Biology subjects

Liu, Q.

Publications and source records attributed to Liu, Q..

At least 163 records · Page 9Linked to original sources

bioRxiv2025

Splicing of HPV16 E6 promotes aggressive invasion in oropharyngeal cancer via endocytosis of E-cadherin

Human papillomavirus-positive oropharyngeal squamous cell carcinoma (HPV+ OPSCC) has become the most common HPV-associated cancer in developed countries, yet a significant subset of patients develops recurrence despite favorable treatment responses. Biomarkers that identify aggressive tumors at diagnosis are therefore needed. In HPV+ cancers, the viral E6 transcript can be expressed as two main variants, the full-length isoform (E6FL) and the spliced E6*I isoform. Here, we investigated the functional and clinical impact of E6FL and E6*I in HPV+OPSCC. Across multiple preclinical models, E6*I promoted migration and aggressive invasion relative to E6FL and was associated with redistribution of E-cadherin away from the cell membrane. In multi-institutional patient cohorts, a previously developed E6FL:E6ALL influence score, which captures E6 splicing-associated host transcriptional biology, was associated with clinical outcomes. Lower scores, reflecting greater E6*I impact, were associated with worse overall survival and recurrence-free survival. Multiplexed immunofluorescence of 75 primary pretreatment biopsies further showed that a lower influence score was linked to reduced membrane and increased cytoplasmic localization of E-cadherin, while a tissue-based E-cadherin localization score was associated with recurrence. Mechanistically, E6*I overexpression promotes E-cadherin internalization, likely through the Rab11-associated trafficking pathway. Splice-switching oligonucleotides that shifted endogenous E6 splicing toward E6FL reduced invasion in two HPV+ OPSCC models. Together, these findings position HPV E6 splicing as a regulatory axis underlying aggressive HPV+ OPSCC biology and support E6 splicing and membrane-to-cytoplasmic ECAD localization as candidate risk-stratification biomarkers.

cancer biology↗

bioRxiv2025

Alzheimer's disease risk factor APOE4 exerts dimorphic effects on female bone

Individuals diagnosed with Alzheimers disease (AD) are at an increased risk of bone fractures. Conversely, a diagnosis of osteoporosis in women is the earliest known predictor for AD. However, mechanisms responsible for the coupled decline in cognitive and skeletal health remain unclear. Proteomic analysis of cortical bone from aged mice revealed neurological disease-associated proteins that are highly enriched in aged mouse bones, including apolipoprotein E (Apoe) and amyloid precursor protein. Further, Apoe localized specifically to bone-embedded osteocytes with expression twice as high in aged female bone as in young or male counterparts. In humans, APOE allele variants carry differing AD risk with age. To investigate APOE allelic roles in bone, we utilized a humanized APOE knock-in mouse model that expresses either the protective APOE2, the neutral APOE3, or the AD risk factor APOE4, and analyzed bone and hippocampus from the same mice. APOE4 exerted strong sex-specific effects on the bone transcriptome and proteome, relative to APOE2 or APOE3. Interestingly, the APOE4-associated perturbation in the female bone proteome was more pronounced than the corresponding alterations observed in the hippocampus. APOE4 protein causes bone fragility in females, but not males, even without changes in cortical bone structure. These bone quality deficits arose from suppression of osteocyte perilacunocanalicular remodeling. We find that APOE4 is a new molecular culprit capable of disrupting osteocyte maintenance of bone quality as early as midlife in a manner that disproportionately affects females. These findings highlight osteocytes as potential targets for early diagnosis of age-related cognitive impairment, and treatment for bone fragility, in females.

molecular biology↗

bioRxiv2025

A correlative quantitative phase contrast and fluorescence super-resolution microscope for imaging molecules in their cellular context

Fluorescence microscopy has been widely used to reveal the spatial distribution of specifically labeled molecules, but it is blind to cellular context. Quantitative phase contrast microscopy (QPC) provides such complementary information. Here we have developed a platform that combines the QPC technique of correlative orientation-independent differential interference contrast (OI-DIC) microscopy with single-molecule super-resolution fluorescence microscopy. We demonstrate a detection sensitivity of 0.05 nm optical path difference, sufficient to detect single microtubules, and show its capability of 3D super-resolution fluorescence imaging in the cellular context. Additionally, we report deep-learning enabled digital staining, identifying nuclei, mitochondria and lipid droplets from OI-DIC data and demonstrate the potential of this approach for long-term live-cell imaging of organelles of interest without the need for fluorescence. OI-DIC can be easily integrated into most fluorescence microscopes and is readily adoptable by microscopy labs. ONE-SENTENCE TEASERA highly sensitive technique to visualize sub-cellular structures, dynamics, and molecules in their cellular context.

cell biology↗

bioRxiv2025

Distinct contributions of anterior and posterior orbitofrontal cortex to outcome-guided behavior

The lateral orbitofrontal cortex (OFC) is critical for flexibly adjusting choices when outcome values change. Anterior and posterior parts of the human lateral OFC differ in cytoarchitecture and connectivity, but whether these subregions make differential contributions to outcome-guided (i.e., goal-directed) behavior remains unclear. Outcome-guided behavior requires (a) representations of stimulus-outcome associations and (b) inferring the current value of options when making decisions. Here, we test whether these two functions are differentially supported by the posterior (pOFC) and anterior (aOFC) parts of the lateral OFC, using transcranial magnetic stimulation (TMS) to selectively disrupt activity in functional networks centered on the pOFC and aOFC during a two-day outcome devaluation task. Participants (n = 48) received pOFC or aOFC network-targeted TMS either on day 1 before learning associations between visual stimuli and sweet or savory food odors, or on day 2 before a meal that selectively devalued one of these outcomes, followed by a choice test. TMS targeting pOFC, but not aOFC, before the meal on day 2 disrupted outcome-guided behavior, as measured by choices of stimuli predicting non-sated rewards in the post-meal choice test. In contrast, TMS targeting aOFC, but not pOFC, before learning on day 1 similarly impaired behavior in the post-meal choice test on day 2. These findings demonstrate that anterior and posterior parts of the lateral OFC make distinct contributions to outcome-guided behavior by supporting learning of stimulus-outcome associations and inferring the current value of options, respectively.

neuroscience↗

bioRxiv2025

Base-editing a single missense mutation in A20 enhances CAR-T cell efficacy

T cell exhaustion limits the efficacy of cancer immunotherapies. Here, we performed genome-wide loss-of-function screening in repetitively stimulated human T cells and identified the mulitfunctional ubiquitin-modifying protein A20/TNFAIP3 as a major negative regulator of exhausted T cell persistence. Protein large language modeling, deep base-editing mutagenesis, and studies in immunocompetent mice with domain-specific inactivating mutations revealed A20s non-enzymatic M1 ubiquitin-binding zinc finger 7 (A20ZF7) motif as critical to suppression of anti-tumor immunity. A20ZF7-deficient CD8+ tumor-infiltrating lymphocytes (TILs) resisted terminal exhaustion and circumvented an unappreciated mechanism restraining perforin degranulation in terminally exhausted cells. Human chimeric antigen receptor (CAR)-T cells engineered via base-editing to inactivate A20ZF7 via a single missense mutation also resisted exhaustion, secreted more perforin and robustly suppressed cancer in vivo. These studies pinpoint A20ZF7 as a novel T cell checkpoint and reveal precision base-editing of missense mutations as an effective approach to enhance CAR-T cell therapy.

immunology↗

bioRxiv2025

In vivo genome-wide CRISPR screens in human T cells to enhance T cell therapy for solid tumors

Large-scale CRISPR screening in human T cells holds significant promise for identifying genetic modifications that can enhance cellular immunotherapy. However, many genetic regulators of T cell performance in solid tumors may not be readily revealed in vitro. In vivo screening in tumor-bearing mice offers greater physiological relevance, but has historically been limited by low intratumoral T cell recovery. Here, we developed a new model system that achieves significantly higher human T cell recovery from tumors, enabling genome-wide in vivo screens with small numbers of mice. Tumor-infiltrating T cells in this model exhibit hallmarks of dysfunction compared to matched splenic T cells, creating an ideal context for screening for genetic modifiers of T cell activity in the tumor microenvironment. Using this platform, we performed two genome-wide CRISPR knockout screens to identify genes regulating T cell intratumoral abundance and effector function (e.g., IFN-{gamma} production). The intratumoral abundance screen uncovered the P2RY8-G13 GPCR signaling pathway as a negative regulator of human T cell infiltration into tumors. The effector function screen identified GNAS (Gs), a central signaling mediator downstream of multiple GPCRs that sense different suppressive ligands, as a key regulator of T cell dysfunction in tumors. Targeted GNAS knockout rendered T cells resistant to multiple suppressive cues and significantly improved therapeutic performance across diverse solid tumor models. Moreover, combinatorial knockout of P2RY8 (trafficking) and GNAS (effector function) further enhanced overall tumor control, demonstrating that genetic modifications targeting distinct T cell phenotypes can be combined to improve therapeutic potency. This flexible and scalable in vivo screening platform can be adapted to diverse tumor models and pooled CRISPR libraries, enabling future discovery of genetic strategies that equip T cell therapies to overcome barriers imposed by solid tumors.

immunology↗

bioRxiv2025

Structure-Guided Development of a Potent BioA Inhibitor ValidatesBiotin Synthesis Inhibition as a Therapeutic Strategy forTuberculosis

Conditionally essential pathways - such as the biotin biosynthesis - represent promising targets for new antibiotics. However, the chemical interrogation of the biotin pathway with an orally effective lead remains elusive, and the preclinical development of biotin inhibitors for mycobacterial infections in vivo is challenging due to the unusually high concentration of biotin in standard mouse models. Structure-guided optimization was applied to develop the first oral lead targeting aminotransferase BioA, a key enzyme in bacterial biotin biosynthesis, resulting in C48, a picomolar inhibitor displaying sub-micromolar MICs against Mycobacterium tuberculosis (Mtb). Mechanism of action was confirmed by biochemical, structural, and genetic studies. C48 demonstrated favorable pharmacokinetics and excellent oral bioavailability resulting in over 39,000-fold improved exposure. We next developed an easy-to-operate, low-biotin mouse model that recapitulates human biotin physiology. C48 significantly reduced Mtb burden in this low-biotin mouse model, providing the first in vivo proof-of-concept for targeting biotin biosynthesis in Mtb.

microbiology↗

bioRxiv2025

The structures of tetrameric Avian Immunoglobulin A are uniquely structured to support mucosal immunity

Birds and mammals assemble polymeric (p) forms of immunoglobulin (Ig) A, which are transported to mucosal surfaces and released as secretory (S) IgA, the predominant mucosal antibody. Mammalian SIgA, which is typically dimeric, is well characterized; however, avian IgA structure-function relationships and how they compare to those in mammals remains unclear. Here we report the cryo-electron microscopy structures of mallard duck pIgA and SIgA at 3.76-[A] and 3.21-[A] resolution, respectively. Both structures revealed four IgA monomers linked through one joining chain (JC) and adopted a non-planar conformation; a heavy chain domain absent in mammals, extended the tetramers non-planar geometry toward antigen binding sites. The SIgA structure revealed four secretory component (SC) domains binding IgA and JC analogous to four of the five mammalian SC domains; however, SC and JC N-terminal extensions, absent in mammals, mediated additional interfaces between complex components. Experiments comparing mammalian and avian SC binding to cognate and non-cognate IgA ligands demonstrated that species-specific structural differences correlated with differences in SC binding and that adding an N-terminal extension to mammalian SC enhanced binding to avian pIgA. Together, results and comparison to published structures indicate that avian IgA components co-evolved unique elements compared to mammalian IgA, including a predominantly tetrameric state, and suggest that birds may employ different IgA effector mechanisms to combat mucosal pathogens compared to mammals. These findings are broadly relevant to understanding IgA evolution and function and combating zoonotic disease such as avian influenza A virus. One Sentence SummaryCryo-electron microscopy structures together with biochemical experiments demonstrate similarities and differences between mammalian and avian secretory immunoglobulin A relevant to understanding differences in immune response to common pathogens such as influenza virus.

immunology↗

bioRxiv2025

E2F3 amplification primes bladder cancer cells for premature mitosis.

The E2F-RB pathway controls the G1/S checkpoint, and tumors often bypass it through RB1 or CDKN2A loss. Unlike these lesions, E2F3 amplification drives persistent excessive E2F-dependent transcription through S and G2 phases. This oncogene is frequently amplified in for example bladder cancer, but its impact on the cancer cell cycle remains unclear. Using isogenic bladder cancer models and patient data, we show that E2F3 amplification hyperactivates a mitotic gene expression program, including cyclin B1. This predisposes cells to unscheduled mitosis when the G2/M checkpoint is inhibited using the PKMYT1 inhibitor lunresertib, alone or in combination with low dosages of the WEE1 inhibitor zederosertib. E2F3-amplified cells acquired resistance to lunresertib by permanently reducing cyclin B1 expression, thereby preventing premature mitotic entry. Importantly, this resistance was reversed by co-treatment with a low dose of WEE1 inhibitor. These findings identify PKMYT1-dependent CDK1 inhibition as a critical safeguard against premature mitosis in E2F3-amplified bladder cancer. Thus, we uncover an opportunity for precision medicine strategies aimed at G2/M checkpoint inhibition to promote catastrophic mitosis in bladder cancer patients with E2F3 amplification and excessive cyclin B1 expression.

cancer biology↗

bioRxiv2025

Decoding Spine Nanostructure in Mental Disorders Reveals a Schizophrenia-Linked Role for Ecrg4

Dendritic spine dysfunction may contribute to the etiology and symptom expression of neuropsychiatric disorders. The intimate relationship between spine morphology and function suggests that decoding disease-related abnormalities from spine morphology can aid in developing synapse-targeted interventions. Here, we describe a population analysis of dendritic spine nanostructure applied to the objective grouping of multiple mouse models of neuropsychiatric disorders. This method has identified two major groups of spine phenotypes linked to schizophrenia and autism spectrum disorder (ASD). An increase in spine subpopulation with small volumes characterized the spines of schizophrenia-associated mouse models, whereas a spine subset with large volumes increased in ASD models. Schizophrenia-associated mouse models showed higher similarity in spine morphology, driven by reduced size and growth of nascent spines. The expression of Ecrg4, a gene encoding small secretory peptides, was increased in schizophrenia-associated mouse models, and functional studies confirmed its critical involvement in impaired spine dynamics and shape. These results suggest that population-level spine analysis provides rich insights into heterogeneous spine pathology, facilitating the identification of new molecular targets related to core synaptic dysfunction.

neuroscience↗

bioRxiv2025

stk32a links sleep homeostasis to suppression of sensory and motor systems

Sleep is regulated by a homeostatic process and associated with an increased arousal threshold, but the genetic and neuronal mechanisms that implement these essential features of sleep remain poorly understood. To address these fundamental questions, we performed a zebrafish genetic screen informed by human genome-wide association studies. We found that mutation of serine/threonine kinase 32a (stk32a) results in increased sleep and impaired sleep homeostasis in both zebrafish and mice, and that stk32a acts downstream of neurotensin signaling and the serotonergic raphe in zebrafish. stk32a mutation reduces phosphorylation of neurofilament proteins, which are co-expressed with stk32a in neurons that regulate motor activity and in lateral line hair cells that detect environmental stimuli, and ablating these cells phenocopies stk32a mutation. Neurotensin signaling inhibits specific sensory and motor populations, and blocks stimulus-evoked responses of neurons that relay sensory information from hair cells to the brain. Our work thus shows that stk32a is an evolutionarily conserved sleep regulator that links neuropeptidergic and neuromodulatory systems to homeostatic sleep drive and changes in arousal threshold, which are implemented through suppression of specific sensory and motor systems.

neuroscience↗

bioRxiv2025

GSDME unlocks astrocyte-driven neurotoxicity in Alzheimer's Disease

Astrocytic calcium dysregulation and reactivity precede A{beta} deposition in amyloid-{beta} deposition in Alzheimers disease (AD) but the neurotoxic mechanisms remain unclear. We show that GSDME acts as a switch, linking MAM-mediated calcium release to astrocyte-driven neurotoxicity. Specifically, A{beta}-activated microglial signals activate astrocytic GSDME, releasing its N-terminal fragment, which targets MAMs and triggers ER calcium efflux. This induces biphasic CaMKII phosphorylation, initially boosting NRF2 defenses, then activating NF-{kappa}B-driven inflammation, shifting astrocytes from protective to toxic states. GSDME activation also drives astrocyte-derived exosomes (ADEs) to carry neurotoxic tau, proinflammatory miRNAs, and toxic lipids, propagating toxicity. GSDME deletion in AD mice reduces A{beta} burden, restores NF-{kappa}B/NRF2 balance, reprograms astrocytes and ADEs to protective states, and rescues cognition. Multi-omics profiling of serum ADEs from AD patients reveals a disease-specific signature with central neurotoxicity and peripheral immune regulation. These findings position GSDME as a promising dual diagnostic and therapeutic target for early AD invention.

neuroscience↗

bioRxiv2025

An RNA polymerase III tissue and tumor atlas uncovers context-specific activities linked to 3D epigenome regulatory mechanisms

RNA polymerase III (Pol III) produces a plethora of small noncoding RNA species involved in diverse cellular processes, from transcription regulation and splicing to RNA stability, translation, and proteostasis. Though Pol III activity is broadly coupled with cellular demands for protein synthesis and growth, a more precise understanding of gene-level dynamics and context-specific expression patterns remains missing, in part due to challenges related to sequencing and mapping Pol III-derived small ncRNAs. Here, we establish a predictive multi-tissue map of human Pol III activity across 19 tissues and 23 primary cancer subtypes by comprehensively profiling the chromatin accessibility of canonical Pol III-transcribed gene classes. Our framework relies on the unique relationship between gene accessibility and Pol III transcription, inferring activity through uniform binary classification of ATAC-seq enrichment at Pol III-transcribed genes. By characterizing multi-context gene uniformity, we provide a definition of the core Pol III transcriptome, broadly active across specialized tissues, and catalog genes with varied levels of context specificity. Our genomic Pol III atlas uncovers variable levels of activity across tissues, including sharp contraction of the Pol III transcriptome in heart and brain tissues and frequent expansion across diverse cancers. We show that both tissue- and tumor-specific genes are significantly enriched within lamina-associated domains (LADs), and that aberrant expression of nuclear lamin proteins is sufficient to induce Pol III-emergent patterns at tumor-specific genes. Together, these findings link Pol III dynamics to subnuclear compartmentalization and provide a resource for better understanding Pol III expansion and small RNA biogenesis in cancer.

genomics↗

bioRxiv2025

High-throughput 3D super-resolution ultrasound imaging

Capturing fast hemodynamics in deep organs is essential for understanding microvascular regulation of organ responses to physiological demands and pathological stress. However, non-invasive three-dimensional (3D) imaging of these microscale processes remains challenging due to trade-offs between spatial resolution, imaging speed, and penetration depth. Here, we present fluctuation-based high-order super-resolution acoustic microscope (FLAME), a tracking-free 3D ultrasound imaging technology capable of fast microvascular angiography and flow measurement. Using as few as 30 volumes, FLAME improves 3D ultrasound resolution by 8-fold ([~]50 m) and shortens data acquisition time by over two orders of magnitude, from tens of seconds to tens of milliseconds, compared with conventional tracking-based super-resolution approaches1-6. This high-throughput capability supports high-fidelity imaging of tissue functions under flexible experimental settings. FLAME achieves an unprecedented 3D super-resolution frame rate of [~]40 Hz, capturing transient hemodynamic responses to various physiological and pathological stimuli in different mouse organs, from the microvascular level to the whole-body scale. With open-sourced implementation, FLAME provides an accessible platform for real-time, in-depth hemodynamic monitoring across diverse biomedical applications and clinical translation.

bioengineering↗

bioRxiv2025

Conserved Heterochromatin-like Structures with Local Regulators Mediate the Iron Stress Response in Mycobacteria

Recent studies have demonstrated the importance of dynamic heterochromatin-like regions in bacterial gene regulation, particularly for adaptation to changing environments. Here, we have measured the dynamic regulatory protein-DNA landscape of the tuberculosis vaccine strain, M. bovis BCG Pasteur, under the pathogenically-relevant condition of iron starvation. Our results capture for the first time the overall protein occupancy landscape of the genome of M. bovis BCG, identifying extended protein occupancy domains likely composed of diverse sets of nucleoid-associated proteins and transcription factors. Importantly, we find chromatin-directed regulation of stress-responsive genes like siderophores. Furthermore, through comparison with the free-living M. smegmatis, we identified a specific class of extended protein occupancy domains that are associated with conserved genomic regions across the two organisms, whereas regions with low protein occupancy often lack conservation. Our findings thus comprehensively reveal the contributions of both local regulators and chromatin structure to gene regulation and evolution in mycobacteria.

microbiology↗

bioRxiv2025

Light-Activated Nucleic Acid Amplification Systems Using Photo-caged DNA Polymerase or Primers

Precise control over nucleic acid amplification is essential for achieving reliable, quantitative, high-throughput, and multiplexed molecular diagnostics, particularly in point-of-care and field settings. However, conventional isothermal amplification methods, especially rapid assays at ambient temperature such as recombinase-aided amplification (RAA), suffer from spontaneous initiation and lack of synchronization across parallel reactions. Here, we report light-activatable RAA systems employing two distinct photocaging strategies to achieve spatiotemporal control. In the first, a photocaged DNA polymerase was engineered via site-specific incorporation of p-azido-L-phenylalanine and conjugation with a 2-nitrobenzyl-modified ssDNA blocker through click chemistry. This approach offers high stability, making it advantageous for long-term storage and lyophilized formats. In the second, 5'-nitrobenzyl-modified primers were synthesized to block hybridization or extension until UV activation, offering operational simplicity and rapid integration into existing workflows. Both strategies independently suppressed background activity in the dark and restored full amplification efficiency upon 365 nm UV exposure. The systems exhibited high sensitivity, low background, and compatibility with portable diagnostics. A custom-built device integrating UV activation and real-time fluorescence detection enabled seamless, on-demand operation. This modular platform provides flexible light-gated amplification solutions, allowing the selection of polymerase- or primer-based caging according to storage stability or workflow requirements, thereby advancing precise and field-ready molecular diagnostics.

molecular biology↗

bioRxiv2025

Target-Stabilized Base Editors Enable Robust High-Fidelity RNA Editing

RNA base editing using engineered deaminases expands target compatibility, offering a powerful tool to correct mutations at the RNA level. However, widespread off-target effects, primarily arising from dissociated free deaminases, remain a significant challenge. Here, we devised the RECODE (RNA editing with conditionally stable and enhanced ADAR1 deaminase variants) system, which employs designer degron-tagged ADAR1 deaminase (ADAR1d) with guide RNA (gRNA)-regulated stability. By promoting degradation of gRNA-unbound ADAR1d, RECODE markedly reduced transcriptome-wide edits while maintaining high on-target efficacy. Engineering gRNA for target RNA-induced conformational switching restricts ADAR1d stabilization, further enhancing editing precision. With structure-guided rational engineering of ADAR1d, RECODE achieved editing efficiencies of 90.3% and 58.8% for an Amyotrophic Lateral Sclerosis-relevant FUS mutation in vitro and in vivo, respectively. These findings establish RECODE as a highly stringent and efficient RNA editing technology and underscore a general principle for enhancing the specificity of RNA-guided protein effectors.

molecular biology↗

bioRxiv2025

Predicting interactions between the SARS-CoV-2 spike glycoprotein and the human proteome using AphaFold and molecular dynamics simulations

AbstractSince the COVID-19 pandemic began, the SARS-CoV-2 virus has caused over 775 million cases and more than 7 million deaths worldwide. Despite progress in treatments and vaccines, we still need better ways to prevent and treat the disease. To do this, a clearer understanding of how SARS-CoV-2 interacts with human proteins is needed. We developed a new computational tool to predict and study these protein-protein interactions. Our method uses two stages of AlphaFold, an AI tool, to predict how SARS-CoV-2 proteins bind to human proteins, followed by molecular dynamics simulation to refine these predictions. We tested this method in a small study focusing on the S1 subunit of the SARS-CoV-2 spike protein interacting with human cell junction and synaptic proteins, and in a larger study screening the spike S1 N- terminal domain against the entire human proteome. We validated the method using experimental virus-human protein interactions. The results provide valuable insights into how SARS-CoV-2 interacts with human proteins, guiding future experiments to better understand COVID-19s short- and long-term effects. This developed method could be utilized to study protein-protein interactions in other biological systems.

biochemistry↗