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Chen, L.

Publications and source records attributed to Chen, L..

At least 109 records · Page 6Linked to original sources

Developing a Multimodal miR-15a Mimic to Overcome PARP Inhibitor Resistance in Epithelial Ovarian Cancer

Epithelial ovarian cancer (EOC) is characterized by high relapse rates and the development of drug resistance, driven by adaptive DNA repair and survival pathways. Here, we develop a multimodal, chemically engineered miRNA therapeutic, MTX-5-FU-Gem-miR-15a, that integrates tumor-suppressive miR-15a activity with chemotherapeutic modifications and tumor-targeting capability. This modified miRNA exhibits potent nanomolar activity across diverse EOC models, including PARP inhibitor-resistant cells, without requiring delivery vehicles. Mechanistically, MTX-5-FU-Gem-miR-15a induces replication stress while suppressing G2/M checkpoint regulators (WEE1 and CHK1), resulting in genomic instability and apoptotic cell death. Transcriptomic and protein-level analyses revealed coordinated suppression of resistance-associated and oncogenic signaling pathways, alongside activation of DNA damage coupled with checkpoint abrogation and potential innate immune response. MTX-5-FU-Gem-miR-15a also demonstrates strong synergy with olaparib and robust antitumor efficacy in vivo. These findings establish a multimodal miRNA-based therapeutic strategy that targets replication stress and checkpoint dependency to overcome PARPi resistance in ovarian cancer.

cancer biology↗

Autoluminescence characteristics of 25 Phalaenopsis orchids following transient transformation with eFBP2

Engineering autoluminescent plants, especially horticultural crops, has recently emerged as a promising research area, with one current approach involving the transgenic introduction of fungal bioluminescence pathway genes. Although autoluminescent plants such as tobacco and petunia have been created, it remains unclear whether all horticultural plants have the potential to be autoluminescent after genetic modification, especially those having flowers with dark colors and thick cuticles. To understand whether, and what if any, floral traits affect autoluminescence potential, we assess the autoluminescence characteristics of 25 representative Phalaenopsis cultivars after transient transformation of fungal bioluminescence pathway genes, alongside several key morphological and biochemical traits. Our results demonstrate that autoluminescence characteristics are correlated with floral color lightness, organ textures and epidermal cell types. In contrast, the content of the substrates of luciferin--caffeic acid and tyrosine, and the infiltration ease of inoculation solution into floral organs after injection, have limited effects on autoluminescence characteristics. Autoluminescence intensity can be reasonably predicted using five floral traits investigated, as 80.4% of variation can be explained by these traits. Our study not only identifies specific Phalaenopsis cultivars with high potential for developing autoluminescent lines but also provides a selection framework applicable to other horticultural crops.

plant biology↗

Structural Mechanism of Electron Shuttling in Inducible Nitric Oxide Synthase

Nitric oxide (NO) signaling is pivotal in numerous physiological processes and is implicated in a spectrum of human diseases. Nitric oxide synthases (NOS) initiate NO signaling and govern its magnitude and duration, making them key drug targets. Despite decades of investigation, the structural mechanism by which NOS enzymes transfer electrons from NADPH to haem remains incompletely understood. Here, we report cryo-electron microscopy (cryo-EM) studies of the inducible NOS (iNOS) homodimer in complex with calmodulin (CaM) captured under catalytic turnover conditions, resolving two important functional states: the electron input state and output state. In the input state, the FMN-binding subdomain (FMND) docks onto the FAD/NADPH-binding subdomain (FNR), positioning the FMN cofactor to accept electrons from FAD. The FMND then undergoes a large rotational movement to engage the oxygenase domain (OXY) of the other protomer, adopting the output state, which enables electron transfer from FMN to the haem center via W366. This dynamic movement of the FMND shuttles electrons from the reductase domain (RED) to the OXY active site in iNOS. A point mutation (S594E) that disrupts the FMND-OXY interface markedly reduces the catalytic activity of iNOS and traps a fraction of enzymes in a non-productive intermediate conformation. Together, these findings elucidate the structural mechanism of FMND-mediated electron transfer in the iNOS catalytic cycle.

biochemistry↗

Immune receptor LILRB1 mediates cis-signalling which is targeted by RIFINs of the malaria parasite

The malaria parasite, Plasmodium falciparum, replicates within human erythrocytes, where it is susceptible to clearance by immune cells. It uses erythrocyte surface proteins, the RIFINs, to signal through immune receptors and to suppress immune cell function. Previous studies identified two groups of RIFINs which bind different sites on inhibitory immune receptor LILRB1. While some RIFINs bind an elongated LILRB1 conformation, triggering inhibitory immune signalling in trans, we show that other RIFINs stabilise a c-shaped LILRB1 conformation. This buckled LILRB1 binds MHC class I found on the same immune cell, which triggers inhibitory cis signalling. Therefore, LILRB1 exists in dynamic equilibrium, with an elongated conformation able to bind to ligands in trans on a target cell, while a buckled conformation signals through MHC class I in cis, setting the signalling threshold. Different clades of RIFINs exist to mediate inhibitory signalling through each of these LILRB1 conformations to prevent parasite destruction.

microbiology↗

Human Lymph Node Cellular Senescence Atlas Reveals Age-Dependent Alteration in Germinal Center B Cell Function and Niches

Immunosenescence, the age-associated decline in immune function, is a key feature of human aging. In human lymphoid organs, however, the specific immune cell populations that acquire senescence-associated phenotypes during aging and how they influence the surrounding tissue microenvironment remain poorly understood. A spatially resolved map of these senescence-associated immune states in human lymphoid tissues could help clarify their relationship with aging and their potential contributions to the progressive decline of immune function. Here, we integrated single-cell and spatial multi-omics to systematically characterize age-related senescence in human lymph nodes (LNs). Single-cell transcriptomics of lymphoid tissues from donors aged 18 to 100 years old identified 34 immune and stromal cell types and revealed age-associated upregulation of senescence signatures in specific populations. Spatial proteomic profiling of 99 LN sections from 51 donors (18-86 years) using high-plex immunofluorescence ([~]20 million cells) mapped senescence markers (p16, p21, HMGB1, -H2AX) at single-cell resolution, revealing diverse senescent-like cell types ("senotypes") and a stepwise shift from extrafollicular to germinal center (GC) localization with age. Notably, we observed focal clonal-like senescence in GC B cells in older donor LNs. Spatial transcriptomics, epigenomics, and metabolic imaging of selected samples further elucidate the multi-omics signatures and underlying mechanisms of functional impairment, metabolic remodeling, and distinct regulatory programs in senescent-like GC B cells. This study presents a comprehensive spatial atlas of senescence-associated immune states in human lymph nodes, revealing cell-type-specific and spatial heterogeneity that may contribute to immunosenescence and the decline of immune function during aging.

immunology↗

Structural Mechanism of TRPC3 Channel Activation by the Moonwalker Mutation

TRPC3 is a calcium-permeable, non-selective cation channel that is activated by DAG. It is expressed in several tissues, especially in the cerebellum, and has been implicated in various human diseases. Despite recent progress in understanding the structural mechanism of TRPC3, how the channel opens remains elusive. Here, we present structures of hTRPC3 in an agonist-free resting state, determined using a DAG-binding site mutant. We also present the structure of hTRPC3 in a DAG-bound open state, determined using a constitutively active "moonwalker" (T561A) mutant. These structures, together with electrophysiological results, reveal that the T561A mutation activates hTRPC3 by disrupting a polar interaction with N652. A newly formed {pi}-bulge in S6 leads to rotation and outward tilting of the lower half of S6, resulting in dilation of the pore and thus channel opening. Agonist DAG stabilizes hTRPC3 in the open conformation. BTDM exerts its inhibitory effect by pushing S5 and S6 back to the center to close the pore, while preserving the {pi}-bulge. These results shed light on the opening mechanism of hTRPC3.

biophysics↗

Generating and navigating single cell dynamics via a geodesic bridge between nonlinear transcriptional and linear latent manifolds

Time-series single-cell RNA sequencing (scRNA-seq) captures cellular processes as sparse and unpaired snapshots, limiting our ability not only to reconstruct continuous cell state transitions, but also to navigate between states in a controlled and interpretable manner. Here we present GeoBridge, a framework modeling cellular dynamics as geodesic trajectories on the transcriptional manifold based on isometric geodesic theory. By learning the geodesic bridge mapping, the method theoretically and computationally transforms time-varying nonlinear transcriptional geodesics (original nonlinear manifold) into constant-velocity straight-line geodesics (latent linear manifold). In the learned geodesic space, continuous interpolation becomes biologically meaningful, enabling reconstruction of unobserved intermediate states and efficient navigation between distinct cellular phenotypes at a single-cell resolution. By mapping interpolated trajectories back to the original gene expression space, GeoBridge recovers smooth transcriptional programs that are robust to noise and snapshot sparsity. Leveraging the derived geodesic potentials, GeoBridge further infers pseudo-temporal trajectories with superior fidelity compared to mainstream approaches from single-snapshot scRNA-seq data without temporal annotation, and directly identifies genes that drive progression along transition paths. We demonstrate the utility of GeoBridge across diverse systems, where GeoBridge resolves EMT-MET progression in cancer stem cells and identifies stage-specific modules as well as the branching cell-fate dynamics in human pluripotent stem cells with higher reconstruction accuracy than state-of-art methods. More importantly, GeoBridge supports single-cell fate navigation in multi-target hematopoietic lineages, allowing neutrophil-biased cells to be virtually guided toward mast-cell fates along biologically plausible paths. Together, GeoBridge establishes a principled method that transforms sparse single-cell measurements into a continuous, controllable landscape for the reconstruction, navigation and manipulation of cellular state transitions.

bioinformatics↗

Integrative Identification and Characterization of PCOS-Associated lncRNAs From the Interface of Genetic Association, Transcriptomics, and Gene Structure Evolution

BackgroundPolycystic ovary syndrome (PCOS) is a prevalent endocrine disorder and a leading cause of female infertility, with complex genetic, metabolic, and hormonal etiologies. Long non-coding RNAs (lncRNAs) have emerged as important regulators of diverse biological processes, yet their roles in PCOS remain underexplored. Here, we identified and characterized PCOS differentially expressed gene-associated lncRNAs (PDEGAL) with an integrative approach combining expression data, genetic association, and evolutionary analysis. MethodsThirty-three PCOS-associated protein-coding genes were obtained from our prior study, and all their nearby and overlapping lncRNAs were annotated. These candidates were analyzed using UCSC Genome Browser-mapped annotations and datasets, including NCBI RefSeq, GENCODE, GTEx, GWAS SNPs, and conservation, as well as the FANTOM5 cap analysis of gene expression (CAGE) promoter data, to assess their expression, regulatory potential, genetic variant overlaps, and evolutionary conservation. ResultsTwenty-three PDEGALs (18 antisense to, and 5 sharing bidirectional promoters with, known PCOS-associated protein-coding genes) were identified. 17 PDEGALs contained GWAS SNPs with statistically significant disease associations, 9 of which were associated with PCOS-related traits. 5 PDEGALs demonstrated expression in the KGN granulosa cell model of PCOS. Key gene structure element (KGSE) analysis revealed that most PDEGALs are primate-specific. Integrating four criteria--GTEx expression, GWAS SNPs, FANTOM promoterome, and KGSE conservation--highlighted HELLPAR as the only lncRNA fulfilling all four, while five others--PGR-AS1, MTOR-AS1, ENSG00000265179, ENSG00000256218, and LOC105377276--fulfilled three of the four criteria. ConclusionsWe have systematically identified candidate PCOS regulatory lncRNAs with convergent genetic, expression, and evolutionary evidence. These results provide a framework for functional validation and highlight lncRNAs as potential biomarkers and therapeutic targets in PCOS that function by regulating their nearby and overlapping protein-coding genes.

genomics↗

A genome-wide CRISPR Screening identifies targets that drive Tolerogenic Dendritic Cells

Tolerogenic dendritic cells (TolDCs) are essential for immune tolerance and offer promise for treating autoimmune diseases. Despite the clinical evidence of their therapeutic potential, the key molecular pathways guiding their differentiation and tolerogenic phenotype remain elusive due to complex interactions identified in functional assays. Here we investigated the molecular profiles and regulatory programs underlying the functional status of tolerogenic dendritic cell populations in response to known tolerizing agents. We identified CD86 as a consistent and robust marker downregulated in tolerogenic state. Using CD86 blocking antibodies or CRISPR-mediated gene inactivation we demonstrated that CD86 is functionally required for TolDC-mediated suppression of T cell proliferation and cytokine secretion, establishing CD86 as both a consensus phenotypic and functional screening marker and a mechanistic regulator of tolerance. Leveraging CD86 as a scalable readout, we performed a pooled genome-wide CRISPR-Cas9 knockout screen to identify regulators of TolDC function. This approach uncovered UBE2L6 as a novel modulator that promotes the tolerogenic phenotype and restricts TolDC-mediated T cell activation. Mechanistically, UBE2L6 deficiency leads to coordinated upregulation of ISG15 and USP18, indicating a possible ISGylation-dependent pathway regulating CD86 expression and tolerogenic function. Together, this study identifies pathways that can be targeted to promote immune tolerance in immune-mediated inflammatory diseases. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=105 SRC="FIGDIR/small/713621v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@4c3636org.highwire.dtl.DTLVardef@17b27e5org.highwire.dtl.DTLVardef@783d95org.highwire.dtl.DTLVardef@1337ce_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

Spindle pole proteins confine chromosomes to ensure their expulsion during female meiosis

Animal oocytes undergo highly asymmetric divisions to expel excess copies of their genome into compact cells called polar bodies. This requires tight clustering and cortical positioning of meiotic chromosomes, yet the mechanism remains incompletely understood. Using C. elegans oocytes, we found that the meiotic spindle pole protein ZYG-9/ch-TOG delocalizes from microtubules to spread along the surface of chromosomes and prevent their dispersal in meiotic anaphase. This effect was more pronounced in the absence of the spindle, where ZYG-9 formed into a micron-scale droplet that enveloped all chromosomes. Purified ZYG-9 was sufficient to bind DNA and coat reconstituted chromatin. Mutations that perturb ZYG-9-DNA binding impaired chromosome packaging into polar bodies, resulting in oocytes carrying extra chromosomes and reduced fertility. We propose that liquid-like assemblies of spindle pole proteins are repurposed as surface-acting glue to tightly package meiotic chromosomes into polar bodies, thus ensuring oocytes have the correct genome copy number.

cell biology↗

SNAP MRI Reveals Association Between Distal Cerebral Arterial Flow and Cognitive Function in an Aging Population

ObjectiveImpaired blood flow has recently been recognized as a critical contributor to cognitive impairment and dementia. It was reported that cerebral distal arterial flow measured from Simultaneous Non-contrast Angiography and Intraplaque Hemorrhage (SNAP) MRI is associated with post-treatment cognitive function improvement in carotid atherosclerosis patients. In this study, we aim to evaluate the value of SNAP-based measurements in assessing cerebrovascular function in an aging population. Materials and MethodsNeurovascular MRI data were collected on 36 aging participants (22 cognitively unimpaired and 14 impaired; 9 mild cognitive impairment (MCI) and 5 Alzheimers Disease (AD)). Neurovascular MRI measurements, including white matter hyperintensities (WMH) volumes, cerebral blood flow (CBF), and SNAP-based distal cerebral arterial flow (dCAF) index, were quantified. Cognitive function was assessed using the Repeatable Battery for the Assessment of Neuropsychological Status (RBANS). ResultsSignificant differences in the dCAF index were observed between cognitively unimpaired and impaired groups, and the dCAF index was significantly correlated with the RBANS total score. While CBF was significantly associated with dCAF index, there is no significant correlation of CBF or WMH with the RBANS score in this population. ConclusionOur findings suggest that the dCAF measured with SNAP MRI is valuable for evaluating the cognition-related cerebrovascular condition in an aging population.

neuroscience↗

A cerebellar cognitive rheostat bidirectionally controls attention

Attention requires filtering distractors and amplifying signals, processes classically attributed to cortico-thalamic networks. Here, we reveal that the cerebellum operates as a bidirectional "cognitive rheostat" to optimize attentional states. In mice, the anterior and posterior cerebellar vermis exert opposing control over attention. Granule cells in the anterior vermis are functionally suppressed to gate sensorimotor noise via reticular nucleus-driven feedforward inhibition. Conversely, posterior granule cells are recruited by pontine inputs to amplify cognitive signals, a process relying on Grin1-mediated NMDA receptor plasticity. Circuit-specific manipulations targeting this push-pull mechanism, or localized pharmacological modulation, successfully rescued attentional deficits in an ADHD mouse model. These findings fundamentally expand the cerebellums role beyond motor coordination, identifying a topographic circuit algorithm essential for cognitive control.

animal behavior and cognition↗

Single-cell Landscape of T Cell Heterogeneity in Kawasaki Disease: STAT3/JAK Axis Regulates the Lineage Differentiation Bias of Th17 Cells

BackgroundKawasaki disease (KD) is a pediatric systemic vasculitis in which T-cell-mediated immune responses play a pivotal role. However, the precise dynamic evolution of T-cell subsets during disease progression remains poorly understood. MethodsSingle-cell RNA sequencing (scRNA-seq) was employed to perform high-resolution annotation of peripheral blood mononuclear cells (PBMCs) from healthy controls and KD patients, both pre- and post- IVIG treatment. T-cell developmental trajectories were reconstructed via Monocle3-based pseudotime analysis. Furthermore, the functional significance of the significant pathway was validated in a CAWS-induced KD murine model. ResultsA high-resolution single-cell landscape identified 13 distinct T-cell subtypes. Pseudotime analysis revealed a significant lineage commitment of CD4+ T cells toward a Th17 phenotype during the acute phase of KD, synchronized with the transcriptional upregulation of the STAT3/JAK signaling axis. Animal experiments further demonstrated that pharmacological inhibition of this pathway substantially attenuated inflammatory infiltration in the cardiac vasculature of KD mice. ConclusionThis study identifies the STAT3/JAK-mediated Th17 differentiation bias as a potential regulatory program associated with acute inflammation in Kawasaki disease, thereby highlighting the STAT3/JAK axis as a potential therapeutic target.

bioinformatics↗

Chromosome-level genome sequence of the C4 grass Themeda triandra reveals karyotype orthology with sorghum and genetic variation in accessions adapted to diverse environments

Themeda triandra (family Andropogoneae) is a pan-continental grass occurring throughout Australia. Recognising its remarkable adaptive capacity, we assembled the nuclear genome sequence of a diploid accession from eastern Australia, finding all ten chromosomes of the 755 Mb assembly highly syntenic with those of Sorghum bicolor. Genotyping and cytometry of range-wide accessions suggested several historical radiation events, with polyploids dominating in arid regions, apart from a notable diploid lineage from the arid north-west of Australia (PAN). A detailed comparison of PAN with two diploids from temperate south-eastern Australia through whole-genome resequencing revealed extensive copy number variation and polymorphism, with changes in genes for heat-shock proteins and flowering regulation reflecting their environmental origin. Exploration of the rich genetic diversity in T. triandra with respect to environmental adaptation is expected to benefit grassland management programs and enable introgression of novel genes into Andropogoneae crops for climate resilience.

genomics↗

PPa1 insufficiency drives lysosomal storage disease and inflammatory macrophage expansion in the bone marrow.

Inorganic pyrophosphatase-1 (PPa1) is an essential enzyme proposed to limit accumulation of the ubiquitous metabolic byproduct inorganic pyrophosphate, yet its role beyond a general housekeeping function remains poorly understood. We generated viable hypomorphic alleles of PPa1 through random mutagenesis in mice and unexpectedly found that PPa1 insufficiency causes a lysosomal storage disease of the bone marrow. Mutant mice developed impaired hematopoiesis and defective skeletal mineralization in a hematopoietic-intrinsic manner. The bone marrow was infiltrated by glycolipid-laden macrophages that were marked by high Spp1 and CD14 expression, blunted lysosomal acidification, metabolic stress, and a distinct inflammatory transcriptional program. Consistent with a lysosomal storage defect, PPa1-deficient bone marrow accumulated elevated levels of long-chain glucosyl-sphingolipids and sphingosine. These findings identify PPa1 as a previously unrecognized regulator of lysosomal function in myeloid cells that restrains inflammatory macrophage expansion and prevents bone marrow lysosomal storage pathology.

immunology↗

Synergistic Inhibition of Notch Signaling and Forced Cell Cycle Re-entry Drive Müller Glia Reprogramming in Uninjured Mouse Retina

In regenerative species, such as teleost fish, Muller glia (MG) autonomously re-enter the cell cycle after injury and give rise to functional retinal neurons. In contrast, the loss of retinal neurons in mammals is irreversible due to the limited proliferative and regenerative ability of MG. Various strategies have been developed to induce proliferation of mature mouse MG with or without injury, yet most MG daughter cells retain glial cell fate. Here, we found that MG progenies maintain high Notch signaling, which may constrain their neurogenic potential. Conditional deletion of Rbpj, the central transcriptional effector of Notch, induced limited MG-to-neuron conversion in mature MG without proliferation. However, Rbpj deletion, combined with forced MG proliferation by overexpressing cyclin D1 and suppressing p27Kip1, significantly promoted MG dedifferentiation and ectopic expression of the neuronal marker Otx2 in MG daughter cells in uninjured mouse retina. Combining Notch inhibition with MG cell cycle re-activation not only increased the numbers of bipolar- and amacrine-like cells generated from MG but also promoted the further differentiation toward ON-cone, OFF-cone, and rod-bipolar subtypes. Single-nucleus RNA and ATAC sequencing data revealed that Notch inhibition facilitated the formation of MG-derived progenitor-like cells while MG proliferation increased chromatin accessibility of neurogenic genes. Notably, most MG-derived cells survived long term despite incomplete maturation. Together, our findings delineate how Notch inhibition and MG proliferation, alone or in combination, influence the regenerative potential of MG in the mammalian retina.

cell biology↗

Benchmarking zero-shot single-cell foundation model embeddings for cellular dynamics reconstruction

Reconstructing cellular trajectories from time-resolved single-cell transcriptomics is fundamental to understanding processes from embryonic development to cancer progression. While single-cell foundation models (scFMs) promise universal biological representations through large-scale pretraining, their capacity to capture the non-linear dynamics governing cell-fate decisions remains uncharacterized. Here we systematically benchmark multiple scFMs across challenging biomedical scenarios involving branching lineages and continuous state transitions. By coupling zero-shot scFM embeddings with dynamic optimal transport, we evaluated their performance against a traditional highly variable gene (HVG) baseline in backtracking progenitor states, interpolating transition intermediates, and extrapolating future fates. We find that zero-shot scFM embeddings underperform the HVG baseline across diverse biological systems, particularly in recovering the distributional complexity of unobserved cells. Mechanistic analysis reveals that current scFM architectures tend to over-compress subtle temporal signals, causing an artificial "linearization" of branched biological structures that may obscure critical divergence points in disease progression. Our findings suggest that while scFMs provide unified cell-state views, the HVG baseline remains more robust for trajectory inference, identifying a fundamental "temporal-compression" bottleneck that must be addressed to develop next-generation, dynamics-aware foundation models.

bioinformatics↗

STING agonist-mediated endothelial cell activation drives NK cells and neutrophils-dependent pulmonary inflammation

Stimulator of interferon genes (STING) agonists and derivative molecules have been extensively developed for tumor immunotherapy. However, systemic exposure toxicity risks have constrained clinical trial progression and even threatened patient lives. Currently, systematic toxicity assessments for STING agonists remain lacking, with the mode of action for major organ injury yet to be elucidated. Here, we focused on STING agonist-induced lung injury, revealing that systemic administration of STING agonists caused pulmonary hemorrhage, inflammatory alterations, and respiratory dysfunction. Through single-cell RNA sequencing and immune deletion studies, we found that lung endothelial cells could be stimulated by STING agonists and then secreted chemokines and IL-15 to recruit and activate NK cells. NK cells could induce endothelial cell apoptosis via IFN-{gamma}. Tbx21+ NK subpopulations, which activated by endothelial cells, could produce chemokines to recruit neutrophils. Neutrophils secreted IL-1{beta} through positive feedback pathways and form neutrophil extracellular traps during lung injury. This study elucidates the critical role of the endothelial cell-NK cell-neutrophil axis in mediating STING agonist-associated pneumonia, offering insights for developing intervention strategies for STING agonist toxicity.

pharmacology and toxicology↗