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Wang, N.

Publications and source records attributed to Wang, N..

At least 109 records · Page 6Linked to original sources

Passive muscle forces in Drosophila are large but insufficient to support a flys weight

Movement of a limb is shaped by active forces generated by muscle contraction but also by passive forces within individual muscles and joints. In small animals such as insects, the contribution of passive forces to limb movement can match the active forces. However, most measurements of passive forces are limited to the femur-tibia joint in large insects. Here we take advantage of genetic tools in Drosophila to measure passive torques at multiple joints in the flys leg. We genetically inactivate all the motor neurons to assess passive forces. We find that the passive torques are well approximated by a linear spring, i.e., the passive torques linearly increase with angular deviation from the rest angle. The torques are much larger than the gravitational torque due to the leg itself. We estimate that the passive torques are seventy times smaller than necessary to support the weight of the animal. We also inactivated all the motor neurons in a freely standing fly and found that, as predicted from the model, the fly falls when the motor neurons are inactivated. We found that the height at which a fly stands, and, therefore the active forces vary. The flys height affects the time to initiate a fall. The time it takes for the fall is consistent with the active forces decaying with a time constant of [~]100 ms. Thus, although passive forces are strong and will have a large effect on limb kinematics, they are not strong enough to support the weight of the fly.

neuroscience↗

FilaBuster: A Strategy for Rapid, Specific, and Spatiotemporally Controlled Intermediate Filament Disassembly

Intermediate filaments (IFs) play key roles in cellular mechanics, signaling, and organization, but tools for their rapid, selective disassembly remain limited. Here, we introduce FilaBuster, a photochemical approach for efficient and spatiotemporally controlled IF disassembly in living cells. FilaBuster uses a three-step strategy: (1) targeting HaloTag to IFs, (2) labeling with a covalent photosensitizer ligand, and (3) light-induced generation of localized reactive oxygen species to trigger filament disassembly. This modular strategy applies broadly across IF subtypes--including vimentin, GFAP, desmin, peripherin, and keratin 18--and is compatible with diverse dyes and imaging platforms. Using vimentin IFs as a model system, we establish a baseline implementation in which vimentin-HaloTag labeled with a photosensitizer HaloTag ligand triggers rapid and specific IF disassembly upon light activation. We then refine this approach by (i) expanding targeting strategies to include a vimentin nanobody-HaloTag fusion, (ii) broadening the range of effective photosensitizers, and (iii) optimizing irradiation parameters to enable precise spatial control over filament disassembly. Together, these findings position FilaBuster as a robust platform for acute, selective, and spatiotemporally precise disassembly of IF networks, enabling new investigations into their structural and functional roles in cell physiology and disease.

cell biology↗

Loss of Kmt2c/d promotes gastric cancer initiation and confers vulnerability to mTORC1 inhibition and anti-PD1 immunotherapy

KMT2C and KMT2D (KMT2C/D) are frequently mutated in gastric adenocarcinoma, yet their function in cancer initiation remains poorly understood. In this study, based on the observation that loss-of-function mutations of KMT2C and KMT2D are enriched and co-occur in gastric adenocarcinoma, we developed genetically engineered mouse models to selectively knock out Kmt2c and Kmt2d in gastric epithelial cells with Tmprss2-CreERT2. Through histological staining and single-cell RNA sequencing, we observed that Kmt2c/d loss led to nuclear dysplasia and expansion of cells with mixed gastric lineage markers. When combined with Pten deletion, Kmt2c/d loss drove rapid development of muscle-invasive gastric adenocarcinoma as early as 3 weeks post Cre-mediated gene deletion. The adenocarcinoma exhibited decreased expression of gastric lineage markers and increased expression of intestinal differentiation markers, phenocopying human gastric adenocarcinoma. Kmt2c/d knockout reduced protein synthesis but upregulated transcription of ribosomal proteins, rendering sensitivity to mTORC1 inhibitors. Additionally, Kmt2c/d knockout increased MHC-I molecule expression and enhanced antigen presentation. Combination of mTROC1 inhibition and anti-PD1 immunotherapy significantly suppressed tumor growth in immune-competent mice. Together, these findings reveal the role of Kmt2c/d loss in gastric cancer initiation and suggest the potential therapeutic strategies for KMT2C/D-deficient gastric cancer.

cancer biology↗

Single-cell multiome and enhancer connectome of human retinal pigment epithelium and choroid nominate pathogenic variants in age-related macular degeneration

Age-related macular degeneration (AMD) is a leading cause of vision loss worldwide. Genome-wide association studies (GWAS) of AMD have identified dozens of risk loci that may house disease targets. However, variants at these loci are largely noncoding, making it difficult to assess their function and whether they are causal. Here, we present a single-cell gene expression and chromatin accessibility atlas of human retinal pigment epithelium (RPE) and choroid to systematically analyze both coding and noncoding variants implicated in AMD. We employ HiChIP and Activity-by-Contact modeling to map enhancers in these tissues and predict cell and gene targets of risk variants. We further perform allele-specific self-transcribing active regulatory region sequencing (STARR-seq) to functionally test variant activity in RPE cells, including in the context of complement activation. Our work nominates new pathogenic variants and mechanisms in AMD and offers a rich and accessible resource for studying diseases of the RPE and choroid.

genomics↗

A humanized 16A antibody conjugated with DNA topoisomerase I inhibitors, targeting a GSTA glycosite-signature epitope.

BackgroundWe previously reported the 16A antibody, which binds to the abnormally glycosylated tandem repeat region of the MUC1 glycoprotein, and developed 16A-MMAE as an antibody-drug conjugate. However, its antitumor efficacy as an antibody-drug conjugate with DNA topoisomerase Iinhibitors remains unknown. MethodsWe humanized the 16A antibody and conjugated it to DXd and MF6, two DNA topoisomerase I inhibitors. The antitumor efficacy of the conjugates was evaluated in vitro and in vivo. ResultsThe humanized 16A-DXd conjugate showed potent antitumoral efficacy, with an IC50 in the nM range against CFPAC1 cells. In vivo, h16A-DXd and h16A-MF6 inhibited tumor growth in asubcutaneous mouse tumor transplantation model using CT26-COSMC KO-hMUC1 cells, administered at a dose of 10 mg/kg. ConclusionsThe high antitumor efficacy of h16A-conjugated DNA topoisomerase I inhibitors supports further clinical development. The relatively low toxicity of h16A-DXd and h16A-MF6 may enable a higher therapeutic window, since MUC1-positive cells internalize the antibody-drug conjugate more efficiently.

pharmacology and toxicology↗

The TALE effector PthA4 of Xanthomonas citri subsp. citri indirectly activates an expansin gene CsEXP2 and an endoglucanase CsEG1 via CsLOB1 to cause citrus canker symptoms

Citrus canker caused by Xanthomonas citri subsp. citri (Xcc) is an important citrus disease worldwide. PthA4 is the most important pathogenicity gene of Xcc and encodes a transcription activator like effector (TALE) secreted by the type III secretion system. PthA4 is known to activate the expression of CsLOB1, the canker susceptibility gene and a transcription factor, to cause citrus canker symptoms. Extensive effort was made to identify downstream targets of CsLOB1 to investigate the mechanism underlying canker symptom development. However, none of identified CsLOB1 target genes have been confirmed to be involved in citrus canker development. Here, we first identified the direct targets of CsLOB1 by generating promoter-uidA (GUS) reporter fusion construct for the 13 genes highly induced by both PthA4 and CsLOB1 and monitored the reporter activity in N. benthamiana leaves co-expressing CsLOB1. Agrobacterium tumefaciens-mediated transient expression of CsLOB1 activated seven gene promoters in N. benthamiana including Cs7g18460, Orange1.1t00600, Cs6g17190, Cs7g32410 (CsEXP2), Cs2g27100, Cs2g20750 (CsEG1), and Cs9g17380. Next, we constructed dTALEs to target unique sequences in the promoters of the seven direct target genes of CsLOB1 and transformed them into XccpthA4::Tn5 mutant. Our results indicate that a combination of 5 and 7 dTALEs caused canker-like symptoms in the inoculated citrus leaves. In addition, dTALECsEXP2 and dTALECsEG1 caused water soaking and pustules, which are typical canker symptoms. Taken together, Xcc indirectly activates CsEXP2 and CsEG1 via PthA4-CsLOB1 to cause canker symptoms. Author summaryPtha4 is responsible for the canker symptoms of Xcc and activate the expression of CsLOB1 of citrus to cause the canker symptoms. Extensive effort by multiple groups has been made to identify downstream targets of CsLOB1 to understand the mechanism underlying canker symptom development. However, none of the CsLOB1 targets have been shown to cause canker symptoms. Here we have demonstrated that Xcc indirectly activates CsEXP2, an expansin gene, and CsEG1, an endoglucanase, via PthA4-CsLOB1 to cause canker symptoms. Identification of direct targets of CsLOB1 provides alternative target genes for genetic improvement of citrus against canker via genome editing.

plant biology↗

clusIBD: Robust Detection of Identity-by-descent (IBD) Segments Using Unphased Genetic Data from Poor-quality DNA Samples

Inferring relatedness through the detection of identity-by-descent (IBD) segments is widely used in many fields. However, existing methods are often powerless for poor-quality DNA samples. Here, we propose a method, clusIBD, which can robustly detect IBD segments using unphased genetic data with high genotype errors. We evaluated and compared the performance of clusIBD with IBIS, TRUFFLE, and IBDseq using simulated data, artificial poor-quality materials and ancient DNA samples. The results showed that clusIBD outperformed these state-of-the-art existing tools and may be a promising tool for kinship inference in fields such as ancient DNA analysis and criminal investigation (freely available at https://github.com/Ryan620/clusIBD/).

genetics↗

Design of solubly expressed miniaturized SMART MHCs

The precise recognition of specific peptide-MHC (pMHC) complexes by T-cell receptors (TCRs) plays a key role in infectious disease, cancer and autoimmunity. A critical step in many immunobiological studies is the identification of T-cells expressing TCRs specific to a given pMHC antigen. However, the intrinsic instability of empty class-I MHCs limits their soluble expression in Escherichia coli (E. coli) and makes it very difficult to characterize even a small fraction of possible pMHC/TCR interactions. To overcome this limitation, we designed small proteins which buttress the peptide binding groove of class I MHCs, replacing {beta}2-microglobulin ({beta}2m) and the heavy chain 3 domain, and enable soluble expression of both H-2Db and A*02:01 in E. coli. We demonstrate that these soluble, monomeric, antigen-receptive, truncated (SMART) MHCs retain both peptide- and TCR-binding specificity, and that peptide-bound structures of both allomorphs are similar to their full-length, native counterparts. With extension to the majority of HLA alleles, SMART MHCs should be broadly useful for probing the T-cell repertoire in approaches ranging from yeast display to T-cell staining. SignificanceDespite the critical role that TCR/pMHC interactions play in human health, it has remained difficult to produce reagents necessary to study them. Requirements for refolding or sequence optimization limit immunologists and biochemists ability to characterize diverse pMHC/TCR interactions. Here, we develop a de-novo designed protein domain that stabilizes the H-2Db and A*02:01 class I MHC allomorphs, allowing soluble expression in E. coli without the need for a stabilizing peptide, and improving display on the yeast surface, while maintaining peptide and TCR binding interactions. These features facilitate a wide range of experiments to more fully understand the nature of pMHC/TCR interactions, and pave the way for the development of stabilizing domains for all MHC allomorphs.

biochemistry↗

Distinguish risk genes functioning at presynaptic or postsynaptic regions and key connectomes associated with pathological α-synuclein spreading

Previous studies have suggested that pathological -synuclein (-Syn) mainly transmits along the neuronal network, but several key questions remain unanswered: (1) How many and which connections in the connectome are necessary for predicting the progression of pathological -Syn? (2) How to identify risk gene that affects pathology spreading functioning at presynaptic or postsynaptic regions, and are these genes enriched in different cell types? Here, we addressed these key questions with novel mathematical models. Strikingly, the spreading of pathological -Syn is predominantly determined by the key subnetworks composed of only 2% of the strongest connections in the connectome. We further explored the genes that are responsible for the selective vulnerability of different brain regions to transmission to distinguish the genes that play roles in presynaptic from those in postsynaptic regions. Those risk genes were significantly enriched in microglial cells of presynaptic regions and neurons of postsynaptic regions. Gene regulatory network analyses were then conducted to identify key drivers of genes responsible for selective vulnerability and overlapping with Parkinsons disease risk genes. By identifying and discriminating between key gene mediators of transmission operating at presynaptic and postsynaptic regions, our study has demonstrated for the first time that these are functionally distinct processes.

neuroscience↗

Single-cell copy number alteration signature analysis reveals masked patterns and potential biomarkers for cancer

Copy number alteration (CNA) is a major type of cancer genome alteration that drives cancer progression. CNA signature analysis can reveal underlying etiology and provide biomarkers for cancer treatment, and existing CNA signature analyzes are all performed using bulk tissue samples. However CNA usually affect large proportion of genome, and the CNA profile of bulk sample does not reflect the actual CNA profiles of the individual cancer cells of the sample, especially in tumors with high heterogeneity, such as hepatocellular carcinoma (HCC). Furthermore, the evolutionary trajectory of CNA mutational processes still remain elusive. Here we build a method to comprehensively analyze the CNA signatures of HCC from single-cell and bulk sample perspective, revealing patterns and potential noise signals from the usually performed bulk tissue CNA signature analysis. Single-cell signature analysis delineated the evolutionary trajectory of HCC CNA signatures, and different CNA signatures consistently emerge in different HCC evolution stages. Single-cell CNA signatures show robust performance in patient prognosis and drug sensitivity prediction. This work not only reveals specific considerations in analyzing CNA signature derived from bulk tissue but also depicts CNA evolution process and provides potential biomarkers for the prognosis and treatment of HCC patients. HighlightSingle-cell analysis reveals CNA signatures masked in bulk tissue. Single-cell analysis delineates the evolutionary trajectory of CNA signature. Small CNAs occur early and large CNAs happens late in HCC evolution. Single-cell CNA signatures show robust performance in guiding cancer clinical treatment.

genomics↗

Macrogenetic atlas of prokaryotes

Macrogenetics investigates patterns and predictors of intraspecific genetic variation across diverse taxa, offering a framework for understanding species diversity and addressing evolutionary hypotheses. Here, we present a macrogenetic atlas of prokaryotes (MAP), integrating genomic data from 15,235 prokaryotic species (30 parameters in 12 categories) and population genetic data from 786 species (22 parameters in 7 categories), together with phylogenetic, phenotypic, and ecological information. MAP enables quantitative species characterization, straightforward cross-species comparisons, and easy generation, testing, and refinement of evolutionary hypotheses. For example, our analyses show that long- and short-range genetic linkage capture distinct evolutionary dynamics and independently shape genetic diversity. Further, we propose that as within-species diversity increases, epistatic selection increasingly contributes to shaping genetic diversity, exemplified by convergent selection-driven structures (ecospecies) identified in Streptococcus mitis and S. oralis. Overall, MAP represents a widely applicable resource (www.genomap.cn) and offers novel insights into the drivers of macroevolution and the life cycle of prokaryotic species.

microbiology↗

Le Petit Prince (LPP) Multi-talker: Naturalistic 7T fMRI and EEG Dataset

Prior neuroimaging datasets using naturalistic listening paradigms have predominantly focused on single-talker scenarios. While these studies have been invaluable for advancing our understanding of speech and language processing in the brain, they do not capture the complexities of real-world multi-talker environments. Here, we introduce the "Le Petit Prince (LPP) Multi-talker Dataset", a high-quality, naturalistic neuroimaging dataset featuring 40 minutes of electroencephalogram (EEG) and 7T functional magnetic resonance imaging (fMRI) recordings from 26 native Mandarin Chinese speakers as they listened to both single-talker and multi-talker speech streams. Validation analyses conducted on both EEG and fMRI data demonstrate the datasets high quality and robustness. Additionally, the dataset includes detailed transcriptions and prosodic and linguistic annotations of the speech stimuli, enabling fine-grained analyses of neural responses to specific linguistic and acoustic features. The LPP Multi-talker Dataset is well-suited for addressing a wide range of research questions in cognitive neuroscience, including selective attention, auditory stream segregation, and working memory processes in naturalistic listening contexts.

neuroscience↗

Themis dominates T cell exhaustion by regulation of TCR and PD-1 signaling

T cell exhaustion is important to protect the host from immunopathology during chronic viral infection, but it also impairs T cell anti-tumor immunity1-5. A fundamental unresolved question is whether and how T cell exhaustion is determined at the onset of TCR signaling6-8. Here we report an unexpected role of Themis, a TCR-proximal signaling molecule9, in T cell exhaustion. Chronic viral infection in mice usually leads to T cell exhaustion and survival of the host. Surprisingly, Themis T-cell conditional knockout mice died from severe CD8+-dependent lung immunopathology in chronic viral infection, showing Themis importance in establishing T cell exhaustion. We found that Themis-deficient CD8+ T cells were hyperactivated at the single-cell level - producing more TNF and IFN{gamma} compared to wild-type counterparts - but defective in population-level expansion. Moreover, TCF-1 and TOX expression were inhibited in Themis-deficient CD8+ T cells, thereby impairing differentiation of exhausted T cell precursors (T-pex) and maintenance of terminally exhausted T cells (T-ex), respectively. Mechanistically, Themis initially promotes TCR signaling to induce PD-1 expression and subsequently mediates PD-1 signaling. In the latter, Themis binds to PD-1 and promotes PD-1 phosphorylation and its recruitment of SHP2, thereby acting as a negative regulator to inhibit T cell effector functions. Without Themis, the orderly regulation of TCR and PD-1 signaling, and therefore exhaustion, is disrupted. Thus, our results unequivocally demonstrate that Themis-mediated early TCR signaling plays a decisive role in T cell exhaustion and provide a novel mechanism of PD-1 signaling through Themis.

immunology↗

Tumor-associated stroma shapes the spatial tumor immune microenvironment of primary Ewing sarcomas

To date, few studies have detailed the tumor microenvironment (TME) of Ewing sarcoma (EwS). The TME has a vital role in cancer survival and progression with implications in drug resistance and immune escape. By performing spatially resolved transcriptomic analysis of primary treatment-naive EwS samples, we discovered greater stromal enrichment in localized EwS tumors compared to metastatic EwS tumors. Through spatial ligand-receptor analysis, we show that the stromal enriched regions harbor unique extracellular matrix related cytokines, immune recruitment and proinflammatory microenvironmental signals, implying EwS stroma may play an anti-tumorigenic role by acting as an immune recruitment center. All EwS tumors expressed pro-tumorigenic MIF-CD74 immune signaling, suggesting a potential immune-evasive mechanism and immunotherapy target. Our findings provide insight into tumor cell/stromal cell interactions in EwS and serve as a valuable resource for further investigations in the tumor immune microenvironment of EwS.

cancer biology↗

Spatiotemporal changes in soil properties predict plant health at continental scale

Abiotic and biotic soil properties are strong predictors of plant yield globally1-5, but they become unreliable over large areas when plant health is threatened by pathogen6-8. Here we present a novel approach to predict plant health based on spatiotemporal changes in soil chemical and biological properties. We first demonstrate that plant health and soil properties consistently respond to environmental change (organic fertilization) regardless of the soil type or geographical origin. Second, we experimentally show that trackable shifts in soil properties reliably explain soil suppressiveness to the Ralstonia solanacearum bacterial pathogen and that a scalable spatiotemporal model predicts plant health with 84% accuracy across multiple climatic zones and cropping systems. Our results suggest that this tight coupling between soil properties and plant health could facilitate the development of agricultural practices aimed at sustainably improving crop yields while safeguarding crop health.

ecology↗

Neuronal LAG3 facilitates pathogenic α-synuclein neuron-to-neuron propagation

Lymphocyte activation gene 3 (LAG3) is a key receptor involved in the propagation of pathological proteins in Parkinsons disease (PD). This study investigates the role of neuronal LAG3 in mediating the binding, uptake, and propagation of -synuclein (Syn) preformed fibrils (PFFs). Using neuronal LAG3 conditional knockout mice and human induced pluripotent stem cells-derived dopaminergic (DA) neurons, we demonstrate that LAG3 expression is critical for pathogenic Syn propagation. Our results show that the absence of neuronal LAG3 significantly reduces Syn pathology, alleviates motor dysfunction, and inhibits neurodegeneration in vivo. Electrophysiological recordings revealed that Syn PFFs induce pronounced neuronal hyperactivity in wild-type (WT) neurons, increasing firing rates in cell-attached and whole-cell configurations, and reducing miniature excitatory postsynaptic currents. In contrast, neurons lacking LAG3 resisted these electrophysiological effects. Moreover, treatment with an anti-human LAG3 antibody in human DA neurons inhibited Syn PFFs binding and uptake, preventing pathology propagation. These findings confirm the essential function of neuronal LAG3 in mediating Syn propagation and associated disruptions, identifying LAG3 as a potential therapeutic target for PD and related -synucleinopathies.

neuroscience↗

Elastase mediated white matter damage in cerebral small vessel disease: Microglia - neutrophils pas de deux

Cerebral small vessel disease (CSVD) leads to an extensive white matter damage associated with cognitive decline, yet the underlying damaging mechanisms remain incompletely understood. Here we established a positive correlation between plasma levels of serine proteinase elastase ELANE and periventricular white matter hyperintensity (PV-WMH) in a cohort of CSVD patients. In a CSVD murine model induced by bilateral carotid artery stenosis (BCAS), upregulated ELANE was detected both in microglia and peripheral blood neutrophils. Genetic ELANE deficiency significantly alleviated oligodendrocyte loss, thereby reducing white matter lesions (WMLs) as well as ameliorating sensorimotor and cognitive impairments in BCAS mice. In vitro studies demonstrated that ELANE triggered time-dependent and dose-dependent oligodendrocyte lineage cell death. Bone marrow transplantation showed that ELANE from microglia and peripheral blood both contributed to WML development and BCAS-induced neurological deficits. Mechanistically, ELANE, accumulated by oligodendrocytes, cleaved the phosphodiesterase domain of 2',3'-cyclic nucleotide 3'-phosphodiesterase (CNPase). Pharmacological inhibition of ELANE with Sivelestat reduced oligodendrocyte loss and WMLs leading to the restoration of white matter integrity and neurological improvements in BCAS mice. In post-mortem brain specimens of CSVD patients ELANE accumulated within WMLs being predominantly localized in microglia (and hence defined as microglial ELANE) rather than in the brain-infiltrating neutrophils. We therefore posit microglial ELANE as an instigator of whiter matter injury in CSVD and suggest its potential therapeutic relevance.

neuroscience↗

De novo design and structure of a peptide-centric TCR mimic binding module

T cell receptor (TCR) mimics offer a promising platform for tumor-specific targeting of peptide-MHC in cancer immunotherapy. Here, we designed a de novo -helical TCR mimic (TCRm) specific for the NY-ESO-1 peptide presented by HLA-A*02, achieving high on-target specificity with nanomolar affinity (Kd = 9.5 nM). The structure of the TCRm/pMHC complex at 2.05 [A] resolution revealed a rigid TCR-like docking mode with an unusual degree of focus on the up-facing NY-ESO-1 side chains, suggesting the potential for reduced off-target reactivity. Indeed, a structure-informed in silico screen of 14,363 HLA-A*02 peptides correctly predicted two off-target peptides, yet our TCRm maintained a wide therapeutic window as a T cell engager. These results represent a path for precision targeting of tumor antigens with peptide-focused -helical TCR mimics.

immunology↗