Biology subjects

Zhang, Q.

Publications and source records attributed to Zhang, Q..

At least 235 records · Page 13Linked to original sources

bioRxiv2025

Somatic repetitive element insertions Define New Biomarkers in Pan-cancer genome

Repetitive elements insertions (REIs), including tandem repeat insertions (TRIs) and transposable element insertions (TEIs), constitute >90% of large-scale (>50bp) somatic insertions and are linked to diseases and cancer biomarkers. However, the genomic landscape of large-scale REIs in pan-cancer has not been well-characterized due to short-read sequencing limitations. Here, we detected somatic REIs in 325 cancer genomes across 12 cancer types using long-read whole-genome sequencing and customized algorithms. The diverse sequence patterns of somatic TRIs and the insertion mechanisms of somatic TEIs were characterized across different cancer types. We identified 152 high-frequency somatic TRIs, with 10 showing pan-cancer characteristics, including TRIs in SHROOM2, PALMD, and the enhancer of PTPRZ1. The MHC class II gene cluster exhibited the highest somatic TEI abundance, affecting [~]40% tumors. Adenocarcinomas and squamous cell carcinomas exhibited differing TEI distributions within this region. Our study highlights REIs as important but under-explored markers for personalized cancer diagnosis and immunotherapy.

genomics↗

bioRxiv2025

Structural basis of ATP release and ion selectivity in Pannexin1 channels

This study investigated the structural basis of adenosine triphosphate (ATP) release and ion selectivity by Pannexin1 (Panx1). The microinjection of active SRC tyrosine kinase increased Panx1-mediated currents in Panx1-expressing oocytes. Furthermore, a mutation mimicking phosphorylation at Y308 turned Panx1 into a constitutively open ATP-releasing channel with broad ion permeability. Cryogenic electron microscopy showed that for most maps, the channel alternated between wide and narrow conformations. However, in the map of the phosphomimetic Y308E mutation, Panx1 remains in a wide ATP-releasing conformation. The pore-lining residues, W74 and R75, are flexible and create, in concert with the sequestered N-terminal helix, a path for ATP. The data point to phosphorylation as a reversible switch that activates ATP permeability by stabilizing Panx1 in the ATP-releasing conformation, which is crucial for developing modulators for diseases such as cancer and chronic pain.

biophysics↗

bioRxiv2025

Clonal memory of colitis accumulates and promotes tumor growth

Chronic inflammation is a well-established risk factor for cancer, but the underlying molecular mechanisms remain unclear. Using a mouse model of colitis, we demonstrate that colonic stem cells retain an epigenetic memory of inflammation following disease resolution, characterized by a cumulative gain of activator protein 1 (AP-1) transcription factor activity. Further, we develop SHARE-TRACE, a method that enables simultaneous profiling of gene expression, chromatin accessibility and clonal history in single cells, enabling high resolution tracking of epigenomic memory. This reveals that inflammatory memory is propagated cell-intrinsically and inherited through stem cell lineages, with certain clones demonstrating dramatically stronger memory than others. Finally, we show that colitis primes stem cells for amplified expression of regenerative gene programs following oncogenic mutation that accelerate tumor growth. This includes a subpopulation of tumors that have exceptionally high AP-1 activity and the additional upregulation of pro-oncogenic programs. Together, our findings provide a mechanistic link between chronic inflammation and malignancy, revealing how long-lived epigenetic alterations in regenerative tissues may contribute to disease susceptibility and suggesting potential therapeutic strategies to mitigate cancer risk in patients with chronic inflammatory conditions.

cancer biology↗

bioRxiv2025

AMPK- and cGAS-Mediated Dual Sensing of Glucose and dsDNA Synergizes to Enhance Antitumor Immunity

Intratumoral glucose availability is linked considerably to tumor growth, immune evasion, and metastasis. However, the precise molecular mechanisms by which glucose levels govern cellular and immune responses against tumors remain incompletely understood. Here, we explored the context of tumors of intersections between AMP-activated protein kinase (AMPK) and cGAS-STING signaling, a key pathway initiating antitumor immunity. We unexpectedly found that AMPK activation robustly enhances cGAS-STING signaling within cancer and immune cells, which potently impacts melanoma and colorectal cell senescence, organoid apoptosis, and the infiltration of CD4+ and CD8+ T lymphocytes. Using classic or newly developed AMPK agonist Aldometanib, TBK1S511E/S511E knock-in (KI) mice, glucose metabolic modulator, as well as AMPK1/2 dKO melanoma, we demonstrated that dual sensing of intratumoral glucose and dsDNA integrated by the AMPK-TBK1 cascade is essential for initiating antitumor immunity and suppressing cancer progressions. Notably, novel AMPK agonists or intervening in glucose glycolysis by Lonidamine synergized effectively with STING agonists, substantially inhibiting melanoma growth. Therefore, these findings unravel a concise mechanism integrating glucose metabolism and innate DNA sensing into cancer cell fate and propose an effective therapeutic strategy to enhance antitumor immunity. HIGHLIGHTSO_LIDual and synergistic sensing of glucose and dsDNA facilitates antitumor immunity in melanoma and colorectal cancer; C_LIO_LIAMPK substitutes intratumoral cGAS-STING-IRF3 signaling through TBK1 phosphorylation at S511; C_LIO_LIGlucose deficiency induces cancer cell senescence, apoptosis, and T lymphocyte infiltration via the AMPK-TBK1 cascade; C_LIO_LINewly developed AMPK agonists synergize with STING agonists to retrieve striking tumor suppression. C_LI

cancer biology↗

bioRxiv2025

Dietary cysteine enhances intestinal stemness via CD8+ T cell-derived IL-22

A critical question in physiology is understanding how tissues adapt and alter their cellular composition in response to dietary cues. The mammalian small intestine, a vital digestive organ that absorbs nutrients, is maintained by rapidly renewing Lgr5+ intestinal stem cells (ISCs) at the intestinal crypt base. While Lgr5+ ISCs drive intestinal adaptation by altering self-renewal and differentiation divisions in response to diverse diets such as high-fat diets and fasting regimens, little is known about how micronutrients, particularly amino acids, instruct Lgr5+ ISC fate decisions to control intestinal homeostasis and repair after injury. Here, we demonstrate that cysteine, an essential amino acid, enhances the ability of Lgr5+ ISCs to repair intestinal injury. Mechanistically, the effects of cysteine on ISC-driven repair are mediated by elevated IL-22 from intraepithelial CD8{beta}+ T cells. These findings highlight how coupled cysteine metabolism between ISCs and CD8+ T cells augments intestinal stemness, providing a dietary approach that exploits ISC and immune cell crosstalk for ameliorating intestinal damage.

cell biology↗

bioRxiv2025

Accurate Somatic SV detection via sequence graph model-based local pan-genome optimization

Somatic structural variations (SVs) are critical genomic alterations in cancer genomes. Long-read sequencing (LRS) is theoretically optimal for detecting somatic SVs. However, influenced by reads-to-reference alignment errors, particularly in low-complexity or highly repetitive genomic intervals, current LRS-based somatic SV callers fail to accurately detect SVs. Moreover, the lack of comprehensive ground-truth datasets hinders accurate evaluation. Here, we introduce SVscope, a novel algorithm that fundamentally addresses these challenges by leveraging full-length sequence information from span-reads and integrating local graph-genome optimization with a random forest strategy. SVscope outperforms state-of-the-art methods on six paired long-read whole-genome sequencing (WGS) benchmark cell lines, achieving a maximum F1-score improvement of 16.7%. In simulated datasets, SVscope demonstrates superior performance in both somatic SV detection and read phasing tasks. Based on the findings from SVscope, we validated 47 somatic SVs, thereby significantly expanding the existing experimentally validated ground-truth somatic SV dataset by 69.1%.

bioinformatics↗

bioRxiv2025

In situ generated vaccine-like pyroptosome for personalized cancer immunotherapy

The efficacy of in situ cancer vaccination has been hampered by poor spatiotemporal orchestration of multiple key steps of cancer-immunity cycle in most tumours and systemic toxicity related to therapeutic strategies. Here, we report a systemic injectable and pyroptosis-enabled nanoadjuvant (SPEN) that precisely evokes the secretion of vaccine-like pyroptosome in tumour area for eliciting robust anti-tumour immunity. SPEN induces vigorous immunogenic pyroptosis, triggering the efficient release of tumour antigen-rich pyroptosomes, DAMPs, and proinflammatory cytokines. Upon the activatable release of a TLR7/8 agonist into pyroptosome, the generated pyroptosome functions as in situ cancer vaccine for cooperatively activating the cancer-immunity cycle while avoiding systemic toxicity. This in situ vaccine boosts both innate and adaptive immune response, facilitating the eradication of primary tumour and long-lasting cancer prevention. Our findings provide new insights into the rational design of pyroptosis-inducing nanomedicines for boosting the cancer-immunity cycle, thus advancing personalized cancer immunotherapy.

cancer biology↗

bioRxiv2025

Mutations in TAC1B drive CDR1 and MDR1 expression and azole resistance in C. auris

ObjectiveCandida auris has emerged as a fungal pathogen of particular concern owing in part to its propensity to exhibit antifungal resistance, especially to the commonly prescribed antifungal fluconazole. In this work we aimed to determine how mutations in the transcription factor gene TAC1B, which are common among resistant isolates and confer fluconazole resistance, exert this effect. MethodsSelected TAC1B mutations from clinical isolates were introduced into a susceptible isolate and reverted to the wild-type sequence in select clinical isolates using CRISPR Cas9 gene editing. Disruption mutants were likewise generated for select genes of interest. TAC1B mutants were subjected to transcriptional profiling by RNA-seq, and relative expression of specific genes of interest was determined by qRT-PCR. Antifungal susceptibilities were determined by modified CLSI broth microdilution. ResultsTAC1B mutations leading to A640V, A657V, and F862_N866del conferred fluconazole resistance, as well as increased resistance to other triazoles, when introduced into a susceptible isolate. RNA-seq revealed that the ATP-Binding Cassette (ABC) transporter gene CDR1 as well as the Major Facilitator Superfamily (MFS) transporter gene MDR1 were both upregulated by these TAC1B mutations. Disruption of CDR1 greatly abrogated resistance in strains with TAC1B mutations whereas disruption of MDR1 had little to no effect. However, disruption of both CDR1 and MDR1 resulted in an additional reduction in resistance as compared to disruption of either gene alone. ConclusionTAC1B mutations leading to A640V, A657V, and F862_N866del all result in increased resistance to fluconazole and other triazole antifungals, and increased expression of both CDR1 and MDR1 in C. auris. CDR1 is the primary driver of resistance conferred by these TAC1B mutations.

microbiology↗

bioRxiv2025

DAZAP2 functions as a pan-coronavirus restriction factor by inhibiting viral entry and genomic replication

The SARS-CoV-2 pandemic and the emergence of novel variants underscore the need to understand host-virus interactions and identify host factors that restrict viral infection. Here, we perform a genome-wide CRISPR knockout screen to identify host restriction factors for SARS-CoV-2, revealing DAZAP2 as a potent antiviral gene. DAZAP2, previously implicated in SARS-CoV-2 restriction, is found to inhibit viral entry by blocking virion fusion with both endolysosomal and plasma membranes. Additionally, DAZAP2 suppresses genomic RNA replication without affecting the primary translation of viral replicases. We demonstrate that DAZAP2 functions as a pan-coronavirus restriction factor across four genera of coronaviruses. Importantly, knockout of DAZAP2 enhances SARS-CoV-2 infection in mouse models and in human primary airway epithelial cells, confirming its physiological relevance. Mechanistically, antiviral activity of DAZAP2 appears to be indirect, potentially through the regulation of host gene expression, as it primarily localizes to the nucleus. Our findings provide new insights into the host defense system against coronaviruses and highlight DAZAP2 as a potential target for host-directed antiviral therapies. IMPORTANCEDuring viral infection, the host defense response is mediated by a variety of host factors through distinct mechanisms that have yet to be fully elucidated. Although DAZAP2 was previously implicated in SARS-CoV-2 restriction, its mechanisms of action and in vivo relevance remain unclear. In this study, we identify the DAZAP2 as a potent pan-coronavirus restriction factor that inhibits viral infection through dual mechanisms: blocking virion fusion with both endolysosomal and plasma membranes, and suppressing genomic RNA replication. We confirm its physiological relevance in host defense using mouse models and primary cell cultures. This study advances our understanding of host-pathogen interactions. Targeting DAZAP2 or its regulatory pathways could provide a new approach to enhance host defense against current and future coronavirus threats.

microbiology↗

bioRxiv2025

PET imaging of an antisense oligonucleotide in the living non-human primate brain using click chemistry

Determination of a drugs biodistribution is critical to ensure it reaches the target tissue of interest. This is particularly challenging in the brain where invasive sampling methods may not be possible. Here, a pretargeted imaging methodology is disclosed that utilizes bioorthogonal click chemistry to determine the distribution of an antisense oligonucleotide in the living brain following intrathecal dosing. A novel PET tracer, [18F]BIO-687, bearing a click-reactive trans-cyclooctene (TCO) was discovered and tested in conjunction with a Malat1 antisense oligonucleotide (ASO) conjugated with a methyltetrazine (MeTz). PET imaging in rats demonstrated that the tracer possesses good kinetic properties for CNS imaging and can react to form a covalent linkage with high specificity to the MeTz-conjugated-ASO in vivo. Further, the amount of tracer reacted by cycloaddition with the Tz was determined to be dependent on the concentration of ASO-MeTz in tissue, as determined through comparison of the imaging signal with the LC-MS of the tissue homogenate. The system was evaluated in cynomolgus monkeys, with PET imaging showing favorable tracer kinetics and specific binding to the ASO in vivo. These results demonstrate that the tracer [18F]BIO-687 can image intrathecally-delivered ASO distribution in the brain, and future studies should leverage this technology to evaluate ASO distribution in human subjects to study distribution. One Sentence SummaryDistribution of an intrathecally administered antisense oligonucleotide can be imaged using a pretargeted approach in the living brains of non-human primates.

neuroscience↗

bioRxiv2025

In silico classification and identification co-purified protein complexes yield new structures and multiple MSP assembly states

Native protein complexes have garnered interest as targets for structural dissemination. Cryogenic electron microscopy (cryoEM) with its ability to image protein mixtures is the most promising tool to enable structural proteomics. Additionally, image processing has evolved to deal with conformational and compositional heterogeneity. Integrative approaches, namely mass spectrometry in conjunction with cryoEM have made it possible to characterize and identify complex mixtures. However, this comes at a cost of generating models and interpreting mass spectra. Here we present a modified approach that only requires electron micrographs and a computer for unsupervised model building and protein identification. We were able to identify co-purified membrane proteins, resulting in a novel structure and unexpected nanodisc assemblies, which imply direct interaction between membrane proteins and membrane scaffolding proteins.

biochemistry↗

bioRxiv2025

Improving American chestnut resistance to two invasive pathogens through genome-enabled breeding

Over a century after two introduced pathogens decimated American chestnut populations, breeding programs continue to incorporate resistance from Chinese chestnut to recover self-sustaining populations. Due to complex genetics of chestnut blight resistance, it is challenging to obtain trees with sufficient resistance and competitive growth. We developed high quality reference genomes for Chinese and American chestnut and leveraged large disease phenotype and genotype datasets to develop accurate genomic selection. Inoculation and simulation results indicate that resistance may be substantially increased in trees that inherited 70% to 100% of their genome from American chestnut. To facilitate gene editing, we integrated multiple lines of evidence to discover candidate alleles for blight resistance and susceptibility. These genomic resources provide a strong foundation to accelerate restoration of this iconic tree.

genomics↗

bioRxiv2025

Gut-Brain Hydraulics: Brain motion and CSF circulation is driven by mechanical coupling with the abdomen

The brain moves within the skull, but the drivers and function of this motion are not understood. We visualized brain motion relative to the skull in awake head-fixed mice using high-speed, multi-plane two-photon microscopy. Brain motion was primarily rostrally and laterally directed, and was tightly correlated with locomotion, but not with respiration or the cardiac cycle. Electromyography recordings in abdominal muscles and microCT reconstructions of the trunk and spinal vasculature showed that brain motion was driven by abdominal muscle contractions that activate a hydraulic-like vascular connection between the nervous system and the abdominal cavity. Externally-applied abdominal pressure generated brain motion similar to those seen during abdominal muscle contractions. Simulations showed that brain motion drives substantial volumes of interstitial fluid through and out of the brain (at volumetric rates several times higher than production) into the subarachnoid space, in the opposite direction of fluid flow seen during sleep. The brain is hydraulically linked to the abdominal compartment, and fluid flow in the brain is coupled to body movements, providing a mechanism by which the mechanics of the viscera directly impact brain health.

neuroscience↗

bioRxiv2025

SpaTM: Topic Models for Inferring Spatially Informed Transcriptional Programs

BackgroundSpatial transcriptomics has revolutionized our ability to characterize tissues and diseases by contextualizing gene expression with spatial organization. Current spatial transcriptomics pipelines require researchers to use a variety of models and tools to explore spatial domains. However, few methods provide researchers with a way to jointly analyze spatial data from both annotation-free and annotation-guided perspectives using consistent inductive biases and levels of interpretability. A single framework with consistent inductive biases ensures coherence and transferability across tasks, reducing the risks of conflicting assumptions. ResultsWe propose the Spatial Topic Model (SpaTM), a topic-modelling framework capable of annotation-guided and annotation-free analysis of spatial transcriptomics data. SpaTM can be used to learn gene programs that represent histology-based annotations while providing researchers with the ability to infer spatial domains with an annotation-free approach if manual annotations are limited or noisy. Our benchmarking experiments reveal SpaTMs competitiveness at spatial label prediction and clustering when compared to state-of-the-art methods. We also demonstrate SpaTMs interpretability with its use of topic mixtures to represent cell states and transcriptional programs in dorsolateral prefrontal cortex and ductal carcinoma samples and how its intuitive framework facilitates the integration of annotation-guided and annotation-free analyses of spatial data with downstream analyses. Finally, we demonstrate how SpaTM can be used to extend the analysis of large-scale snRNA-seq atlases with the inference of cell proximity and spatial annotations in human brains with Major Depressive Disorder. ConclusionsSpaTM provides researchers with a unified analysis framework for spatial transcriptomics data. By enabling competitive performance in a variety of tasks, SpaTM helps researchers undertake biologically-driven analyses through the identification of interpretable and biologically informed gene programs.

bioinformatics↗

bioRxiv2025

Avoidance of fratricide and improved efficacy of CD33-MSLN CAR-iNK cells in treating acute myeloid leukemia

Acute myeloid leukemia (AML) patients are often older, which brings challenges of endurance and persistent efficacy of autologous CAR-T cell therapies. Allogenic CAR-NK cell therapies may offer reduced toxicities and enhanced anti-leukemic potential against AML. In this study, we designed a novel CD33-mesothelin loop CAR (Loop CAR) and evaluated its anti-tumor efficacy in human umbilical cord blood-derived NK (UCB-NK) cells and human pluripotent stem cell-derived NK (hPSC-iNK) cells. The Loop CAR exhibited superior cytotoxicity against dual-antigen-positive tumor cell lines and primary AML cells. To further avoid fratricide caused by endogenous CD33 expression in NK cells, we established a hPSC-derived cell line via knockout of CD33 gene (CD33KO) and engineered Loop CAR. Rather than enforced expression of exogenous CD16, we generated abundant mature CD33KO-Loop CAR-iNK cells highly expressing endogenous CD16 via an organoid induction approach. This innovative strategy effectively mitigated NK cell fratricide and significantly enhanced CD33 and mesothelin-mediated specific cytotoxicity. Moreover, the CD33KO-Loop CAR-iNK cells demonstrated superior tumor-killing activity in AML xenograft mice and significantly prolonged survival. hPSC-derived CD33KO-Loop CAR-iNK cells possess unique advantages and translational potential for treating AML.

cancer biology↗

bioRxiv2025

Wearable Photonic Device for Multiple Biomarker Sampling and Detection Without Blood Draws

Blood draws or phlebotomy using needles have been practiced in clinics for several centuries and it often causes pain, discomfort, and inconvenience. Herein, we create a wearable photonic device by integrating a microlens array (MLA) and an optic microneedle array (OMNA) functionalized with immunobinding capacity for safe and needle-free biomarker sampling and detection. The MLA-integrated OMNA amplified and transmitted LED light at 595 nm into the skin through the OMNA, bypassing the light-absorbing melanin in the epidermal layer, and evenly distributing it in the capillary-enriched dermis. The 595 nm light was preferably absorbed by hemoglobin (Hb) and oxygen-Hb within the capillaries, triggering thermal dilation of capillaries without damaging them or causing petechiae. The light illumination resulted in remarkable increases in the concentrations of various blood biomarkers in the skin owing to capillary dilation and biomarker extravasation. These extravasated biomarkers bound specifically to the OMNA, which was covalently decorated with capture antibodies, each microneedle immobilized with one specific antibody. The multi-functional OMNA was extensively modified to amplify the immunobinding signals and achieve sensitivity superior to that of enzyme-linked immunosorbent assay (ELISA) kits. As a proof of concept, we validated the functionality of the prototype for minimally invasive sampling and precise multiplexed blood biomarker detection in two mouse models to quantify acute inflammation and specific antibody production. This cost-efficient device provides a promising platform for blood-free, multiplexed detection of blood biomarkers.

bioengineering↗

bioRxiv2025

Unsupervised multi-animal tracking for quantitative ethology

Quantitative ethology necessitates accurate tracking of animal locomotion, especially for population-level analyses involving multiple individuals. However, current methods rely on laborious annotations for supervised training and have restricted performance in challenging conditions. Here we present an unsupervised deep-learning method for multi-animal tracking (UDMT) that achieves state-of-the-art performance without requiring human annotations. By synergizing a bidirectional closed-loop tracking strategy, a spatiotemporal transformer network, and three sophisticatedly designed modules for localization refining, bidirectional ID correction, and automatic parameter tuning, UDMT can track multiple animals accurately in various challenging conditions, such as crowding, occlusion, rapid motion, low contrast, and cross-species experiments. We demonstrate the versatility of UDMT on five different kinds of model animals, including mice, rats, Drosophila, C. elegans, and Betta splendens. Combined with a head-mounted miniaturized microscope, we illustrate the power of UDMT for neuroethological interrogations to decipher the correlations between animal locomotion and neural activity. UDMT will facilitate advancements in ethology by providing a high-performance, annotation-free, and accessible tool for multi-animal tracking.

animal behavior and cognition↗

bioRxiv2025

Type-I nNOS neurons orchestrate cortical neural activity and vasomotion

It is unknown how the brain orchestrates coordination of global neural and vascular dynamics. We sought to uncover the role of a sparse but unusual population of genetically distinct interneurons known as type-I nNOS neurons, using a novel pharmacological strategic to unilaterally ablate these neurons from the somatosensory cortex of mice. Region-specific ablation produced changes in both neural activity and vascular dynamics, decreased power in the delta-band of the local field potential, reduced sustained vascular responses to prolonged sensory stimulation, and abolished the post-stimulus undershoot in cerebral blood volume. Coherence between the left and right somatosensory cortex gamma-band power envelope and blood volume at ultra-low frequencies was decreased, suggesting type-1 nNOS neurons integrate long-range coordination of brain signals. Lastly, we observed decreases in the amplitude of resting-state blood volume oscillations and decreased vasomotion following the ablation of type-I nNOS neurons. This demonstrates that a small population of nNOS-positive neurons are indispensable for regulating both neural and vascular dynamics in the whole brain, raising the possibility that loss of these neurons could contribute to the development of neurodegenerative diseases and sleep disturbances.

neuroscience↗