Biology subjects

Qiu, M.

Publications and source records attributed to Qiu, M..

At least 19 recordsLinked to original sources

bioRxiv2026

An adjuvant for in vivo CAR-T therapy potentiation against solid tumors

In vivo CAR-T therapy offers rapid and controllable T-cell engineering but has yet to achieve durable efficacy against solid tumors. Rather than focusing solely on CAR-T cells, we harness the intact immune system via an in vivo CAR-T adjuvant (iCTA). Composed of aluminum-manganese hydrogel, iCTA can form a spatially confined antigenic and immunostimulatory niche in-situ. By coupling controlled antigen exposure with STING-type I interferon signaling, iCTA not only recruited and reactivated CAR-T cells, but engage the CAR-negative immunocytes with enhanced dendritic-cell antigen presentation and mobilized endogenous antigen-specific T-cell responses. Combined with mRNA-LNP-mediated in vivo CAR-T generation, a single administration of iCTA increased CAR+ T-cell abundance in draining lymph nodes and blood by 2-fold. It also increased T and NK cell infiltration, established an IFNgamma-enriched tumor microenvironment, and reduced exhaustion-associated T-cell states. iCTA improved tumor regression and survival, establishing an adjuvant strategy to enhance in vivo CAR-T therapy.

bioengineering↗

bioRxiv2026

Constructing Virtual Viruses in A Spatial Minimal Cell

Viral development links gene expression and genome replication to particle formation within a cell. Here we construct virtual viruses in a JCVI-syn3A-based spatial minimal cell. For mycoplasma virus P1, molecular events connect expression and replication to coarse-grained packaging, followed by a spatial reconstruction of membrane opening and particle release. Individual finite-size particles coexist, move across the boundary and undergo partial crossings and returns before complete exit. In contrast, Acholeplasma phage MV-L1 (L1) expresses its genes and accumulates genomes as the host continues to grow and develops a constricted shape. The coexistence of viral activity and continued host growth is qualitatively consistent with the non-lytic biology of group 1 acholeplasmaviruses. These reconstructions extend the virtual cell to the viruses that develop within it, linking molecular activity, particle behavior and host growth.

synthetic biology↗

bioRxiv2026

Disordered brain circuits linked to diagnostic specificity and comorbidity revealed by multivariate symptom modeling

Modeling how functional network connectivity underlies transdiagnostic symptomatology has promised to advance psychiatric medicine by revealing neurobiological mechanisms related to comorbidity. However, network mapping methods have yet to yield clinically-actionable insights, largely due to complexities in the neurobiological underpinnings of symptom comorbidity across disorders and symptom heterogeneity within disorders. Here, we sought to address this problem by leveraging a large (n=317) transdiagnostic dataset of adults with extensive fMRI scanning (>50 min), using connectome-based predictive modeling (CPM) to identify network correlates of an array of psychiatric symptoms. The symptom networks spanned a complex web of shared and unique networks, in which individuals displayed significant heterogeneity in their edge-level dysfunction. We then constructed disordered circuit models that jointly accounted for an individuals symptom severity, the multivariate network space, and network heterogeneity. Although all the symptoms were highly comorbid and none showed specificity to any single diagnostic category, many features within the disordered circuit models were uniquely associated with individual diagnoses and comorbidity patters. These findings shed mechanistic insights into how transdiagnostic symptoms arise from different neurobiological processes depending on a patients diagnostic profile. Thus, this approach provides key insights into where an individuals disordered circuits are located, a critical first step in precision psychiatry frameworks.

neuroscience↗

bioRxiv2026

Expression of amyloid-β antibody via AAV of CNS tropism alleviates Alzheimer's disease in mice

Alzheimers disease (AD), the leading cause of dementia, affects over 33 million people worldwide, with pathogenesis tied to amyloid-{beta} (A{beta}) accumulation. Although anti-A{beta} monoclonal antibodies have shown clinical benefits, they often cause side effects including amyloid-related imaging abnormalities and brain microhemorrhage, especially in APOE E4 allele carriers. Here we used PHP.eB serotype adeno-associated virus (AAV), a vector with enhanced central nervous system (CNS) tropism, to deliver an A{beta} antibody expression vector (AAV-LEC) into the CNS of APP/PS1 and 5xFAD mice intravenously. The AAV-LEC-mediated expression of anti-A{beta} antibodies in the CNS significantly reduced the number and size of A{beta} plaques at various stages in both APP/PS1 and 5xFAD mice, alongside improved spatial learning and memory. It also reversed abnormal glial activation with reduced disease-associated microglia and astrocytes, and restored oligodendrocyte differentiation and myelin formation. No brain microhemorrhage or liver damage was detected following the AAV-antibody treatment. Thus, this AAV-mediated strategy offers a promising, convenient and safe AD therapeutic approach in the future.

neuroscience↗

bioRxiv2026

Hypoxia-activated scleraxis a mediates epicardial progenitor differentiation into a unique cardiac perivascular cell type

The epicardium is a crucial source of progenitor cells and paracrine signals that support heart development and regeneration. However, the molecular mechanisms that guide epicardial cell fate decisions remain incompletely understood. Here, we identify the transcription factor Scleraxis a (encoded by scxa) as a key regulator of epicardial progenitor differentiation in zebrafish. Through single-cell transcriptomics, genetic lineage tracing, and cardiac injury models, we show that scxa is transiently induced in activated epicardial progenitor cells (aEPCs) during both heart regeneration and developmental coronary angiogenesis. scxa+ epicardial cells primarily give rise to a previously uncharacterized cardiac population of perivascular cells marked by col18a1a, molecularly distinct from classical pericytes and vascular smooth muscle cells. We refer to this population as epicardial-derived perivascular mesenchymal cells (Epi-PMCs). These Epi-PMCs closely associate with coronary vessels and may contribute to vascular stabilization and remodeling, potentially through the anti-angiogenic but vessel-stabilizing activity of endostatin derived from collagen XVIII. Loss of scxa increases coronary vessel density. Mechanistically, we identify hypoxia and Hif1a signaling as upstream regulators of scxa, with systemic hypoxia or Hif factor stabilization robustly inducing scxa expression in the epicardium. Together, these findings uncover a hypoxia-responsive Scxa-Col18a1a axis that drives epicardial differentiation toward a vascular-supportive fate, offering new insight into the regulation of coronary vessel development and the regenerative potential of the epicardium.

developmental biology↗

bioRxiv2025

RPRM (Reprimo) triggers SCF(FBXW11)-mediated DNA-PKcs degradation to block non-homologous end joining and radiosensitize tumors

Targeting DNA damage repair pathways represents a promising strategy in cancer radiotherapy, however, the limited insight into the regulation of the non-homologous end joining (NHEJ) repair pathway in cancer cells severely restricts the development of precise radiosensitization approaches. Here, we identify Reprimo (RPRM), a p53-inducible tumor suppressor, is a potent inhibitor of NHEJ in which RPRM promotes proteasomal degradation of DNA-dependent protein kinase catalytic subunit (DNA-PKcs) phosphorylated at the T2609 site. Upon irradiation, RPRM quickly translocates into the nucleus to enhance the transcription of FBXW11, a F-box protein gene that encodes the substrate recognition component of SCF (SKP1-CUL1-F-box protein) E3 ubiquitin-protein ligase complex. In the nucleus, RPRM is also able to scaffold the assembly of the SCFFBXW11 E3 ligase complex by binding to both CUL1 and FBXW11. This complex can specifically ubiquitylate phosphorylated DNA-PKcs (T2609), leading to reduced levels of both phosphorylated DNA-PKcs (T2609) and total DNA-PKcs, thereby suppressing NHEJ-driven repair and enhancing tumor radiosensitivity. In consistence, inhibiting the SCFFBXW11 E3 ligase complex eliminates RPRM-mediated radiosensitization by protecting DNA-PKcs. Clinically, high RPRM expression in non-small cell lung cancer (NSCLC) predicts better patient prognosis. Moreover, RPRM expression correlates positively with FBXW11 and PRKDC (DNA-PKcs) in the tumor tissues of the NSCLC patient cohort. Significantly, high expression of RPRM protein is linked to enhanced radiosensitivity of patient-derived organoids (PDOs) from these NSCLC patients. These results establish RPRM as a key negative regulator in NHEJ repair pathway and the RPRM-SCFFBXW11-DNA-PKcs axis as a potential target to enhance cancer radiosensitivity.

cancer biology↗

bioRxiv2025

GatorSC: Multi-Scale Cell and Gene Graphs with Mixture-of-Experts Fusion for Single-Cell Transcriptomics

Single-cell RNA sequencing (scRNA-seq) enables high-resolution characterization of cellular heterogeneity, but its rich, complementary structure across cells and genes remains underexploited, especially in the presence of technical noise and sparsity. Effectively leveraging this multi-scale structure is essentially an information fusion problem that requires integrating heterogeneous graph-based views of cells and genes into robust low-dimensional representations. In this paper, we introduce GatorSC, a unified representation learning framework that models scRNA-seq data through multi-scale cell and gene graphs and fuses them with a Mixture-of-Experts architecture. GatorSC constructs a global cell-cell graph, a global gene-gene graph, and a local gene-gene graph derived from neighborhood-specific subgraphs, and learns graph neural network embeddings that are adaptively fused by a gating network. To learn noise-robust and structure-preserving embeddings without labels, we couple graph reconstruction and graph contrastive learning in a unified self-supervised objective applied to both cell- and gene-level graphs. We evaluate GatorSC on 19 publicly available scRNA-seq datasets covering diverse tissues, species, and sequencing platforms. Experiments showed that GatorSC consistently outperforms state-of-the-art deep generative, graph-based, and contrastive methods for cell clustering, gene expression imputation, and cell-type annotation. The learned embeddings are used for accurate trajectory inference, recovery of canonical marker gene programs, and cell-type-specific pathway signatures in an Alzheimers disease single-nucleus dataset. GatorSC provides a flexible foundation for comprehensive single-cell transcriptomic analysis and can be readily extended to multi-omic and spatial modalities.

bioinformatics↗

bioRxiv2025

Morphogen gradients applied basally to human embryonic stem cells to control and dissect tissue patterning

Morphogen gradients are used repeatedly during development to pattern embryonic tissues. Absolute concentrations, duration or even temporal derivative of morphogen concentration have all been proposed to carry positional information. However, establishing the causal relationship between the gradient spatio-temporal profile and resulting cellular diversity and tissue patterning is difficult to address in live embryos because of lack of tools to control those variables. Here, we developed microfluidics devices able to apply spatio-temporally well-defined morphogen landscapes on the basal side of human embryonic stem cells colonies, thus mimicking how BMP4 is delivered to the pluripotent epiblast during mouse gastrulation. Combining live imaging and theoretical modelling, we show that in this configuration the absolute concentration of BMP4 provides positional information and the cell identities emerging during differentiation can vary according to the shape of the gradient. Our toolbox provides a powerful means to dissect the logic of patterning and to engineer tissues precisely.

developmental biology↗

bioRxiv2025

Zebrafish otic vesicle and mouse epididymis as model systems for studying columnar epithelial cell division

Epithelial cell division maintains tissue architecture through coordinated nuclear migration, cell shape changes, and spindle orientation. In columnar epithelia, interkinetic nuclear migration (INM) involves apical nuclear translocation in G2 phase and basal return post-mitosis, yet its regulation remains incompletely understood in vertebrates, in part due to limited in vivo live-imaging models. In this methodological study, we adapted the zebrafish embryonic otic vesicle as an in vivo model to investigate cell division dynamics in simple columnar epithelium using high-resolution live imaging and genetic tools. We demonstrated that apical INM initiates in mid-to-late G2 and is driven by dynein, not myosin II. Mitotic rounding is achieved via actomyosin-mediated basolateral constriction while maintaining basal attachment. Inhibiting myosin II impairs rounding and planar division, causing apical retention of daughter cells, suggesting planar division ensures proper integration. We additionally analyzed the mouse epididymal epithelium, a simple columnar epithelial tissue, to allow cross-species comparison of nuclear migration dynamics. Together, these optimized in vivo vertebrate models uncover conserved and tissue-specific mechanisms underlying epithelial organization and function, and importantly, provide tools for deeper mechanistic dissection in the future.

cell biology↗

bioRxiv2025

Transdiagnostic connectome-based predictive modeling of many behavioral phenotypes reveals brain network mediators of clinical-cognitive relationships

A key assumption of the NIMHs RDoC framework is that disordered circuits in the brain should manifest in observable behaviors, including psychiatric symptomatology and cognitive deficits. However, how disordered circuitry impacts multiple behaviors remains poorly understood. Connectome-based predictive modeling (CPM) applied to functional MRI connectivity data can identify networks associated with specific behavioral measures across individuals. Prediction strength reflects how closely a measure relates to network connectivity, while derived networks provide evidence of where an individuals disordered circuits are located. Using CPM, we predicted a broad range of self-reported clinical and objective cognitive measures in a large, transdiagnostic sample with extensive fMRI data (n = 317). Prediction performance varied substantially across instruments, with objective cognitive tests yielding stronger models than self-reported clinical measures (p < 0.001). To test whether circuits underlying cognitive deficits related to symptomatology reside in regions where networks overlap, we examined the prediction strength of these sparsely shared circuits. Their connectivity strongly predicted cognitive performance and were primarily localized within the frontoparietal network and between the frontoparietal and default mode networks. These findings reveal how much various behavioral measures reflect brain networks and how circuits within the shared network space contribute to cognitive deficits associated with symptomatology.

neuroscience↗

bioRxiv2025

Changes in endophytic microbial diversity and function in the root system affect the growth of continuously planted Casuarina equisetifolia

Withdrawal StatementThe authors have withdrawn this manuscript because additional experimental data are necessary to strengthen the conclusions and improve the overall quality of the study. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

microbiology↗

bioRxiv2025

TIP-seq: A Single-cell Multiomics Approach for Simultaneous Transcriptome and Intracellular Protein Profiling

Single-cell multiomics technologies have significantly advanced our understanding of cellular heterogeneity; however, the concurrent profiling of mRNA transcripts and target proteins continues to pose a substantial challenge. To bridge the gap between single-cell sequencing and proteomic methods, we developed an innovative single-cell multiomics methodology, termed TIP-seq, which facilitates the simultaneous profiling of the transcriptome and intracellular proteins without prior cell manipulation. In TIP-seq, microfluidic technology is leveraged to integrate oligonucleotide-labeled antibodies with hydrogel beads, allowing for the capture of mRNAs and proteins from individual cells within droplets, thereby enabling high-throughput and precise dual-omics data acquisition. When applied to lung cell lines and non-small cell lung cancer (NSCLC) tissues, TIP-seq analysis revealed notable cellular heterogeneity and molecular dynamics, emphasizing the distinct immune cell interactions within NSCLC tissues. Key immune checkpoint interactions in NSCLC, such as SPP1-CD44, NECTIN2-TIGIT, and NECTIN2-CTLA4, along with functional alterations in tumor-associated dendritic cells (DCs) and T cells, were identified via TIP-seq, underscoring their pivotal roles in mediating immune suppression within the tumor microenvironment. Collectively, TIP-seq represents a powerful methodology for identifying novel therapeutic targets and biomarkers, thereby holding significant potential for the advancement of precision medicine in the treatment of lung cancer and other complex diseases.

biochemistry↗

bioRxiv2025

SLC44A1 deficiency impedes myelin development in the central nervous system

Axon-wrapping myelin sheath is essential for the proper functioning of the central nervous system (CNS). Defects in myelination occur in various neurodevelopmental disorders. Human deficiency of the solute carrier 44A1 (SLC44A1) causes a new type of childhood-onset neurodegeneration with leukoencephalopathy. Currently, there is no effective treatment for this devastating disease, and little is known about its pathological mechanisms. In this study we identified that SLC44A1 is enriched in oligodendrocytes and required for myelin development in the CNS of zebrafish and rodents, which is crucial for normal motor coordination and cognitive function. Defective oligodendroglial maturation and myelinogenesis can be visualized by in vivo time-lapse imaging in the spinal cord of zebrafish with Slc44a1b deficiency. Mechanistically, SLC44A1 deficiency disrupts the expression of genes involved in phosphatidylcholine production pathway, and subsequently inhibiting phospholipid biosynthesis and disturbing the lipid composition of myelin sheaths. More importantly, supplementation with citicoline, a natural choline metabolite, restores developmental myelination in SLC44A1-deficient animals. These findings demonstrate that SLC44A1 is essential for CNS myelination and citicoline supplementation represents a potential therapeutic strategy to address the developmental hypomyelination.

neuroscience↗

bioRxiv2025

scBiopsy-seq: a platform for temporal single-cell RNA-seq analysis

The development of temporal single-cell RNA-seq (scRNA-seq) assay enabled us to systemically investigate the effects of various types of perturbations in a time course with single-cell resolution. However, the existing temporal scRNA-seq technologies have certain limitations in reliability, detection efficacy and detection diversity. In the current study, we develop scBiopsy-seq assay, which combines a synergistic electroosmosis-electrophoresis extraction method for efficient RNA extraction and digital microfluidics with contamination-isolated hydrophobic interface for high-performance sample processing. scBiopsy-seq extracts the cytoplasm at well-controlled volume to detect >10K genes per extraction with 90% successful rate. Functional enrichment analysis revealed that the genes robustly detected by scBiopsy-seq were associated to diverse biological processes, demonstrating its superb diversity of detection. scBiopsy-seq can perform the sequential extraction of the cytoplasm from the same cell multiple times, which allows us to associate the cell phenotypic responses with its transcriptional dynamics. We employed scBiopsy-seq to analyze the temporal response to a BRD4 degrader induced transcriptional suppression, which identified the key roles of fatty acid beta oxidation in this biological process. scBiopsy-seq with similar data quality as scRNA-seq will dramatically expand the application of temporal scRNA-seq towards a broader spectrum of cell biology research.

bioengineering↗

bioRxiv2025

Cell-Surface LAMP1 is a Senescence Marker in Aging and Idiopathic Pulmonary Fibrosis

The accumulation of senescent cells (SEN) with aging produces a chronic inflammatory state that accelerates age-related diseases. Eliminating SEN has been shown to delay, prevent, and in some cases reverse aging in animal disease models and extend lifespan. There is thus an unmet clinical need to identify and target SEN while sparing healthy cells. Here, we show that Lysosomal-Associated Membrane Protein 1 (LAMP1) is a membrane-specific biomarker of cellular senescence. We have validated selective LAMP1 upregulation in SEN in human and mouse cells. Lamp1+ cells express high levels of prototypical senescence markers p16, p21, Glb1, and have low Lmnb1 expression as compared to Lamp1- cells. The percentage of Lamp1+ cells is increased in mice with fibrotic lungs after bleomycin instillation. Finally, we use a dual antibody-drug conjugate (ADC) strategy to eliminate LAMP1+ senescent cells.

molecular biology↗

bioRxiv2025

Hydroxychloroquine-functionalized Ionizable Lipids Mitigate Inflammatory Responses in mRNA Therapeutics

Lipid nanoparticle (LNP)-based mRNA therapeutics, highlighted by the success of SARS-CoV-2 vaccines, face challenges due to inflammation caused by ionizable lipids. These ionizable lipids can activate the immune system, particularly when co-delivered with nucleic acids, leading to undesirable inflammatory responses. We introduce a novel class of anti-inflammatory ionizable lipids functionalized with hydroxychloroquine (HCQ), which suppresses both lipid-induced and nucleic acid-induced immune activation. These HCQ-functionalized LNPs (HL LNPs) exhibit reduced proinflammatory responses while maintaining efficient mRNA delivery. Structural and physicochemical analyses revealed that HCQ-functionalization results in a distinct particle structure with significantly improved stability. The efficacy of HL LNPs was demonstrated across various therapeutic contexts, including a prophylactic vaccination model against varicella-zoster virus (VZV) and CRISPR-Cas9 gene editing targeting PCSK9. Notably, HL LNPs showed robust mRNA expression after repeated administration, addressing concerns of inflammation and ensuring sustained therapeutic effects. These findings highlight the potential of HCQ-functionalized LNPs in expanding the safe use of mRNA therapeutics, particularly for applications requiring repeated dosing and in scenarios where inflammation-induced side effects must be minimized.

bioengineering↗

bioRxiv2025

LCORL and STC2 variants increase body size and growth rate in cattle and other animals

Using ancestral recombination graphs, we investigated recent selection signatures in European beef cattle breeds, pinpointing sweep-driving variants in the LCORL and STC2 loci with notable effects on body size and growth rate. The ACT-to-A frameshift mutation in LCORL occurs mainly in central-European cattle, and stimulates growth. Remarkably, convergent truncating mutations were also found in commercial breeds of sheep, goats, pigs, horses, dogs, rabbits, and chickens. In the STC2 gene, we identified a missense mutation (A60P) located within the conserved region across vertebrates. We validated the two natural mutations in gene-edited mouse models, where both variants in homozygous carriers increase the average weight by 11%. Our findings provide insights into a seemingly recurring gene target of body size enhancing truncating mutations across domesticated species, and offer valuable targets for gene editing-based breeding in animals.

genetics↗

bioRxiv2025

Flaviviruses Hijack HuR to Suppress CNPY3: A Novel Pathway for Immune Evasion and Therapeutic Intervention

Flaviviruses represent a serious global health threat, infecting millions annually with high rates of cross-infection among different flaviviruses, yet no broad-spectrum antiviral therapy currently targets these pathogens. Through biological big data analysis, we observed a significant downregulation of Canopy FGF Signaling Regulator 3 (CNPY3), a positive regulator of defense responses, in flavivirus-infected patients, with the level of downregulation correlating with infection severity. This observation was validated in cellular and animal models. Mechanistically, we demonstrate that flaviviruses hijack the RNA-binding protein Human antigen R (HuR) to destabilize CNPY3 mRNA via adenine-uridine-rich elements (AREs), thus downregulating CNPY3 expression and promoting viral replication. Our findings identify CNPY3 as a novel antiviral mediator essential for the TLR-mediated type I interferon (IFN-I) pathway in defense against flaviviruses. In vitro, CNPY3 overexpression reduced DENV and ZIKV replication, confirming its antiviral role. To explore therapeutic potential, we developed lipid nanoparticles (LNPs) encapsulating CNPY3 mRNA (LNP-CNPY3), and early administration in flavivirus-infected mice improved survival, reduced viral loads, and attenuated neuroinflammation by enhancing antiviral and interferon responses. Together, these findings establish CNPY3 as a critical antiviral target and support LNP-CNPY3 as a promising therapeutic approach against flavivirus infections.

microbiology↗