Biology subjects

Qi, X.

Publications and source records attributed to Qi, X..

At least 37 records · Page 2Linked to original sources

bioRxiv2025

Ethylene Glycol Monomethyl Ether Altered Rat Sperm Small RNAs with Critical Developmental Roles

Abstract/SummaryEthylene glycol monomethyl ether (EGME) is a testicular germ cell toxicant that selectively targets spermatocytes. In rats, male-only EGME exposure reduces mating success and can lead to an increase in resorbed fetuses. In a previous study, five-day exposure to 50, 60, or 75 mg/kg/d EGME in male rats led to a decrease in sperm motility and increase in retained spermatid heads with a lowest observed adverse effect level (LOAEL) of 75 mg/kg/d. At 60 mg/kg/d, EGME exposure altered the proportion of sperm small RNA reads mapped to different small RNA categories and the distribution of read lengths. To understand the possible role of sperm sncRNAs in EGME-mediated reduction in spermatogenesis, fertility, and embryonic development, we analyzed sperm sncRNA data from EGME-treated male rats to identify differential expression at the individual RNA level. EGME treatment resulted in dose-dependent increases in the expression levels of microRNAs (miRNAs), piRNAs, and tRNA-derived small RNAs (tsRNAs), and mixture of dose-dependent increases and decreases in abundance of rsRNA reads. We identified 12 miRNAs that were differentially expressed at all EGME doses, with a monotonic, dose-dependent increase. High-confidence targets of these 12 miRNAs are known to be expressed in pre-implantation embryos and statistically enriched for Gene Ontology (GO) biological processes related to early development, such as cell fate commitment and regulation of developmental growth. These results demonstrated that the EGME-induced changes in sperm sncRNA levels were reproducible, dose-dependent, and provided a putative mechanism of paternal EGME effects on embryonic development, which will be investigated in future studies.

pharmacology and toxicology↗

bioRxiv2025

Tibetan near-complete pangenome reveals complex variants underlying high-altitude adaptation

Genomic diversity in indigenous populations offers critical insights into human evolution and population-specific adaptation. Here, we generated 70 near-complete, fully phased genome assemblies from 35 high-altitude Tibetan trios and identified 4.55 million small variants and 63,031 structural variants (SVs) absent from the current global pangenome reference. Comparative analyses with a 595 globally diverse long-read genome dataset revealed 207 previously uncharacterized Tibetan-enriched SVs spanning 275 genes implicated in high-altitude physiological adaptation. Genotyping these SVs in 1,164 Tibetan and Han individuals with 88 physiological traits reveals five variants significantly associated with cardiopulmonary and hematological phenotypes central to hypoxia adaptation. We further map 2.45 Gb of archaic hominin sequences in Tibetans and uncover 18 previously unrecognized introgressed regions enriched in Tibetans with genes related to hematopoiesis and lung function. These regions harbor five Tibetan-enriched SVs, indicating that archaic introgression contributed SVs relevant to human adaptation. Together, these findings reveal substantial uncharacterized genomic diversity in Tibetans and highlight a previously underappreciated role of SVs and archaic SVs in shaping human evolution and high-altitude adaptation.

genomics↗

bioRxiv2025

Patient-Specific Midbrain Organoids with CRISPR Correction Reveal Disease Mechanisms and Enable Therapeutic Evaluation in Neuronopathic Gaucher Disease

Neuronopathic Gaucher disease (nGD) is a lysosomal storage disorder caused by GBA1 mutations, leading to defective acid {beta}-glucosidase (GCase) and accumulation of glycosphingolipid substrates, causing inflammation and neurodegeneration. Patients with nGD manifest severe neurological symptoms, but current animal models fail to fully recapitulate human condition, posing a major barrier to the development of effective therapies targeting the brain. To bridge this gap, we have developed midbrain-like organoids (MLOs) from human induced pluripotent stem cells (hiPSCs) of nGD patients with GBA1L444P/P415R and GBA1L444P/RecNcil mutations to model nGD brain pathogenesis. These nGD MLOs exhibited GCase deficiency, resulting in diminished enzymatic function, accumulation of lipid substrates, widespread transcriptomic changes, and impaired dopaminergic neuron differentiation, mirroring nGD pathology. GBA1 mutation correction mediated by CRISPR/Cas9 restored GCase activity, normalized lipid substrate levels, and rescued dopaminergic neuron function, confirming the causal role of GBA1 mutations during early brain development. Using this novel platform, we further evaluated therapeutic strategies, including SapC-DOPS nanovesicles delivering GCase, AAV9-GBA1 gene therapy, and substrate reduction therapy with GZ452, a glucosylceramide synthase inhibitor currently under clinical investigation. These treatments either restored GCase activity, reduced lipid substrate accumulation, improved autophagic and lysosomal abnormalities, or ameliorated dysregulated genes involved in neural development. These patient-specific, 3D neural models offer a transformative, physiologically relevant platform for unravelling disease mechanisms and accelerating the discovery of therapies for patients with nGD.

neuroscience↗

bioRxiv2025

Accessing Meaning During Encoding Shapes Subsequent Memory Reactivation in the Brain

Semantic access can occur in many forms, ranging from retrieving specific exemplars to linking concepts with related meanings. We hypothesized that accessing meaning at different levels during encoding would lead to distinct neural reactivation patterns during later memory retrieval. Human participants learned novel word-image associations through prompts that queried item-specific, categorical, or thematic features, while undergoing fMRI. Multivariate pattern analysis shows that encoding histories leave distinct neural signatures even when behavioral performances is equivalent. Encoding history could be decoded by classifiers from recognition activity across the ventral visual stream and higher-order regions. Category-based encoding reduced item-specific reinstatement in perceptual regions, while item-based encoding modified cross-phase item-level similarity in the anterior temporal lobe, suggesting a transition from detailed to integrative conceptual representations. Together, these findings demonstrate that semantic access during encoding shapes how memories are neurally reinstated to integrate perceptual and conceptual information across systems supporting semantic and episodic memory.

neuroscience↗

bioRxiv2025

Direct In-Sample Sequencing of the 3' Transcriptome Expands the Capabilities of Optical Pooled Screens

We present a platform that directly sequences single guide RNAs and endogenous 3'UTRs in fixed cells while simultaneously measuring protein abundance and cellular morphology. We demonstrate platform capability by performing optical pooled screening of CRISPR-perturbed lung cancer cells. This approach unites direct in-sample RNA sequencing with complementary phenotypic readouts, enabling comprehensive, scalable, and functional genomics analyses within a single experiment.

genomics↗

bioRxiv2025

Dual effects of nicotinamide on aging-related arrhythmia: protective at low dose, proarrhythmic at high doses

BackgroundCardiac arrhythmia and dysfunction progressively increase with age, both of which are closely associated with a decline in NAD+. Supplementation with nicotinamide (NAM), a critical NAD+ precursor, has shown protection in experimental models of aging-related cardiac diseases, including atrial fibrillation (AF) and heart failure, especially heart failure with preserved ejection fraction. With the potential rise of NAM in treatment of various cardiometabolic diseases, its dose-dependent cardiac-specific adverse effects and underlying mechanisms warrant investigation. MethodsThe effects of NAM on aging-related arrhythmia and cardiac dysfunction were assessed using ex vivo Langendorff mouse hearts and adult Drosophila heart preparations. Different doses of NAM (10-100 mM) were tested for their impact on the contractility of HL-1 cardiomyocytes, lifespan and cardiac function of Drosophila, as well as arrhythmia susceptibility of ex vivo mouse hearts. Acetylation of sarcoplasmic/endoplasmic reticulum Ca{superscript 2} ATPase 2a (SERCA2a) was measured by immunoprecipitation followed by Western blotting. ResultsAcute perfusion with 10 mM NAM had limited influence on aging-related AF susceptibility in ex vivo mouse hearts. Short-term dietary intervention with 10 mM NAM in late-life protected against aging-induced cardiac arrhythmia and contractile dysfunction exclusively in male Drosophila. In contrast, life-long exposure or NAM concentrations above 20 mM led to dose-dependent adverse cardiac effects, including impaired contractility in HL-1 cardiomyocyte and shortened lifespan in Drosophila, with increased arrhythmia observed in both models. In ex vivo mouse hearts, 100 mM NAM increased SERCA2a acetylation, suggesting inhibition of sirtuin1 and impaired calcium handling, which likely underlies the observed effects of high-dose NAM on arrhythmia and cardiac dysfunction. ConclusionsNAM exhibits a narrow therapeutic window in aging-related cardiac dysfunction and arrhythmia, with its efficacy highly dependent on dose, duration, and biological context. While a moderate dose in late-life may be protective, chronic or excessive intake of NAM can induce arrythmia and impair cardiac function, likely through disruption of the SERCA2a activity. These findings underscore the importance of cautious and context-specific application of NAM in clinical settings.

physiology↗

bioRxiv2025

A molecularly defined basalo-prefrontal-thalamic circuit regulates sensory and affective dimensions of pain

Both the medial prefrontal cortex (mPFC) and thalamus have been implicated in pain regulation. However, the roles of the mPFC-thalamus connection in pain and how the mPFC modulates nociceptive processing remain unclear. Here, we show that the mPFC neurons projecting to thalamus, marked by Foxp2 expression, are deactivated in both acute and chronic pain in male mice. Persistent inactivation of the mPFC Foxp2+ neurons enhances nociceptive sensitivity, while their activation alleviates multiple aspects of pain. Circuit-specific manipulations revealed that the projections to parataenial nucleus, mediodorsal and ventromedial thalamus differentially modulate sensory and affective pain. Additionally, the mPFC Foxp2+ neurons receive cholinergic input from the basal forebrain, particularly the horizonal diagonal band (HDB). Notably, activation of the 4{beta}2-containing nicotinic acetylcholine receptor in mPFC exerts antinociceptive effects in Foxp2+ neuron-dependent manner. Together, our study defines an HDB[->]mPFCFoxp2[->]thalamus circuit essential for sensory and affective pain modulation and underscores the therapeutic potential of targeting mPFC cholinergic signaling in chronic pain management.

neuroscience↗

bioRxiv2025

DeepHalo: Deep Learning-Powered Exploration of Halogenated Metabolites Uncovering Antibacterial Depsipeptides

In the omics era, confident high-throughput analytical tools are crucial for the efficient identification of metabolites. Here, we present DeepHalo, a deep learning-integrated and hierarchically optimized workflow designed for high-throughput exploration of halogenated metabolites from high-resolution mass spectrometry-based metabolomics. DeepHalo leverages deep learning models combined with a comprehensive scoring to enhance the reliability of halogen predictions. It integrates PyOpenMS for fast isotope pattern detection and incorporates a halogen-based dereplication algorithm with GNPS molecular networking to efficiently exploit and annotate halogenates from complex biological matrices. To validate its performance, DeepHalo was applied to explore halogenated metabolites from 1,296 microbial culture crude, leading to the discovery of six families of structurally diverse halogenated molecules. This included a new class of cyclic depsipeptides, aglomycins A-E, featuring rare 3-chloroanthranilic acid and/or epoxyvaline blocks. Additionally, a plausible biosynthetic pathway of aglomycins was proposed through bioinformatics analyses and targeted gene knockout experiments. Bioassays revealed that aglomycin A exhibits synergistic antibacterial activity with linezolid against vancomycin-resistant Enterococcus faecium (VRE) both in vitro and in vivo. We envision that DeepHalo (freely available at https://github.com/xieyying/DeepHalo) will become a powerful tool for accelerating the discovery of halogenated "dark matter".

biochemistry↗

bioRxiv2025

Semantic Memory Traces Reflect How They Were Last Retrieved

Episodic memories are known to change with each act of retrieval. We hypothesize that accessing semantic knowledge in different ways during episodic retrieval--from unique perceptual features to taxonomic and thematic context--shapes how those memories are subsequently represented during recognition. In this functional magnetic resonance imaging (fMRI) study, human participants learned novel word-image pairs and underwent re-exposure that required accessing semantic knowledge at one of three different levels: item, category, or theme. Participants then completed a recognition task. Although behavioral memory performance was matched across conditions, neural activity during recognition varied based on prior semantic access history. Recognition patterns could be classified according to prior semantic access in early visual cortex, ventral temporal cortex and the hippocampus for remembered concepts. A whole-brain searchlight analysis revealed bilateral clusters along the ventral visual stream where semantic access history was decodable. To further characterize how prior semantic access history shaped neural representations during recognition, we tested whether memories accessed at the same semantic level were expressed more similarly or distinctly in the brain. Category-level access increased similarity among items in early visual cortex, while item-level access led to more differentiated representations in the visual word form area. Together, these findings show that how we access semantic knowledge during episodic retrieval leaves measurable traces in subsequent neural representations, revealing how semantic-episodic interactions shape memory representations.

neuroscience↗

bioRxiv2025

Mechanical Responses of the Giant Nesprin-2

The nesprin protein family serves as a critical physical bridge between the cytoskeleton-a fundamental structural scaffold and mechanotransduction hub of the cell, and the nucleus-an intriguing and emerging mechano-responsive element. Due to the external mechanical cues and the nucleo-cytoskeletal dynamics, the nesprins are physiologically under forces. However, the dynamics of nesprins within physiological forces and loading rates remain largely unexplored. In this study, we employ magnetic tweezers based single-molecule manipulation alongside molecular dynamic simulations and AlphaFold structural predictions to comprehensively investigate the dynamics of force-bearing spectrin repeat (SR) domains of the giant nesprin-2 protein. Through direct quantification, we unveil that the numerous SRs undergo mechanical unfolding and refolding dynamics with distinct transition rates within several pN scale. Furthermore, we show that the giant nesprin-2 could act as an effective molecular absorber adeptly maintaining forces on the nucleoskeleton and cytoskeleton linkage within a few pN across displacement spans exceeding {micro}m. Notably, our findings imply that subtle pN-level mechanical forces intricately modulate nesprin-protein interactions via the dynamics of domain folding and unfolding. Collectively, our study offers a comprehensive understanding of the mechanical characteristics of giant nesprin-2, shedding light on its pivotal role in nucleoskeleton-cytoskeleton mechanotransduction.

biophysics↗

bioRxiv2025

Mechanism of clinically relevant neurosecretory and metabolic impairment in Alzheimers and identification of engineered nanotherapy

A central challenge in Alzheimers disease is understanding the mechanism of neuronal secretory dysfunction. By exploiting AI, we reveal how beta-amyloid disrupts key protein interactions within the neuronal secretory machinery. In a combinatorial strategy of reprogramming the neuronal secretory and metabolic components, we established a dual-target therapeutic framework that repairs synaptic and mitochondrial defects to counteract neurodegeneration in Alzheimers.

neuroscience↗

bioRxiv2025

One Tracer, Dual Platforms: Unlocking Versatility of Fluorescent Probes in TR-FRET and NanoBRET Target Engagement Assays

Target engagement assays are essential for drug discovery, utilizing Time-Resolved Fluorescence Resonance Energy Transfer (TR-FRET) and Nano Bioluminescence Resonance Energy Transfer (NanoBRET) as complementary methods for biochemical and cellular evaluation. Traditional platforms require distinct fluorescent tracers, increasing costs and complexity. This study systematically evaluates the cross-platform performance of T2-BODIPY-FL and T2-BODIPY-589, tracers developed for receptor-interacting protein kinase 1 (RIPK1) target engagement in TR-FRET and NanoBRET applications, respectively. Our results demonstrate both tracers effectively bridge biochemical and cellular assays, providing reliable measurements. T2-BODIPY-589 demonstrates superior performance in NanoBRET (Z up to 0.80) and acceptable functionality in TR-FRET (Z=0.53). Conversely, T2-BODIPY-FL performs optimally in TR-FRET (Z=0.57) and exhibits NanoBRET potential (Z up to 0.72). Competition assays with an unlabeled inhibitor yielded consistent binding constants across all combinations. These findings suggest a single tracer can integrate diverse assay platforms, enhancing consistency and comparability in drug discovery. Table of Content Graphic O_FIG O_LINKSMALLFIG WIDTH=198 HEIGHT=200 SRC="FIGDIR/small/645143v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1cad1eforg.highwire.dtl.DTLVardef@9ccef0org.highwire.dtl.DTLVardef@d611c1org.highwire.dtl.DTLVardef@279f90_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2025

A simplified hybrid capture approach retains high specificity and enables PCR-free workflow

Hybrid capture is a critical technology for selective enrichment of genomic regions of interest, enabling cost-effective focused sequencing in both clinical and research applications. We present a simplified hybrid capture approach that eliminates complexities typically associated with hybridization-based selection methods by directly loading the hybridization product onto the sequencing flow cell. The workflow removes bead-based steps, washes, and post-hybridization PCR, while retaining high capture specificity and library complexity. The approach is enabled by the development of a streptavidin flow cell surface, a method to circularize and amplify captured targets on the flow cell, and a fast hybridization protocol. We demonstrate application across targeted panel sizes and improvements to library complexity and variant calling. We also show how the approach can be used to create an entirely PCR-free targeted sequencing workflow that further improves variant calling and enables the detection of repeat expansions.

genomics↗

bioRxiv2025

Genome-wide analysis reveals the genetic basis of key agronomic traits and modern wheat breeding in Henan Province

Despite the continuous improvement of wheat cultivars in Henan Province, the largest Chinese wheat-producing area, there have been no reports of studies on their breeding advances in the past decades. This study aims to elucidate their genetic basis and breeding advances. A total of 351 landraces and 265 cultivars in Henan Province were employed in selective sweep studies and genome-wide association studies. All the wheat accessions were planted in five locations in Henan Province in 2016-2017, 2017-2018 and 2018-2019. Candidate genes were identified through differential expression, GO annotation, gene homology, and haplotype analyses. Breeding advances were summarized based on four breeding periods (1950s, 1960s-1970s, 1980s-1990s, and post-2000s) of all 265 cultivars. The results demonstrated that 263 known genes with selection signals were found to be associated with important traits. Around the detected quantitative trait loci, 51 genes had been previously reported, while 252 genes were identified as candidate genes. Of the 303 genes and loci identified, 80 genes and 50 loci contributed to the improvement of 12 traits like plant height, and 12 key candidate genes was verified by qRT-PCR, while superior haplotypes of 24 genes explained cultivar climate adaptation. The superior haplotypes of 164 genes are available for future breeding. Transmission of superior haplotypes in four varietal pedigrees revealed pyramiding of superior haplotypes in elite cultivars. The analysis of post-2000 cultivars suggests a broader range of germplasm resources should be considered in parental selection than only recent accessions. This study provides a genetic basis and guide for wheat improvement.

genetics↗

bioRxiv2025

Targeting the ClpP-αSynuclein Interaction with a Decoy Peptide to Mitigate Neuropathology in Parkinson's Disease Models

Parkinsons disease (PD), the most prevalent neurodegenerative movement disorder, is characterized by the progressive loss of dopaminergic (DA) neurons and the accumulation of -synuclein (Syn)-rich inclusions. Despite advances in understanding PD pathophysiology, disease-modifying therapies remain elusive, underscoring gaps in our knowledge of its underlying mechanisms. Mitochondria are key targets of Syn toxicity, and growing evidence suggests that Syn-mitochondrial interactions contribute to PD progression. Our recent findings identify mitochondrial protease ClpP as a crucial regulator of Syn pathology, with pathological Syn binding to and impairing ClpP function, thereby exacerbating mitochondrial impairment and neurodegeneration. To disrupt this deleterious interaction, we developed a decoy peptide, CS2, which directly binds to the non-amyloid-{beta} component (NAC) domain of Syn, preventing its association with ClpP. CS2 treatment effectively mitigated Syn toxicity in an Syn-stable neuronal cell line, primary cortical neurons inoculated with Syn pre-formed fibrils (PFFs), and DA neurons derived from PD patient-induced pluripotent stem cells (iPSCs). Notably, subcutaneous administration of CS2 in transgenic mThy1-hSNCA PD mice rescued cognitive and motor deficits while reducing Syn aggregation and neuropathology. These findings establish the ClpP-Syn interaction as a druggable target in PD and position CS2 as a promising therapeutic candidate for PD and other Syn-associated neurodegenerative disorders.

neuroscience↗

bioRxiv2025

Inhibition of MAPK signaling suppresses cytomegalovirus reactivation in CD34+ Kasumi-3 cells

Reactivation of latent human cytomegalovirus (CMV) can lead to severe complications in individuals with dysregulated immune systems. While antiviral therapies for CMV are approved, these compounds are limited by their toxicity and inability to specifically target the latent reservoir or prevent reactivation. Herein we show that CMV reactivation in Kasumi-3 cells, a CD34+ hematopoietic cell line, requires mitogen-activated protein kinase (MAPK) activation. Importantly, pharmacological inhibition of the MAPK signaling pathway, including MEK and ERK, restricts viral reactivation in Kasumi-3 cells. In sum, our findings show MAPK signaling is critical for CMV reactivation, revealing a potential avenue for therapeutic intervention to prevent viral reactivation and downstream pathogenesis that is often detrimental for immunosuppressed and immunocompromised patients.

microbiology↗

bioRxiv2025

Time-dependent Mitochondrial Remodeling in Experimental Atrial Fibrillation and Potential Therapeutic Relevance

BACKGROUNDChanges in mitochondria have been implicated in atrial fibrillation (AF), but their manifestations and significance are poorly understood. Here, we studied changes in mitochondrial morphology and function during AF and assessed the effect of a mitochondrial-targeted intervention in a large animal model. METHODS AND RESULTSAtrial cardiomyocytes (ACMs) were isolated from dogs in electrically-driven AF for periods of 24 hours to 3 weeks and from humans with/without longstanding persistent AF. Mitochondrial Ca2+-concentration ([Ca2+]Mito), reactive oxygen species (mtROS) production, membrane potential ({Delta}{Psi}m), permeability transition-pore (mPTP) opening and flavin adenine dinucleotide (FAD) were measured via confocal microscopy; nicotine adenine dinucleotide (NADH) under ultraviolet light. mtROS-production increased within 24 hours and superoxide-dismutase type-2 was significantly reduced from 3-day AF. [Ca2+]Mito and mPTP-opening frequency/duration increased progressively during AF. Mitochondrial depolarization was detectable 24 hours after AF-onset. NADH increased by 15% at 24-hour AF, concomitant with increased pyruvate-dehydrogenase expression, then gradually decreased. Mitochondria enlarged and elongated at 24-hour and 3-day AF, followed by progressive fragmentation, rupture and shrinkage. Mitochondrial fusion protein-1 (MFN1) was reduced from 3-day to 3-week AF and phosphorylated dynamin-related protein-1 (p-DRP1ser-616) increased after 1 week of canine AF and in human AF. Addition of the mitochondrial antioxidant MitoTempo attenuated action-potential shortening and L-type Ca2+-current (ICaL)-downregulation in canine and human AF ACMs in vitro. Administration of the orally-active mitochondrial-targeted ubiquinone mitoquinone to dogs during 3-week AF prevented mitochondrial Ca2+-overload, mtROS-overproduction, structural damage and abnormalities in {Delta}{Psi}m and respiration. Functionally, mitoquinone reduced AF-induced Ca2+-current downregulation, action-potential abbreviation, contractile dysfunction and fibrosis, preventing AF-substrate development and AF-sustainability. CONCLUSIONSMitochondria show a series of changes during AF, with early hyperfunction and enhanced ROS-generation, followed by progressive damage and dysfunction. Mitochondrial-targeted therapy prevents mitochondrial dysfunction and attenuates adverse AF-related remodeling, positioning mitochondrial protection as a potential novel therapeutic target in AF.

pathology↗

bioRxiv2025

Title: Cell-autonomous and non-cell-autonomous effects of TRIM72 on ALS disease progression

Dysfunction of RNA-binding proteins, including TDP-43 and FUS, has been associated with amyotrophic lateral sclerosis (ALS); however, the underlying mechanisms are largely unknown. Here, we reported that a neuronal upregulation of TRIM72 (Tripartite Motif Containing 72) in FUS mutation knockin ALS models slows disease progression. TRIM72 interacts with Commander, a protein complex for recycling of membrane proteins, facilitating membrane repair and antioxidation. Exosomal TRIM72 is detected in ALS patient cerebrospinal fluid (CSF) and extracellular application of exosomal TRIM72 protects cell from membrane damage. In a sporadic ALS cohort, CSF TRIM72 level associates ALS disease progression. AAV-mediated neuronal expression of TRIM72 slows down the disease progressions in ALS models and in an ALS patient without adverse effects over a year treatment course. Taken together, our results suggest a universal neuronal protection of a TRIM family protein in cell-autonomous and non-cell-autonomous manners in ALS.

neuroscience↗