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Wu, S.

Publications and source records attributed to Wu, S..

At least 91 records · Page 5Linked to original sources

Innate immune sensing via the cGAS-STING pathway restricts extrachromosomal DNA-driven tumorigenesis

Extrachromosomal DNAs (ecDNAs) are circular DNA fragments frequently found in human cancers, where they amplify oncogenes, drive tumor heterogeneity, and promote therapy resistance and poor prognosis. Despite their prevalence, how ecDNAs interact with the immune system remains poorly understood. Here, we show that the cytosolic DNA sensor cGAS detects ecDNA fragments in the cytoplasm and activates the innate immune response. cGAS and STING are frequently silenced in ecDNA+ tumors through promoter hypermethylation. Restoring cGAS or STING in human and murine ecDNA+ cancer cells reactivates innate immune signaling and selectively suppresses ecDNA+ tumor growth in an immunocompetent mouse model. Using two ecDNA biogenesis models, we show that the cGAS-STING pathway restricts de novo ecDNA formation. Together, our findings identify innate immune sensing as a natural barrier to ecDNA-driven oncogenesis and establish cGAS-STING reactivation as a therapeutic strategy for ecDNA+ cancers. HighlightsO_LIThe cGAS-STING pathway is frequently silenced in ecDNA+ tumors C_LIO_LIRestoration of cGAS in ecDNA+ cells activates innate immune responses C_LIO_LIcGAS expression suppresses ecDNA+ tumor growth in vivo C_LIO_LIThe cGAS-STING pathway restricts de novo ecDNA biogenesis C_LI

cancer biology↗

Systematic microcircuit reconfigurations underlie early experience-induced visual cortical plasticity

Experience-dependent reorganization of neuronal connections during a postnatal critical period (CP) is essential for the functional maturation of developing primary visual cortex (V1). However, the systematic reconfigurations across microcircuit synapses underlying this plasticity were poorly defined. Paired recording from excitatory pyramidal cells and other three major interneurons (INs) within layers 2/3 and 4 microcircuits in the developing mouse V1 monocular region, we find that monocular deprivation (MD) for one-day during the CP transiently reconfigures local excitatory synapses on inhibitory INs that specifically express parvalbumin (PV) or vasoactive intestinal peptide (VIP), whereas prolonged MD primarily strengthens inhibitory transmission from somatostatin (SST)-expressing INs to PV-INs and VIP-INs in both layers. A physiologically based microcircuit model suggests these coordinated synaptic changes in specific inhibitory neurons mediate differential MD-induced plasticity in visual responses across layer 2/3 neurons in vivo. Together, our findings define a systematic microcircuit basis for cortical critical-period plasticity. HighlightsO_LIInhibitory-to-inhibitory connectivity is conserved in cortical layer 2/3 and 4 circuits. C_LIO_LIEarly experience sequentially modifies excitatory and dis-inhibitory synapses in both layers. C_LIO_LISystematic microcircuit reconfigurations underlie plasticity of cortical visual responses. C_LIO_LIModeling suggests a pivotal role of disinhibitory microcircuits in mediating the plasticity. C_LI

neuroscience↗

Identification of Vector Organisms and Their Carried Pathogens by Metagenomic Sequencing

Vector surveillance is vital for public health, yet traditional methods often face limitations. This study assessed the use of metagenomic sequencing for analyzing mosquitoes, cockroaches, flies, and rodents from Zhongshan, China. The results revealed a high concordance between metagenomic and Sanger sequencing for species identification (Kappa = 0.667, P = 0.011). Metagenomic analysis identified vector-specific dominant bacteria, including Wolbachia in mosquitoes, Blattabacterium sp. in cockroaches, Bartonella tribocorum and Leptospira interrogans in rodents, and Vagococcus teuberi in flies. It also detected numerous classical pathogens, such as Enterococcus faecalis, L. interrogans, and Klebsiella pneumoniae. Among the identified fungi and viruses, 19 were human pathogens, while seven posed a threat to agriculture, notably Pepper mild mottle virus and Tomato brown rugose fruit virus. These findings systematically characterize the microbial communities associated with various vectors, highlight the potential of metagenomics for broad pathogen screening, and underscore its utility in large-scale vector surveillance and public health protection. ImportanceVectors are major carriers of numerous diseases and present risks fot cross-border transmission. Existing detection methods for vectors and their pathogens remain inefficient, insensitive, and prone to difficulties in species identification. Despite extensive efforts in vector identification, the potential threats posed by their associated pathogens remain unclear, demonstrating the need for more effective diagnostic strategies. Metagenomic sequencing offers a promising solution to this challenge. In this study, we applied metagenomic sequencing to vectors collected from urban and port areas in Zhongshan, China, to evaluate its efficacy in pathogen detection. Overall, our work contributes to a better understanding of the public health risks posed by vector-borne pathogens.

microbiology↗

Serotonergic neuron-glioma interactions drive high-grade glioma pathophysiology

High-grade gliomas are lethal brain cancers that are powerfully regulated by glutamatergic neurons through activity-dependent paracrine factors and functional neuron-to-glioma synapses. Here, we report that serotonergic neurons promote the proliferation of high-grade gliomas throughout the brain. Serotonergic neuronal activity drives circuit-specific increases in high-grade glioma proliferation, calcium transients, and reduced survival. This growth-promoting effect is chiefly mediated by activation of the serotonin (5-hydroxytryptamine; 5HT) receptor 5HT2A on glioma cells. Knock out or pharmacological blockade of 5HT2A receptors in glioma abrogated the glioma growth-promoting effects of serotonergic neuronal activity, while serotonergic psychedelic drugs robustly promote malignant cell proliferation. Gliomas alter serotonergic neuronal activity patterns, resulting in elevated serotonin release into the tumor microenvironment. Together, these findings uncover pathogenic, feed-forward interactions between serotonergic neurons and glioma cells.

neuroscience↗

Machine perfusion and single-cell spatial transcriptome mapping identifies novel immune escape mechanisms in colorectal cancer liver metastasis

Liver metastasis is the terminal stage of colorectal cancer. Immune checkpoint blockade (ICB) has heralded remarkable clinical success across a range of cancer types, but with limited efficacy in replacement-type colorectal liver metastasis (CRLM), the most common and lethal histological subtype. Using a novel human normothermic perfusion model, we demonstrate for the first time, that T-cells preferentially extravasate within the peri-tumoural liver rather than the CRLM. We use single-cell spatial transcriptomics and multiplexed immunofluorescence to validate CRLM T-cell exclusion and show that CRLM endothelia are anergic, lacking key receptors required for T-cell extravasation. CD4 T-cells that extravasate within the peri-tumoural liver are TCR-reactive, yet exhausted, whilst CD4 T-cells within the CRLM demonstrate a stress response, impaired cytokine expression and lack of TCR reactivity. We identify the spatial cellular and molecular interactions underlying these observations, providing novel targets for future attempts to sensitise to immunotherapeutics and a justification for failed ICB efficacy in CRLM.

cancer biology↗

Dorsomedial hypothalamus cold-sensitive neurons drive shivering thermogenesis

Hypothermia, a decline in core body temperature below 35{degrees}C in homeotherms, elicits rapid, asynchronous involuntary shivering thermogenesis; however, the hypothalamic neurons responsible for initiating this response remain uncharacterized. Here, retrograde transsynaptic tracing combined with RNA-seq identified a distinct population of VGLUT2-positive neurons enriched with Calbindin D28k (CALB1) within the dorsomedial hypothalamic nucleus (DMHCalb1/Vglut2). Convergent evidence from chemogenetic, optogenetic, fiber photometry calcium imaging, and electromyography (EMG) experiments demonstrated that these neurons selectively mediate hypothermia-triggered shivering thermogenesis. Bidirectional perturbation of DMHCalb1/Vglut2 activity modulated shivering intensity, while CALB1-negative VGLUT2-expressing DMH neurons were responsible for non-shivering thermogenesis (NST). Genetic ablation of afferent inputs from LSI/POA/VLPAG projecting to DMHCalb1/Vglut2, as well as ex vivo pharmacological synaptic blockade, failed to eliminate shivering responses during hypothermia, indicating that their activation is independent of canonical cold-responsive circuits. Hypothermia significantly suppressed transient A-type K (IA) currents, without affecting delayed rectifier K (IK) currents, accompanied by a pronounced reduction in the IA inactivation time constant relative to normothermic 36 {degrees}C. Collectively, hypothermia elevates DMHCalb1/Vglut2 excitability through IA-dependent reshaping of action potential dynamics. Shortened action potential repolarization and afterhyperpolarization duration cooperatively boost neuronal firing, constituting an intrinsic mechanism for DMHCalb1/Vglut2 neuron-driven shivering initiation.

neuroscience↗

A non-canonical top-down pathway regulating relapse to opioid

The high relapse rates are major challenges in treating opioid addiction. However, it remains poorly understood the mechanisms underlying long-lasting vulnerability to relapse. Here, we identify the cortico-subthalamic projection from the granular retrosplenial cortex (RSG) to the zona incerta (ZI) as a key circuit for controlling relapse to opioid. We uncover that an ensemble of RSG glutamatergic neurons that locate in layer 5 and express B subtype cholecystokinin receptor (RSGGlu-Cckbr ensemble) are critically implicated in the encoding and retrieval of opioid-associated memories, leading to relapse to opioid via innervating ZI GABAergic (ZIGABA) rather than dopaminergic neurons. We further identify that the Cckergic neurons from anterodorsal nucleus of thalamus (AD thalamus) orchestrates RSGGlu-Cckbr-ZIGABA circuit function via release of cholecystokinin (Cck) in RSG. These results elucidate a previously unknown non-canonical top-down pathway regulating relapse to opioid and shed new light on the development of new therapeutic strategies to treat relapse to opioids.

neuroscience↗

Melody: Decoding the Sequence Determinants of Locus-Specific DNA Methylation Across Human Tissues

DNA methylation is a fundamental epigenetic modification that plays crucial roles in transcriptional regulation, cellular differentiation, and genome stability. However, how locus-specific DNA methylation is determined by intrinsic DNA sequence remains poorly understood. Here, we introduce Melody, a deep learning framework that predicts DNA methylation from 10-kb genomic sequences, enabling the integration of both local and long-range sequence signals. Across 39 human tissues, Melody accurately predicts methylation profiles and consistently outperforms existing state-of- the-art methods in whole-chromosome, hypomethylated-region, and cell-type-specific benchmarks. Melody also generalizes to methylation quantitative trait locus (meQTL) effect prediction and identifies regulatory sequence motifs associated with methylation variability. To extend prediction beyond profiled tissues, we further develop Melody-G, which incorporates single-cell RNA-seq foundation model embeddings to infer methylation states in previously unseen cell types directly from transcriptomic data. Together, Melody provides a unified framework for linking genomic sequence and cellular state to DNA methylation and offers new insights into the regulatory logic governing the human methylome.

bioinformatics↗

Isolation of the first cultured representative from a deep-branching phylum in serpentinite-hosted ecosystems

Serpentinization drives abiotic synthesis of organics (e.g., hydrocarbon) potentially conducive to the emergence of life, making serpentinite-hosted systems and associated microbial community key windows into nature of lifes origin. Although cultivation-independent studies uncovered the Candisdatus Bipolaricaulota widely distributed in serpentinizing environments, cultivation of this phylum has been unsuccessful. Here we cultured the first pure strain, J31, of Ca. Bipolaricaulota from the Lost City hydrothermal field, a well-characterized marine serpentinite system, using hydrocarbons as the primary nutrient source. As an early-branching bacterial lineage, strain J31 exhibits an unusual morphology composed of a central rod and elongated Toga-like extensions at both ends, and divides by binary fission. Strain J31 absorbs hexadecane through Toga ends via coordinated processes resembling inhalation and swallowing, after which hexadecane is efficiently transported to the central rod in the vesicle-like structures and subsequently converted into membrane lipids to support Toga synthesis and cellular growth. Hydrocarbon-degrading capability is widespread among the globally distributed members of Ca. Bipolaricaulota. Strain J31 colonizes serpentine minerals, facilitating the utilization of hydrocarbons derived from serpentines and promoting the release of soluble iron and silicon, thereby linking microbial activity to geochemical cycling. Thus, our study presents a novel strategy for cultivating deep-branching bacteria and offers insights into the metabolic foundations of early life on Earth--and potentially on other rocky planets undergoing serpentinization.

microbiology↗

ecDNA-driven oncogene super-expressors shape immunoevasive tumor microenvironment

ecDNA contributes to cancer genetic heterogeneity through random segregation during mitosis. Emerging evidence links ecDNA to immune evasion, but the mechanism remains elusive. Using genetically engineered mouse models of pancreatic ductal adenocarcinoma (PDAC), we show that Kras and Myc oncogenes are amplified either on ecDNAs or as homogeneously staining regions (HSRs) on chromosomes. ecDNA-driven tumors are more aggressive in immunocompetent mice. Single-cell transcriptomic and histological analyses reveal that ecDNA-driven tumors rapidly establish an immunoevasive tumor microenvironment (TME), marked by increased myofibroblastic cancer-associated fibroblasts (myCAFs) and reduced T cell infiltration. Mechanistically, ecDNA heterogeneity generates a subset of cancer cells with extremely high Kras expression, termed super-expressors, which secrete amphiregulin to promote myCAF expansion and suppress T cell infiltration. Clonally organized super-expressors establish an immunoevasive niche in the TME from patients with PDAC. Our findings demonstrate a causal role of ecDNA in TME remodeling, offering insights into cancer heterogeneity and immune evasion.

cancer biology↗

A novel 18F-labeled brain penetrant PET ligand for imaging poly(ADP-ribose) polymerase-1

Poly(ADP-ribose) polymerase-1 (PARP-1) is a key mediator of DNA repair, and its inhibition has become a validated therapeutic strategy in homologous recombination-deficient cancers. However, tools for non-invasive assessment of PARP-1-specific expression remain limited. Here, we evaluated [18F]AZD9574, a next-generation PARP-1-selective PET radiotracer. [18F]AZD9574 was tested in a panel of breast, glioblastoma, prostate, and pancreatic cancer cell lines. Uptake correlated with PARP-1 expression and was dose-dependently blocked by a variety of clinically relevant PARP inhibitors, confirming its binding specificity. In 22Rv1 xenograft mouse models, the tracer demonstrated significant tumor accumulation that was specific to PARP-1, and ex vivo biodistribution confirmed organ uptake consistent with specific tumor binding and PARP-1 expression. Together, these findings establish [18F]AZD9574 as a promising PARP-1-targeted imaging agent with strong potential for advancing cancer research and therapeutic monitoring.

cancer biology↗

In-Cell Synthesis of Nε-acetyl-L-lysine for Facile Protein Acetylation

N{varepsilon}-acetylation of proteins is a crucial post-translational modification (PTM) that occurs across all kingdoms of life and plays key roles in nearly every cellular process. Due to its broad significance, there is a strong demand for chemical biology tools that enable efficient, site-specific acetylation of target proteins in live cells. Genetic code expansion (GCE) has emerged as a powerful tool for introducing N{varepsilon}-acetylation at specific lysine residues in proteins. However, achieving adequate expression levels typically requires adding 2-10 mM of chemically synthesized N{varepsilon}-Acetyl-L-lysine (AcK) to the culture medium, which can be cumbersome and costly. To overcome this limitation, we present the first proof-of-concept for a one-pot acetylation platform that simplifies protein acetylation in both E. coli and mammalian cells. Our approach begins with the discovery of 10 novel lysine acetyltransferases (KATs) capable of biosynthesizing AcK from basic carbon sources. When these enzymes are co-expressed with the genetic incorporation machinery for AcK, they facilitate streamlined, site-specific acetylation of any target protein without compromising E. coli viability. This innovative platform not only broadens the range of unnatural amino acids (UAAs) that can be biosynthesized and incorporated but also provides a powerful tool for probing the histone and non-histone acetylation events in live cells. In addition, this technique offers an eco-friendly and scalable method to produce synthetic acetylated proteins, which will provide practical value in acetylation/deacetylation-related research such as chemical biology, biotechnology, and drug development.

synthetic biology↗

Hemin Inhibits the Activation of STING in Macrophages by Inducing HO-1, Promoting Endometriosis Development

IntroductionEndometriosis (EMS) is an estrogen-dependent inflammatory disorder characterized by immune dysregulation. This condition profoundly affects the quality of life and reproductive health of nearly 200 million women of reproductive age worldwide and poses significant clinical challenges due to lack of diagnosis tools and effective treatment. Peritoneal macrophages play a central role in promoting the initiation and progression of EMS. Bioinformatics studies have indicated that the STimulator of INterferon Gene (STING) was downregulated in the macrophages in EMS, and this influenced their polarization and functional. However, the specific contribution of STING pathway alterations to EMS pathogenesis remains unclear. MethodsWe integrated scRNA-seq data from EMS patients and healthy controls-including lesions, eutopic endometrium, non-lesional tissue, and peritoneal fluid from EMS patients and healthy controls(n = 19,291 total samples)-to analyze macrophage STING expression and function. Mouse EMS model was generated by injecting uterus fragments into WT or STING-/- mice. Peritoneal fluid was collected and macrophage proportions and subtypes were assessed via flow cytometry. Macrophages were depleted in STING-/- mice prior to EMS induction to evaluate their role in disease progression. In vitro, hemin was used to treat macrophages to investigate how heme oxygenase-1 (HO-1) modulates the STING pathway, assessed through immunoblotting, co-immunoprecipitation, ELISA, and multiplex immunofluorescence. ResultsBioinformatic analysis revealed that macrophages within the EMS lesions are primarily derived from peritoneal macrophages and exhibit decreased STING expression, which correlated negatively with HO-1. STING-/- mice developed more numerous and larger EMS lesions, accompanied by a decreased proportion of large peritoneal macrophages and an increase in small peritoneal macrophages. A marked elevation in M2-type macrophages within the lesions was detected in STING-/- mice. In vitro, hemin-induced HO-1 suppressed STING pathway activation in macrophages. Mechanistically, HO-1 inhibited the translocation of STING from the endoplasmic reticulum to the Golgi, thereby suppressing STING signaling and facilitating EMS. ConclusionMacrophages are essential for lesion formation in STING-/- mice. In vitro, hemin promotes EMS progression via HO-1 - mediated suppression of the STING pathway. Our findings identify the heme-HO-1-STING axis as a key immunomodulatory pathway in EMS and suggest its potential as a therapeutic target. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=157 SRC="FIGDIR/small/683839v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@6901beorg.highwire.dtl.DTLVardef@1f18d44org.highwire.dtl.DTLVardef@1716f6forg.highwire.dtl.DTLVardef@4ae22d_HPS_FORMAT_FIGEXP M_FIG Graphical abstract (Created in BioRender.com) Retrograde menstruation leads to the accumulation of heme in the peritoneal cavity, which upregulates HO-1 expression in peritoneal macrophages. HO-1 inhibits the translocation of STING from the endoplasmic reticulum to the Golgi apparatus in macrophages, thereby suppressing the STING pathway and promoting the development and progression of EMS. The progression of EMS, in turn, reinforces this mechanism, creating a self-sustaining vicious cycle. C_FIG

immunology↗

Unfolding the Black Box of Recurrent Neural Networks for Path Integration

Path integration is essential for spatial navigation. Experimental studies have identified neural correlates for path integration, but exactly how the neural system accomplishes this computation remains unresolved. Here, we adopt recurrent neural networks (RNNs) trained to perform a path integration task to explore this issue. After training, we borrow neuroscience prior knowledge and methods to unfold the black box of the trained model, including: clarifying neuron types based on their receptive fields, dissecting information flows between neuron groups by pruning their connections, and analyzing internal dynamics of neuron groups using the attractor framework. Intriguingly, we uncover a hierarchical information processing pathway embedded in the RNN model, along which velocity information of an agent is first forwarded to band cells, band and grid cells then coordinate to carry out path integration, and finally grid cells output the agent location. Inspired by the RNN-based study, we construct a neural circuit model, in which band cells form one-dimensional (1D) continuous attractor neural networks (CANNs) and serve as upstream neurons to support downstream grid cells to carry out path integration in the 2D space. Our study challenges the conventional view of considering grid cells as the principal velocity integrator, and supports a neural circuit model with the hierarchy of band and grid cells.

neuroscience↗

TyCHE enables time-resolved lineage tracing of heterogeneously-evolving populations

Phylogenetic methods for cell lineage tracing have driven significant insights into organismal development, immune responses, and tumor evolution. While most methods estimate mutation trees, time-resolved lineage trees are more interpretable and could relate events like cellular migration and differentiation to perturbations like vaccines and drug treatments. However, somatic mutation rates vary dramatically by cell type, significantly biasing existing methods. We introduce TyCHE (Type-linked Clocks for Heterogeneous Evolution), a Bayesian phylogenetics package that infers time-resolved phylogenies of populations with distinct evolutionary rates. We demonstrate that TyCHE improves tree accuracy using a new simulation package SimBLE (Simulator of B cell Lineage Evolution). We use TyCHE to infer patterns of memory B cell differentiation during HIV infection, dynamics of recall germinal centers following influenza vaccination, evolution of a glioma tumor lineage, and progression of a bacterial lung infection. TyCHE and SimBLE are available as open-source software packages compatible with the BEAST2 and Immcantation ecosystems.

immunology↗

Stromal subsets modulate T-cell infiltration in early breast cancer

Recent studies of the tumour microenvironment have elucidated the heterogeneity of stromal cells, with increasing evidence suggesting that stromal subsets play an important role in regulating anti-tumour immunity in breast cancer. However, the functional diversity of these cells within the tumour immune microenvironment and how they interact with immune cells in a spatial and clinical context remain poorly understood. We performed multiplex immunofluorescence on tumour microarrays from two cohorts consisting of 591 breast cancer patients to assess the abundance and spatial co-localisation of stromal and immune subsets and their correlation with clinicopathological features and patient outcomes. We found that stromal cells were spatially distinct. A perivascular-like subset that was disseminated throughout the stroma rather than restricted to vessel-adjacent regions was enriched in an immune cold environment and associated with T-cell exclusion. An inflammatory-like cancer-associated fibroblast subset was associated with segregation of T cells from cancer cells. Our findings highlight the differential impact of stromal subsets on immune infiltration and activation within the breast cancer tumour microenvironment with potential implications for patient outcomes. SignificanceThis study characterised spatially-defined interactions between stromal and immune subsets in large clinical cohorts of early breast cancer. Findings from this study will contribute to gaps in current knowledge in how diverse stromal cell subsets, particularly novel subsets, interact with immune cells in a clinically-relevant context.

cancer biology↗

Structural basis for MurJ inhibition by phage lysis protein SglPP7 suggesting convergence

Some bacteriophages encode lysis proteins that inhibit essential bacterial processes, the elucidation of which is valuable for developing antibacterial strategies against drug-resistant pathogens. We determined the cryo-EM structure of the complex between the essential E. coli lipid II flippase MurJ and a phage lysis protein, SglPP7. MurJ was locked in an outward-facing conformation by SglPP7, similar to the MurJ/LysM complex; however, distinct interactions suggest convergent evolution among phage lysis proteins.

molecular biology↗

Aberrant Neural Entrainment to Word-Level Speech Patterns in Fragile X Syndrome: Evidence for a Statistical Learning Deficit

Fragile X syndrome (FXS), the most common inherited cause of intellectual disability and autism spectrum disorder, causes significant language and cognitive impairments. Statistical learning refers to the ability to extract patterns from sensory input through mere exposure and plays a central role in language acquisition. Surprisingly, statistical learning in FXS has not been explored. Given that children with FXS typically follow a delayed developmental trajectory for language, we hypothesized that they would show impaired statistical learning. To test this hypothesis, we used an EEG measure of neural entrainment to index statistical learning of hidden trisyllabic words within a continuous speech stream in children with FXS (n = 17) and in typically developing controls (n = 31). Children with FXS showed significantly reduced neural entrainment to words compared to controls, particularly in the superior temporal gyrus and transverse temporal gyrus (primary auditory cortex), providing evidence of statistical learning impairment. Notably, syllable-level entrainment was preserved or even enhanced in FXS, indicating that word-level deficits cannot be attributed to general auditory processing impairments. In addition, while typically developing controls showed an increase in word-level entrainment over the course of learning, children with FXS failed to show a similar increase over time. Taken together, this pattern of results demonstrates that children with FXS can process rapid, lower-order acoustic structure but struggle to integrate these syllables into longer, chunk-like word representations. Overall, these findings suggest that statistical learning is impaired in FXS, and also suggest neural entrainment to statistical structure as a potential therapeutic target.

neuroscience↗