Biology subjects

Hong, Y.

Publications and source records attributed to Hong, Y..

At least 91 records · Page 5Linked to original sources

bioRxiv2024

Development of a Two-Leaf Photosynthetic Model Sensitive to Chlorophyll and Its Coupling with a Wheat Growth Model

Crop growth models (CGMs) commonly simulates the response of photosynthetic rate to nitrogen (N) dynamic by calculating critical N concentration. However, critical N concentration makes it hard to describe the physiological effect of N dynamic on photosynthesis. Meanwhile, the effect of diffuse light on photosynthesis was limited in previous studies. In this study, we introduced a Two-leaf Photosynthetic Model Sensitive to Chlorophyll Content (TPMSCC) and coupled it with the crop growth model (WheatGrow) to enhance our understanding of how N dynamic and diffuse light affects photosynthesis. By coupling the Farquhar-von Caemmerer-Berry (FvCB) C3 photosynthesis model with a canopy radiative transfer model (PROSAIL), TPMSCC simulated the light interception of direct and diffuse light, and employed leaf chlorophyll content (LCC) to simulate the light absorption and electron transfer rate of leaves. Result showed that TPMSCC well simulated the light absorption of the wheat canopy and found the canopy photosynthetic rate benefited from the increase of diffuse radiation fraction (DRF) except for when the condition of a dense canopy at a high solar zenith angle was present. Research found the logarithmic and linear relationships of LCC to the initial light use efficiency ([a]) and the maximum photosynthetic rate (Amax), respectively, which followed the field measurements. Additionally, the optimized WheatGrow model outperforms its predecessor in describing the response of N application rate on photosynthesis.

biophysics↗

bioRxiv2024

Synchronization of Circadian Clock Gene Expression in Arabidopsis and Hyaloperonospora arabidopsidis and its Impact on Host-Pathogen Interactions

Organisms across all kingdoms have an internal circadian clock running in 24h cycles. This clock affects a variety of processes, including innate immunity in plants. However, the role of pathogen circadian clocks had not been extensively explored. We previously showed that light can influence infection of the oomycete Hyaloperonospora arabidopsidis (Hpa, downy mildew disease) on its natural host Arabidopsis thaliana. Here, we identified Hpa orthologs of known circadian clock genes (CCGs) Drosophila TIMELESS (TIM) and Arabidopsis Sensitive to Red Light Reduced 1 (AtSRR1) genes. Expression of both HpaTIM and HpaSRR1 showed a circadian rhythm when Hpa was exposed to constant light. Contrastingly, these two genes were negatively regulated by constant dark exposure. Furthermore, the expression patterns of HpaTIM and HpaSRR1 correlate with those of AtCCA1 and AtLHY, indicating a synchronisation of biological clock genes between the host and the pathogen. In addition, screening mutants of Arabidopsis Clock Regulated Genes (AtCRGs) with three virulent Hpa isolates revealed that mutations in AtCRGs influenced HpaTIM and HpaSRR1 expression and Hpa development, indicating a functional link between the plant biological clock and virulence. Moreover, sporulation of Hpa was reduced by targeting HpaTIM and HpaSRR1 with short synthesized small interfering RNAs, indicating that the pathogen clock is also relevant to virulence. We propose that plant and pathogen clocks are synchronized during infection and that proper regulation of both clocks are genetically necessary for pathogen virulence.

plant biology↗

bioRxiv2024

Augmentation of DNA exonuclease TREX1 in macrophages as a therapy for cardiac ischemic injury

Noncoding RNAs (ncRNAs) are increasingly recognized as bioactive. Here we report the development of TY1, a synthetic ncRNA bioinspired by a naturally-occurring human small Y RNA with immunomodulatory properties. TY1 upregulates TREX1, an exonuclease that rapidly degrades cytosolic DNA. In preclinical models of myocardial infarction (MI) induced by ischemia/reperfusion, TY1 reduced scar size. The cardioprotective effect of TY1 was abrogated by prior depletion of macrophages and mimicked by adoptive transfer of macrophages exposed either to TY1 or TREX1. Inhibition of TREX1 in macrophages blocked TY1 cardioprotection. Consistent with a central role for TREX1, TY1 attenuated DNA damage in the post-MI heart. This novel mechanism--pharmacologic upregulation of TREX1 in macrophages--establishes TY1 as the prototype for a new class of ncRNA drugs with disease-modifying bioactivity. One Sentence SummaryUpregulation of three prime exonuclease, TREX1, in macrophages enhances tissue repair post myocardial infarction.

molecular biology↗

bioRxiv2024

Multitask Knowledge-primed Neural Network for Predicting Missing Metadata and Host Phenotype based on Human Microbiome

Microbial signatures in the human microbiome have been linked to various human diseases, and Machine Learning (ML) models have been developed for microbiome-based disease prediction, although improvements remain to be made in accuracy, reproducibility and interpretability. On the other hand, confounding factors, including hosts gender, age and BMI can have a significant impact on humans microbiome, complicating microbiome-based human phenotype predictions. We recently developed MicroKPNN, an interpretable ML model that achieved promising performance for human disease prediction based on microbiome data. MicroKPNN explicitly incorporates prior knowledge of microbial species into the neural network. Here we developed MicroKPNN-MT a unified model for predicting human phenotype based on microbiome data, as well as additional metadata including age, body mass index (BMI), gender and body site. In MicroKPNNMT, the metadata information, when available, will be used as additional input features for prediction, or otherwise will be predicted from microbiome data using additional decoders in the model. We applied MicroKPNN-MT to microbiome data collected in mBodyMap, covering healthy individuals and 25 different diseases, and demonstrated its potential as a predictive tool for multiple diseases, which at the same time provided predictions for much of the missing metadata (e.g., the BMI information was missing for 94% of the samples). Our results showed that incorporating real or predicted metadata helped improve the accuracy of disease predictions, and more importantly, helped improve the generalizability of the predictive models. Finally, our model enables the interpretation of predictive models and the identification of potential microbial markers affecting host phenotypes.

bioinformatics↗

bioRxiv2024

Stimulated Prorocentrum donghaiense cell growth by in-situ mariculture dissolved organic matter

Mixotrophic dinoflagellates frequently cause harmful algal blooms (HAB) in eutrophic mariculture waters that contain diverse excreted dissolved organic matter (DOM). The phagotrophy and the utilization of single organic small molecules have been extensively investigated in the bloom-forming mixotrophic dinoflagellates. However, their ability to utilize the in-situ DOM via absorbtrophy still remains unexplored. Here we examined the growth promotion effect of the in-situ mariculture DOM on Prorocentrum donghaiense, a representative HAB-forming species in coastal waters. Our results showed that the cell growth and photosynthesis of P. donghaiense were significantly promoted under in-situ DOM culture conditions. Additionally, parallel cultures were set up to disclose the potential role of the bacterioplankton in the free-living community (helper), where they aid in the remineralization of the in-situ DOM, and the phycosphere community (competitor), where they compete against the algal host to acquire nutrients from the in-situ DOM. Meanwhile, we determined the cellular stoichiometry under different culture conditions, showing that mariculture DOM can shape cellular stoichiometry significantly. Elevated cellular N (84.96%) and P (48.3%) were observed in spring DOM groups compared with the control groups. For the first time, this study quantifies the efficient utilization of the in-situ DOM via absorbtrophy, indicating the vital role in the outbreak and maintenance of HAB events.

ecology↗

bioRxiv2024

Deciphering the molecular mechanism of DNA-protein interactive co-condensates

Nucleic acid and protein co-condensates exhibit diverse morphologies crucial for fundamental cellular processes. Despite their significance, the molecular mechanisms governing morphology transitions remain poorly understood. To address this gap in knowledge, we investigated DNA and the human transcription factor p53 as a model system, specifically focusing on DNA-protein interactive co-condensates (DPICs)--a scenario where neither dsDNA nor the protein demonstrates phase-separation behavior individually. Through a combination of experimental assays and theoretical approaches, we elucidated: (i) the phase diagram of DPICs, identifying two distinct transition phenomena--a phase transition between viscoelastic fluid and viscoelastic solid states, and a morphology transition from droplet-like to "pearl chain"-like DPICs; (ii) the growth dynamics of DPICs. Droplet-like and "pearl chain"-like DPICs, although with dramatically distinct final morphologies and material properties, share a common initial critical microscopic cluster (CMC) size at the nanometer scale during the early stage of phase separation. These findings provide novel insights into the biophysical mechanisms underlying multi-component phase separations within cellular environments. Significance StatementNucleic acids and proteins have the capacity to form co-condensates, exhibiting various morphologies, including droplet-like and "pearl chains" formations. Despite this observation, the underlying biophysical mechanisms remain poorly understood. In this study, we employed DNA and the protein p53 as a model system. Our investigation revealed that the strength of the DNA-p53 interactions dictates the material properties of the co-condensates, leading to a transition from a viscoelastic fluid to a viscoelastic solid phase. This transition is accompanied by a morphological shift from droplet-like formations to structures resembling "pearl chains". Additionally, we explored the growth dynamics of these co-condensates and demonstrated that the strength of p53-DNA interactions influences the relaxation time of the co-condensates, thereby potentially determining their morphological features.

biophysics↗

bioRxiv2024

JNK1 And Downstream Signalling Hubs Regulate Anxiety-Like Behaviours In A Zebrafish Larvae Phenotypic Screen

Current treatments for anxiety and depression show limited efficacy in many patients indicating that research into new underlying mechanisms is needed. Inhibition of JNK1 has been shown to evoke an anxiolytic-and antidepressant-like phenotype in mice however the downstream effectors that elicit these behavioural effects are unknown. Here we employ a zebrafish (D. Rerio) larvae behavioural assay to identify an antidepressant-/anxiolytic-like phenotype based on 2759 measured stereotypic responses to clinically proven antidepressant and anxiolytic (AA) drugs. Employing machine learning, we classify an AA phenotype from behavioural features measured during and after a startle battery in fish exposed to AA drugs (fluoxetine, imipramine, diazepam, lithium chloride, ketamine). We demonstrate that structurally independent JNK inhibitors replicate the AA classification with high accuracy, consistent with findings in mice. We go on to identify signalling hubs downstream from JNK1 by comparing phosphoproteome data from wildtype and Jnk1-/- mouse brains, and test these hubs as possible mediators of the AA phenotype in zebrafish larvae. Among these, we find that AKT, GSK-3, 14-3-3{zeta}/{varepsilon} and PKC{varepsilon}, when pharmacologically targeted, phenocopy clinically proven AA drugs. This assay shows promise as an early phase screening for compounds with anti-stress-axis/anxiolytic-like properties, and for mode of action analysis.

pharmacology and toxicology↗

bioRxiv2023

Lactose and its derivatives are a new class of immune checkpoint inhibitors for cancer therapy

Understanding the mechanisms by which the immune system surveils cancer is the key to developing better tumor immunotherapy strategies. By CRISPR/Cas9 screenings, we identified that inactivation of beta-1,4-galactosyltransferase-1 (B4GALT1), a key enzyme in glycoconjugate biosynthesis, leads to enhanced T-cell receptor (TCR) activation and functions of CD8+ T-cells. Via proximity-dependent-intercellular-protein-spreading (PDICPS), cancer cells transfer surface-bound galectin-1 (Gal-1) proteins, which recognize and bind galactosylated membrane proteins, to CD8+ T-cells, thereby suppressing T-cell-mediated cytolysis. B4GALT1-deficiency leads to reduced cell-surface galactosylation and Gal-1 binding of CD8+ T-cells. Proteomic analysis revealed reduced binding of Gal-1 with TCR and its coreceptor CD8 on B4GALT1-deficient CD8+ T-cells, leading to enhanced TCR-CD8 colocalization and T-cell activation. Lactose, a structure-mimicking competitive inhibitor of N-glycan galactosylation, enhances the functions of CD8+ T-cells and tumor immunosurveillance. Results from various preclinical tumor models demonstrate that lactose and its derivatives are a new class of immune checkpoint inhibitors for tumor immunotherapy.

immunology↗

bioRxiv2023

Determining glycosyltransferase functional order via lethality due to accumulated O-antigen intermediates, exemplified with Shigella flexneri O-antigen biosynthesis

The O antigen (OAg) polysaccharide is one of the most diverse surface molecules of Gram-negative bacterial pathogens. The structural classification of OAg based on serological typing and sequence analysis is important in epidemiology and surveillance of outbreaks of bacterial infections. Despite the diverse chemical structures of OAg repeating units (RUs) described, the genetic basis of the assembly of these RUs remains poorly understood and represents a major limitation in our understanding of the gene functions in the polysaccharide biosynthesis. Here we describe a genetic approach to interrogate the functional order of glycosyltransferases (GTs). Using Shigella flexneri as a model, we established an initial glycosyltransferase (IT) controlled system to allocate the functional order of the subsequent GT in a two-fold manner. First by reporting the growth defects caused by the sequestration of UndP through disruption of late GTs, and second by comparing the molecular sizes of stalled OAg intermediates when each putative GT is disrupted. Using this approach, we demonstrate that for RfbF and RfbG, the GTs involved in the assembly of S. flexneri backbone OAg RU, RfbG is responsible for both the committed step of OAg synthesis, as well as the third transferase for the second L-Rha. We also show that RfbF functions as the last GT to complete the S. flexneri OAg RU backbone. We propose that this simple and effective genetic approach can be also extended to define the functional order of enzymatic synthesis of other diverse polysaccharides produced both by Gram-negative and Gram-positive bacteria. ImportanceThe genetic basis of enzymatic assembly of structurally diverse OAg repeating units in Gram-negative pathogens is poorly understood, representing a major limitation in our understanding of gene functions for the synthesis of bacterial polysaccharides. We present a simple genetic approach to assigning glycosyltransferase (GT) functions and the order in which they act in the assembly of the OAg RU in their native background strain with reasonable confidence. We demonstrated with this approach the functional allocation of GTs for Shigella flexneri O antigen assembly. This approach can be generally applied in interrogating GT functions encoded by other bacterial polysaccharides to advance our understanding of diverse gene functions in the biosynthesis of polysaccharides, key knowledge in advancing biosynthetic polysaccharide production.

microbiology↗

bioRxiv2023

Interpretable Inflammation Landscape of Circulating Immune cells

Inflammation is a biological phenomenon involved in a wide variety of physiological and pathological processes. Although a controlled inflammatory response is beneficial for restoring homeostasis, it can become unfavorable if dysregulated. In recent years, major progress has been made in characterizing acute and chronic inflammation in specific diseases. However, a global, holistic understanding of inflammation is still elusive. This is particularly intriguing, considering the crucial function of inflammation for human health and its potential for modern medicine if fully deciphered. Here, we leverage advances in the field of single-cell genomics to delineate the full spectrum of circulating immune cell activation underlying inflammatory processes during infection, immune-mediated inflammatory diseases and cancer. Our single-cell atlas of >6.5 million peripheral blood mononuclear cells from 1047 patients and 19 diseases allowed us to learn a comprehensive model of inflammation in circulating immune cells. The atlas expanded our current knowledge of the biology of inflammation of immune-mediated diseases, acute and chronic inflammatory diseases, infection and solid tumors, and laid the foundation to develop a precision medicine framework using unsupervised as well as explainable machine learning. Beyond a disease-centered analysis, we charted altered activity of inflammatory molecules in peripheral blood cells, depicting discriminative inflammation-related genes to further understand mechanisms of inflammation. Finally, we have laid the groundwork for developing precision medicine diagnostic tools for patients experiencing pathologic inflammation by learning a classifier for inflammatory diseases, presenting cells in circulation as a powerful resource for patient diagnosis.

immunology↗

bioRxiv2023

Identification of A Potential Inhibitor for Anticancer Target MTHFD2 by Consensus Docking and Molecular Dynamics

The bifunctional methylenetetrahydrofolate dehydrogenase/cyclohydrolase (MTHFD2) has been recognized as a promising anticancer drug target because it is overexpressed in various types of cancer and is associated with poor prognosis. In the present study, we aimed to discover potential inhibitors from the Enamine HTS library which consists of over one million compounds. A consensus docking-based virtual screening workflow was adopted and two hits, E96 and E41, were identified for being ranked in the top 5 in all docking programs used. To validate the virtual screening result, the binding modes of the two hits were visually inspected with reference to previously published inhibitors B01 and D56, and a similar pattern of binding was observed between the hits and established ligands, indicating the reliability of the docking protocol. The subsequent molecular dynamics simulation and a series of analyses including root mean square deviation, root mean square fluctuation, and radius of gyration reveal that E96 achieved a more stable binding to the receptor than E41. The binding free energy predicted by MM/GBSA calculation confirms E96s potential to be a potent inhibitor for the target MTHFD2 as it outperforms E41 and the established ligands. In conclusion, this computational study contributes to the drug discovery efforts for the anticancer drug target MTHFD2 by suggesting ligand E96 for further structure-based optimization and in vitro/vivo experimental validation.

biochemistry↗

bioRxiv2023

Evidence for impaired hippocampal circuitry in schizophrenia and its link to memory dysfunction

Pattern separation and pattern completion are opposing yet complementary components of mnemonic processing that heavily rely on the hippocampus. It has been shown that processing within the dentate gyrus (DG) subfield promotes pattern separation while operations within the CA3 subfield are important for pattern completion. Schizophrenia has been associated with anatomical and functional hippocampal abnormalities, including within the DG and CA3. We hypothesized that an impairment in hippocampal circuitry in individuals with first-episode schizophrenia leads to deficits in pattern separation (mnemonic discrimination) and pattern completion (recognition memory), that these deficits contribute to delusions, and that antipsychotic treatment improves circuit functioning. We measured behavioral and neural responses during the identification of new, repeated, and similar stimuli using high-resolution fMRI in 45 medication-free or minimally-treated patients with first-episode schizophrenia and 49 matched controls. We found recognition memory and pattern separation deficits in patients and a negative association between memory performance and the severity of delusions. Neural analyses revealed deficits in both univariate BOLD responses and multivariate patterns in the hippocampus during mnemonic discrimination in patients compared to controls. Importantly, by investigating the association between trial-level neural activity and behavior before and after treatment, we found that antipsychotics normalized DG activity during pattern separation and CA3 activity during pattern completion. Lastly, trial-level cortical responses during mnemonic discrimination predicted performance in patients at baseline, suggesting a compensatory role. This study provides new insight into the impact of schizophrenia and antipsychotic treatment on memory systems and uncovers systems-level contributions to pattern separation and pattern completion.

neuroscience↗

bioRxiv2023

Respiration and growth of Paracoccus denitrificans R-1 with nitrous oxide as an electron acceptor

In the nitrogen biogeochemical cycle, the reduction of nitrous oxide (N2O) to N2 by N2O reductase, which is encoded by nos gene cluster, is the only biological pathway for N2O consumption. However, the capability and mechanisms of microbial N2O reduction are poorly understood. In this study, we investigated the ability to obtain energy for growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N2O reduction. This strain has strong N2O reduction capability, and the average N2O reduction rate was 5.10{+/-}0.11x10-9 mol{middle dot}h-1{middle dot}cell-1 under anaerobic condition at 30 using acetate as the electron donor in a defined medium. This reduction was accompanied by the stoichiometric consumption of acetate over time when N2O served as the sole electron acceptor and the reduction can yield energy to support microbial growth, suggesting that microbial N2O reduction is an electron transport process. Cu2+, silver nanoparticles, O2, and acidic conditions can strongly inhibit the reduction, whereas NO3- or NH4+ can promote it. Genomic analysis showed that the gene cluster encoding N2O reductase of P. denitrificans R-1 was composed of nosR, nosZ, nosD, nosF, nosY, and nosL, and nosZ, which was identified as clade I. The respiratory inhibitors test indicated that the pathway of electron transport for N2O reduction was different from that of the traditional electron transport chain for aerobic respiration. These findings suggest that modular N2O reduction by P. denitrificans R-1 is linked to the electron transport chain and energy conservation, and that dissimilatory N2O reduction is a form of microbial anaerobic respiration. IMPOETANCEIn the nitrogen biogeochemical cycle, the reduction of N2O to N2 by N2O reductase, which is encoded by nos genes, is the only biological pathway for N2O consumption. However, the capacity and mechanisms of microbial N2O reduction are poorly understood. We investigated the ability to obtain energy for growth of Paracoccus denitrificans R-1 by coupling the oxidation of various electron donors to N2O reduction. Our study showed that the nosZ type I bacterium, P. denitrificans R-1, can respire N2O as the sole electron donor. Thus, the modular N2O reduction process of clade I denitrifiers not only can consume N2O produced by themselves but can also consume the external N2O generated from non-denitrification biological or abiotic pathways under suitable conditions, which is critical for controlling the release of N2O from ecosystems into the atmosphere.

microbiology↗

bioRxiv2023

Single-cell RNA sequencing unveils the hidden powers of zebrafish kidney for generating both hematopoiesis and adaptive antiviral immunity

The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of kidney in fish immune systems remain to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cell types from zebrafish kidney via single-cell transcriptome profiling analysis. These populations included almost all known cells associated with innate and adaptive immunity, and displayed differential responses to viral infection, indicating their diverse functional roles in antiviral immunity. Remarkably, HSPCs were found to have extensive reactivities to viral infection, and the trained immunity can be effectively induced in certain HSPCs. In addition, the antigen-stimulated adaptive immunity can be fully generated in kidney, suggesting kidney acting as a secondary lymphoid organ. These results indicated that fish kidney is a dual-functional entity with functionalities of both primary and secondary lymphoid organs. Our findings illustrated the unique features of fish immune system, and highlighted the multifaced biology of kidney in ancient vertebrates.

immunology↗

bioRxiv2023

Chromatinization Modulates Topoisomerase II Processivity

Type IIA topoisomerases are essential DNA processing enzymes that must robustly and reliably relax DNA torsional stress in vivo. While cellular processes constantly create different degrees of torsional stress, how this stress feeds back to control type IIA topoisomerase function remains obscure. Using a suite of single-molecule approaches, we examined the torsional impact on supercoiling relaxation of both naked DNA and chromatin by eukaryotic topoisomerase II (topo II). We observed that topo II was at least [~] 50-fold more processive on plectonemic DNA than previously estimated, capable of relaxing > 6000 turns. We further discovered that topo II could relax supercoiled DNA prior to plectoneme formation, but with a [~]100-fold reduction in processivity; strikingly, the relaxation rate in this regime decreased with diminishing torsion in a manner consistent with the capture of transient DNA loops by topo II. Chromatinization preserved the high processivity of the enzyme under high torsional stress. Interestingly, topo II was still highly processive ([~] 1000 turns) even under low torsional stress, consistent with the predisposition of chromatin to readily form DNA crossings. This work establishes that chromatin is a major stimulant of topo II function, capable of enhancing function even under low torsional stress.

biophysics↗

bioRxiv2023

Hallmark molecular and pathological features of POLG disease are recapitulated in cerebral organoids

In our research, we developed a 3D brain organoid model to study POLG-related encephalopathy, a mitochondrial disease stemming from POLG gene mutations. We utilized induced pluripotent stem cells (iPSCs) derived from patients with these mutations to generate cortical organoids, which exhibited typical POLG disease features, such as altered morphology, neuronal loss, and mtDNA depletion. We also identified significant dysregulation in pathways crucial for neuronal development and function, alongside upregulated NOTCH and JAK-STAT signaling pathways. Metformin treatment ameliorated many of these abnormalities, except for the persistent affliction of inhibitory DA GLU neurons. This novel model effectively mirrors both the molecular and pathological attributes of POLG disease, providing a valuable tool for mechanistic understanding and therapeutic screening for POLG-related disorders and other conditions characterized by compromised neuronal mtDNA maintenance and complex I deficiency. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=127 SRC="FIGDIR/small/558087v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@1759de3org.highwire.dtl.DTLVardef@d0a3dborg.highwire.dtl.DTLVardef@1b58eaborg.highwire.dtl.DTLVardef@a986a8_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIWe have successfully developed cortical organoid model that represents POLG-related disease. C_LIO_LIThis model effectively replicates both histological and molecular signatures seen in the brains of patients. C_LIO_LIThe cortical organoid model displays a range of features common in POLG-related disease, including neurodegeneration, mtDNA depletion, and neuronal complex I deficiency. C_LIO_LIThe use of metformin supplementation in this model improved mitochondria protein and reduced cell death. C_LI

cell biology↗

bioRxiv2023

NRF2 Regulates Contractile Vascular Smooth Muscle Cells Phenotypic Switching In Abdominal Aortic Aneurysm

OBJECTIVEEvidence from previous studies has demonstrated that NRF2 can protect cardiovascular progression,which prompted us to study if NRF2 is involved in AAA development. APPROACH AND RESULTSThe difference and function of NRF2 in AAA were verified on human aortic tissues combined with scRNA-seq samples.We then used angiotensin II (Ang II) infusion mouse model with VSMCs-specific knockout to study the role of NRF2 in AAA formation.Primary cultured VSMCs were used to study how NRF2 regulates contractile VSMCs phenotype.Patient specimens were obtained to investigate the relevance of NRF2 expression to human AAA disease. NRF2 was induced in abdominal aortic VSMCs in both mouse and human AAA tissues. VSMCs-specific NRF2 knockout increased experimental AAA formation. Mechanistically, NRF2 regulates the contractile VSMCs phenotypic through miRNA145, leading to increased classic contractile protein level to prevent the development of AAA. CONCLUSIONSNRF2 is a negative regulator of AAA development, and thus may represent a potentially new therapeutic target to inhibit AAA growth and rupture.

bioinformatics↗

bioRxiv2023

Chemotherapeutic regulation of the ROS/MondoA-dependent TXNIP/GDF15 axis; and derivation of a new organoid metric as a predictive biomarker

Chemotherapy, the standard of care treatment for cancer patients with advanced disease, has been increasingly recognised to activate host immune responses to produce durable outcomes. Here, in colorectal adenocarcinoma (CRC) we identify chemotherapy-induced Thioredoxin Interacting Protein (TXNIP), a MondoA-dependent tumor suppressor gene, as a negative regulator of Growth/Differentiation Factor 15 (GDF15). GDF15 is a negative prognostic factor in CRC and promotes the differentiation of regulatory T cells (Tregs), through CD48 ligation. Intriguingly, multiple models including patient-derived tumor organoids demonstrate that loss of TXNIP/GDF15 axis functionality is associated with advanced disease or chemotherapeutic resistance, with transcriptomic or proteomic GDF15/TXNIP ratios showing potential as a prognostic biomarker. These findings illustrate a potentially common pathway where chemotherapy-induced epithelial stress drives local immune remodelling for patient benefit, with disruption of this pathway seen in refractory or advanced cases.

cancer biology↗