Biology subjects

Xu, Y.

Publications and source records attributed to Xu, Y..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Segmented poly(A) tails with microRNA target sites confer tissue-specific regulation for mRNA therapeutics

Targeted delivery and controlled expression of mRNA-LNPs are critical for the development of safe and effective mRNA medicines. However, efficient post-delivery regulation of mRNA-LNP expression remains challenging. In this study, we engineered segmented poly(A) tail variants that function as gene-specific regulatory elements for synthetic mRNAs. Specifically, we inserted microRNA target sites (MTS) for miR-122 or miR-142 at various positions of the poly(A) tail of synthesized luciferase reporter mRNA. These modifications significantly reduced luciferase expression in non-target tissues in vitro and in vivo, demonstrating position-dependent selective expression control. Furthermore, by incorporating triple-MTS sequences for miR-142, miR-126, and miR-148a in all possible combinations at the 5 end of the poly(A) tail, we identified triple-MTS arrangements that simultaneously decrease luciferase activities in three non-target hepatic cell types, while preserving robust expression in hepatocytes. The results highlighted the importance of MTS insertion order for optimal mRNA silencing. These triple-MTS modules significantly expanded the utility of single miRNA-responsive elements, enabling cell-type selective regulation for mRNA therapeutics. By complementing tissue-tropic delivery LNPs, our mRNA cargo regulatory elements have the potential to improve tissue and cell type selectivity as a novel platform for post-delivery regulation of mRNA-LNP.

bioengineering↗

bioRxiv2025

Design of a novel multi-epitope mRNA vaccine against BtHKU5-CoV-2 using immunoinformatics

Bat HKU5-CoV-2 (BtHKU5-CoV-2), a recently discovered bat-infecting merbecovirus, was found to infect human cell lines by utilizing the human angiotensin-converting enzyme 2 (ACE2) receptor, similar to SARS-CoV-2, which caused millions of deaths. Moreover, its broad host tropism has raised significant concerns about potential human spillover risk. Therefore, there is an urgent need to develop vaccines to combat the potential outbreak of BtHKU5-CoV-2. However, research focusing on BtHKU5-CoV-2 remains limited. In this study, we designed a novel multi-epitope vaccine against BtHKU5-CoV-2 using an immunoinformatic approach. Eight cytotoxic T lymphocyte (CTL) epitopes, seven helper T lymphocyte (HTL) epitopes, and five linear B lymphocyte (LBL) epitopes were screened from the spike glycoprotein of BtHKU5-CoV-2. The selected epitopes were joined together with an appropriate linker, and {beta}-defensin II and MHC I-targeting domain (MITD) were incorporated into the construct to enhance vaccine immunogenicity. Biological characteristic analysis revealed that the designed vaccine exhibited strong antigenicity and immunogenicity while being non-toxic and non-allergenic. The tertiary structure of the multi-epitope vaccine was modeled, refined, and validated, demonstrating its structural stability and near-native conformation. Molecular docking studies showed that the vaccine successfully docked with Toll-like receptor 2 (TLR2) and TLR4. Moreover, its mRNA exhibits strong interactions with TLR3, TLR7, and TLR8 receptors. Additionally, in silico immune simulations have suggested that vaccination could trigger robust humoral and cellular immunity. These findings suggest that the proposed mRNA vaccine is a potential candidate for targeting BtHKU5-CoV-2. Further experiments are necessary to validate its protective efficacy. Author summaryBtHKU5-CoV-2, a newly discovered merbecovirus isolated from bats, exhibits potential for spillover into humans. It was found to utilize human ACE2 as functional receptors for infection. A functional receptor acts like a "key" that fits into the "lock" on the host cell, enabling viral entry. BtHKU5-CoV-2 warrants significant attention, because it shares the same functional receptor with SARS-CoV-1 and SARS-CoV-2, which caused the 2003 SARS epidemic and the 2019 pandemic, respectively. Thus, developing vaccines to prevent potential global outbreaks of BtHKU5-CoV-2 is urgently needed. Theoretically, within the bodys immune surveillance system, proteins from BtHKU5-CoV-2 are processed via proteasomal degradation into short peptides. The peptides with immunogenicity bind to MHC molecules and are presented on the cell surface. These peptides, known as epitopes, can initiate immune reaction. In this study, we designed a multi-epitope mRNA vaccine against BtHKU5-CoV-2 using immunoinformatics methods. Epitopes were screened from the spike glycoprotein, a promising target of BtHKU5-CoV-2. Our results suggest that the vaccine is safe and capable of inducing strong humoral and cellular immunity. Therefore, this mRNA vaccine represents a promising candidate for preventing furture BtHKU5-CoV-2 outbreak.

microbiology↗

bioRxiv2025

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

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

bioinformatics↗

bioRxiv2025

An HMA-like integrated domain in the wheat tandem kinase WTK4 recognises an RNase-like pathogen effector

Proteins with a tandem kinase structure have recently emerged as new players in race-specific resistance in cereal crops. However, the molecular understanding of these novel immune receptors resistance mechanisms is limited by the lack of knowledge about the pathogen effectors that they recognise. In this work, we identify AvrWTK4, the wheat powdery mildew RNase-like effector recognised by the wheat tandem kinase immune receptor WTK4, through a combination of bi-parental genetic mapping and mutagenesis. We demonstrate that mutations in the AvrWTK4 gene or a reduction of its expression lead to virulence on WTK4. Transfection of AvrWTK4 specifically induced cell death in WTK4-containing Aegilops tauschii protoplasts. The avirulent AvrWTK4 variant interacts more strongly than the virulent variant with the N-terminal heavy metal-associated (HMA)-like domain of WTK4. These findings further highlight that integrated domains in tandem kinase proteins serve as decoys for pathogen effectors, which could be leveraged to design novel recognition specificities.

molecular biology↗

bioRxiv2025

Mild weight loss promotes plaque growth and synthesis of pro-atherogenic lipids in ApoE-deficient mice fed a high-fat, high-cholesterol diet

BackgroundAccording to the recent ACC/AHA Guideline on the Primary Prevention of Cardiovascular Disease, achieving an initial weight loss of [≥]5% over six months in individuals with obesity is associated with clinically meaningful reductions in cardiovascular risk factors. However, emerging evidence suggests that weight loss may paradoxically increase the risk of CVD and atherosclerosis in certain populations. Motivated by these counterintuitive findings, we hypothesized that mild weight loss may induce metabolic reprogramming that promotes atherogenesis, potentially via an upregulation of pro-atherogenic lipids. MethodsApolipoprotein E-deficient mice were fed either a standard Chow or a high-cholesterol/high-fat (HCHF) diet for six months. A subset in each group underwent mild caloric restriction to achieve [~]5% body weight reduction. Atherosclerotic plaque burden in the brachiocephalic artery was assessed histologically. Hepatic lipidomic profiling was conducted via ESI-MS/MS, and lipid changes were compared with published plasma lipidomic data from obese human subjects stratified by CVD and diabetes status. Cardiovascular risk was further evaluated using the ceramide risk score (CERT1). ResultsMild weight loss induced significant plaque growth, increasing lesion area by 28% in Chow-fed and 53.8% in HCHF-fed mice relative to controls. In HCHF-fed mice, caloric restriction markedly elevated free cholesterol and multiple pro-atherogenic phospholipids, including nine phosphatidylcholine, six phosphatidylethanolamine, one lysophosphatidylcholine, two sphingomyelin, and three ceramide species. Seven cholesterol esters also increased, and a CERT1 score of 8.1 indicated high CVD risk. These pro-atherogenic lipids were confirmed by comparison with published plasma lipidomic data from CVD and diabetes patients. In contrast, weight loss under Chow conditions caused minimal lipid alterations, with only isolated increases in phosphatidylcholine and lysophosphatidylcholine species. ConclusionsMild weight loss under high-fat dietary conditions accelerates atherosclerosis through increased production of pro-atherogenic lipids. These findings underscore the need to monitor lipidomic responses during weight loss interventions in obese individuals with CVD risk. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=187 HEIGHT=200 SRC="FIGDIR/small/670993v1_ufig1.gif" ALT="Figure 1"> View larger version (71K): org.highwire.dtl.DTLVardef@1330150org.highwire.dtl.DTLVardef@19b2ee1org.highwire.dtl.DTLVardef@122c910org.highwire.dtl.DTLVardef@be7270_HPS_FORMAT_FIGEXP M_FIG C_FIG Graphical Abstract model of phospholipid-driven atherosclerosis progression. Graphical summary depicting the mechanistic link between hypercholesterolemia, phospholipid composition, and atherosclerotic plaque development. The left panel highlights pro-atherogenic phospholipids, while the right panel shows anti-atherogenic phospholipids, both grouped by class and correlated with plaque size. Phospholipids enclosed within the dashed box represent those exhibiting statistically significant changes. HighlightsO_LIMild weight loss ([~]5%) in ApoE-deficient mice fed a high-fat, high-cholesterol diet led to a paradoxical increase in atherosclerotic plaque burden. C_LIO_LIWeight loss under metabolically adverse dietary conditions may induce pro-atherogenic lipid remodelling that exacerbates atherosclerosis. C_LIO_LICareful monitoring of atherogenic lipid species may be warranted in obese patients with existing cardiovascular disease undergoing dietary interventions. C_LIO_LIComprehensive, tailored lifestyle interventions--beyond caloric restriction alone--may be necessary to avoid unintended cardiovascular harm during weight loss. C_LI

pathology↗

bioRxiv2025

SARS-CoV-2 NSP14 inhibitor exhibits potent antiviral activity and reverses NSP14-driven host modulation

The emergence of SARS-CoV-2 variants and drug-resistant mutants highlights the urgent need for novel antiviral therapeutics. SARS-CoV-2 NSP14, an N7-guanosine methyltransferase, plays a critical role in viral RNA capping, enabling viral replication and immune evasion. While NSP14 has emerged as a promising drug target, its role in host-virus crosstalk and the cellular consequences of NSP14 inhibition remain poorly understood. Here, we present the identification and characterization of C10, a highly potent and selective first-in-class non-nucleoside inhibitor of the NSP14 S-adenosylmethionine (SAM)-binding pocket. C10 demonstrates robust antiviral activity against SARS-CoV-2, including its variants, with EC50 values ranging from 64.03 to 301.9 nM, comparable to the FDA-approved drug remdesivir in our cell-based assays. C10 also exhibits broad-spectrum activity against other betacoronaviruses and inhibits SARS-CoV-2 at the replication stage. C10 suppresses viral translation and exhibits immunostimulatory effect. Additionally, C10 specifically reversed NSP14-mediated alterations in host transcriptome. The antiviral efficacy of C10 was further validated in a transgenic mouse model of SARS-CoV-2 infection. Our findings highlight C10 as a promising candidate for the development of effective treatments against SARS-CoV-2 and its emerging variants. This study also uncovers a novel mechanism of NSP14 in SARS-CoV-2 pathogenesis and its therapeutic potential, providing insights that may extend to other viral capping methyltransferases.

microbiology↗

bioRxiv2025

Telomere 3'-overhang attrition and persistent telomeric DNA damage response in failing human hearts

BackgroundTelomere homeostasis is critical for normal cellular and organ function, and its dysregulation is implicated in aging and chronic diseases. Although telomere length (TL) is critical for normal telomere function, its functional status can also be altered by many other factors. The organization and protective status of telomere in failing human heart (FHH) remains incompletely understood. MethodsUsing left ventricular tissues from patients with idiopathic dilated cardiomyopathy (IDC), ischemic heart disease (IHD), and non-failing heart (NFH), we performed a comprehensive analysis that included measurements of overall TL and 3 overhang length in left ventricles and cardiomyocytes (CM), assessment of telomere-binding protein associations, and transcriptomic profiling through RNA sequencing. ResultsAlthough TL varied among individuals, reduced median TL was observed only in IDC, while both IDC and IHD showed an increased frequency of very short telomeres, falling below the 5th percentile, in CMs. Strikingly, significant telomere 3-overhang attrition was detected in both disease groups and strongly correlated with elevated H2AX phosphorylated on serine 139 ({gamma}H2AX) in heart tissues, indicating DNA damage. This was accompanied by persistent activation of ataxia telangiectasia mutated (ATM) protein-mediated DNA damage responses and the formation of telomere dysfunction-induced foci (TIFs) in CMs from FHH. Concomitantly, the association of telomeres with the single-stranded telomere-binding protein, Protection of Telomeres 1 (POT1), and the double-stranded telomere-interacting protein, telomere repeat-binding factor 2 (TERF2), was markedly reduced, accompanied by an increase in association of {gamma}H2AX and ssDNA binding protein, RPA with telomeres in IDC and IHD relative to NFH, signifying telomere de-protection. ConclusionsCM telomere dysfunction, characterized by 3 overhang attrition and de-protection, is a common feature in FHH, leading to persistent DNA damage response in telomeres. Better understanding of telomere biology throughout the progression of different heart diseases to heart failure will provide more effective prevention and treatment strategies. GRAPHICAL ABSTRACTHuman telomeres safeguard chromosome ends through a higher-order telomere-loop (t-loop) structure and the shelterin complex, preventing their recognition as DNA double-strand breaks (DSBs). In the failing human heart (FHH) with idiopathic dilated cardiomyopathy (IDC) and ischemic heart disease (IHD), cardiomyocyte telomeres lose protection due to disruption of the shelterin complex, driven by oxidative DNA damage from reactive oxygen species (ROS) targeting G-rich telomeric sequences. This leads to t-loop unfolding, DDR cascade activation, 3 overhang excision, and persistent DNA damage responses with Telomere Dysfunction-Induced Foci (TIFs) formation at the telomeric regions of cardiomyocytes in FHH. The ATM-mediated DDR, along with engagement of both classical non-homologous end joining (cNHEJ) and homologous recombination (HDR) repair pathways, is integral to FHH progression. This study underscores the significance of telomere 3 overhang attrition in the pathogenesis of FHH with IDC and IHD. Unlike changes in overall telomere length, 3 overhang shortening directly correlates with increased DNA damage in human myocardial tissue. Preventing telomere 3 overhang attrition and oxidative damage offers a promising avenue for attenuating heart disease progression toward heart failure. In particular, selective ATM inhibition, as opposed to ATR inhibition, presents a potential therapeutic strategy for patients with IDC and IHD. Future efforts to pinpoint deficiencies in cNHEJ and HDR pathways in failing human hearts may reveal novel targets for heart failure prevention and treatment, providing new strategies in the management of this patient population. CMs, cardiomyocytes; DDR, DNA double-strand break repair; FHH, failing human heart; ROS, reactive oxygen species; t-loop, telomere-loop. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=120 SRC="FIGDIR/small/669993v1_ufig1.gif" ALT="Figure 1"> View larger version (43K): org.highwire.dtl.DTLVardef@1d21937org.highwire.dtl.DTLVardef@757f54org.highwire.dtl.DTLVardef@1fa7472org.highwire.dtl.DTLVardef@1f2e961_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Guided by Noise: Correlated Variability Channels Task-Relevant Information in Sensory Neurons

Shared trial-to-trial variability across sensory neurons is reliably reduced when perceptual performance improves, yet this variability is low-dimensional, so it could be ignored by an optimal readout mechanism. Why then is it so consistently related to behavior? We propose that shared variability both reflects circuit structure and reveals the information communicated to downstream areas. In this framework, the same connectivity that shapes signal propagation also shapes shared variability. Using a circuit model, we show that when sensory signals align with shared variability, behaviorally relevant information is amplified without compromising coding fidelity. Analyses of neural population recordings from multiple brain areas and tasks reveal that the dominant axis of shared variability consistently aligns with task-relevant stimulus features and action plans. Finally, the behavioral impact of microstimulation can be explained by the extent to which it changes projections onto the shared variability axis. These findings suggest that shared variability may illuminate, rather than obscure, the neural dimensions that guide behavior. Significance StatementThe brains ability to use different features of sensory information flexibly across many tasks is essential for complex decision-making. Our study reveals that the correlated variability in neural responses in mid-level visual areas indicates the visual feature that is relevant for behavior. Our biologically plausible network model predicted that it is beneficial for the representation of behaviorally relevant visual information to be aligned with the correlated variability in neurons. We tested and confirmed this in five independent neural data sets. Our results suggest that trial-by-trial variability does not affect the information encoded in sensory neurons but instead is a valuable signal for us to understand which combination of the encoded features is being used by the brain to guide choices.

neuroscience↗

bioRxiv2025

Selective abundance of the stemness-promoting cluster miR-290-295 within the adult substantia nigra dopamine neurons is neuroprotective via preservation of protein synthesis

Locomotor, reward and other critical functions of the body are regulated by the ventral midbrain, with the central role played by dopamine (DA) neurons. The function of these cells from the early development to maturity is critically dependent on the orchestrated expression of coding and non-coding genes. For example, in the stem cells the miR-290-295 cluster constitutes the majority of expressed microRNAs and is critical for stemness in rodents. During development towards various terminally differentiated lineages, such as neurons, the cells typically switch off transcription of these stem cell-specific microRNAs. Here we report that within the adult Substantia Nigra pars compacta (SNpc), the miR-290-295 cluster is exclusively expressed in DA neurons (SNDA), preventing the locomotor deficits and maintaining an adequate expression of proteins involved in DA biogenesis, such as tyrosine hydroxylase (TH), dopa decarboxylase (DDC) and DA transporter (DAT). Importantly, a global knock-out of the miR-290-295 cluster leads to decreased numbers of SNDA neurons in adult mice. Using in vitro and in vivo DA cell-specific loss-of-function models, we demonstrated that miR-292a-3p, the most abundant microRNA in this cluster, directly targets PTEN, a phosphatase antagonizing the neuroprotective phosphatidylinositol-4,5-bisphosphate 3-kinase (PI3K)-AKT-mechanistic target of rapamycin kinase (mTOR) pathways regulating translation initiation. Accordingly, when labelled with the click chemistry-compatible methionine analogue L-azidohomoalanine, miR-290-295 cluster-deficient SNDA neurons revealed a drastic impairment of protein synthesis, which is critical for DA biogenesis. Our surprising findings demonstrate for the first time a selective expression of stem cell-specific and stemness-promoting microRNAs in a distinct population of mature neurons to maintain their physiological functions in the adulthood, suggesting that similar epigenetic disinhibition mechanisms may be also critical for other terminally differentiated cells across species.

neuroscience↗

bioRxiv2025

KiF1a-regulated neuronal infrastructures in sensory and prefrontal cortices essential for fear memory and anxiety

Stress in social activities induces fears. Cellular infrastructures and molecular profiles underlying fear-relevant psychosis remain elusive. By giving psychological stress to mice that watched fear scenes in the resident/intruder paradigm, we have studied the features of neuronal infrastructures in visual, auditory and medial prefrontal cortices correlated to fear-induced anxiety by approaches of behavior task, neural tracing, molecular biology and electrophysiology in vivo. This psychological stress causes observational mice fears specific to resident mouse and anxiety. This social phobia is associated with the interconnections newly emerged among visual, auditory and medial prefrontal cortices as well as among intramodal neurons. These cortical neurons receive the new synapse innervations from their interconnected neurons alongside the innate synapse innervations, and become to encode the stress signals including battle image and battle sound. The KiF1a knockdown in the medial prefrontal cortex precludes the formations of neuronal infrastructures and social phobia. KiF1a-mediated intracellular transportation in the medial prefrontal cortex is essential for the recruitment of associative memory neurons that encode fear scenes and anxiety. HighlightO_LIPsychological stress induces fears and interconnections among sensory and prefrontal cortices. C_LIO_LIAssociative memory neurons in these cortices are recruited to encode fear scenes and anxiety. C_LIO_LIKiF1a-mediated transportation essential for these cellular infrastructures relevant to learned fear. C_LI

neuroscience↗

bioRxiv2025

TopoLa: A Universal Framework to Enhance Cell Representations for Single-cell and Spatial Omics through Topology-encoded Latent Hyperbolic Geometry

Recent advances in cellular research demonstrate that scRNA-seq characterizes cellular heterogeneity, while spatial transcriptomics reveals the spatial distribution of gene expression. Cell representation is the fundamental issue in the two fields. Here, we propose Topology-encoded Latent Hyperbolic Geometry (TopoLa), a computational framework enhancing cell representations by capturing fine-grained intercellular topological relationships. The framework introduces a new metric, TopoLa distance (TLd), which quantifies the geometric distance between cells within latent hyperbolic space, capturing the networks topological structure more effectively. With this framework, the cell representation can be enhanced considerably by performing convolution on its neighboring cells. Performance evaluation across seven biological tasks, including scRNA-seq data clustering and spatial transcriptomics domain identification, shows that TopoLa significantly improves the performance of several state-of-the-art models. These results underscore the generalizability and robustness of TopoLa, establishing it as a valuable tool for advancing both biological discovery and computational methodologies.

bioinformatics↗

bioRxiv2025

Adaptive Immunity Governs Regional Aortic Remodeling in Hypertension via Perivascular Adipose Tissue Plasticity

Hypertension drives heterogeneous aortic remodeling, but the mechanisms underlying regional disparities remain unclear. Here, we demonstrate that adaptive immunity orchestrates spatial differences in vascular dysfunction by modulating perivascular adipose tissue (PVAT) phenotype and immune-metabolic crosstalk. Using angiotensin II (AngII)-infused wild-type (WT) and Rag1-/-mice lacking T and B cells, we integrated biaxial mechanical testing, bulk transcriptomics, and PVAT analyses. In WT mice, AngII induced pronounced descending thoracic aorta (DTA) remodeling, marked by wall thickening, reduced circumferential stiffness and inflammatory gene upregulation (Il6, Ccl2). These changes were attenuated in Rag1-/- mice, implicating T cells in thoracic maladaptation. Conversely, the infrarenal abdominal aorta (IAA) exhibited hypertensive resilience in WT mice but unmasked PPAR{gamma}-associated metabolic reprogramming (Pparg, Adipoq) in Rag1-/- mice, suggesting T cells suppress protective abdominal adaptations. PVAT heterogeneity emerged as a key regulator wherein thoracic PVAT (T-PVAT) adopted a pro-inflammatory phenotype (CCL5, TIMP-1) in WT mice, exacerbating DTA damage, while Rag1-/- mice showed thermogenic plasticity (Ucp1 upregulation) in abdominal PVAT (A-PVAT). T cell reconstitution restored maladaptive remodeling in Rag1-/- mice, confirming adaptive immunitys dual role in promoting thoracic injury and restraining metabolic resilience. This work identifies PVAT as an immune-metabolic switch governing regional susceptibility to vascular remodeling, offering spatially resolved strategies to preserve aortic compliance in hypertensive disease.

bioengineering↗

bioRxiv2025

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.

plant biology↗

bioRxiv2025

Remodeling of the immune-metabolic landscape triggered by long-term high-altitude exposure

Growing evidence indicates that immunological and metabolic outcomes are key mediators of long-term high-altitude exposure (LTHAE) adaption, but the underlying mechanisms remain poorly understood. This study employs plasma metabolomics and peripheral blood single-cell transcriptomic sequencing to analyze the metabolic and immune dynamic regulation in 46 young male lowlanders following a 90-day adaptation period at high altitude. Single-cell analysis shows a pattern of "innate immune activation and adaptive immune suppression" under LTHAE, characterized by facilitated maturation of neutrophils, enhanced cytotoxicity of CD56dim NK cells, and increased immune responsiveness of cDC2 and pDC, while inhibited maturation of plasmablasts and suppressed immune responsiveness of CD8{square}TEM and CD4+ T cells. Plasma metabolic analysis reveals significant alterations, involving enhanced steroid hormone synthesis, unsaturated fatty acid and amino acid metabolism under LTHAE, which in turn are associated with immune remodeling. Moreover, transcriptomic-metabolic integration analysis indicates the molecular mechanisms of enhanced aerobic oxidation efficiency under LTHAE. Collectively, these findings provide integrated insights into immune-metabolic landscape remodeling and suggest potential mutual regulatory relationship between immune and metabolic state following LTHAE, offering a molecular foundation for high-altitude adaptation research.

genomics↗

bioRxiv2025

Comprehensive profiling of antibiotic resistance, virulence genes, and mobile genetic elements in the gut microbiome of Tibetan antelopes

Tibetan antelopes, native to high-altitude plateau regions, play a vital role in the local ecosystem. However, their gut microbiota harbors diverse antibiotic resistance genes (ARGs) and virulence genes (VFGs), raising concerns about the potential spread of antibiotic resistance in wildlife. In this study, in addition to collecting 26,608 metagenome-assembled genomes (MAGs) from public databases, we performed gut metagenomic sequencing on 68 Tibetan antelopes and obtained 7,318 MAGs through binning. A total of 2,968 ARGs were identified, conferring resistance to 23 antibiotic classes, with elfamycin resistance being the most prevalent. Comparative analysis revealed 7 ARGs unique to Tibetan antelopes, suggesting species-specific adaptations. Additionally, during the analysis of shared antibiotic resistance profiles between Tibetan antelopes and humans, two bacterial strains were identified within the Tibetan antelope gut microbiota: Enterococcus gallinarum exhibiting resistance to extended-spectrum class A beta-lactamases and Klebsiella grimontii demonstrating vancomycin resistance. Mobile genetic elements played a key role in ARG dissemination. ARGs were significantly correlated with VFGs, particularly those linked to adherence and effector delivery systems. These findings underscore for the first time the potential ecological and health implications of ARG dissemination in Tibetan antelopes, highlighting the need for further surveillance to assess its impact on wildlife and environmental resistomes.

microbiology↗

bioRxiv2025

Graph pangenome reveals structural variation dynamics during cucumber breeding

Structural variants (SVs) represent a significant yet underexplored component of plant genome diversity. Analyzing SV dynamics is important for understanding their contributions to phenotypic variation and their influence on genome evolution. Here, we present a graph-based pangenome for cucumber, constructed from 39 reference-level genome assemblies. The pangenome captures 171,892 high-confidence SVs and enables genotyping of these SVs across 443 cucumber accessions, representing diverse geographic origins and spanning wild progenitors, landraces, and modern cultivars. Our analyses reveal that during cucumber domestication, a substantial portion of mildly deleterious SNPs are retained, whereas SVs are consistently purged, highlighting their potentially highly deleterious nature. During the geographic expansion of cucumber, a reduction in SV burden and a younger age of SVs than SNPs were observed, suggesting stronger purifying selection acting on SVs. Additionally, notable gene flow from wild population to African and European populations was detected, resulting in an increased SV burden, potentially due to hitchhiking effects. Importantly, incorporating SV burden into genomic prediction models improved the prediction accuracy for several agronomically important traits. This study illuminates the dynamics of SVs during cucumber domestication and improvement, highlights the complex interplay between SVs and selection pressures, and underscores the extensive implications of SVs for future cucumber breeding.

plant biology↗

bioRxiv2025

Mgl2+ cDC2 triggering of fungal allergic inflammation depends on a spore induced glycolytic shift fuelled by local availability of glucose

Fungal spores are a major cause of severe asthmatic disease. However, the precise events that cause individuals to become sensitised to spores are poorly understood. Mgl2+ type 2 conventional dendritic cells (Mgl2+ cDC2s) are critical in coordinating allergic airway inflammation in mice following repeated exposure to inhaled spores. Yet, whether these DCs are directly acquiring spores from the airway, and the downstream mechanism(s) upon fungal uptake causing DCs to trigger allergic inflammation are unknown. Here we find that spores are acquired by lung DCs after inhalation although these events are rare ([~] 0.5% of the cDC2 population). Transcriptomics on isolated spore+ Mgl2+ cDC2s, compared to spore- Mgl2+ cDC2s from the same environment, revealed that a major consequence of fungal uptake was a boost in metabolic activity. Single-cell metabolic profiling revealed this increase in Mgl2+ cDC2 metabolism upon spore acquisition was fuelled by a glycolytic shift. To pinpoint if nutrient availability and acquisition is an important determinant of this response, mass spectrometry-based metabolomics revealed that, during fungal allergic inflammation, the local airway nutrient environment is altered. To ascertain which of these could be fuelling DC responses, we identified which substrates that feed into glycolysis were crucial. Of these, we found that glucose availability acts as a key rheostat in shaping cDC2 responses to spores. These data highlight a crucial role for glycolytic metabolism in driving cDC2 responses to spores, which is governed by glucose availability, defining novel targets for future therapeutic development of fungal allergic inflammation.

immunology↗

bioRxiv2025

The cryo-EM-delineated mechanism underlying mimicry of CXCR4 agonism enables widespread stem cell neuroprotection in a mouse model of ALS

G-protein coupled receptors (GPCRs) are transmembrane proteins that mediate a range of signaling functions and, therefore, offer targets for a number of therapeutic interventions. Chemokine receptor CXCR4, a GPCR, plays versatile roles in normal and abnormal physiological processes. Synthetic CXCR4 antagonists have been extensively studied and approved for the clinical treatment of cancer and other diseases. We recently elucidated the structural mechanisms underlying CXCR4 antagonism using cryogenic electron microscopy (cryo-EM). CXCR4 agonism by synthetic molecules is an unanticipated therapeutic intervention we recently unveiled. The structural mechanisms underlying those actions remain poorly understood yet could help elucidate a new class of drugs. Here we demonstrate a synthetic dual-moiety strategy that combines simplified agonistic and antagonistic moieties taken from natural agonistic and antagonistic chemokines, respectively, to design de novo peptide mimics of biological function of natural CXCR4 agonist SDF-1. Two peptides so generated, SDV1a and SDVX1 were shown to mimic the action of SDF-1 in activating CXCR4 signaling pathways and cell migration. The structural mechanism of these peptides in the mimicry of CXCR4 agonism was illustrated by cryo-EM structures of CXCR4 bound and activated by the peptides in the presence of G protein, revealing common interactions with the receptor by these peptides in comparison with SDF-1 that explain their close mimicry and conformational changes leading to CXCR4 signal activation. The therapeutic benefit of one of these peptides, SDV1a, was demonstrated in the SOD1G93A mouse model of the spinal motor neuron degenerative disease, amyotrophic lateral sclerosis (ALS) wherein the success of neuroprotective actions of transplanted human neural stem cells (hNSCs) is directly correlated with the expanse of diseased neuroaxis traversed by the donor cells; SDV1a enabled broader neuroprotective coverage while also permitting a much less invasive route of cell administration for extending life. Taken together, these results provide insights into the structural determinants of therapeutic CXCR4 agonism which may allow the design of adjunctive drugs that improve cell-based treatments of central nervous system (CNS) diseases.

neuroscience↗