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Biology subjects

Huang, P.

Publications and source records attributed to Huang, P..

At least 55 records · Page 3Linked to original sources

An intercellular signaling pathway in the mouse retina connects Kv2.1, GLT-1, and nitric oxide synthase 1 to optic nerve regeneration

We report here that a multicellular signaling pathway in the mouse retina targeting glutamate homeostasis and nitric oxide production is activated upon optic nerve injury and modulates reti-nal ganglion cells (RGCs) ability to mount a robust regenerative response. A novel highly sen-sitive and specific NO sensor (FL2) revealed that optic nerve injury leads to a rapid, prolonged elevation of NO in the inner retina. Amacrine cell-specific genetic deletion of the neuron-specific isoform of nitric oxide synthase (NOS1, nNOS) or the NOS1 inhibitor N(w)-propyl-L-arginine (L-NPA) suppressed optic nerve regeneration. Steps leading to NOS1 activation are shown to in-clude Kv2.1 phosphorylation and activation, reversal of glutamate uptake by the glutamate transporter GLT-1 (EAAT2), and subsequent NMDA receptor activation. Conditional knockout of the glutamate transporter GLT-1 in bipolar cells, intraocular injection of the GLT-1 blockers dihydrokainate (DHK) or WAY213613, the N-methyl-D-aspartate (NMDA) receptor antagonist D-2-amino-5-phosphonovalerate (D-AP5), or the Kv2.1 blockers RY796 or stromatoxin all sup-pressed NO generation and strongly diminished RGCs ability to respond to Pten deletion and other factors. Thus, optic nerve injury activates a sequence of pathophysiological changes in retinal interneurons that gates RGCs ability to regenerate injured axons. Significance StatementCells use extracellular signals to coordinate responses to injury and to promote repair and re-generation. The NMDA receptor, which has a high affinity for glutamate and is functionally cou-pled to nitric oxide synthase, has the potential to mediate such responses by responding to changes in extracellular glutamate. In the mouse retina after optic nerve injury, potassium channels in retinal ganglion cells, glutamate transporters in neighboring cells, and NMDA recep-tors in amacrine cells, are all involved in a pathway that regulates the generation of nitric oxide, which we show promotes axon regeneration after injury.

neuroscience↗

Expression and Characterization of SARS-CoV-2 Spike Protein in Thermothelomyces heterothallica C1

The COVID-19 pandemic demonstrated a pressing need for rapid, adaptive, and scalable manufacturing of vaccines and reagents. With the transition into an endemic disease and rising threats of other emerging pandemics, production of these biologicals requires a stable and sustainable supply chain and accessible distribution methods. In this study, we demonstrate the strength of an engineered filamentous fungal platform, Thermothelomyces heterothallica C1, for high volumetric productivity of the full-length spike glycoprotein. Spike protein produced in this system is highly thermostable and immunization of mice with spike made in C1 or mammalian platforms resulted in a similar humoral response. Additionally, it was shown that the native N-glycan profile can be redecorated with complex sialylated structures, if necessary, resulting in a more human-like glycan profile, without impacting binding characteristics as shown experimentally and in simulations. Through extensive physicochemical analysis, the C1 produced spike performs similarly to spike proteins produced in other commercially available systems. The data presented is evidence that C1 can be a strong platform for production of complex glycosylated recombinant proteins such as subunit antigen vaccines.

bioengineering↗

Somites are a source of nephron progenitors in zebrafish

For over a century it has been believed that the vertebrate kidney arises exclusively from the intermediate mesoderm. Here, we overturn this paradigm by demonstrating that some nephrons, the functional units of the kidney, originate from the somites--blocks of paraxial mesoderm best known for their contribution to muscle and connective tissues. Using a combination of the GESTALT technique to assign developmental ancestry, somite transplantation experiments and Cre-lox fate-mapping, we show that somites can contribute to the nephrons in the adult zebrafish kidney. Our findings uncover an unexpected developmental connection between the somites and kidneys, potentially offering new pathways for developing regenerative treatments for kidney diseases.

developmental biology↗

Sex differences in human IgG1-mediated angiogenesis inhibition depend on Y chromosome-encoded DDX3Y

Prevalent diseases of angiogenesis such as age-related macular degeneration (AMD) exhibit sex-specific prevalence, with female sex being an independent risk factor for the advanced neovascular form of AMD. The basis for these sex differences is poorly understood. Here, we quantify the impact of sex on suppression of aberrant choroidal angiogenesis by human immunoglobulin 1 (hIgG1), which possesses class-wide, antigen-independent anti-angiogenic activity. Males exhibited significantly more robust hIgG1-induced chemotaxis inhibition in primary human and mouse macrophages and anti-angiogenic activity in mouse laser-induced choroidal neovascularization (CNV). Four core genotypes and XY* Turner Syndrome mouse models revealed the Y chromosome as a sex-biasing factor contributing to hIgG1 responses. Transcriptomic and RNAi screening identified DEAD-Box Helicase 3 Y-Linked (DDX3Y) as necessary for the robust inhibitory effects of hIgG1 in males. Male mice as well as human and mouse macrophages lacking DDX3Y exhibited blunted hIgG1 responses in CNV and macrophage chemotaxis, resembling those of females. These results unveil a novel mechanism through which sex chromosome complement differences can impact key processes involved in AMD, carrying implications for various sex-related disorders and conditions involving angiogenesis.

pathology↗

Inhibiting B-cell-mediated Immunosuppression to Enhance the Immunotherapy Efficacy in Hepatocellular Carcinoma

BackgroundImmunotherapy is efficacious in hepatocellular carcinoma (HCC), but the benefits are limited to a minority of patients. Most HCC patients show resistance to immune checkpoint blockade (ICB). Agonists of the stimulator of interferon genes (STING), potent immune stimulators, showed limited effectiveness. Using preclinical models, we studied the mechanisms of resistance to ICB and STING agonism. MethodsMurine HCA-1 and RIL-175 HCCs were orthotopically grown in mice with underlying liver fibrosis, to mimic the presentation of human HCC. Established tumors were treated with a STING agonist (BMS-986301) or anti-PD1 ICB, and mice were followed to evaluate safety and efficacy, as well as the mechanisms of treatment resistance by RNA sequencing, flow cytometry, and immunofluorescence, B-cell depletion and T-cell immunoglobulin and mucin domain 1 (TIM-1) ICB. ResultsUnbiased analyses of transcriptomic data from murine HCC tissues from ICB-treated mice showed an increased abundance of intratumoral CD8+ T cells and B cells. STING agonism alone showed efficacy in the ICB-responsive RIL-175 HCC model but more limited efficacy in the ICB-resistant HCA-1 model. STING agonism increased circulating IL-10 and intratumoral infiltration by B-cells, including TIM-1+ B cells, and promoted the formation of tertiary lymphoid structure (TLS)-like structures, especially in the peritumoral areas. Strikingly, adding B cell depletion to ICB or STING agonism treatment significantly increased survival. Interestingly, unlike ICB, STING agonism also had a pronounced anti-metastatic activity. In addition, the combination of STING agonism and TIM-1 blockade augmented B cell differentiation and antigen presentation in vitro and improved the anti-tumor effects in murine HCC in vivo. This approach decreased the number of TIM-1+ B cells in the tumor and shifted B cells to higher expression of CD86 and MHC class II, enhancing the antigen presentation capability and further boosting the antitumor efficacy of CD8+ cytotoxic T cells. ConclusionOur findings demonstrate that B cells are associated with ICB- and STING-mediated therapy resistance, and that depleting B-cells or targeting TIM-1 enhances both innate and acquired therapeutic efficacy in HCC.

cancer biology↗

TEMI: Tissue Expansion Mass Spectrometry Imaging

The spatial distribution of diverse biomolecules in multicellular organisms is essential for their physiological functions. High-throughput in situ mapping of biomolecules is crucial for both basic and medical research, and requires high scanning speed, spatial resolution, and chemical sensitivity. Here, we developed a Tissue Expansion method compatible with matrix-assisted laser desorption/ionization Mass spectrometry Imaging (TEMI). TEMI reaches single-cell spatial resolution without sacrificing voxel throughput and enables the profiling of hundreds of biomolecules, including lipids, metabolites, peptides (proteins), and N-glycans. Using TEMI, we mapped the spatial distribution of biomolecules across various mammalian tissues and uncovered metabolic heterogeneity in tumors. TEMI can be easily adapted and broadly applied in biological and medical research, to advance spatial multi-omics profiling.

molecular biology↗

Sidechain conditioning and modeling for full-atom protein sequence design with FAMPNN

Leading deep learning-based methods for fixed-backbone protein sequence design do not model protein sidechain conformation during sequence generation despite the large role the three-dimensional arrangement of sidechain atoms play in protein conformation, stability, and overall protein function. Instead, these models implicitly reason about crucial sidechain interactions based on backbone geometry and known amino acid sequence labels. To address this, we present FAMPNN (Full-Atom MPNN), a sequence design method that explicitly models both sequence identity and sidechain conformation for each residue, where the per-token distribution of a residues discrete amino acid identity and its continuous sidechain conformation are learned with a combined categorical cross-entropy and diffusion loss objective. We demonstrate that learning these distributions jointly is a highly synergistic task that both improves sequence recovery while achieving state-of-the-art sidechain packing. Furthermore, benefits from explicit full-atom modeling generalize from sequence recovery to practical protein design applications, such as zero-shot prediction of experimental binding and stability measurements.

bioengineering↗

Bioinformatic analysis reveals the molecular mechanisms of Trefoil factor 3 involved in asthma pathogenesis

ObjectiveInvestigate the expression, regulatory network and function of TFF3 in asthma from a multi-omics perspective through bioinformatics and cellular experiments to provide clues for understanding its molecular mechanisms in asthma. MethodsDownloaded two asthma-related datasets (GSE67472 and GSE147878) from GEO. Conducted differential expression analysis and WGCNA to find common genes related to asthma phenotype and TFF3 expression. Constructed a PPI network to identify key genes interacting with TFF3. Performed GO and pathway enrichment analysis using DAVID. Analyzed the relationship between TFF3 and immune cell infiltration with CIBERSORTx. Used molecular docking to validate interactions. In vitro, induced 16HBE cells with HDM to establish asthma model and detected inflammatory indicators and TFF3 by RT-qPCR and western blotting. ResultsTFF3 expression was significantly increased in asthma patients in both datasets. ROC analysis showed good diagnostic specificity and sensitivity. 57 co-expressed genes related to asthma and TFF3 were screened, with 11 genes directly interacting with TFF3 and upregulated. Functional enrichment analysis indicated involvement in asthma-related processes. Immune infiltration analysis showed increased M2 macrophages and mast cells, decreased M1 macrophages, and positive correlation with TFF3. Molecular docking confirmed stable binding. In vitro experiments showed increased inflammation index and TFF3 expression after HDM intervention. ConclusionThe study used bioinformatics and cellular experiments to show TFF3s key roles in asthma pathogenesis in aspects like gene expression, protein interaction, and immune microenvironment. TFF3 may regulate genes like AGR2 and AKT1, affect immune cells, and be involved in processes like cell migration and immune response. It provides clues for exploring molecular mechanisms and may offer new directions for asthma diagnosis and treatment.

genomics↗

Zymoseptoria tritici show local differences in within-field diversity and effector variation

Zymoseptoria tritici is a cosmopolitan hemibiotrophic wheat pathogen with a high mutation rate and a mixed reproduction system, leading to challenges in traditional farming management. For successful integration of pest management, especially for early diagnostics of new aggressive or fungicide-resistant lineages, it is critical to understand population diversity in the field. We look at whole-genome sequence data for three datasets to differentiate within field diversity in fields of similar size: one dataset from a newly sampled field population from the United Kingdom and two publicly available datasets from fields from the United States and Switzerland. Inspection of population structure and diversity features, such as minor allele frequency distribution and clonality, show no within-field structure, the most abundant SNPs are present in low frequency, and European fields have higher clonality. Knowing that effectors play particularly important roles in (a)virulence, we specifically assess effector diversity characteristics. Whereas on a whole-genome scale, we can see separation of the populations at the regional scale, we do not find such separation for the effectors. Moreover, we find that multiple effector haplotypes can be found interspersed within the field and even occur within what has been considered clonal isolates or isolates from a single lesion. Our analyses highlight that within-field Z. tritici diversity is higher than previously reported. Our finding that multiple effector haplotypes can be found within a single lesion might explain the large resistance gene-breaking potential of Z. tritici.

microbiology↗

The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution

Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities. Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3,234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral species-level clusters (VSCs), nearly 90% of which are absent from current databases. Analysis of single nucleotide variations (SNVs) in 233 globally prevalent VSCs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. This foundational resource underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.

microbiology↗

Nectin-4 PET For Optimizing Enfortumab Vedotin Dose-Response In Urothelial Carcinoma

The optimization of dosing strategies is critical for maximizing efficacy and minimizing toxicity in drug development, particularly for drugs with narrow therapeutic windows such as antibody-drug conjugates (ADCs). This study demonstrates the utility of Nectin-4-targeted positron emission tomography (PET) imaging using [68Ga]AJ647 as a non-invasive tool for real-time assessment of target engagement in enfortumab vedotin (EV) therapy for urothelial carcinoma (UC). By leveraging the specificity of [68Ga]AJ647 for Nectin-4, we quantified dynamic changes in target engagement across preclinical models and established its correlation with therapeutic outcomes. PET imaging revealed dose-dependent variations in Nectin-4 engagement, with suboptimal EV doses resulting in incomplete Nectin-4 engagement and reduced tumor growth. Importantly, target engagement measured by PET emerged as a more reliable predictor of therapeutic efficacy than dose or baseline Nectin-4 expression alone. Receiver operating characteristic (ROC) analysis identified a target engagement threshold that is determinant of response, providing a quantitative benchmark for dose optimization. Furthermore, PET imaging measures provide a promising framework to account for key challenges in ADC development, including tumor heterogeneity, declining drug-to-antibody ratios over time, and limitations of systemic pharmacokinetic measurements to account for tumor-drug interactions. These findings underscore the transformative potential of integrating PET pharmacodynamic measures as early biomarkers to refine dosing strategies, improve patient outcomes, and accelerate the clinical translation of next-generation targeted therapeutics.

cancer biology↗

Aurora kinase A promotes trained immunity via regulation of endogenous S-adenosylmethionine metabolism

Innate immune cells can acquire a memory phenotype, termed trained immunity, but the mechanism underlying the regulation of trained immunity remains largely elusive. Here, we demonstrate that inhibition of Aurora kinase A (AurA) dampens trained immunity induced by {beta}-glucan. ATAC-seq and RNA-seq analysis reveals that AurA inhibition restricts chromatin accessibility of genes associated with inflammatory pathways such as JAK-STAT, TNF and NF-{kappa}B pathways. Specifically, AurA inhibition promotes nuclear localization of FOXO3 and the expression of glycine N-methyltransferase (GNMT), a key enzyme responsible for S-adenosylmethionine (SAM) consumption. Metabolomic analysis confirms a reduction in SAM level upon AurA inhibition. As a result of SAM deficiency, trained mouse macrophages exhibit decreased H3K4me3 and H3K36me3 enrichment on gene regions of Il6 and Tnf. Additionally, the tumor inhibition effect of {beta}-glucan is notably abolished by AurA inhibition. Together, our findings identify an essential role of AurA in regulating trained immunity via a methylation-dependent manner by maintaining endogenous SAM level through mTOR-FOXO3-GNMT axis.

immunology↗

Irx3/5 define the cochlear sensory domain and regulate vestibular and cochlear sensory patterning in the mammalian inner ear

The mammalian inner ear houses the vestibular and cochlear sensory organs dedicated to sensing balance and sound, respectively. These distinct sensory organs arise from a common prosensory region, but the mechanisms underlying their divergence remain elusive. Here, we showed that two evolutionarily conserved homeobox genes, Irx3 and Irx5, are required for the patterning and segregation of the saccular and cochlear sensory domains, as well as for the formation of auditory sensory cells. Irx3/5 were highly expressed in the cochlea, their deletion resulted in a significantly shortened cochlea with a loss of the ductus reuniens that bridged the vestibule and cochlea. Remarkably, ectopic vestibular hair cells replaced the cochlear non-sensory structure, the Greater Epithelial Ridge. Moreover, most auditory sensory cells in the cochlea were transformed into hair cells of vestibular identity, with only a residual organ of Corti remaining in the mid-apical region of Irx3/5 double knockout mice. Conditional temporal knockouts further revealed that Irx3/5 are essential for controlling cochlear sensory domain formation before embryonic day 14. Our findings demonstrate that Irx3/5 regulate the patterning of vestibular and cochlear sensory cells, providing insights into the separation of vestibular and cochlear sensory organs during mammalian inner ear development.

developmental biology↗

Genomic diversity and underlying metabolic variations of the human gut microbiome between populations at single nucleotide resolution

BackgroundA comprehensive and representative reference database is crucial for accurate taxonomic and functional profiling of the human gut microbiome in population-level studies. However, with 70% of current microbial reference data derived from Europeans and the Americans, East Asia, especially China, remain underrepresented. MethodsWe constructed the human Gut Microbiome Reference (GMR), comprising 478,588 high-quality microbial genomes from Chinese (247,134) and non-Chinese (231,454) populations. Species-level clustering and protein annotations were performed to characterize microbial diversity and function. We further integrated novel genomes into taxonomic profiling database and validated the improvements using independent cohort data. ResultsThe GMR dataset spans 6,664 species, including 26.4% newly classified species, and encodes over 20 million unique proteins, with 47% lacking known functional annotations. Notably, we observed that 35.35% and 32.46% of species unique to Chinese and non-Chinese populations, respectively. For 2,145 species shared between populations, 74% of 304 species with balanced prevalence between populations exhibited population-specific phylogenetic stratification, involving health relevant functionalities such as antibiotic resistance. Integration of novel genomes into taxonomic improved population-level species profiling by up to 23% and uncovered replicable associations between novel species and host physiological traits. ConclusionsOur study largely expands the compositional and functional landscape of the human gut microbiome, providing a crucial resource for studying the role of gut microbiome for regional health disparities.

genomics↗

Creating a biomedical knowledge base by addressing GPT inaccurate responses and benchmarking context

We created GNQA, a generative pre-trained transformer (GPT) knowledge base driven by a performant retrieval augmented generation (RAG) with a focus on aging, dementia, Alzheimers and diabetes. We uploaded a corpus of three thousand peer reviewed publications on these topics into the RAG. To address concerns about inaccurate responses and GPT hallucinations, we implemented a context provenance tracking mechanism that enables researchers to validate responses against the original material and to get references to the original papers. To assess the effectiveness of contextual information we collected evaluations and feedback from both domain expert users and citizen scientists on the relevance of GPT responses. A key innovation of our study is automated evaluation by way of a RAG assessment system (RAGAS). RAGAS combines human expert assessment with AI-driven evaluation to measure the effectiveness of RAG systems. When evaluating the responses to their questions, human respondents give a "thumbs-up" 76% of the time. Meanwhile, RAGAS scores 90% on answer relevance on questions posed by experts. And when GPT-generates questions, RAGAS scores 74% on answer relevance. With RAGAS we created a benchmark that can be used to continuously assess the performance of our knowledge base. Full GNQA functionality is embedded in the free GeneNetwork.org web service, an open-source system containing over 25 years of experimental data on model organisms and human. The code developed for this study is published under a free and open-source software license at https://git.genenetwork.org/gn-ai/tree/README.md.

scientific communication and education↗

Cytosolic delivery of anionic cyclic dinucleotide STING agonists with locally supercharged viral capsids

Cyclic dinucleotide (CDN) STING agonists represent a powerful new immunotherapy treatment modality and are a class of nucleotide-based therapies with broad clinical potential. However, they face practical challenges for administration, largely due to their poor pharmacological properties. We report the development of a drug delivery platform for CDNs and other anionic small-molecule drugs using bacteriophage MS2 viral capsids with engineered cationic residues. Relative to viral capsids lacking locally supercharged regions, these assemblies exhibit substantial increases in mammalian cell uptake while avoiding cell toxicity and hemolysis. CDN drugs were covalently attached to the interior capsid surfaces through reductively cleavable disulfide linkers, which allowed for traceless drug release upon cell entry and exposure to reductive cytosolic environments. MS2-mediated CDN delivery into immune cell populations resulted in an approximately 100-fold increase in delivery efficiency compared to free drugs and showed enhanced STING activation as well as downstream cytokine release.

biochemistry↗

A Paradoxical Tumor Antigen Specific Response in the Liver

Functional tumor-specific CD8+ T cells are essential for an effective anti-tumor immune response and the efficacy of immune checkpoint inhibitor therapy. In comparison to other organ sites, we found higher numbers of tumor-specific CD8+ T cells in primary, metastatic liver tumors in murine tumor models. Despite their abundance, CD8+ T cells in the liver displayed an exhausted phenotype. Depletion of CD8+ T cells showed that liver tumor-reactive CD8+ T failed to control liver tumors but was effective against subcutaneous tumors. Similarly, analysis of single-cell RNA sequencing data from patients showed a higher frequency of exhausted tumor-reactive CD8+ T cells in liver metastasis compared to paired primary colon cancer. High-dimensional, multi-omic analysis combining proteomic CODEX and scRNA-seq data revealed enriched interaction of SPP1+ macrophages and CD8+ tumor-reactive T cells in profibrotic, alpha-SMA rich regions in the liver. Liver tumors grew less in Spp1-/- mice and the tumor-specific CD8+ T cells were less exhausted. Differential pseudotime trajectory inference analysis revealed extrahepatic signaling promoting an intermediate cell (IC) population in the liver, characterized by co-expression of VISG4, CSF1R, CD163, TGF-{beta}R, IL-6R, SPP1. scRNA-seq of a third data set of premetastatic adenocarcinoma showed that enrichment of this population may predict liver metastasis. Our data suggests a mechanism by which extrahepatic tumors facilitate the formation of liver metastasis by promoting an IC population inhibiting tumor-reactive CD8+ T cell function.

immunology↗

Pdgfab/Pdgfra-mediated chemoattraction guides the migration of sclerotome-derived fibroblast precursors in zebrafish

In vertebrates, the sclerotome is a transient embryonic structure that gives rise to various tissue support cells, including fibroblasts. However, how fibroblast precursors are guided to diverse tissues remain poorly understood. Using zebrafish, our lab has previously shown that sclerotome-derived cells undergo extensive migration to generate distinct fibroblasts subtypes, including tenocytes along the myotendinous junction and fin mesenchymal cells in the fin fold. Interestingly, the pan-fibroblast gene platelet-derived growth factor receptor a (pdgfra), which has been implicated in cell migration across various contexts, is specifically expressed in the sclerotome and its descendants. Loss of functional Pdgfra in a pdgfra gene-trap mutant results in severe defects in the migration of sclerotome- derived cells, leading to a dose-dependent loss of tenocytes and fin mesenchymal cells. By combining live imaging and mosaic labeling with a membrane-bound dominant-negative tool, we demonstrate that Pdgfra acts cell-autonomously to regulate the migration of sclerotome- derived cells. In the absence of ligand pdgfab, which is expressed in the medial somite, sclerotome-derived cells fail to migrate medially, resulting in a loss of tenocytes, although they can migrate normally toward the fin fold and generate fin mesenchymal cells. Strikingly, localized expression of Pdgfab in pdgfab mutants can direct the migration of sclerotome- derived cells to both normal and ectopic locations, suggesting a chemoattractive role for the Pdgfab ligand. Together, our results demonstrate that Pdgfab/Pdgfra-mediated chemoattraction guides the migration of sclerotome-derived fibroblast precursors to specific locations, where they diversify into distinct fibroblast subtypes.

developmental biology↗