Biology subjects

Hai, Y.

Publications and source records attributed to Hai, Y..

15 recordsLinked to original sources

bioRxiv2025

LSH-mediated resolution of R-loops mitigates transcription-replication conflicts to preserve genomic stability in prostate cancer cells

Prostate cancer cells exhibit heightened transcriptional activity to sustain their aggressive phenotype, yet this creates DNA topological stress, leading to RNA: DNA hybrids (R-loops) and DNA damage that compromise genomic stability. LSH, an SNF2-family chromatin remodeler, is frequently dysregulated in cancers and linked to tumor progression, but its mechanistic role in genome maintenance remains unclear. Here, we demonstrate that LSH resolves R-loops in an ATP-dependent manner, mitigating transcription- replication (TR) conflicts in prostate cancer cells. LSH depletion caused R- loop accumulation due to reduced FANCD2 recruitment, exacerbating DNA damage and impairing Rad51 filament formation. Strikingly, LSH deficiency also increased R-loops at promoters of MYC and E2F target genes, stalling RNA polymerase II elongation and disrupting transcriptional programs critical for proliferation. Our findings reveal LSH is a key guardian of genome integrity, resolving R-loops to prevent TR conflicts and maintaining DNA repair fidelity. By linking LSH to R-loop resolution and transcriptional regulation, this study reveals its dual role in prostate cancer pathogenesis-- supporting malignant proliferation while safeguarding genomic stability. These insights nominate LSH as a potential therapeutic target to disrupt oncogenic transcription and induce synthetic lethality in prostate cancer.

cancer biology↗

bioRxiv2025

Inhibition of DHODH Activates Pyroptosis and cGAS-STING Pathways to Enhance NK cell Infiltration Mediated Anti-tumor Immunity in Melanoma

Cancer cells are heavily reliant on de novo pyrimidine synthesis. Suppression of pyrimidine metabolism directly inhibits tumor growth and fosters immune activation within the tumor microenvironment. Dihydroorotate dehydrogenase (DHODH), a crucial enzyme governing de novo pyrimidine synthesis, is a critical player in this context. Inhibition of DHODH not only reverses immunosuppression but also instigates a mild innate immune response. However, the impact of DHODH inhibition on natural killer (NK) cells remains unexplored. In this study, we found that inhibition of DHODH efficiently promotes NK cells infiltration in tumors. Suppression of DHODH led to increased oxidative stress in mitochondria, the release of mtDNA, and activation of caspase 3, which in turn activated the cGAS-STING pathway and pyroptosis in cancer cells, respectively, contributing to NK cells induced antitumor immune responses in melanoma. Additionally, we developed EA6, a novel DHODH inhibitor with higher efficacy in promoting NK cells infiltration. In summary, this study underscores that modulation of pyrimidine metabolism can effectively trigger antitumor immune responses, with a specific emphasis on NK cells. This finding opens new avenues for enhancing the efficacy of targeted nucleotide metabolism in cancer therapy. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=141 SRC="FIGDIR/small/644471v1_ufig1.gif" ALT="Figure 1"> View larger version (60K): org.highwire.dtl.DTLVardef@88d4fcorg.highwire.dtl.DTLVardef@156fe1aorg.highwire.dtl.DTLVardef@448086org.highwire.dtl.DTLVardef@152079c_HPS_FORMAT_FIGEXP M_FIG C_FIG The anti-tumor mechanisms of DHODH inhibition. Inhibition of DHODH activates cGAS-STING pathways to enhance NK cell infiltration. And the tumor-infiltrating NK cells facilitate melanoma cells pyroptosis which providing a positive feedback mechanism for DHODH-mediated anti-tumor immunity.

cancer biology↗

bioRxiv2024

Biochemical dissection of a fungal highly reducing polyketide synthase condensing region reveals basis for acyl group selection.

Fungal highly reducing polyketide synthases (hrPKSs) are remarkable multidomain enzymes that catalyse the biosynthesis of a diverse range of structurally complex compounds. During biosynthesis, the ketosynthase (KS) and acyltransferase (AT) domains of the condensing region are visited by the acyl carrier protein (ACP) domain during every cycle, catalysing chain priming and elongation reactions. Despite their significance, our comprehension of how these steps contribute to biosynthetic fidelity remains poorly understood. Herein, we report the full in vitro reconstitution of each catalytic step carried out by a hrPKS condensing region. Application of intact protein mass spectrometry shows that the AT domain operates selective acyl transfer to the ACP domain, ensuring loading of the correct starter / extender units, which is governed by a substrate recycling mechanism and kinetic parameters towards each substrate. The KS domain is shown to select for the correct starter unit for transacylation and subsequent chain elongation, yet harbours flexibility towards the extender unit supplied. This work provides the first comprehensive interrogation of a fungal hrPKS condensing region, which both affirms and expands our understanding of how these systems function, and provides a framework for future bioengineering efforts.

biochemistry↗

bioRxiv2024

Biosynthesis of the alpha-D-Mannosidase Inhibitor (-)-Swainsonine

(-)-Swainsonine is a polyhydroxylated indolizidine alkaloid with potent inhibitory activity against -D-mannosidases. In this work, we successfully reconstituted swainsonine biosynthetic pathway both in vivo and in vitro. Our study unveiled an unexpected epimerization mechanism involving two -ketoglutarate-dependent non-heme iron dioxygenases (SwnH2 and SwnH1), and an unusual imine reductase (SwnN), which displays substrate-dependent stereospecificity such that the stereochemical outcome of SwnN-catalyzed iminium reduction is ultimately dictated by SwnH1-catalyzed C8-hydroxylation. We also serendipitously discovered that an O-acetyl group can serve as a detachable protecting/directing group, altering the site-selectivity of SwnH2-catalyzed hydroxylation while maintaining the stereoselectivity. Insights gained from the biochemical characterization of these tailoring enzymes enabled biocatalytic synthesis of a new polyhydroxylated indolizidine alkaloid, opening doors to the biosynthesis of diverse natural product-based glycosidase inhibitors.

biochemistry↗

bioRxiv2023

Novel DNA methylation changes in mouse lungs associated with heavy smoking

Smoking is a potent cause of asthma, chronic obstructive pulmonary disease (COPD) and many other health defects, and changes in DNA methylation (DNAm) have been identified as a potential link between smoking and these health outcomes. However, most links between smoking and DNAm have been made using blood and other easily accessible tissues in humans, while evidence from more directly affected tissues such as the lungs is greatly lacking. Here, we identified DNAm patterns which are altered by smoking directly in the lungs. We used a well-established mouse model to measure the effects of heavy smoking first on lung phenotype immediately after smoking and then after a period of smoking cessation. Next, we determined whether our mouse model could recapitulate previous DNAm patterns observed in smoking humans by measuring DNAm at a candidate gene responsive to cigarette smoke (CS), Cyp1a1. Finally we carried out epigenome-wide DNAm analyses using the newly released Illumina mouse methylation microarrays. Our results recapitulate some of the phenotypes and DNAm patterns observed in human studies but reveal 32 differentially methylated genes specific to the lungs which have not been previously associated with smoking. The affected genes are known to be involved in nicotine dependency, tumorigenesis and metastasis, immune cell dysfunction, lung function decline, and COPD. This research emphasizes the need to study CS-mediated DNAm signatures in directly affected tissues like the lungs, as that may be essential in understanding mechanisms underlying CS-mediated health outcomes.

molecular biology↗

bioRxiv2023

Three Conserved Immune Dysfunction and Exclusion Subtypes in Bladder and Pan-cancers: Prognostic and Immunotherapeutic Significance

Molecular subtyping is expected to enable bladder cancer (BC) precise treatment. However, its clinical application remains defective and controversial. Given the significance of tumor immune dysfunction and exclusion (TIDE) in tumor immune escape and immunotherapy, we aimed to develop a novel TIDE-based subtyping method to facilitate personalized management. Transcriptome data of BC was used to evaluate the heterogeneity and the status of TIDE patterns. We identified 69 TIDE biomarker genes and classified BC samples into three subtypes. Subtype I showed the lowest TIDE status and malignancy with the best prognosis and highest sensitivity to immune checkpoint blockade (ICB) treatment, which was enriched of metabolic related signaling pathways. Subtype III represented the highest TIDE status and malignancy with the poorest prognosis and resistance to ICB treatment, resulting from its inhibitory immune microenvironment and T cell terminal exhaustion. Subtype II was in a transitional state with intermediate TIDE level, malignancy, and prognosis. We further confirmed the existence and characteristics of our novel TIDE subtypes using real-world BC samples. This subtyping method was proved to be more efficient than known methods in identifying non-responders to immunotherapy. We also found that combining our TIDE subtypes with known biomarkers can improve the sensitivity and specificity in predicting ICB response. Moreover, besides guiding ICB treatment, this classification approach can assist in selecting the frontline or recommended drugs. Finally, the TIDE subtypes are conserved across pan-tumors. In conclusion, our novel TIDE-based strategy is a powerful clinical tool for BC and pan-cancer patients, and potentially guiding personalized immunotherapy.

bioinformatics↗

bioRxiv2023

Early life exposure to cigarette smoke is associated with lung function changes and primes gene expression and DNA methylation changes at Cyp1a1 upon exposure later in life

Prenatal and early life exposure to cigarette smoke (CS) have repeatedly been shown to induce stable, long-term changes in DNA methylation (DNAm) in offspring. It has been hypothesized that these changes might be functionally related to the known outcomes of prenatal and early life CS exposure, which include impaired lung development, altered lung function and increased risk of asthma and wheeze. However, to date, few studies have examined DNAm changes induced by prenatal CS in tissues of the lung, and even fewer have attempted to examine the specific influences of prenatal versus early postnatal exposures. Here, we have established a mouse model of CS exposure which isolates the effects of prenatal and early postnatal CS exposures in early life. We have used this model to measure the effects of prenatal and/or postnatal CS exposures on lung function and immune cell infiltration as well as DNAm and expression of Cyp1a1, a candidate gene previously observed to demonstrate DNAm differences upon CS exposure in humans. Our study revealed that exposure to CS prenatally and in the early postnatal period cause long-lasting differences in offspring lung function, gene expression and lung Cyp1a1 DNAm, which wane over time but are reestablished upon re-exposure to CS in adulthood. This study creates a testable mouse model which can be used to investigate the effects of prenatal and early postnatal CS exposures and will contribute to the design of intervention strategies to mediate these detrimental effects.

genetics↗

bioRxiv2022

Elucidating the molecular programming of a nonlinear nonribosomal peptide synthetase responsible for fungal siderophore biosynthesis.

Siderophores belonging to the ferrichrome family are essential for the viability of fungal species and play a key role for virulence of numerous pathogenic fungi. Despite their biological significance, our understanding of how these iron-chelating cyclic hexapeptides are assembled by non-ribosomal peptide synthetase (NRPS) assembly lines remains poorly understood, primarily due to the nonlinearity exhibited by the domain architecture. Herein, we report the biochemical characterization of the SidC NRPS, responsible for construction of the intracellular siderophore ferricrocin. In vitro reconstitution of purified SidC revealed its ability to produce ferricrocin and its structural variant, ferrichrome. Application of intact protein mass spectrometry uncovered several non-canonical events during peptidyl siderophore biosynthesis, including inter-modular loading of amino acid substrates and an adenylation domain capable of poly-amide bond formation. This work expands the scope of NRPS programming, allows biosynthetic assignment of ferrichrome NRPSs, and sets the stage for reprogramming towards novel hydroxamate scaffolds.

biochemistry↗

bioRxiv2019

A novel vaccine targeting the viral protease cleavage sites protects Mauritian cynomolgus macaques against vaginal SIVmac251 infection

After over three decades of research, an effective anti-HIV vaccine remains elusive. Unconventional and novel vaccine strategies are needed. Here, we report that a vaccine focusing the immune response on the sequences surrounding the 12 viral protease cleavage sites (PCSs) provides greater than 80% protection of Mauritian cynomolgus macaques (MCMs) against repeated intravaginal SIVmac251 challenges. The PCS-specific T cell responses are correlated with vaccine efficacy. The PCS vaccine does not induce immune activation and inflammation known to be associated with increased susceptibility to HIV infection. Machine learning analyses revealed that the immune environment generated by the PCS vaccine predicts vaccine efficacy. Our study demonstrates for the first time that a novel vaccine which targets viral maturation, but lacks full Env and Gag proteins as immunogens, can prevent intravaginal infection in a highly stringent NHP/SIV challenge model. Targeting HIV maturation thus offers a novel approach to developing an effective HIV vaccine. One Sentence SummaryThe anti-PCS T cell responses and the immune environment induced by the novel PCS vaccine are key correlates of vaccine efficacy

microbiology↗

bioRxiv2019

Nix induced mitochondrial fission, mitophagy, and myocyte insulin resistance are abrogated by PKA phosphorylation.

Lipotoxicity is a form of cellular stress caused by the accumulation of lipids resulting in mitochondrial dysfunction and insulin resistance in muscle. Previously, we demonstrated that the mitophagy receptor Nix is responsive to lipotoxicity and accumulates in response to diacylglycerols induced by high-fat (HF) feeding. In addition, previous studies have implicated autophagy and mitophagy in muscle insulin sensitivity. To provide a better understanding of these observations, we undertook gene expression array and shot-gun metabolomics studies in soleus muscle from rodents on an HF diet. Interestingly, we observed a modest reduction in several autophagy-related genes including Beclin-1, ATG3, and -5. Moreover, we observed alterations in the fatty acyl composition of cardiolipins and phosphatidic acids. Given the previously reported roles of these phospholipids and Nix in mitochondrial dynamics, we investigated aberrant mitochondrial fission and turn-over as a mechanism of myocyte insulin resistance. In a series of gain-of-function and loss-of-function experiments in rodent and human myotubes, we demonstrate that Nix accumulation triggers mitochondrial depolarization, fragmentation, calcium-dependent activation of DRP1, and mitophagy. In addition, Nix-induced mitochondrial fission leads to myotube insulin resistance through activation of mTOR-p70S6 kinase inhibition of IRS1, which is contingent on phosphatidic acids and Rheb. Finally, we demonstrate that Nix-induced mitophagy and insulin resistance can be reversed by direct phosphorylation of Nix by PKA, leading to the translocation of Nix from the mitochondria and sarcoplasmic reticulum to the cytosol. These findings provide insight into the role of Nix-induced mitophagy and myocyte insulin resistance during an overfed state when overall autophagy-related gene expression is reduced. Furthermore, our data suggests a mechanism by which exercise or pharmacological activation of PKA may overcome myocyte insulin resistance. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=98 SRC="FIGDIR/small/825828v2_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@15d0a4org.highwire.dtl.DTLVardef@34f358org.highwire.dtl.DTLVardef@5427f3org.highwire.dtl.DTLVardef@10ae48a_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2019

Structure-guided function discovery of an NRPS-like glycine betaine reductase for choline biosynthesis in fungi

Nonribosomal peptide synthetases (NRPS) and NRPS-like enzymes have diverse functions in primary and secondary metabolism. By using a structure-guided approach, we uncovered the function of an NRPS-like enzyme with unusual domain architecture, catalyzing two sequential two-electron reductions of glycine betaine to choline. Structural analysis based on homology model suggests cation-{pi} interactions as the major substrate specificity determinant, which was verified using substrate analogs and inhibitors. Bioinformatic analysis indicates this NRPS-like glycine betaine reductase is highly conserved and widespread in fungi kingdom. Genetic knockout experiments confirmed its role in choline biosynthesis and maintaining glycine betaine homeostasis in fungi. Our findings demonstrate that the oxidative choline-glycine betaine degradation pathway can operate in a fully reversible fashion and provide new insights in understanding fungal choline metabolism. The use of an NRPS-like enzyme for reductive choline formation is energetically efficient compared to known pathways. Our discovery also underscores the capabilities of structure-guided approach in assigning function of uncharacterized multidomain proteins, which can potentially aid functional discovery of new enzymes by genome mining.

biochemistry↗

bioRxiv2018

Structural Basis for Stereoselective Dehydration and Hydrogen-Bonding Catalysis by the SAM-Dependent Pericyclase LepI

LepI is an S-adenosylmethionine (SAM)-dependent pericyclase that catalyzes the formation of 2-pyridone natural product leporin C. Biochemical characterization showed LepI can catalyze the stereoselective dehydration to yield a reactive (E)-quinone methide which can undergo a bifurcating intramolecular Diels-Alder (IMDA) and hetero-Diels-Alder (HDA) cyclization from an ambimodal transition state, and a [3,3]-retro-Claisen rearrangement to recycle the IMDA product into leporin C. Here we solved the X-ray crystal structures of SAM-bound LepI, and in complex with a substrate analog, the product leporin C, and a retro-Claisen reaction transition-state analog to understand the structural basis for the multitude of reactions. Structural and mutational analysis revealed how Nature evolves a classic methyltransferase active site into one that can serve as a dehydratase and a multifunctional pericyclase. Catalysis of both sets of reactions employ His133 and Arg295, two active site residues that are not found in canonical methyltransferases. An alternative role of SAM, which is not found to be in direct contact of the substrate, is also proposed.

biochemistry↗

bioRxiv2018

Trans-ethnic genome-wide association study provides insight into effector genes and molecular mechanisms for kidney function and highlights a causal effect on kidney-specific disease aetiologies

Chronic kidney disease (CKD) affects [~]10% of the global population, with considerable ethnic differences in prevalence and aetiology. We assembled genome-wide association studies (GWAS)1-3 of estimated glomerular filtration rate (eGFR), a measure of kidney function that defines CKD, in 312,468 individuals from four ancestry groups. We identified 93 loci (20 novel), which were delineated to 127 distinct association signals. These signals were homogenous across ancestries, and were enriched for protein-coding exons, kidney-specific histone modifications, and transcription factor binding sites for HDAC2 and EZH2. Fine-mapping revealed 40 high-confidence variants driving eGFR associations and highlighted potential causal genes with cell-type specific expression in glomerulus, and proximal and distal nephron. Mendelian randomisation (MR) supported causal effects of eGFR on overall and cause-specific CKD, kidney stone formation, diastolic blood pressure (DBP) and hypertension. These results define novel molecular mechanisms and effector genes for eGFR, offering insight into clinical outcomes and routes to CKD treatment development.

genetics↗

bioRxiv2018

High Postoperative Monocyte Predicts Worse Lung Adenocarcinoma or Squamous Cell Carcinoma Outcomes

BackgroundPeripheral monocyte count is an assessable parameter. Recently, evidence suggested an elevated preoperative monocyte counts predicting poor prognosis in malignancies. The aim of this study was to determine the prognostic effect of early postoperative (within 4 days) blood monocyte count in patients with lung adenocarcinoma or squamous cell carcinoma following lobectomy.\n\nMethodsWe retrospectively reviewed patients with operated lung adenocarcinoma or squamous cell carcinoma from 2006 to 2011 in Western China Lung Cancer database. Both the preoperative and postoperative monocyte counts were divided into two groups. Univariate analysis on disease-free survival (DFS) and overall survival (OS) was performed using the Kaplan-Meier and log-rank tests, and multivariate analysis was conducted using the Cox proportional hazards regression model.\n\nResultsThere were 433 patients enrolled in our analysis. The cut-off values were 0.375*109/L and 0.845*109/L for preoperative and early postoperative monocyte count respectively which were calculated by receiver operating characteristic curve. Two-tailed log-rank test indicated patients with an early postoperative elevated monocyte count predicted a poor DFS and OS overall (P<0.001, P<0.001, respectively) as well as in subgroup analysis. On univariate and multivariate analysis, early postoperative elevated monocyte count presented as a promising independent prognostic factor for both DFS and OS (HR=2.991, 95%CI: 2.243-3.988, P<0.001; HR=2.705, 95%CI: 1.977-3.700, P<0.001, respectively). However, no significance was detected for preoperative monocyte in multivariate analysis.\n\nConclusionsElevated early postoperative peripheral monocyte count is an independent predictor of poor prognosis for patients with operable lung adenocarcinoma or squamous cell carcinoma by lobectomy.

cancer biology↗

bioRxiv2018

Misoprostol regulates Bnip3 repression and alternative splicing to control cellular calcium homeostasis during hypoxic stress.

The cellular response to hypoxia involves the activation of a conserved pathway for gene expression regulated by the transcription factor complex called hypoxia-inducible factor (HIF). This pathway has been implicated in both the adaptive response to hypoxia and in several hypoxic-ischemic related pathologies. Perinatal hypoxic injury, often associated with prematurity, leads to multi-organ dysfunction resulting in significant morbidity and mortality. Using a rodent model of neonatal hypoxia and several representative cell lines, we observed HIF1 activation and down-stream induction of the cell death gene Bnip3 in brain, large intestine, and heart which was mitigated by administration of the prostaglandin E1 analog misoprostol. Mechanistically, we determined that misoprostol inhibits full-length Bnip3 (Bnip3-FL) expression through PKA-mediated NF-{kappa}B (P65) nuclear retention, and the induction of pro-survival splice variants. We observed that the dominant small pro-survival variant of Bnip3 in mouse cells lacks the third exon (Bnip3{Delta}Exon3), whereas human cells produce a pro-survival BNIP3 variant lacking exon 2 (BNIP3{Delta}Exon2). In addition, these small Bnip3 splice variants prevent mitochondrial dysfunction, permeability transition, and necrosis triggered by Bnip3-FL by blocking calcium transfer from the sarco/endoplasmic reticulum to the mitochondria. Furthermore, misoprostol and Bnip3{Delta}Exon3 promote nuclear calcium accumulation, resulting in HDAC5 nuclear export, NFAT activation, and adaptive changes in cell morphology and gene expression. Collectively, our data suggests that misoprostol can mitigate the potential damaging effects of hypoxia on multiple cell types by activating adaptive cell survival pathways through Bnip3 repression and alternative splicing.

cell biology↗