Biology subjects

Meng, Q.

Publications and source records attributed to Meng, Q..

At least 19 recordsLinked to original sources

bioRxiv2026

Vascularized Organoids Emerge from a Heart-Foregut-like Intermediate Recapitulating Early Human Development

During early cardiogenesis, the heart regions lie in close contact with foregut endoderm, which supplies essential nutrients and signaling cues to orchestrate primitive heart tube assembly. Here, we show that self-organized heart/foregut like-structures emerge from human pluripotent stem cells (hPSCs). The initial heart/foregut-like structures, termed the Seed, are encased by surrounding supportive cells termed Soil, which provide a matrix microenvironment; the Seed progressively develops into chambered human cardiac organoids (hCOs) containing cardiomyocytes (CMs), epicardial cells, cardiac fibroblasts, and endothelial cells. Optimization of the induction system further enhanced hCO maturation and vascularization. Therefore, this Soil-Seed system provides a model to dissect human early heart/foregut self-organization.

developmental biology↗

bioRxiv2026

Prenatal 3i-0777 treatment attenuates left ventricular hypertrabeculation and dysfunction in a retinoic acid-induced mouse model

Excessive left ventricular trabeculation and thinning of the compacted myocardium arise during cardiac development and may be accompanied by myocardial dysfunction. Gestational exposure to all-trans retinoic acid (ATRA) induces a comparable phenotype in mice, providing a model for evaluating prenatal pharmacological intervention. We examined whether 3i-0777, a small-molecule enhancer of GATA4-NKX2-5 transcriptional synergy, could attenuate these structural and functional abnormalities. Pregnant C57BL/6NCrl dams were randomly assigned to untreated control, vehicle control, ATRA, or ATRA plus 3i-0777 groups (12 independent litters per group). Both ATRA-exposed groups received ATRA (50 mg/kg) on embryonic day (E)12.5. In the ATRA plus 3i-0777 group, 3i-0777 (15 mg/kg) was administered as a separate injection concurrently with ATRA at E12.5, followed by 5 mg/kg every 8 h (three doses per day) on E13.5-E15.5. At postnatal day 1, one pup was randomly selected from each litter for echocardiography and subsequent histomorphometry. The echocardiographic and histomorphometric ratios of non-compacted to compacted myocardial layer thickness (N/C ratios) were higher, and the absolute magnitude of global longitudinal strain (|GLS|) was lower, in the ATRA group than in either control group (all adjusted P < 0.001). Compared with the ATRA group, the ATRA plus 3i-0777 group had lower echocardiographic and histomorphometric N/C ratios (0.58 {+/-} 0.19 vs 2.19 {+/-} 0.18 and 0.90 {+/-} 0.33 vs 2.46 {+/-} 0.48, respectively), higher |GLS| (25.9 {+/-} 2.5% vs 15.3 {+/-} 2.7%), and a smaller left ventricular internal diameter at end-diastole (1.15 {+/-} 0.06 vs 1.42 {+/-} 0.10 mm; all adjusted P < 0.001). These findings provide proof of concept that ATRA-induced left ventricular hypertrabeculation and dysfunction can be pharmacologically attenuated in utero.

developmental biology↗

bioRxiv2026

Novel Dissymmetric Ionizable Lipid-Assembled Lipid Nanoparticles for Delivery of Ferroptosis-Related siRNA in Diabetic Treatment

Small interfering RNA (siRNA) enables precise post-transcriptional gene silencing for refractory diseases, yet its clinical translation remains limited by the lack of safe and efficient delivery vectors. Inspired by the dissymmetric alkyl chain architecture of natural membrane phospholipids, we designed and synthesized 34 novel ionizable lipids with dissymmetric hydrophobic tails and formulated them into lipid nanoparticles (LNPs). Through systematic physicochemical and biological assessments, we established clear structure-activity relationships and identified two lead LNPs (O14-LNP, H18a-LNP) with superior endosomal escape capacity, enhanced in vivo gene silencing potency, and favorable biosafety relative to the clinical benchmark MC3-LNP. In both streptozotocin-induced and spontaneous db/db type 2 diabetes (T2D) mouse models, lead LNPs delivering ferroptosis-related siRNAs effectively ameliorated glucose and lipid metabolic disorders, restored islet function, and alleviated hepatic steatosis. This study not only lays a theoretical foundation for the rational design of novel ionizable lipids, but also validates the therapeutic potential of siRNA therapy targeting ferroptosis, providing a versatile delivery platform and targeted therapeutic strategy for the treatment of T2D.

pharmacology and toxicology↗

bioRxiv2026

A biointegrated living brain stimulator evokes specific neural signalling

Implanted brain stimulators play a crucial role in treating various neurological disorders, including Parkinsons disease (PD), Alzheimers disease, epilepsy, and depression. However, none of the existing implanted brain stimulators can realize specific neuromodulation due to fundamental disparities in signal transmission between electrical signal-induced neuronal responses and neurotransmitter-evoked neural signalling in natural neural circuits, leading to persistent challenges in biosafety and therapeutic effectiveness. Inspired by the dopaminergic neural circuit, we report a biointegrated living brain stimulator (BBS) that integrates ferroelectric bioelectronics, dopaminergic cells, and a gelatin hydrogel matrix, enabling dopamine neurotransmitter-evoked neural signalling. In contrast to conventional brain stimulators, the BBS are capable of programmed secretion of physiological-level dopamine, specifically activating nigral dopamine pathways and restoring motor function in a rodent PD model. By integrating the advantages of both bioelectronics and medicine, this lifelike BBS offers a great promise for next-generation bioelectronics, medicine, and brain-machine interfaces.

bioengineering↗

bioRxiv2026

Mature Citrus Leaves Undergo Coordinated Photosynthetic Downregulation to Support Flush-Driven Carbon and Nitrogen Sink Demand

The source{square}sink attenuation hypothesis suggests that plants regulate carbon fixation in response to fluctuations in sink demands. Many evergreen trees exhibit flushing growth patterns, where new shoot development generates a strong, transient demand for both carbon and nitrogen that may influence the function of mature leaves. This study examined the source-sink attenuation hypothesis in the context of vegetative sink growth by investigating the photosynthetic capacity and nitrogen dynamics in mature citrus leaves across three stages of flush development. In contrast to expectations, photosynthesis declined as flush growth progressed. Early flush initiation induced stomatal limitation in mature leaves, whereas as sink demand from further shoot growth continued carboxylation capacity and Rubisco abundance declined, despite relatively stable total leaf nitrogen. These results suggest that mature leaves undergo selective protein retooling under prolonged sink demand, constraining CO{square} fixation while maintaining C export. Overall, this study revealed that under strong combined N and C sink demands, mature citrus leaves function primarily as regulated carbon conduits rather than dynamically upregulating photosynthesis, providing new insight into source-sink coordination in woody perennial species. HighlightCitrus flush growth shows that mature leaves suppress photosynthesis through stomatal and biochemical regulation while reallocating carbon and nitrogen to support new shoot development, challenging classic source-sink theory.

plant biology↗

bioRxiv2026

HSC71 acetylation confers protection against Spiroplasma eriocheiris infection by inhibiting apoptosis and promoting ROS production in arthropods

Heat shock proteins (HSP) are increasingly recognized as pivotal regulators of host innate immunity. However, the role of HSP70 post-translational modifications in modulating the immunologic functions during pathogenic infection remains poorly understood. Here, we demonstrated that heat shock cognate 71 kDa protein (HSC71), a member of the HSP70 family, was deacetylated following infection with intracellular pathogen Spiroplasma eriocheiris. HSC71 deficiency exacerbated hemocyte apoptosis and increased host susceptibility to S. eriocheiris infection. Conversely, ectopic expression of hyperacetylation-mimetic HSC71(K579Q) in Drosophila S2 cells conferred robust protection against S. eriocheiris by suppressing apoptosis and augmenting reactive oxygen species (ROS) production. Mechanistically, carnitine O-acetyltransferase (Crat) was identified as the specific acetyltransferase for HSC71. Crat acetylated HSC71 at lysine 579 (K579), which in turn impeded its interaction with the E3 ubiquitin ligase CHIP, thereby stabilizing HSC71 by attenuating ubiquitin-mediated degradation. Crat deficiency induced apoptosis and reduced ROS levels in hemocytes, thereby exacerbating S. eriocheiris intracellular proliferation. Furthermore, acetylation of HSC71 at K579 weakened its binding to superoxide dismutase (SOD), resulting in impaired SOD activity and consequent accumulation of microbicidal ROS. Pharmacological inhibition of the deacetylase SIRT1 with EX-527 enhanced HSC71 acetylation and ROS production, conferring resistance to S. eriocheiris infection in crabs. Notably, EX-527 similarly enhanced the acetylation of Drosophila HSC71 homolog, HSPA8, which in turn impaired its interaction with SOD. This led to elevated ROS levels and restricted intracellular proliferation of S. eriocheiris in S2 cells, demonstrating evolutionary conservation of this mechanism among arthropods. Therefore, this study established the modulation of HSC71 acetylation as a promising strategy to enhance arthropod immunity. Author summaryMembers of the HSP70 family are indispensable components of host innate immunity, and their functions are finely tuned by post-translational modifications. This study investigated the mechanisms that underlie acetylation modification of HSC71 mediated resistance to S. eriocheiris infection in crab. Our results revealed that the acetyltransferase Crat and the antioxidant enzyme SOD directly interacted with HSC71. Mechanistically, Crat acetylated HSC71 at K579, which prevented its ubiquitination by promoting the disassociation of E3 ubiquitin ligase CHIP, thereby improving HSC71 stability. In HSC71-deficient or Crat-deficient crabs, hemocyte apoptosis was markedly enhanced, leading to higher host mortality upon S. eriocheiris challenge. Meanwhile, K579 acetylation on HSC71 weakened the interaction between HSC71 and SOD, resulting in the accumulation of intracellular ROS and thereby restricting S. eriocheiris propagation. Administration of the SIRT1 inhibitor EX-527 enhanced HSC71 acetylation, elevated ROS production and reduced host susceptibility to S. eriocheiris infection. These findings revealed a novel role for Crat-mediated acetylation of HSC71 in orchestrating host defense through two synergistic mechanisms: suppressing apoptosis and promoting ROS accumulation. Thus, targeting HSC71 acetylation may represent a promising avenue to combat S. eriocheiris infection.

immunology↗

bioRxiv2026

Lung-Targeting Interleukin-10 mRNA Lipid Nanoparticles Ameliorate Acute Lung Injury

Acute respiratory distress syndrome (ARDS) is the most severe manifestation of acute lung injury (ALI), characterized by diffuse pulmonary inflammation, impaired gas exchange, and high morbidity and mortality. Despite its clinical significance, no specific or effective pharmacological therapies are currently available for its treatment. In this study, we developed a lung -targeted mRNA-sulfonium lipid nanoparticle (mRNA/sLNP) delivery system for the treatment of ALI in a mouse model. We first optimized sulfonium lipid structures, and the optimized sLNP was comprehensively characterized and subsequently loaded with interleukin-10 (IL-10) mRNA. In a lipopolysaccharide (LPS)-induced ALI mousemodel, IL-10/sLNPdemonstrated both prophylactic and therapeutic efficacy, significantly attenuating pulmonary and systemic inflammation, restoring barrier integrity, and reducing tissue injury.

bioengineering↗

bioRxiv2026

EOLA1, a novel mitochondria-localized protein critical for heart functions via regulating mitochondrial translation

Mitochondria possess their own mRNA translation system, mediated by specialized mitoribosomes. Dysregulation of mitochondrial translation disrupts metabolic homeostasis and is linked to various pathologies, including metabolic syndromes, neurological disorders, and cardiac diseases. Using CRISPR/Cas9 screening, we identified EOLA1 (endothelial-overexpressed lipopolysaccharide-associated factor 1) as a novel mitochondrial matrix protein essential for metabolic homeostasis. Knockout of Eola1 severely affects mitochondrial translation and consequently the oxidative phosphorylation in mammalian cells. Mechanistically, EOLA1 physically interacts with mitochondrial 12S ribosomal RNA (12S mt-rRNA) and the mitochondrial Tu translation elongation factor (TUFM), facilitating efficient translation elongation of mitochondrial-encoded mRNAs. Furthermore, genetic ablation of Eola1 in mice induced severe cardiac dysfunction, demonstrating its indispensable role in maintaining heart function through mitochondrial translation control. Together, our findings establish EOLA1 as a key regulator of mitochondrial translation via its interactions with 12S mt-rRNA and TUFM, highlighting its importance in cellular metabolism and a potential role in cardiac disease pathogenesis.

molecular biology↗

bioRxiv2026

Phosphorylation Protects Oncogenic RAS from LZTR1-Mediated Degradation

Oncogenic KRAS and NRAS mutations are common in hematologic malignancies, but how they signal is less well characterized than in carcinomas. To uncover novel RAS biology and potential therapeutic vulnerabilities, we employed a multi-omics screening approach in multiple myeloma to identify regulators of RAS activity. We report that the phosphatase PP1C dephosphorylates the conserved T148 residue on RAS, which in turn permits LZTR1-dependent proteasomal degradation. Notably, LZTR1 is ineffective against KRAS A146 gain-of-function mutations, which are adjacent to T148 and prevalent in hematologic cancers. Remarkably, we find that KRAS protein is four-fold less stable in hematologic versus carcinoma cells, offering a unique therapeutic opportunity targeting RAS protein stability mechanisms. The kinases PAK1 and PAK2 shield RAS from LZTR1-dependent degradation by phosphorylating T148, and targeting PAK1/2 activity improves RAS-directed therapy. Collectively, our findings reveal a novel regulatory circuit governing RAS stability that is preferentially active in blood cancers and potentially druggable.

cancer biology↗

bioRxiv2025

Cross-species etiologically informed stratification enables T cell receptor-based diagnosis of Parkinson's Disease

BackgroundDeveloping peripheral blood-based diagnostic models for idiopathic Parkinsons disease (iPD), particularly those leveraging the T-cell receptor (TCR) repertoire, has long been considered infeasible because patient-derived TCRs appear to lack convergent sequence motifs. We reasoned that this apparent absence of shared TCR features likely reflects both insufficient sample sizes and unaccounted immune heterogeneity within the iPD population. MethodsWe reconstructed TCR repertoires from the two largest iPD cohorts currently available, anchoring them with three mechanistically distinct mouse models to stratify patients into model-anchored informed subtypes. Within these data-driven subtypes, we trained subtype-specific, multimodal multi-instance classifiers. ResultsWe demonstrated that iPD patients can be successfully stratified into model-anchored informed subtypes. Furthermore, the trained subtype-specific, multimodal multi-instance classifiers achieved an Area Under Curve (AUC) exceeding 0.8 for both subtypes. ConclusionsOur findings underscore the critical role of disease stratification in enabling TCR repertoire-based modeling in neurodegenerative diseases.

neuroscience↗

bioRxiv2025

AI-based Predictive Signaling Pathway Profiling in Cardiac Fibrosis Suggests a Novel Combinatorial Treatment Strategy

BackgroundCardiovascular disease (CVD) remains the leading cause of global mortality, with myocardial fibrosis characterized by excessive extracellular matrix (ECM) deposition representing a common endpoint associated with progressive cardiac dysfunction. While studies in animal models of heart disease suggest that preventing or reducing fibrosis can antagonize negative ventricular remodeling, current therapeutic strategies remain clinically limited and ineffective, in part due to an incomplete understanding of the multifactorial nature of the fibrotic process. Methods and ResultsWe employed artificial intelligence (AI) trained from 6,528 cardiac fibrosis publications over the past decade, which suggested 10 nodal signaling pathways underlying the fibrotic process. Single-cell RNA sequencing was used to quantify pathway activities across mouse models and clinical samples encompassing acute and chronic cardiac injury. Dynamic enrichment analysis revealed 2 critical pathways involved in acute myocardial infarction (MI) injury driven temporally-regulated fibrosis whereby Janus kinase - Signal transducer and activator of transcription (JAK-STAT) signaling peaked early (day 7) while transforming growth factor-{beta} (TGF-{beta}) pathway activity peaked mid-phase (day 14). With more chronically-driven fibrosis, JAK-STAT signaling again emerged, which this time was persistently active during chronic transverse aortic constriction (TAC) injury. Experimentally, single-cell analysis identified a pathogenic myofibroblast subpopulation characterized by high JAK-STAT signaling and ECM secretion capacity. Fibroblast-specific Jak1/2 gene-deleted mice significantly reduced TAC-induced fibrosis by blocking myofibroblast formation from this subpopulation, although these same mice failed to show attenuated fibrosis following MI injury, suggesting a pathway that would be ideal to therapeutically target for chronic fibrosis without affecting necessary acute scar formation. Indeed, based on the predictive AI driven algorithm, a temporal inhibitory strategy was generated for JAK-STAT and TGF-{beta} that permitted compensatory scar formation while more effectively preventing progressive fibrosis and worsened cardiac function versus either singular pathway or chronic antagonism. ConclusionHere we employed the wealth of past signaling pathway data underlying cardiac fibrosis to train an AI model, which suggested an optimized approach of inhibiting 2 nodal signaling pathways but with differential timing as a more effective therapeutic strategy that reduces pathologic cardiac fibrosis without negatively impacting compensatory fibrotic activity with acute MI injury. The therapeutic approach involves altering the timing of JAK-STAT signaling blockade with ruxolitinib (RUX) in combination with delayed and temporary TGF-{beta} signaling inhibition post MI injury with pirfenidone (PFD).

cell biology↗

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↗

bioRxiv2025

Low-coverage whole-genome sequencing facilitates accurate and cost-effective haplotype reconstruction in complex mouse crosses

The search for the underlying genetic contributions to complex traits and diseases relies on accurate genetic data from populations of interest. Outbred populations, like the Diversity Outbred (DO), are commonly genotyped using commercial SNP arrays, such as the Giga Mouse Universal Genotyping Array (GigaMUGA). However, array genotypes are expensive to collect, subject to significant ascertainment bias, and too sparse to capture the genetic structure of highly recombined mouse crosses. We investigated the efficacy of sequencing-based genotyping by comparing genotyping results between the GigaMUGA, double-digest restriction-site associated DNA sequencing (ddRADseq), and low-coverage whole-genome sequencing (lcWGS). We aligned reads at [~]1X coverage and imputed segregating SNPs from the eight DO founder strains onto 48 DO genomes and reconstructed their haplotypes using R/qtl2. Haplotype reconstructions derived from all three methods were highly concordant. However, lcWGS more faithfully recapitulated crossover counts and identified more small (< 1 Mb) haplotype blocks at as low as 0.1X coverage. Over 90% of local expression quantitative trait loci identified in a set of 183 DO-derived embryoid bodies using the GigaMUGA were recalled by lcWGS at coverages as low as 0.1X. We recommend that lcWGS be adopted as the primary method of genotyping complex crosses, and cell-based resources derived from them because they are as accurate as array-based reconstructions, robust to ultra-low sequencing depths, may more accurately model haplotypes of the mouse genome that are difficult to resolve with dense reference data, and cost-effective.

genetics↗

bioRxiv2025

Super-omics and PCAS reveal rheumatoid arthritis as a tumor-like disease

Rheumatoid arthritis (RA) is a debilitating systemic autoimmune disorder that significantly impairs quality of life. To elucidate the molecular alterations in RA progression, we performed comprehensive super-omics analyses on synovial tissues from patients with joint trauma, arthritis, and RA. These analyses included transcriptomics, proteomics, metabolomics, microbiomics, and fourteen PTMs (phosphorylation, acetylation, lactylation, O-GlcNAc glycosylation, arginine monomethylation, lysine monomethylation, lysine dimethylation, lysine trimethylation, succinylation, malonylation, glutarylation, tyrosine nitration, N-glycosylation, and O-glycosylation). Additionally, we developed a protein-centered association study (PCAS) method to integrate these complex datasets. Using this approach, we identified key proteins, such as STK17B, and its interactors, which may be crucial in RA pathogenesis. Tumor-like features, including aberrant angiogenesis and epithelial-mesenchymal transition, were observed in RA, alongside the potential involvement of oncogenes and tumor suppressor genes. Finally, we constructed a molecular interaction blueprint of RA, providing a comprehensive framework for advancing RA pathogenesis, diagnosis, and therapy.

immunology↗

bioRxiv2024

Bridging the Gap in Immunotherapy Prediction: The AGAE Score as a Pan Cancer Biomarker for Immune Checkpoint Inhibitor Response

BackgroundImmune checkpoint inhibitor (ICI) therapy efficacy varies among cancer patients, necessitating precise predictive biomarkers for optimized treatment strategies. MethodsWe developed the Adaptive best subset selection algorithm and Genetic algorithm Aided Ensemble learning (AGAE) score through multi-cohort transcriptomic analysis of ICI-treated patients. The AGAE score incorporated gene-pairing, Adaptive Best Subset Selection for feature optimization, and a Genetic Algorithm for optimal basic learner identification. We explored correlations between AGAE score and immune microenvironments using multi-omics data. Potential targets were screened using 17 CRISPR datasets and validated through in vitro and in vivo experiments. ResultsThe AGAE score demonstrated robust predictive power for ICI therapy outcomes, with lower scores correlating with enhanced treatment response. The AGAE score outperformed published signatures and conventional biomarkers. Lower AGAE scores were associated with increased immune cell infiltration, higher immunogenicity, and enhanced antitumor immune activity. The CEP55 was identified as a potential key target driving immune evasion through AGAE scoring and CRISPR screening. Experimental validation showed CEP55 downregulation attenuated tumor cell malignancy and augmented ICI therapy efficacy by modulating T cell responses. ConclusionsThe AGAE score was a potent predictor of ICI therapy efficacy, facilitating refined patient stratification. CEP55s role in the tumor microenvironments immune response highlights its potential as a therapeutic target. Targeted interventions against CEP55 may improve immunotherapy precision.

cancer biology↗

bioRxiv2024

Complete Genomic Characterization of Global Pathogens, Respiratory Syncytial Virus (RSV), and Human Norovirus (HuNoV) Using Probe-based Capture Enrichment.

Respiratory syncytial virus (RSV) is the leading cause of lower respiratory tract infections in children worldwide, while human noroviruses (HuNoV) are a leading cause of epidemic and sporadic acute gastroenteritis. Generating full-length genome sequences for these viruses is crucial for understanding viral diversity and tracking emerging variants. However, obtaining high-quality sequencing data is often challenging due to viral strain variability, quality, and low titers. Here, we present a set of comprehensive oligonucleotide probe sets designed from 1,570 RSV and 1,376 HuNoV isolate sequences in GenBank. Using these probe sets and a capture enrichment sequencing workflow, 85 RSV positive nasal swab samples and 55 (49 stool and six human intestinal enteroids) HuNoV positive samples encompassing major subtypes and genotypes were characterized. The Ct values of these samples ranged from 17.0-29.9 for RSV, and from 20.2-34.8 for HuNoV, with some HuNoV having below the detection limit. The mean percentage of post-processing reads mapped to viral genomes was 85.1% for RSV and 40.8% for HuNoV post-capture, compared to 0.08% and 1.15% in pre-capture libraries, respectively. Full-length genomes were>99% complete in all RSV positive samples and >96% complete in 47/55 HuNoV positive samples--a significant improvement over genome recovery from pre-capture libraries. RSV transcriptome (subgenomic mRNAs) sequences were also characterized from this data. Probe-based capture enrichment offers a comprehensive approach for RSV and HuNoV genome sequencing and monitoring emerging variants. IMPORTANCERespiratory syncytial virus (RSV) and human noroviruses (HuNoV) are NIAID category C and category B priority pathogens, respectively, that inflict significant health consequences on children, adults, immunocompromised patients, and the elderly. Due to the high strain diversity of RSV and HuNoV genomes, obtaining complete genomes to monitor viral evolution and pathogenesis is challenging. In this paper, we present the design, optimization, and benchmarking of a comprehensive oligonucleotide target capture method for these pathogens. All 85 RSV samples and 49/55 HuNoV samples were patient-derived with six human intestinal enteroids. The methodology described here results has a higher success rate in obtaining full-length RSV and HuNoV genomes, enhancing the efficiency of studying these viruses and mutations directly from patient-derived samples.

molecular biology↗

bioRxiv2024

Differential Immunoregulation by Human Surfactant Protein A Variants Determines Severity of SARS-CoV-2-induced Lung Disease

AbstractCOVID-19 remains a significant threat to public health globally. Infection in some susceptible individuals causes life-threatening acute lung injury (ALI/ARDS) and/or death. Human surfactant protein A (SP-A) is a C-type lectin expressed in the lung and other mucosal tissues, and it plays a critical role in host defense against various pathogens. The human SP-A genes (SFTPA1 and SFTPA2) are highly polymorphic and comprise several common genetic variants, i.e., SP-A1 (variants 6A2, 6A4) and SP-A2 (variants 1A0, 1A3). Here, we elucidated the differential antiviral and immunoregulatory roles of SP-A variants in response to SARS-CoV-2 infection in vivo. Six genetically-modified mouse lines, expressing both hACE2 (SARS-CoV-2 receptor) and individual SP-A variants: (hACE2/6A2 (6A2), hACE2/6A4 (6A4), hACE2/1A0 (1A0), and hACE2/1A3(1A3), one SP-A knockout (hACE2/SP-A KO (KO) and one hACE2/mouse SP-A (K18) mice, were challenged intranasally with 103 PFU SARS-CoV-2 or saline (Sham). Infected KO and 1A0 mice had more weight loss and mortality compared to other mouse lines. Relative to other infected mouse lines, a more severe ALI was observed in KO, 1A0, and 6A2 mice. Reduced viral titers were generally observed in the lungs of infected SP-A mice relative to KO mice. Transcriptomic analysis revealed an upregulation in genes that play central roles in immune responses such as MyD88, Stat3, IL-18, and Jak2 in the lungs of KO and 1A0 mice. However, Mapk1 was significantly downregulated in 6A2 versus 1A0 mice. Analysis of biological pathways identified those involved in lung host defense and innate immunity, including pathogen-induced cytokine, NOD1/2, and Trem1 signaling pathways. Consistent with the transcriptomic data, levels of cytokines and chemokines such as G-CSF, IL-6 and IL-1{beta} were comparatively higher in the lungs and sera of KO and 1A0 mice with the highest mortality rate. These findings demonstrate that human SP-A variants differentially modulate SARS-CoV-2-induced lung injury and disease severity by differentially inhibiting viral infectivity and regulating immune-related gene expressions.

immunology↗

bioRxiv2024

Calorie Restriction Induces Degeneration of Neurons with Mitochondrial DNA Depletion by Altering ER-Mitochondria Calcium Transfer

Mitochondrial DNA (mtDNA) mutations and/or depletion are implicated in epilepsy and many neurodegenerative diseases. However, systematic investigation into how mtDNA alterations relate to epilepsy and neural degeneration is needed. Here, we established a mouse model where in mtDNA depletion induced by Herpes Simplex Virus Type 1 (HSV-1) protein-UL12.5 in the brain led to an epileptic phenotype characterized by abnormal electroencephalography (EEG) patterns and increased neural excitability in hippocampus. We also found that UL12.5 mediated mtDNA depletion in neurons in vitro (rho-) causes epilepsy-like abnormal EEG. Caloric restriction (CR) is a strategy proven to reduce epileptic activity, however CR mimetic 2-deoxy-D-glucose (2-DG), induced degeneration in mtDNA depleted neurons. Mechanistically, mtDNA depletion increased mitochondria-endoplasmic reticulum (ER) contacts, facilitating CR-induced mitochondrial calcium overload. Rho- neurons did not show changes in mitochondrial motility or membrane potential. Our study revealed an unexpected axis of mtDNA depletion, ER-mitochondrial contacts, and calcium overload in the rho- neuron model. This is the first description of animal and neuronal models of mitochondrial epilepsy. Our findings with these models suggest that CR may not be a viable clinical intervention in patients with mtDNA depletion.

cell biology↗