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Huang, T.

Publications and source records attributed to Huang, T..

At least 37 records · Page 2Linked to original sources

Ablation of microglial estrogen receptor alpha predisposes to diet-induced obesity in male mice

Estrogen receptor alpha (ER) signaling has metabolic and anti-inflammatory properties in addition to its impact on reproductive function. In male but not female mice, inflammatory activation of microglia, the resident macrophages of the brain, has been implicated in the pathogenesis of diet-induced obesity (DIO), raising the possibility that differences in microglial estrogen signaling may account for the sexual dimorphism. In this study, we assessed metabolic and CNS histopathological properties in a mouse model with inducible microglia-specific ablation of ER (MG-ERKO). Male MG-ERKO mice developed increased weight gain and insulin resistance relative to controls during high-fat diet (HFD) feeding. Indirect calorimetry analysis revealed that reduced energy expenditure was the main driver of the obese phenotype. In contrast, female MG-ERKO mice fed HFD developed mild insulin resistance with no change in body weight gain compared to controls. Immunohistochemical analyses of the microglial activation marker IBA1 in the mediobasal hypothalamus (MBH) revealed that female MG-ERKO mice had an increased number of microglia without showing morphological signs of activation. In contrast, MBH microglial number was unchanged in MG-ERKO male mice, but the cells adopted more activated morphological profiles. Finally, HFD-fed MG-ERKO male mice had increased POMC neuron-microglia interactions but fewer overall hypothalamic POMC neurons, suggesting microglia may disrupt POMC neuron integrity to promote DIO. Together, these findings indicate that sex-specific actions of estrogen in microglia limit the metabolic complications of HFD feeding.

neuroscience↗

Modulating inter-mitochondrial contacts to increase membrane potential for mitigating blue light damage

Mitochondrial membrane potential (MMP) is essential for mitochondrial functions, yet current methods for modulating MMP lack precise spatial and temporal control. Here, we present an optogenetic system that enables reversible formation of inter-mitochondrial contacts (mito-contacts) with high spatiotemporal precision. Blue light stimulation induces rapid formation of mito-contacts, which fully dissipate upon cessation of illumination. These light-induced mito-contacts can enhance MMP, leading to increased ATP production under stress conditions. Moreover, in human retinal cells and C. elegans, high MMP induced by mito-contacts alleviates the deleterious effects of prolonged blue light exposure, restoring energy metabolism and extending organismal lifespan. This optogenetic approach provides a powerful tool for modulating MMP and offers potential therapeutic applications for diseases linked to mitochondrial dysfunction.

biophysics↗

Deep multiplexed 50-marker imaging of circulating tumor cells expands actionable biomarker profiling for precision oncology

Liquid biopsy-derived circulating tumor cells (CTCs) offer a minimally invasive avenue for precision oncology by enabling longitudinal monitoring of actionable molecular and cell-phenotypic biomarkers. However, conventional immunofluorescence imaging-based CTC profiling captures just 4-5 markers per cell, restricting crucial insights into oncogenic and resistance drivers, as well as tumor cell heterogeneity. Here we present an integrated pipeline employing deep multiplexed imaging to profile up to 50 molecular markers per CTC, capturing expression, phosphorylation, and subcellular localization of diverse biomarkers. Validated in a multi-stage prostate cancer resistance model and applied to prostate cancer patient-derived CTCs, this approach enhances CTC classification and reveals inter- and intra-patient heterogeneity correlating with therapy response. Machine learning identified therapeutically actionable signatures, suggesting patient-specific treatment strategies. This deep multiplexed imaging pipeline advances the utility of CTCs in guiding personalized cancer therapy by providing comprehensive molecular and phenotypic insights through minimally invasive liquid biopsies. Highlights- Multiplexed immunofluorescence imaging of circulating tumor cells captures up to 50 molecular markers per cell with subcellular localisation. - Single-cell and subcellular analyses identify quantitative signatures correlating with patient outcome, as well as therapeutically actionable biomarkers. - This method transforms the utility of CTCs for future use in patient stratification and for guiding personalised therapies. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=181 SRC="FIGDIR/small/684075v1_ufig1.gif" ALT="Figure 1"> View larger version (47K): org.highwire.dtl.DTLVardef@a36ff4org.highwire.dtl.DTLVardef@b06c1org.highwire.dtl.DTLVardef@1e8a572org.highwire.dtl.DTLVardef@c60753_HPS_FORMAT_FIGEXP M_FIG Graphical Abstract C_FIG

cancer biology↗

A Population-scale Single-cell Spatial Transcriptomic Atlas of the Human Cortex

The genetic and spatial determinants of cell type diversity in human cerebral cortices remain poorly defined. Here, we present a population-level single-cell spatial transcriptomic atlas of human cortices from 71 donors across the lifespan. We identified 906 layer-specific genes showing conserved and divergent laminar expression patterns between humans and other species. Spatial analysis revealed neuronal vulnerability and glial activation during aging, together with a decline in the proportion of superficial SST neurons and their interactions with other cells. Disease-associated genes exhibited high cell-type and layer-specific expression, implicating the pathogenic role of spatially specific gene expression. Spatial cis-eQTL analysis identified regulatory variants linked to genes related to diseases like Tourette syndrome. Cross-species comparison demonstrated glial expansion in the human cortex, accompanied by enhanced neuron-glia communication via the neuregulin signaling. Together, we provide a comprehensive single-cell atlas of the human cortex that is essential for understanding aging, evolution, and disease pathogenesis.

neuroscience↗

Study on Early pregnancy diagnosis in sows based on joint analysis of vaginal secretion metabolomics and machine learning

ObjectiveMetabolic transformations in female mammals throughout gestation manifest in the metabolite profiles of bodily fluids, potentially serving as biomarkers for the diagnosis of pregnancy. This investigation concentrated on sows 18 days post-mating, with the objective of identifying biomarkers pertinent to early pregnancy diagnosis through the analysis of variations in metabolic molecules within vaginal secretions. MethodsVaginal secretion samples were procured from both pregnant and non-pregnant sows 18 days post-mating, subsequently subjected to untargeted metabolomic analysis utilizing liquid chromatography-mass spectrometry (LC-MS). The samples were partitioned into training and testing datasets, and machine learning algorithms--specifically, Random Forest (RF) and support vector machine (SVM)--were integrated with metabolite weight ranking to identify key biological markers. ResultsA total of 3,249 metabolic molecules were identified, among which 534 exhibited significant differential expression in the vaginal secretions of pregnant versus non-pregnant sows. Notably, three hormones that correlate with the pregnant status of the sow were discerned: Progesterone, 3-Deoxyestradiol, and Prostaglandin E1. KEGG pathway analysis revealed that the differentially expressed metabolites were predominantly enriched in nucleotide metabolic pathways. The RF model demonstrated an impressive accuracy of 1.00 in the training dataset and 0.88 in the testing dataset, while the SVM model maintained an accuracy of 1.00 across both datasets. Utilizing model weights and differential expression data, three pivotal metabolites were identified: Indolepropionic acid, cis-Aconitate, and 4-p-Coumaroylquinic acid, which exhibited ROC curve AUC values of 0.90, 0.89, and 0.79, respectively. ConclusionThis study validates the viability of utilizing vaginal secretions for the early diagnosis of pregnancy in sows, thereby establishing a foundation for the advancement of non-invasive diagnostic methodologies.

zoology↗

The rupture and independent extension of sister membranes in C. elegans embryos

Cell division, the physical separation of a cell into two daughter cells, is classically thought to require continuous plasma membrane invagination driven by equatorial contractile forces. Here, we challenge this paradigm by uncovering an unexpected mechanism in C. elegans embryos: the plasma membrane ruptures as early as metaphase. Instead of invaginating as a continuous sheet, the separated membranes extend independently to partition the cytoplasm. The membrane rupture and independent extension of sister membranes create membrane discontinuities--widely observed in electron microscopy (EM) sections. Without plasma membrane coverage, the exposed cytoplasmic regions are shielded either by plasma membrane from neighboring, likely kinship, cells or extracellular matrix components, preventing massive leakage. Our findings overturn the long-standing assumption that cytokinesis requires persistent membrane integrity, and offer fresh insights into cell division, particularly in fast dividing embryonic cells.

cell biology↗

Epithelial-mesenchymal cell state heterogeneity predetermines differential phospho-signaling responses to epidermal growth factor stimulation

Understanding why isogenic cancer cells respond differently to equivalent oncogenic stimuli is vital for optimizing anticancer therapies. Emerging evidence suggests that pre-existing differences in cell state may modulate signaling responses to new stimuli, but the interplay of specific cell states and signals remains unclear. We investigated whether epithelial-mesenchymal (E/M) state, a major axis of cancer cell heterogeneity, influences signaling responses to epidermal growth factor (EGF), a critical oncogenic stimulus in non-small cell lung cancer (NSCLC). We imaged >64,000 A549 NSCLC cells labeled for DNA, F-actin and alternate signaling markers (p-AKT-S473, p-AKT-T308, p-ERK or p-S6) after acute stimulation. Quantitative single-cell morphological and spatial profiling defined a stimulus-invariant E/M state landscape over which EGF signaling responses were compared. This revealed state-dependent differences in signal-activation magnitudes, dynamics and subcellular routing. AKT responses exhibited phosphosite- and compartment-specific dynamics across states, with epithelial cells showing strong, transient membrane-localized S473 and higher internalized T308, whereas mesenchymal cells displayed weaker but sustained nuclear and ruffle-localized S473. Regression-based computational multiplexing concurrently inferred all signaling responses per cell, mapping state-dependent divergence in multi-molecular signaling trajectories. E/M state thus pre-determines distinctive spatiotemporal profiles of EGF-induced signaling, with implications for signaling functions and anti-signaling therapy responses across E/M state-diverse tumors.

cancer biology↗

Microglial GSDMD-Mediated Pyroptosis Drives Neuroinflammation in Parkinson's Disease

RationaleParkinsons disease (PD), a globally prevalent neurodegenerative disorder, is characterized by substantia nigra dopaminergic neuron degeneration and striatal dopamine depletion. While microglial pyroptosis is implicated in neuroinflammation and neural injury via inflammatory cytokine release, the role of the CASPASE-1/GSDMD pathway in PD pathogenesis remains incompletely defined. Methods1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP) was used to construct PD model in vivo, GSDMD-knockout mice was employed to assess pyroptotic mechanisms. MPP-stimulated BV2 microglia were treated with a CASPASE-1 inhibitor in vitro. Microglia-specific GSDMD conditional knockout mice were generated to evaluate cell-type contributions to neuroinflammation and motor deficits. ResultsGSDMD deficiency attenuated MPTP-induced neuroinflammation, dopaminergic neuron loss, and motor dysfunction in vivo. MPP exposure triggered NLRP3 inflammasome activation and pyroptosis in BV2 microglia, which was suppressed by CASPASE-1 inhibition. Critically, microglia-specific GSDMD ablation mitigated nigrostriatal degeneration and dyskinesia in PD mice, confirming the centrality of microglial pyroptosis. ConclusionOur findings demonstrate that microglia drive neuroinflammation in PD via CASPASE-1/GSDMD-mediated pyroptosis, directly linking this pathway to dopaminergic neurodegeneration and motor impairment. Targeting GSDMD-dependent pyroptosis represents a promising therapeutic strategy.

neuroscience↗

Multi-omics analyses reveal the effect of DNA methylation on iridoid glycosides biosynthesis in Rehmannia glutinosa

Rehmannia glutinosa roots produce a group of lipophilic bioactive components known as iridoid glycosides. However, the molecular mechanisms by which DNA methylation regulates the biosynthesis of iridoid glycosides in R. glutinosa remain unknown. Herein, the development of R. glutinosa roots and the content of iridoid glycosides in the Wenxian region were significantly higher than those in Xinxiang. Low methylation level contributed to the accumulation of iridoid glycosides and the expression of related enzyme genes. Demethylation promoted both roots growth and development, as well as the accumulation of iridoid glycosides. Up-regulated RgALDH13, RgHDR1, RgG10H4, RgDXR1, RgG10H3, and RgUPD1, along with transcription factors (TFs), form the regulatory network for the biosynthesis of iridoid glycosides. Furthermore, the primary active region of the RgG10H4 promoter is located in the -164 bp region, where the RgMYB2 protein specifically binds to the TAACCA motif in the RgG10H4 promoter. Collectively, low levels of DNA methylation enhance the expression of core genes, followed by inducing the accumulation of iridoid glycosides, which suggests that RgMYB2-RgG10H4 plays a positive role in this process. These findings will contribute to a deeper understanding of the role of DNA methylation in the accumulation of iridoid glycosides. HighlightLow levels of DNA methylation contribute to the accumulation of iridoid glycosides and the expression of key enzyme genes in R. glutinosa.

molecular biology↗

Bona fide hematopoietic stem cells in zebrafish originate from the supra-intestinal artery

Hematopoietic stem cells (HSCs) in vertebrates are widely believed to originate from hemogenic endothelial cells (HECs) in the dorsal aorta (DA) through endothelial-to-hematopoietic transition. However, conclusive in vivo DA-specific lineage-tracing studies to confirm this origin are lacking. Here, leveraging infrared light-mediated temporospatial-resolution lineage-tracing technology, we demonstrate that in zebrafish, HSCs do not originate from the DA. Instead, following the DA hematopoiesis, which produces hematopoietic precursors with limited renewal potential, lifelong renewable HSCs emerge from the supra-intestinal artery (SIA). Remarkably, while the DA produces hematopoietic cells from unipotent HECs, the SIA generates hematopoietic cells from both unipotent HECs and bipotent vessel-resident hemangioblasts (VRHs). These VRHs undergo multiple rounds of division and budding, generating both hematopoietic cells and SIA-resident endothelial cells. The distinct characteristics of DA and SIA cells are further reinforced by single-cell transcriptomic profiling. Our findings challenge the current paradigm of HSC development, underscoring the complexity of vertebrate hematopoiesis.

developmental biology↗

An ATM-PPM1D Circuit Controls the Processing and Restart of DNA Replication Forks

In response to DNA replication stress, DNA damage signaling kinases inhibit origin firing and promote the remodeling and stabilization of replication forks, leading to a systemic reduction in DNA synthesis, which collectively protects genomic integrity. Little is understood about the regulatory mechanisms of replication stress recovery, including the mechanisms involved in the restart of stalled replication forks. Here, we identify the oncogenic phosphatase PPM1D/WIP1 as a regulator of replication fork restart. During recovery from replication stress, PPM1D prevents excessive MRE11- and DNA2-dependent nucleolytic degradation of stalled forks. Loss of PPM1D function leads to defects in RAD51 recruitment to chromatin and impairs RAD51-dependent fork restart. Phosphoproteomic analysis reveals that PPM1D regulates a network of ATM substrates, several of which are phosphorylated at an S/T-Q-(E/D)n motif. Strikingly, inhibition of ATM suppresses the deleterious consequences of impaired PPM1D function at replication forks, enabling timely fork restart. The dominant effect of ATM hyper-signaling in suppressing fork restart occurs, in part, through the excessive engagement of 53BP1 and consequent RAD51 antagonization. These findings uncover a new mode of ATM signaling responding to fork stalling and highlight the need for PPM1D to restrain ATM signaling and facilitate proper fork restart.

biochemistry↗

spRefine Denoises and Imputes Spatial Transcriptomics with a Reference-Free Framework Powered by Genomic Language Model

The analysis of spatial transcriptomics is hindered by high noise levels and missing gene measurements, challenges that are further compounded by the higher cost of spatial data compared to traditional single-cell data. To overcome this challenge, we introduce spRefine, a deep learning framework that leverages genomic language models to jointly denoise and impute spatial transcriptomic data. Our results demonstrate that spRefine yields more robust celland spot-level representations after denoising and imputation, substantially improving data integration. In addition, spRefine serves as a strong framework for model pre-training and the discovery of novel biological signals, as highlighted by multiple downstream applications across datasets of varying scales. Notably, spRefine enhances the accuracy of spatial ageing clock estimations and uncovers new aging-related relationships associated with key biological processes, such as neuronal function loss, which offers new insights for analyzing ageing effect with spatial transcriptomics.

genomics↗

STPath: A Generative Foundation Model for Integrating Spatial Transcriptomics and Whole Slide Images

Spatial transcriptomics (ST) has shown remarkable promise in pathology applications, shedding light on the spatial organization of gene expression and its relationship to the tumor microenvironment. However, its clinical adoption remains constrained due to the limited scalability of current sequencing technologies. While recent methods attempt to infer ST from whole slide images (WSIs) using pretrained image encoders, they remain restricted by limited gene coverage, organ-specific training, and the need for dataset-specific fine-tuning. In light of this, we introduce STPath, a generative foundation model pretrained on a large-scale collection of WSIs paired with ST profiles. This extensive pretraining enables STPath to directly predict gene expression across 38,984 genes and 17 organs without requiring downstream fine-tuning. STPath integrates multiple data modalities, including histological images, gene expressions, organ type, and sequencing technology information, within a novel geometry-aware Transformer architecture. Unlike previous methods that directly map WSIs to gene expression, STPath is trained using a masked gene expression prediction objective guided by tailored noise schedules, effectively balancing between capturing gene-gene dependencies and performing high-quality predictions. We evaluate STPath across 6 tasks spanning 23 datasets and 14 biomarkers, including gene expression prediction, spot imputation, spatial clustering, biomarker prediction, gene mutation prediction, and survival prediction. These results demonstrate STPaths strong ability to infer spatially resolved gene expression and reveal crucial pathological structures within tissue samples, underscoring its promise for scalable ST-based pathology applications.

pathology↗

The H3K27me3 reader UAD-2 recruits a TAF-12-containing transcription condensates to initiate piRNA expression within heterochromatic clusters

Metazoans utilize the small RNA pathway to regulate gene expression and maintain genome integrity. This pathway directs histone H3 lysine 9 tri-methylation (H3K9me3) or histone H3 lysine 27 tri-methylation (H3K27me3) at target loci to induce transcriptional gene silencing. Interestingly, some small RNAs are generated from genomic loci enriched in H3K9me3 or H3K27me3. However, the transcription mechanism of small RNA precursors from these heterochromatic regions remains unclear. In C. elegans, piRNAs originate from two genomic clusters enriched with H3K27me3 marks, which recruit the H3K27me3 reader UAD-2 and the upstream sequence transcription complex (USTC). Here, we demonstrate that piRNA transcription in C. elegans relies on TAF-12, a subunit of the basal transcription factor IID (TFIID). Depletion of TAF-12 reduces the production of both piRNA precursors and mature piRNAs. TAF-12 interacts with UAD-2 and facilitates piRNA focus formation in germ cell nuclei. We further show that TAF-12 triggers piRNA transcription by recruiting the RNA polymerase II subunit RPB-5, the Mediator complex subunit MDT-8, and the general transcription factors GTF-2F2 and GTF-2H2C. Thus, piRNA transcription within heterochromatic regions depends on the collaboration between histone modification readers, piRNA-specific transcription factors, and core transcription machinery.

genetics↗

A reference genome assembly of the alpine forage grass Elymus nutans

Elymus nutans Griseb. (Poaceae: Triticeae, 2n=6x=42) is a dominant perennial plant species in the Qinghai-Tibetan Plateau in China, which is an important forage resource in high-altitude and cold regions and is the most popular species used for high yield artificial grassland planting because of its rich nutritional value and good palatability for herbivorous ruminant animals. In this study, using advanced sequencing technology, we generated an allohexaploid reference genome for E. nutans, representing the three sets of chromosomes (subgenomes St, Y, and H). This is the first study to our knowledge to confirm the origin of the Y subgenome, which shares a close relationship with the V subgenome. We predict that E. nutans arose via two-step hybridization and that its speciation occurred [~]3.16 MYA. The whole genome in this study will update the Triticeae family genomics information and provide theoretical basis for the evolutionary of its related speicies.

plant biology↗

Methylome and transcriptome analysis reveals the impact of psychological stress on the skin

Psychological stress has been shown to impact skin and DNA methylome, but the mechanisms are poorly understood. Here, we collected multi-omics data from 60 stressed and 60 relaxed individuals to test the hypothesis that psychological stress may impact skin via epigenetic modification and downstream altered gene expression. Each volunteer completed a series of questionnaires and assessments to measure their psychological stress levels and skin condition. Suction blister samples were collected for analyze skin cytokines, DNA methylome, and transcriptome. The dataset generated allowed for the identification of 289 differentially methylated probes(DMPs) and 10 differentially expressed genes (DEGs). Integration of methylation and expression data revealed seven functional epigenetic modules(P<0.05), which were involved in the glutamatergic synapse. In line with previous studies on the prefrontal cortex/hippocampus, we found that psychological stress also affects the glutamatergic synapse in the skin. There was no significant group difference in cytokines, while the stressed group had more severe skin darkening (P=7.36x10-6). This study provides important insight into the impact of psychological stress on the skin and contributes a comprehensive multi-omics dataset resource for the healthy epidermis.

genetics↗

Intersecting impact of CAG repeat and Huntingtin knockout in stem cell-derived cortical neurons

Huntingtons Disease (HD) is caused by a CAG repeat expansion in the gene encoding Huntingtin (HTT). While normal HTT function appears impacted by the mutation, the specific pathways unique to CAG repeat expansion versus loss of normal function are unclear. To understand the impact of the CAG repeat expansion, we evaluated biological signatures of HTT knockout (HTT KO) versus those that occur from the CAG repeat expansion by applying multi-omics, live cell imaging, survival analysis and a novel feature-based pipeline to study cortical neurons (eCNs) derived from an isogenic human embryonic stem cell series (RUES2). HTT KO and the CAG repeat expansion influence developmental trajectories of eCNs, with opposing effects on the growth. Network analyses of differentially expressed genes and proteins associated with enriched epigenetic motifs identified subnetworks common to CAG repeat expansion and HTT KO that include neuronal differentiation, cell cycle regulation, and mechanisms related to transcriptional repression and may represent gain-of-function mechanisms that cannot be explained by HTT loss of function alone. A combination of dominant and loss-of-function mechanisms are likely involved in the aberrant neurodevelopmental and neurodegenerative features of HD that can help inform therapeutic strategies.

cell biology↗

Genomic Insights into the Demographic History and Local Adaptation of Wild Boars Across Eurasia

Wild boars exhibit genetic and phenotypic diversity shaped by migrations and local adaptations. Its expansion across Eurasia, especially in central Asia, remains underexplored. Here, we present newly sequenced whole-genome data of 47 wild boars from Eastern Asia, Central Asia, and Europe, combined with 49 existing genomes, creating a comprehensive dataset of 96 individuals. Our analyses show that Asian wild boars and Southeast Asian Suids split [~]3.6 Mya, with Central Asian and Southern Chinese ancestors diverging [~]1.8 Mya. The split between Central Asian and European-Near East ancestors occurred [~]0.9 Mya, followed by a European-Near East divergence [~]0.6 Mya. We identify signatures of local adaptation in Central Asian populations, including two positively selected variants in LPIN1, associated with cold adaptation, and a missense mutation in ALPK2, linked to meat traits. These findings provide insights into wild boar dispersal and adaptation, and shed light on domestic pigs breeding.

evolutionary biology↗