is capable of restricting Mus musculus papillomavirus (MmuPV1) in cellulo and in vivo. First, we created human A3B and catalytic mutant A3B-E255A expressing FVB/N mice. Second, MmuPV1 gene expression and replication was quantified in primary keratinocytes from these animals and, surprisingly, enzymatically active human A3B caused no measurable impairment in viral transcript or DNA accumulation. Third, A3B, catalytic mutant A3B-E255A, and nontransgenic FVB/N animals were infected with MmuPV1 and similar pathologies were found regardless of A3B functionality. Thus, despite likely never being exposed to human A3B during evolution, MmuPV1 appears to be unaffected by this potent, primate-specific antiviral factor. These results suggest that MmuPV1 and perhaps papillomaviruses more broadly possess a conserved mechanism to efficiently escape restriction by human A3B and related DNA deaminases. IMPORTANCEHuman papillomaviruses (HPVs) are nearly ubiquitous, and persistent infection with high-risk types causes approximately 5% of cancers worldwide. Although HPV vaccination is effective for preventing infection, insufficient global coverage and a rising incidence of HPV-associated malignancies, such as oropharyngeal carcinoma, highlight the need to understand innate virus clearance mechanisms. APOBEC3 enzymes are a central component of the mammalian innate immune system and are hypothesized to restrict papillomavirus infection, particularly between species. Here, we establish mice that express the human antiviral enzyme APOBEC3B (A3B). Surprisingly, we find that human A3B is incapable of blocking the replication of a murine papillomavirus (Mus musculus papillomavirus 1, MmuPV1) in relevant primary cells from these animals or in infected tissues in vivo. These findings highlight the complexity of teasing apart host-pathogen interactions and suggest that papillomaviruses may have a general mechanism for escaping restriction by antiviral enzymes such as A3B.

microbiology↗

bioRxiv2025

deCYPher: Star Allele-Resolution Computational Framework of Pharmacogenes for Haplotype-Resolved Long-Read Assemblies

Although existing next-generation sequencing (NGS) tools, such as Aldy and Cyrius, have been applied for allele typing, they cannot achieve complete accuracy due to various genomic challenges including pseudogenes, structural variations, hybrid genes, copy number variations, and gene deletions. These complexities make accurate pharmacogene interpretation more challenging, despite the crucial role pharmacogenomics plays in precision medicine. We developed deCYPher, a tool that generates personalized pharmacogenomic reports from haplotype-resolved assemblies. The tool enables analysis of all PharmVar 1A level genes, such as CYP2B6, CYP2C9, CYP2C19, CYP2D6, CYP3A5, CYP4F2, DPYD, NUDT15, and SLCO1B1. Applied to all HPRC haplotypes (including both release 1 and release 2 data), deCYPher demonstrated high accuracy in resolving complex gene structures. In the case of CYP2D6, release 1 identified 6% gene multiplications, 6% full gene deletions, and 4% CYP2D6/CYP2D7 hybrids. By contrast, release 2 demonstrated an increased prevalence of multiplications (14%) and hybrids (11%), while the frequency of full gene deletions remained comparable at 5%. Comparison with pb-StarPhase revealed discrepancies in 12 of 94 assemblies in the release 1 dataset. For instance, in sample HG02257, Aldy, Cyrius, and deCYPher consistently identified the genotype as *2/*35, whereas pb-StarPhase reported *2/*2. Notably, the *35-defining variants were present in the BAM and VCF files in the pb-StarPhase pipeline, but the local read depth over the *35-specific region was only 5x in HG02257-p, suggesting that the misclassification likely resulted from insufficient coverage - a known limitation of pb-StarPhase under low-depth conditions.

bioinformatics↗

bioRxiv2025

Respiratory exposure to inert particulate matter during pregnancy leads to oxidative stress and cardiac proteome remodeling

Withdrawal StatementThe authors have withdrawn this manuscript because upon peer review major revisions have been identified as needed to ensure that the conclusions are in par with the presented data. Current studies are ongoing to provide a more complete version of the manuscript for peer review publication. Therefore, the authors do not wish this work to be cited as reference for the project in its current form. If you have any questions, please contact the corresponding author.

molecular biology↗

bioRxiv2025

A high-affinity split-HaloTag for live-cell protein labeling

We introduce a high-affinity split-HaloTag comprised of a short peptide tag (Hpep, 14 residues) and a large, inactive fragment (cpHalo{Delta}3). Hpep binds to cpHalo{Delta}3 spontaneously with nanomolar affinity, enabling subsequent labeling with fluorescent HaloTag ligands. The small size of Hpep facilitates cloning-free endogenous protein tagging using CRISPR/Cas9 and the complementation of Hpep-tagged proteins can be achieved in live cells through co-expression with cpHalo{Delta}3 and in fixed cells through incubation with cpHalo{Delta}3. The approach is compatible with advanced microscopy techniques such as expansion microscopy and live-cell STED imaging. Additionally, variants of Hpep that modulate the spectral properties of labeled fluorophores enable simultaneous imaging of two different Hpep-tagged proteins via fluorescence lifetime microscopy. In summary, our high-affinity split-HaloTag is a robust and versatile tool for live-cell imaging and diverse applications in chemical biology.

biochemistry↗

bioRxiv2025

Unmasking Human T Cell Receptor Germline Diversity: 335 Novel Alleles Identified in 47 Pangenome Reference Individuals Using the gAIRR Suite

The adaptive immune receptor repertoire (AIRR), composed of V(D)J-recombined T cell receptors (TR) and immunoglobulins (IG), is central to adaptive immunity. Accurate AIRR profiling depends on a comprehensive and diverse germline gene set encoding AIRR (gAIRR). Furthermore, gAIRR alleles themselves are associated with immune-related phenotypes and diseases. However, for TR genes, the IMGT database - the primary gAIRR reference - has not been updated since 2020 and lacks sufficient population diversity and complete flanking sequences. To address these limitations, we investigated 47 high-quality genomes from the Human Pangenome Reference Consortium (HPRC) using the gAIRR Suite and identified 335 novel TR alleles - 305 TRV and 30 TRJ - representing 91.6% and 30.9% increases over IMGT records. All novel alleles were crosschecked using two orthogonal pipelines. We also established a comprehensive flanking sequence database, including recombination signal sequences (RSS). We have made all resources publicly available to support immunogenomics research and clinical applications.

genomics↗

bioRxiv2025

Cardiac Adaptations in the Cave Nectar Bat Eonycteris spelaea: Insights into Metabolic Resilience and Stress Response

AimsBats are unique mammals with remarkable adaptations, including powered flight, which demands significant energy expenditure. While previous studies have documented basic structural characteristics of bat hearts, a comprehensive understanding of their response to physiological stress remains unexplored. This study investigates the cardiac adaptations of the cave nectar bat Eonycteris spelaea to elucidate the mechanisms underlying their unique physiological capabilities. Methods and ResultsWe performed RNA sequencing to analyse the cardiac gene expression profile of E. spelaea and 6 other bat species in comparison to mouse and human hearts, revealing enriched transcriptomic signatures related to oxidative phosphorylation and fatty acid metabolism across multiple bat species. Metabolomic profiling compared acylcarnitine metabolites and tricarboxylic acid (TCA) cycle intermediates between bat and mouse hearts, indicating a distinct acylcarnitine profile and increased levels of TCA cycle intermediates in bats, suggesting enhanced metabolic capacity. Structural adaptations were assessed through anatomical and histological analyses on cardiac tissues, showing thicker left ventricular walls and increased vascular density in bats without pathological hypertrophy. Functional characteristics were evaluated using dobutamine stress echocardiography, demonstrating superior cardiac reserve in bats with significant increases in ejection fraction, stroke volume, and cardiac output under stress conditions. Additionally, isolated cardiomyocytes were treated with Angiotensin II (Ang II) to assess stress responses. Bat cardiomyocytes displayed resistance to Ang II-induced hypertrophy and mitochondrial dysfunction compared to mice, further highlighting their resilience to stress-induced damage. ConclusionThe unique adaptations observed in bat hearts, including enhanced metabolic pathways, structural remodelling, and cellular resilience contribute to their ability to meet the high energy demands of powered flight while maintain cardiac function under stress. These insights into bat cardiac physiology provide valuable information on cardioprotective mechanisms that could be applicable to other species. Translational PerspectiveBats exhibit remarkable cardiac adaptations that sustain the high energy demands of powered flight while resisting stress-induced damage. These insights into evolutionarily conserved cardioprotective mechanisms highlight potential therapeutic pathways for preventing heart failure, including resistance to hypertrophy and mitochondrial dysfunction under stress. Studying non-model organisms like bats may offer innovative approaches to enhance metabolic and stress resilience in human hearts, paving the way for translational research in cardiovascular disease management and treatment.

systems biology↗

bioRxiv2025

Interplay between Skin Sympathetic Nerve Activity and Gut Microbiota, the Neurocardiac Axis in Acute Coronary Syndrome

BACKGROUNDPrevious studies have linked gut dysbiosis to the acute coronary syndrome (ACS) and sympathetic nervous system disturbances. However, the relationship between skin sympathetic nerve activity (SKNA) and gut microbiota in ACS patients remains largely unexplored. We hypothesize that elevated SKNA may interact with specific microbial profiles in ACS. METHODS AND RESULTSFifteen ACS patients with age- and sex-matched controls were enrolled in the cross-sectional study. Subjects with type 2 diabetes or on antibiotics, proton pump inhibitors, or metformin were excluded. Demographic and clinical data were recorded, and SKNA was measured by neuECG. Gut microbial profiles were analyzed by sequencing the V3-V4 region of the 16S rRNA gene. Significant differences in alpha diversity, including Chao 1 index and Faiths phylogenetic diversity, were observed between the ACS and control groups (P<0.001). Distinct beta diversity between the two groups was also identified using unweighted normalized UniFrac analysis (P=0.001). Redundancy analysis and Mantel test revealed a significant relationship between SKNA and microbial profiles. Several butyrate-producing bacteria were decreased in the ACS group, while the genus Hungatella, a trimethylamine producer, showed a significant increase and was positively correlated with SKNA. Additionally, predicted microbial functional analysis indicated an elevation in branched-chain amino acid biosynthesis in the ACS group. CONCLUSIONSThis study is the first to establish an association between SKNA and gut microbial profiles in ACS patients. SKNA can serve as a biomarker for ACS, offering a simple and non-invasive tool to explore the interaction between the nervous system and gut microbiota in cardiovascular diseases. Clinical PerspectiveO_ST_ABSWHAT IS NEW?C_ST_ABSThe Skin sympathetic nerve activity (SKNA) is a novel and non-invasive recording of the sympathetic nervous system from the skin of patients. The NEW findings in our study from acute coronary syndrome (ACS) patients are (1) to establish the correlation between SKNA, heart rate variability and microbiota, (2) the Hungatella is correlated with SKNA and standard deviation of NN intervals (SDNN). WHAT ARE THE CLINICAL IMPLICATIONS?Since microbiota and sympathetic nervous system (SNS) might be essential factors of ACS, it is important to assess the abundance of microbiota and SNS activity for accurate management of ACS. The Hungatella, one of the microbiota involved in atherosclerotic cardiovascular disease, heart failure, inflammatory process, and anxiety disorder, might be the link between SNS and ACS. In our study, we prove the positive association between Hungatella and SKNA. Therefore, by checking the SKNA of patients with ACS, we might discover the SNS activity and also the underlying microbiota etiology of ACS. Then, it is critical and accurate to target Hungatella in ACS patients with high SKNA to reduce the risk of ACS.

microbiology↗

bioRxiv2025

Disrupted priming within draining lymph nodes drives immune quiescence in gastric cancer

The gastric mucosa is characterized by continuous innate immune surveillance and inflammatory signaling, yet a high proportion of gastric carcinomas (GCs) are recalcitrant to immune-directed therapies. The mechanisms by which GCs evade adaptive immune surveillance within the highly antigenic microenvironment of the gastric mucosa remains unknown. To address this, we collected patient-matched tumor tissue, distant normal tissue, metastasis, and draining lymph nodes to generate a large-scale single-cell immune profiling dataset from 64 patients (n=179 samples, >150,000 cells). From single cell analysis, we identified two distinct sources of impaired tumor surveillance within tumor draining lymph nodes. First, we observed that a significant fraction of tumor draining lymph nodes had undergone cytokine-driven reprogramming, leading to reduced dendritic cell homing and limited T cell priming. Second, T cells undergoing successful activation exhibited limited expansion and constrained differentiation, marked by expression of the quiescence-associated transcription factor Kruppel-like Factor 2 (KLF2). Overexpression of KLF2 in primary T cells limited both their differentiation and cytotoxic capacity. These findings implicate both impaired T cell priming and KLF2-dependent T cell quiescence in limiting T cell immunity in gastric adenocarcinoma. We suggest these findings represent an emerging model for immune silencing in tumors developing from tissues with chronic inflammation.

immunology↗