Biology subjects

Dang, R.

Publications and source records attributed to Dang, R..

10 recordsLinked to original sources

bioRxiv2026

Neurogenin-2 Reprograms Human Microglial Lineage Cells into Neurons In Vitro and in Chimeric Brains

Progressive neuronal loss is a hallmark of many neurological disorders, yet the adult human brain has a limited capacity for endogenous neuronal replacement. Direct neuronal reprogramming represents an alternative strategy for generating new neurons. Microglia, the brains resident immune cells, are uniquely positioned as candidate cellular substrates due to their abundance, self-renewal capacity, high motility, and rapid recruitment to sites of injury. Here, using live-cell imaging and electrophysiological recordings, we show that human pluripotent stem cell (hPSC)-derived primitive macrophage progenitors (PMPs) and their microglial derivatives exhibit neuronal reprogramming competence. Inducible expression of NEUROG2 in hPSC-derived PMPs drives acquisition of neuronal morphology, sequential expression of early and mature neuronal markers, organization of synaptic proteins, and functional excitability characterized by action potential firing. Single-nucleus RNA sequencing reveals a continuous, directionally ordered reprogramming trajectory marked by suppression of myeloid transcriptional programs, progression through intermediate remodeling states, and progressive activation of neuronal gene regulatory networks, consistent with a regulated lineage conversion rather than partial identity switching. Using a xenotransplantation-based human microglia chimeric brain model, we further demonstrate that inducible NEUROG2 expression reprograms donor-derived human microglia toward a neuronal identity in vivo. Together, these findings establish human microglial lineage cells as a previously unexplored substrate for neuronal reprogramming, providing a conceptual framework for microglia-based strategies aimed at neuronal replacement and neural repair.

neuroscience↗

bioRxiv2026

Gut inflammation promotes adverse food reactions by disrupting the microbial metabolism of food triggers

Background & AimsFood-related adverse reactions are frequently reported by patients with inflammatory bowel disease (IBD), but the underlying mechanisms are poorly understood. We investigated how intestinal inflammation and the microbiota contribute to the development of adverse food reactions. MethodsWe sensitized mice to different foods (dairy and gluten) after intestinal inflammation (chemically- and hapten-induced models), and then re-exposure to the sensitized foods through diet enrichment. To study whether inflamed microbiota facilitates adverse food reactions, we employed gnotobiotic models and bacterial supplementation experiments. We assessed markers of intestinal inflammation and sensitization, clinical responses, RNA transcripts, and microbiota composition and function. In a translational approach, we recruited IBD patients in remission and healthy controls, recorded self-reported food intolerances and clinical responses to triggering foods, and feces for gut microbiota analyses were collected. ResultsIntestinal inflammation facilitates food sensitization by disrupting microbial antigen metabolism, recruiting mast cells to the colon, and promoting mucosal IgE production. In gnotobiotic models, inflammation-driven depletion of colonic bacteria involved in food digestion contributed to food sensitization. Upon re-exposure to triggering foods, sensitized mice experienced visceral pain and low-grade inflammation through mast-cell mediated mechanisms, which also worsened experimental colitis. Supplementation with depleted bacteria or treatment with mast cell stabilizers attenuated food-driven responses. In IBD patients, self-reported food intolerances were common and associated with microbial disruption and depletion of food-metabolizing bacteria. ConclusionMicrobial metabolism of foods is disrupted after intestinal inflammation. This facilitates food sensitization, through colonic mast cell-mediated immune responses, which may explain the high number of adverse food reactions reported by IBD patients. WHAT YOU NEED TO KNOWO_ST_ABSBackground and contextC_ST_ABSPatients with inflammatory bowel disease (IBD) frequently report adverse food reactions, but the underlying mechanisms are not well understood. New findingsIntestinal inflammation promotes food sensitization by depleting bacteria that degrade food triggers. IBD patients in remission with food intolerances show reduced microbial diversity and loss of bacteria involved in digesting food triggers. LimitationsWe used chemically- and hapten-induced mouse models in this study due to the importance of monitoring inflammation onset. Food-driven immune reactions in the mucosa of IBD patients were not performed. Clinical research relevanceImpaired microbial food metabolism is linked to adverse food reactions in IBD. Microbiome-based therapies, such as probiotics capable of degrading dairy or gluten, should be considered for IBD patients with food intolerances. Basic research relevanceWe identified a novel mechanism in which microbial disruption caused by intestinal inflammation leads to adverse food reactions and worsened colitis in preclinical models. Restoring the microbial capacity to digest trigger foods reverses these effects. Lay AbstractIntestinal inflammation facilitates sensitization to gluten and dairy proteins by depleting microbes that digest them, contributing to the increase in adverse food reactions among IBD patients.

microbiology↗

bioRxiv2025

Dietary tryptophan enhances aryl hydrocarbon receptor activation and reduces colitis through microbial metabolism

Background & AimDisrupted microbial tryptophan metabolism and impaired aryl hydrocarbon receptor (AhR) activation are implicated in inflammatory bowel disease (IBD) pathogenesis. However, strategies to restore this pathway through diet or microbial modulation remain poorly defined. This study investigates how dietary tryptophan and human and mouse microbiota modulate metabolism, AhR activation, and intestinal inflammation in preclinical models. MethodsGnotobiotic mice colonized with microbiota of varying complexity or human fecal microbiota from ulcerative colitis (UC) patients and healthy controls were used to assess the impact of microbiota and dietary tryptophan supplementation on AhR activation and colitis severity. Chemically induced and spontaneous colitis models were investigated. ResultsIBD fecal samples showed reduced AhR activation compared to healthy controls, and fecal microbiota transplantation into germ-free mice demonstrated that impaired AhR is microbiota-dependent. Mice colonized with minimal microbiota had impaired microbial tryptophan metabolism, lower AhR activation, and worsened colitis severity compared to those colonized with complex microbiota. Dietary tryptophan supplementation in conventional and UC-humanized mice enhanced microbial production of AhR agonists, restored AhR activation, and reduced colitis severity in an AhR-dependent manner. Co-colonization with a tryptophan-metabolizing bacterium, Clostridium sporogenes, further improved tryptophan metabolism and colitis severity in mice with impaired microbial tryptophan metabolism. ConclusionsMicrobial tryptophan metabolism is critical for determining intestinal inflammation. Dietary tryptophan supplementation restores microbial metabolic pathways, mitigates colitis severity in preclinical models, and may address key metabolic deficiencies in IBD patients with impaired tryptophan metabolism. This study demonstrates the therapeutic potential of targeting microbial metabolism with diet in IBD management.

physiology↗

bioRxiv2025

Determine Protein Interaction Affinity without Purification Reveals a Two-enzyme Co-recognition of SUMOylation Substrate using Quantitative FRET (qFRET) Technology

Protein-protein interaction is the most fundamental process in life, and the quantification and manipulation of protein interaction activation or inhibition are critical for a comprehensive understanding of physiological processes and the development of new medicines that modulate protein-protein interactions. Due to its essential roles in physiology and pathology, many methodologies and technologies have been developed to determine the interaction events and parameters of interaction affinity. However, due to the nature of these methodologies, interactive partner needs to be purified, and large quantities of proteins are needed. This significantly limits quantitatively understanding of protein interaction and its application in therapeutics development. Recently, a quantitative FRET(qFRET) method was developed to determine purified protein-protein interaction affinity for purified proteins in vitro. Here, for the first time, we report the development of a high-throughput approach to determining the protein interaction affinity between two un-purified proteins using a quantitative FRET assay(qFRET). Two proteins, SUMO E2 conjugating enzyme, Ubc9, and RanGap1c, were first employed for the methodology development. We then determined the interaction affinities of Ubc9 and PIAS1 with influenza A virus NS1 protein without purifying two interactive partners. We found that both enzymes have high affinities to interaction affinity to the NS1, and this provides a kinetics explanation for the SUMOylation two-enzyme co-recognition mechanism to achieve high substrate specificity in vivo. The protein interaction affinity determination without purification provides several advantages over the current methods, including high accuracy, no tedious protein purification process, and high-throughput assay. The novel approach, so-called High-throughput determination of protein interaction affinity, KD, without purification using quantitative FRET assay, and scientific discoveries, representing a significant advancement in technology and scientific discovery, holds great potential for large-scale protein-protein interaction affinity determinations in vitro and in vivo. TeaserA novel qFRET technology for protein interaction affinity determination without protein purification for two-enzyme recognition.

bioengineering↗

bioRxiv2025

Microbial metabolism of food allergens determines the severity of IgE-mediated anaphylaxis

Anaphylaxis is an acute, potentially life-threatening reaction, often triggered by foods and largely mediated by IgE. Critically important to anaphylaxis are the factors that modulate its severity. The human microbiota is known to influence oral tolerance, but the microbial mechanisms directly involved in IgE-mediated anaphylaxis remain unknown. Here, we demonstrate that human saliva and jejunum harbor peanut-degrading bacteria that metabolize immunodominant allergens (Ara h 1 and 2) and alter IgE-binding. Additionally, we provide in vivo evidence that oral bacteria metabolize peanut allergens, influencing systemic allergen exposure and anaphylaxis severity. Finally, in clinical studies, we observe that common peanut-degrading bacteria, such as Rothia, from the oral cavity, are more abundant in peanut-allergic patients who exhibit better tolerance to allergen exposure. Altogether, these results demonstrate that human microbiota modulates IgE-mediated reactions through allergen metabolism. We reveal a novel microbial mechanism with potential to prevent, or reduce, the severity of IgE-mediated anaphylaxis.

immunology↗

bioRxiv2024

Co-Transplantation-Based Human-Mouse Chimeric Brain Models to Study Human Glial-Glial and Glial-Neuronal Interactions

Human-mouse chimeric brain models, generated by transplanting human induced pluripotent stem cell (hiPSC)-derived neural cells, are valuable for studying the development and function of human neural cells in vivo. Understanding glial-glial and glial-neuronal interactions is essential for unraveling the complexities of brain function and developing treatments for neurological disorders. To explore these interactions between human neural cells in vivo, we co-engrafted hiPSC-derived neural progenitor cells together with primitive macrophage progenitors into the neonatal mouse brain. This approach creates human-mouse chimeric brains containing human microglia, macroglia (astroglia and oligodendroglia), and neurons. Using super-resolution imaging and 3D reconstruction techniques, we examine the dynamics between human neurons and glia, and observe human microglia pruning synapses of human neurons, and often engulfing neurons themselves. Single-cell RNA sequencing analysis of the chimeric brain uncovers a close recapitulation of the human glial progenitor cell population, along with a dynamic stage in astroglial development that mirrors the processes found in the human brain. Furthermore, cell-cell communication analysis highlights significant neuronal-glial and macroglial-microglial interactions, especially the interaction between adhesion molecules neurexins and neuroligins between neurons and astroglia, emphasizing their key role in synaptogenesis. We also observed interactions between microglia and astroglia mediated by SPP1, crucial for promoting microglia growth and astrogliosis, and the PTN-MK pathways, instrumental in homeostatic maintenance and development in macroglial progenitors. This innovative co-transplantation model opens up new avenues for exploring the complex pathophysiological mechanisms underlying human neurological diseases. It holds particular promise for studying disorders where glial-neuronal interactions and non-cell-autonomous effects play crucial roles.

neuroscience↗

bioRxiv2024

A Trisomy 21-linked Hematopoietic Gene Variant in Microglia Confers Resilience in Human iPSC Models of Alzheimers Disease

SUMMARYWhile challenging, identifying individuals displaying resilience to Alzheimers disease (AD) and understanding the underlying mechanism holds great promise for the development of new therapeutic interventions to effectively treat AD. Down syndrome (DS), or trisomy 21, is the most common genetic cause of AD. Interestingly, some people with DS, despite developing AD neuropathology, show resilience to cognitive decline. Furthermore, DS individuals are at an increased risk of myeloid leukemia due to somatic mutations in hematopoietic cells. Recent studies indicate that somatic mutations in hematopoietic cells may lead to resilience to neurodegeneration. Microglia, derived from hematopoietic lineages, play a central role in AD etiology. We therefore hypothesize that microglia carrying the somatic mutations associated with DS myeloid leukemia may impart resilience to AD. Using CRISPR-Cas9 gene editing, we introduce a trisomy 21-linked hotspot CSF2RB A455D mutation into human pluripotent stem cell (hPSC) lines derived from both DS and healthy individuals. Employing hPSC-based in vitro microglia culture and in vivo human microglia chimeric mouse brain models, we show that in response to pathological tau, the CSF2RB A455D mutation suppresses microglial type-1 interferon signaling, independent of trisomy 21 genetic background. This mutation reduces neuroinflammation and enhances phagocytic and autophagic functions, thereby ameliorating senescent and dystrophic phenotypes in human microglia. Moreover, the CSF2RB A455D mutation promotes the development of a unique microglia subcluster with tissue repair properties. Importantly, human microglia carrying CSF2RB A455D provide protection to neuronal function, such as neurogenesis and synaptic plasticity in chimeric mouse brains where human microglia largely repopulate the hippocampus. When co-transplanted into the same mouse brains, human microglia with CSF2RB A455D mutation phagocytize and replace human microglia carrying the wildtype CSF2RB gene following pathological tau treatment. Our findings suggest that hPSC-derived CSF2RB A455D microglia could be employed to develop effective microglial replacement therapy for AD and other age-related neurodegenerative diseases, even without the need to deplete endogenous diseased microglia prior to cell transplantation.

neuroscience↗

bioRxiv2023

Machine learning-based investigation of regulated cell death for predicting prognosis and immunotherapy response in glioma patients

BackgroundGlioblastoma is a highly aggressive and malignant type of brain cancer that originates from glial cells in the brain, with a median survival time of 15 months and a 5-year survival rate of less than 5%. Regulated cell death (RCD) is the autonomous and orderly cell death under genetic control, controlled by precise signaling pathways and molecularly defined effector mechanisms, modulated by pharmacological or genetic interventions, and plays a key role in maintaining homeostasis of the internal environment. The comprehensive and systemic landscape of the RCD in glioma is not fully investigated and explored. MethodAfter collecting 18 RCD-related signatures from the opening literatures, we comprehensively explored the RCD landscape, integrating the multi-omics data, including large-scale bulk data, single-cell level data, glioma cell lines, and proteome level data. We also provided a machine learning framework for screening the potentially therapeutic candidates. ResultHere, we explored RCD-related phenotypes, investigated the profile of the RCD, and developed a RCD gene pair scoring system, named RCD.GP signature. Using the machine learning framework consisting of Lasso, RSF, XgBoost, Enet, CoxBoost and Boruta, we identified seven RCD genes as potential therapeutic targets in glioma and verified the SLC43A3 by q-PCR in glioma grades and glioma cell lines. ConclusionOur study provided comprehensive insights into the RCD roles in glioma, developed a robust RCD gene pair signature for predicting the prognosis of glioma patients, constructed a machine learning framework for screening the core candidates and identified the SLC43A3 as an oncogenic role and a prediction biomarker in glioblastoma.

bioinformatics↗

bioRxiv2022

Regulation of Nuclear Transcription by Mitochondrial RNA

Chromatin-associated RNAs (caRNAs) form a relatively poorly recognized layer of the epigenome. The caRNAs reported to date are transcribed from the nuclear genome. Here, leveraging a recently developed assay for detection of caRNAs and their genomic association, we report that mitochondrial RNAs (mtRNAs) are attached to the nuclear genome and constitute a subset of caRNA, which we termed mt-caRNA. In four human cell types analyzed, mt-caRNAs preferentially attach to promoter regions. In human endothelial cells (ECs), the level of mt-caRNA-promoter attachment changes in response to environmental stress that mimics diabetes. Suppression of a non-coding mt-caRNA in ECs attenuates stress-induced nascent RNA transcription from the nuclear genome, including that of critical genes regulating cell adhesion, and abolishes stress-induced monocyte adhesion, a hallmark of dysfunctional ECs. Finally, we report increased nuclear localization of multiple mtRNAs in the ECs of human diabetic donors, suggesting many mtRNA translocate to the nucleus in a cell stress and disease-dependent manner. These data nominate mt-caRNAs as messenger molecules responsible for mitochondrial-nuclear communication and connect the immediate product of mitochondrial transcription with the transcriptional regulation of the nuclear genome.

genomics↗

bioRxiv2018

Penton-dodecahedron of fowl adenovirus serotype 4 as a vaccine candidate for the control of related diseases

In some serotypes of adenovirus (Ad), the penton base protein and attached trimeric fiber assemble into dodecameric virus-like particles called penton-dodecahedron (Pt-Dd), which can internalize into cells and can be used to deliver the vaccine antigen and drugs. Fowl adenovirus serotype 4 (FAdV-4) is an important poultry pathogens and causing seriously economic lost to poultry industry in China and several other counties. The produce of Pt-Dd in FAdV-4 infected cells as well as in those infected with the recombinant human Ad expressing fiber-1, fiber-2, and penton base was determine by Transmission electron microscopy (TEM). For the First time, we proved that FAdV-4 produced Pt-Dd in infected cells, which can also be assembled by the overexpressed recombinant proteins fiber-1, fiber-2, and penton base. Pt-Dd, as well as the recombinant proteins fiber-1, fiber-2, and penton base, were then used to immunize chickens. The humoral immune response, cell mediate immune response (CMI), and challenge results were used to evaluate the immune efficacy of the vaccine candidates. Pt-Dd induced the highest level of enzyme-linked immunosorbent assay antibodies and high levels of CMI, showing a significantly (p < 0.05) high level of interferon {gamma}, interleukin-4, and major histocompatibility complex II expressions in peripheral blood mononuclear cells at 48 h post-infection. The challenge results showed that Pt-Dd, inactivated FAdV-4 vaccine, as well as fiber-1 induced the best protection (100%), followed by fiber-2 (80%) and penton (67%). The present study showed that FAdV-4-Pt-Dd and recombinant fiber-1 are good FAdV-4 vaccine candidates and could be used to replace the tissue-sourced inactivated FAdV-4 vaccine.\n\nImportanceFAdV-4-Pt-Dds were discovered in FAdV-4 infected cells, and which were also assembled in cells transduced with recombinant human adenovirus expressing fiber-1, fiber-2, and penton base. FAdV-4-Pt-Dds internalize into cells with high efficiency, so that it can be used for delivery vaccine antigen or drugs. Immunization chickens with Pt-Dd and fiber-1 obtained by transduction HEK-293T cells induced significant high level humoral and cellular mediated immune responses, and also 100% challenge protection in chickens indicating that they are good FAdV-4 vaccine candidates. What more, the Pt-Dd obtained by transduction HEK-293T cell would have no DNA and adenovirus contamination as adenovirus could not package in HEK-293T cells.

immunology↗