Biology subjects

Qu, Y.

Publications and source records attributed to Qu, Y..

At least 55 records · Page 3Linked to original sources

bioRxiv2025

ZMS-6659, a selective Polθ helicase inhibitor, demonstrates anti-tumor activity as monotherapy and synergy effect with PARP inhibitors and topoisomerase inhibitors

The repair of DNA double strand break (DSB) is crucial for genome stability. Homologous recombination (HR) is a high-fidelity, error-free DSB repair pathway, and its dysfunction leads to genome instability and can result in tumorigenesis. In HR deficient contexts, microhomology-mediated end joining (MMEJ), dependent on DNA polymerase theta (Pol{theta}), is up-regulated to serve as a backup pathway for DSB repair. Several studies have proved that Pol{theta} inhibition causes synthetic lethality with HR deficiency, and Pol{theta} emerges as a potential DNA damage repair (DDR) target for the treatment of HR deficient tumors both as single agent or in combination with PARP inhibitors (PARPi). In addition, evidences show that the blockage of Pol{theta} can enhance the sensitivity to DNA damage agents. Herein, we characterized ZMS-6659, a highly potent small-molecule Pol{theta} inhibitor targeting the helicase domain. ZMS-6659 induces synthetic lethality in HR deficient models, elicits synergistic effects with even low dose of PARPi and delays PARPi resistance without additional hematotoxicity. Besides, ZMS-6659 also enhance the sensitivity to topoisomerase inhibitors in HR proficient cell lines. These findings support the clinical exploration of ZMS-6659 in combination with PARPi in HR deficient tumors, and suggest a potential application expansion beyond HR deficiency.

cancer biology↗

bioRxiv2025

On-demand insulin manufacturing using cell-free systems with an "on-column" conversion approach

Recent studies project that the prevalence of diabetes is expected to increase significantly and lead to escalating demand on the insulin supply chain. Despite being the first recombinant therapeutic approved by the FDA, insulin remains challenging to access for many around the globe. Here we report on advancements in manufacturing insulin using cell-free protein synthesis (CFPS) systems to rapidly produce mature desB30-insulin in less than a day. This is a major advance towards decentralizing insulin manufacturing and bringing production closer to the point-of-care, thereby improving diabetic patient accessibility. To this end, a purified cell-free extract, PUREfrex(R) 2.1, was utilized to synthesize a tagged proinsulin construct that can be captured and converted into mature insulin using an on-column affinity chromatography process. Notably, two chaperones, peptidyl prolyl isomerase (FkpA), and seven kilodalton protein (Skp) were observed to play a critical role during cell-free expression of proinsulin. The proinsulin was then immobilized on a Ni-NTA column where the purification and conversion of cell-free products were performed sequentially to yield desB30-insulin. Following further optimization, this method serves as a time and resource-efficient production process as compared to current methods. When applied simultaneously, the cell-free expression and on-column conversion methods reported here can be adopted to enable rapid on-demand insulin manufacturing in order to improve the accessibility of insulin and prevent future shortages.

synthetic biology↗

bioRxiv2025

Development of Replay-DMN Coordination Predicts Entorhinal Grid Codes

Neural replay, the reactivation of experience-related activity patterns during offline periods, has been implicated in organising memories into cognitive maps. However, how replay processes mature through childhood and adolescence remains unclear. Here we studied 106 participants aged 8-25 who learned a hidden two-dimensional (2D) associative structure and then underwent magnetoencephalography (MEG) during a map-based inference task and post-task rest to detect spontaneous replay. We found that during post-task rest, younger individuals relied primarily on replay alone to represent the 2D relationships, whereas older individuals showed increasingly precise timing alignment between replay events and activity in the default mode network (DMN), particularly when replay occurred at the trough of a DMN theta oscillation. Such replay-DMN coupling predicted the strength of a grid-cell-like code in the entorhinal cortex identified in this cohort with fMRI. Furthermore, resting-state fMRI revealed that DMN functional connectivity strengthened with age, in parallel with reduced reliance on replay and more efficient inference performance. These results reveal a developmental progression in which replay shifts from an isolated process in youth to a coordinated DMN mechanism by adulthood. This transition predicts the maturation of grid-like schema representations, shedding light on how children gradually build internal knowledge structures to support flexible inference.

neuroscience↗

bioRxiv2025

AT1R and Integrin β3 Synergize to Drive Aortic Dissection via Non-Canonical Wnt/β-Catenin Signaling

Aortic dissection (AD), a life-threatening cardiovascular emergency, continues to impose high mortality due to insufficient therapeutic options, as monotherapy targeting angiotensin II type 1 receptor (AT1R) demonstrates limited clinical efficacy. Utilizing single-cell RNA sequencing, we identified integrin {beta}3 as a critical driver of AD progression, with expression levels positively correlated with disease severity. Histopathological validation in human AD specimens and a murine angiotensin II (AngII)-infusion model confirmed marked upregulation of integrin {beta}3 activation. Pharmacological blockade of integrin {beta}3 with Cyclo(-RGDfK) significantly attenuated aortic pathogenesis in vivo, reducing dissection incidence and aortic degeneration. Mechanistically, AngII-mediated AT1R activation induced formation of a receptor complex with integrin {beta}3, triggering its conformational activation. Transcriptomic profiling revealed that activated integrin {beta}3 potentiates vascular endothelial dysfunction by binding glycogen synthase kinase 3{beta} (GSK3{beta}), which stabilizes {beta}-catenin via a non-canonical Wnt signaling axis. This pathway drives endothelial barrier disruption, hallmarks of aortic wall destabilization in AD. Our findings unveil a previously unrecognized synergy between AT1R and integrin {beta}3, implicating aberrant Wnt/{beta}-catenin signaling as a nexus of endothelial injury in AD pathogenesis. These results advocate for a paradigm-shifting dual-therapeutic strategy concurrently targeting AT1R and integrin {beta}3 to restore vascular homeostasis, offering a mechanistically grounded approach to mitigate this lethal disease. This work bridges critical gaps in understanding AD pathophysiology and provides a transformative framework for precision therapeutics.

pharmacology and toxicology↗

bioRxiv2025

Functional redundancy in chicken ANP32A mediates species-specific support of avian influenza virus polymerase

Host restriction of avian influenza virus (AIV) polymerase in human cells is driven by species-specific differences in ANP32A/B proteins. While AIV polymerase relies on ANP32A/B containing a 33-amino-acid insert unique to avian species, the structural and/or mechanistic basis for this requirement remains poorly characterized. Here, we demonstrate that chicken ANP32A (chANP32A) displays three functional determinants enabling its species-specific support of AIV polymerase: (1) a SUMO-interacting motif (SIM), (2) SUMOylation at residues K68/K153, and (3) a 28-amino-acid segment within the avian-specific insertion. These determinants function synergistically and redundantly, requiring at least two for optimal activity, to enhance interactions between AIV viral ribonucleoprotein (vRNP) and chANP32A, thereby promoting AIV vRNP assembly. In contrast, human ANP32A/B--which lack the other two determinants and rely solely on SUMOylation--exhibit a limited capacity to support AIV polymerase activity. Our findings unveil a cooperative mechanism where SUMO-dependent processes and structural motifs in chANP32A enforce species-specific adaptation of AIV polymerase, shedding light on how ANP32A/B governs host restriction of AIV polymerase.

microbiology↗

bioRxiv2025

C9orf50 is a Targetable Spliceosome Regulator for Cancer Immunotherapy

Cancer cells harbor cell-intrinsic programs capable of sculpting immunogenic landscapes, yet molecular brakes that enforce immune evasion remain poorly defined. Here, we identify C9ORF50, a previously uncharacterized intrinsically disordered protein, as a liquid-liquid phase separation-driven regulator of RNA processing and actionable immunotherapy target. Genetic ablation of C9ORF50 induces selective intron retention in spliceosome component transcripts, leading to cytoplasmic accumulation of immunogenic double-stranded RNA (dsRNA). This dsRNA activates type I interferon pathway that in turn orchestrates a chemokine secretory program critical for T cell recruitment. The resultant enhancement of tumor immunogenicity and reprogramming of tumor immune microenvironment drives robust antitumor immunity, effectively converting immunologically "cold" tumors to "hot" phenotypes. Therapeutic targeting of C9ORF50 via RNA interference achieved robust tumor suppression in syngeneic models, suggesting its translational relevance. Notably, C9ORF50 exhibits tumor-predominant expression, with minimal baseline levels detected in healthy tissues or immune cell populations, underscoring its potential safety as a therapeutic target. Our study not only identifies C9ORF50 as a novel LLPS-dependent regulator of RNA splicing but also establishes it as a promising and potentially safe therapeutic target for cancer immunotherapy.

cancer biology↗

bioRxiv2025

Deep-learning-based interpolation of longitudinal microbiome data powers biologically informative discovery

The human microbiome is a foundational and dynamic foundation for several health-related functions and disease processes. Advances in microbiome sequencing have enabled the characterization of microbial communities in several niches. Longitudinal microbiome studies further strive to discover clinically informative microbial community trajectories. However, these data are fraught with dropout events, high noise, and irregular sampling that limit and prevent the use of many available longitudinal analysis tools. To address these challenges, we introduce Bidirectional GRU-ODE-Bayes (BGOB), a deep learning framework developed for longitudinal microbiome interpolation. BGOB combines bidirectional information flow and ODE-based continuous modeling to jointly interpolate and smoothen trends across individual participants, providing uniform, denoised time intervals across patients. BGOB enables vastly improved performance in differential abundance testing and time-to-event analysis, and makes possible longitudinal analyses requiring uniformity, such as lead-lag detection and temporal clustering. After interpolation, previously low-powered datasets are able to broadly recapitulate known microbiology and elucidate interacting microbial communities. We highlight several associations between microbial taxa and disease, including novel species associated with Early Childhood Caries and disruption of key healthy gut microbiota in Inflammatory Bowel Disease. The BGOB package is publicly available at https://github.com/Rachel-Lyu/BGOB_n_test.

microbiology↗

bioRxiv2025

Clonal relationships between Tph and Tfh cells in patients with SLE and in murine lupus

Pathologic T cell-B cell interactions drive disease in systemic lupus erythematosus (SLE). The T cells that activate B cell responses include T peripheral helper (Tph) and T follicular helper (Tfh) cells, yet the developmental and clonal relationships between these B cell-helper T cell populations are unclear. Here we use T cell receptor (TCR) profiling to demonstrate substantial clonal overlap between Tph and Tfh cells in the circulation of patients with SLE. Expanded Tph and Tfh cell clones persist over the course of 1 year in patients with a new diagnosis of SLE, and clones are observed to shift both from Tfh to Tph cells and from Tph to Tfh cells over time. High resolution analysis of cells sorted as Tph cells (CXCR5- PD-1hi) from SLE patients revealed considerable heterogeneity among these cells and highlighted a subpopulation of cells with transcriptomic features of activated B cell-helper T cells. This cell population, marked by expression of TOX and CXCL13, was found in both sorted Tph and Tfh cells, and was clonally linked in these two populations. Analysis of B cell-helper T cells in murine pristane-induced lupus demonstrated similar populations of Tph and Tfh cells in both lung and spleen with strong clonal overlap. T cell-specific loss of Bcl6 prevented accumulation of Tfh cells and reduced accumulation of Tph cells in pristane-treated mice, indicating a role for Bcl6 in the survival and expansion of both populations. Together, these observations demonstrate a shared developmental path among pathologically expanded Tph and Tfh cells in SLE. The persistence of expanded Tph and Tfh cells clones over time may explain the lack of stable tolerance induction by immunosuppressive medications or by B cell depletion.

immunology↗

bioRxiv2025

Ancient gene clusters initiate monoterpene indole alkaloid biosynthesis and C-3 stereochemistry inversion

The inversion of C3 stereochemistry in monoterpenoid indole alkaloids (MIAs), derived from the central precursor strictosidine (3S), is a critical step for the biosynthesis of numerous 3R MIAs and spirooxindoles, including the antihypertensive drug reserpine. While early MIA biosynthesis preserves the 3S configuration, the mechanism underlying C3 inversion has remained unresolved. Here, we identify and biochemically characterize a conserved oxidase-reductase pair in the Gentianales order: the heteroyohimbine/yohimbine/corynanthe C3-oxidase (HYC3O) and C3-reductase (HYC3R), which together invert the 3S stereochemistry to 3R across diverse substrates. Notably, HYC3O and HYC3R reside in gene clusters in Rauvolfia tetraphylla and Catharanthus roseus, homologous to an elusive geissoschizine synthase (GS) cluster we also uncovered. In R. tetraphylla, these clusters are in tandem on a single chromosome, likely derived from segmental duplication, whereas in C. roseus they reside on separate chromosomes due to translocation. Comparative genomics indicate the GS cluster originated at the base of Gentianales ([~]135 Mya), coinciding with the evolution of the strictosidine synthase cluster, while the reserpine cluster arose later in rauvolfioid Apocynaceae. Together, these findings uncover the genomic and biochemical basis for key events in MIA evolution and diversification, providing insights beyond the canonical vinblastine and ajmaline biosynthetic pathways.

biochemistry↗

bioRxiv2025

Replay builds an efficient cognitive map offline to avoid computation online

How do humans integrate fragmented experiences into a coherent structure that supports novel inferences? Addressing this question requires tracking learning from the very first encounters. Using magnetoencephalography, we recorded human neural activity throughout the full process - from initial learning to inference. Participants first learned one-dimensional, pairwise rank relationships that collectively formed a two-dimensional (2D) conceptual map, and then inferred unobserved relationships. During rest, offline replay integrated piecemeal memories into a coherent 2D representation, predicting the emergence of a grid-cell-like code that reflected a generalizable task schema. This schema reduced the need for effortful computations during subsequent inference. During inference, two types of on-task replay emerged: a fast replay, resembling offline replay and representing the full map, and a slow replay, focused on trial-specific details. Notably, slow replay negatively correlated with both grid-like coding and inference performance. Together, these results suggest that replay builds an efficient cognitive map offline, thereby reducing reliance on deliberate computation online.

neuroscience↗

bioRxiv2025

Human hippocampal ripples predict the alignment of experience to a grid-like schema

Humans create internal cognitive maps that allow us to make inferences beyond direct experience. These maps often rely on hexagonal grid-cell-like neural codes, serving as a schema for two-dimensional (2D) spaces. Yet it remains unclear how new experiences become aligned with this schema, especially in non-spatial contexts. Here, we show that hippocampal ripples - brief bursts of neuronal activity during rest - predict the emergence of grid-like codes in a novel 2D inference task. We recorded intracranial neuronal activity in 42 epilepsy patients as they learned rank relationships among feature objects (for example, objects differing in "magic" or "speed"). After learning, these objects were combined to form "compounds" occupying a 2D conceptual space defined by two feature dimensions. During learning, hippocampal ripple activity increased during pauses between trials, suggesting that ripples integrated newly acquired information offline. Subsequently, ripple activity during post-learning rest predicted the later emergence of grid-like codes in the entorhinal cortex (EC) and medial prefrontal cortex (mPFC), a core region of the default mode network (DMN), when participants inferred unseen relationships among the compounds. Critically, coordination during rest between hippocampal ripples and DMN activity in the mPFC predicted participants ability to infer complex relationships beyond direct memory retrieval. These findings provide the first direct evidence that hippocampal ripples, working with the DMN, align new experiences with a grid-like schema offline, transforming discrete learning events into structured knowledge that supports flexible and adaptive reasoning in human cognition.

neuroscience↗

bioRxiv2025

Chloroplast genome editing of Rubisco boosts photosynthesis and plant growth

Photosynthetic inefficiencies limit the productivity and sustainability of crop production and the resilience of agriculture to future societal and environmental challenges. Ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) has inherently low catalytic efficiency, making it a key target for photosynthesis and crop improvement. However, introducing mutations to the chloroplast-encoded Rubisco large subunit (rbcL), which contains the enzymes catalytic sites, is technically challenging. In this study, we successfully generated a range of chloroplast-genome-edited Arabidopsis thaliana plants targeting rbcL by a targeted base editor, ptpTALECD. The M309I and D397N substitutions in rbcL resulted in an increased Rubisco catalytic rate (kcat) without any reductions of Rubisco content, thereby enhancing photosynthetic rates and plant growth under both current atmospheric CO2 concentrations (i.e., 381 mol mol-1) and projected future concentrations (i.e., 549 mol mol-1). Cryo-electron microscopy (cryo-EM) structural analysis showed that the M309I and D397N substitutions, although located far from the catalytic site, induce structural alterations in the catalytic (60s) loops. Our findings highlight the potential of Rubisco engineering to improve plant photosynthesis and growth, and underscore the unique opportunities that chloroplast genome editing offers for enhancing photosynthesis and crop productivity and reducing atmospheric CO2 levels in a non-GMO context.

plant biology↗

bioRxiv2024

The Mitochondrial Brown Adipose Tissue Maintenance Factor Nipsnap1 Interfaces Directly with the Beta-Oxidation Protein Machinery.

BackgroundThe activation of brown adipose tissue (BAT) is associated with improved metabolic health in humans. We previously identified the mitochondrial protein 4-Nitrophenylphosphatase Domain and Non-Neuronal SNAP25-Like 1 (Nipsnap1) as a novel regulatory factor that integrates with lipid metabolism and is critical to sustain the long-term activation of BAT, but the precise mechanism and function of Nipsnap1 is unknown. ObjectivesDefine how the regulatory factor Nipsnap1 integrates with lipid metabolism. MethodsWe generated adeno-associated viral (AAV) constructs that overexpress Nipsnap1 in the thermogenic fat of mice. We then measured both whole-body and cellular mitochondrial metabolism and mapped the first Nipsnap1 interacting protein-protein network. ResultsHerein, we show that adipose-specific overexpression of Nipsnap1 in mice increases energy expenditure through the utilization of lipids as an energy substrate. The increase in energy expenditure results in reduced weight gain. Additionally, we show that Nipsnap1 overexpression in primary adipocytes increases lipid beta-oxidation. Moreover, we mapped the first protein- protein network of Nipsnap1 in brown adipocytes and show that Nipsnap1 interacts with proteins that regulate both peroxisomal and mitochondrial fatty acid beta-oxidation. ConclusionThis study elucidates a mechanistic function of Nipsnap1 in thermogenic fat where Nipsnap1 facilitates a functional connection between peroxisomal and mitochondrial beta-oxidation pathways. By enhancing lipid utilization as energy substrates, Nipsnap1 plays a pivotal role in sustaining thermogenic fat activation to increase energy expenditure. These findings underscore the potential of Nipsnap1 as a therapeutic target for metabolic health.

cell biology↗

bioRxiv2024

AtKC1 inhibits AtAKT1 activation via its amino-terminal inhibitory domain

AKT1 is a plant Shaker-like, hyperpolarization-activated K+ channel which plays a crucial role in K+ absorption. Besides phosphorylation, AKT1 is subject to negative regulation by AtKC1, a silent channel of the same family. Previous structural studies unveiled that AKT1 and AtKC1 form 2:2 heterotetramer in purified samples. However, the structural analysis failed to offer more insight into the inhibition mechanism of AKT1 activation by AtKC1. Here, inspecting the complex structure of AKT1-AtKC1 reveals that a stable domain of AtKC1 (residues 53 to 80), named inhibitory domain or I-domain, may inhibit AKT1 activation by stabilizing its depolarized, closed conformation. We confirmed this hypothesis with electrophysiological experiments. Interestingly, a single-point mutation (G315D) in AtKC1 has been reported to abolish its ability to inhibit AKT1. We solved the structure of AKT1-AtKC1(G315D) at a resolution of 2.8 [A] which revealed an unexpected stoichiometry alteration between AKT1 and AtKC1 from 2:2 to 3:1. This stoichiometry change further supports the hypothesis as we reason that single I-domain of AtKC1 in the channel complex is insufficient to effectively inhibit channel activation. Our findings reveal the inhibition mechanism of AtKC1 on AKT1 and offer insight into the regulatory mechanisms of hyperpolarization-activated channels.

biochemistry↗

bioRxiv2024

Stereochemical Insights into Sarpagan and Akuammiline Alkaloid Biosynthesis

The Apocynaceae family produces a diverse array of monoterpenoid indole alkaloids (MIAs) with significant pharmaceutical value. Among these, sarpagan and akuammiline alkaloids stand out for their complex stereochemistry, derived from the enzymatic cyclization and rearrangement of geissoschizine. This study investigates the stereochemical outcomes of sarpagan bridge enzymes (SBEs) and rhazimal synthases (RHS), key players in geissoschizine cyclization and MIA diversification. Using two known and five newly identified enzymes from six plant species, we show that RHS enzymes from Alstonia scholaris, Vinca minor, and Amsonia tabernaemontana exclusively produce the 16R rhazimal stereoisomer. Meanwhile, SBEs from Catharanthus roseus, Tabernaemontana elegans, Vinca minor, and Rauvolfia serpentina likely generate 16R polyneuridine aldehyde; however, downstream aldehyde reductase, deformylase, and esterase activities further epimerize and alter the C16 stereochemistry, yielding naturally occurring alkaloids with distinct C16 stereochemistry across species. These findings, supported by in vitro assays and in planta silencing of C. roseus CrSBE after we reroute biosynthetic flux toward mutated sarpagan MIAs, further reveal enzymatic control over C16 stereochemistry in sarpagan MIA biosynthesis. By elucidating the transformation of diastereomeric intermediates, this work provides key insights into the stereochemical and enzymatic diversification of MIAs in nature.

biochemistry↗

bioRxiv2024

Development of Non-Spatial Grid-Like Neural Codes Predicts Inference and Intelligence

Piagets theory posits that children develop structured knowledge schemas for inferring and assimilating new information, yet the underlying neural mechanisms remain unclear. In 203 participants aged 8-25 years, we investigated how maturation of a two-dimensional (2D) knowledge map underpins inferential reasoning and knowledge assimilation. Grid-cell-like codes in the entorhinal cortex (EC) strengthened with age, reflecting schema representations in non-spatial conceptual spaces, and were directly linked to improved inferential reasoning. These grid-like codes also supported the medial prefrontal cortex (mPFC) in encoding distance relationships between objects on the 2D map. As participants assimilated new information, they integrated it into existing grid patterns in the EC. Moreover, the maturation of these neural codes predicted real-world intelligence measures, particularly in reasoning abilities. Our findings demonstrate that the development of non-spatial grid-like neural codes offers a mechanistic account of cognitive development, bridging psychological theory with a fundamental cellular representation of cognitive map.

neuroscience↗

bioRxiv2024

Activation of hypothalamic-pontine-spinal pathway promotes locomotor initiation and functional recovery after spinal cord injury in mice

The hypothalamus is critical for regulating behaviors essential for survival and locomotion, but how it integrates internal needs and transmits locomotion commands to the spinal cord (SC) remains unclear. We found that glutamatergic neurons in lateral hypothalamic area (LHA) are essential for regulating motivated locomotor activity. Using single-neuron projectome analysis, trans-synaptic tracing, and optogenetic manipulation, we showed that LHA facilitates motivated locomotion during food seeking via pontine oral part (PnO) projection neurons, rather than direct SC projections or indirect stress signaling via medial septum and diagonal band. Activating PnO-SC projection neurons also initiated locomotion. Importantly, LHA-PnO projection neurons were crucial for regulating locomotor recovery following mouse spinal cord injury (SCI). Closed-loop deep brain stimulation (DBS) of LHA via gating by motor cortex signals markedly promoted long-term restoration of hindlimb motor functions after SCI. Thus, we have identified a hypothalamic-pontine- spinal pathway and the stimulation paradigm for potential therapeutic intervention after SCI.

neuroscience↗

bioRxiv2024

A Mouse-adapted SARS-CoV-2 Model for Investigating Post-acute Sequelae of COVID infection

The coronavirus disease of 2019 (COVID-19), caused by the Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2), remains a major health issue after nearly 7 millions of death toll in the last four years. As the world is recovering with improving vaccines and antiviral treatments, the alarming rate of long-COVID, or Post-acute Sequelae of COVID-19 (PASC), calls for further investigations. Among a list of symptoms associated with multi-organ dysfunctions, the neurological complications are particularly intriguing, yet the underlying mechanisms remain elusive. With the recently developed mouse adapted SARS-CoV-2 stain, we are now able to model the mild COVID infection in C57BL/6 mice and study the chronic immune responses and subsequent damages in different organs long after the viruses are clearly naturally in the body. More specifically, we found adult C57BL/6J mice developed neurological impairments, including behavior changes related to sensorimotor coordination, depression- and anxiety-like behaviors, and inflammation in multiple organs including lung, liver and brain, which persisted over at least 4 weeks in mice even with mild infection. Therefore, this model can be used to further explopred the mechanisms of PASC, as well as potential intervention or therapeutic approaches.

neuroscience↗