Biology subjects

Wang, J.

Publications and source records attributed to Wang, J..

At least 1,243 records · Page 69Linked to original sources

bioRxiv2024

Identifying new cancer genes based on the integration of annotated gene sets via hypergraph neural networks

MotivationIdentifying cancer genes remains a significant challenge in cancer genomics research. Annotated gene sets encode functional associations among multiple genes, and cancer genes have been shown to cluster in hallmark signaling pathways and biological processes. The knowledge of annotated gene sets is critical for discovering cancer genes but remains to be fully exploited. ResultsHere, we present the DIsease-Specific Hypergraph neural network (DISHyper), a hypergraph-based computational method that integrates the knowledge from multiple types of annotated gene sets to predict cancer genes. First, our benchmark results demonstrate that DISHyper outperforms the existing state-of-the-art methods and highlight the advantages of employing hypergraphs for representing annotated gene sets. Second, we validate the accuracy of DISHyper-predicted cancer genes using functional validation results and multiple independent functional genomics data. Third, our model predicts 44 novel cancer genes, and subsequent analysis shows their significant associations with multiple types of cancers. Overall, our study provides a new perspective for discovering cancer genes and reveals previously undiscovered cancer genes. AvailabilityDISHyper is freely available for download at https://github.com/genemine/DISHyper. Contactjxwang@mail.csu.edu.cn

systems biology↗

bioRxiv2024

LRG1 promotes atherosclerosis by activating macrophages

BackgroundAtherosclerosis is a chronic inflammatory disease of the arterial wall characterized by the accumulation of cholesterol-rich lipoproteins in macrophages. Leucine-rich alpha-2 glycoprotein 1 (LRG1) is a circulating protein associated with inflammation, however, its role in atherosclerosis remains unclear. This study identified its role in macrophage pro-inflammatory differentiation and revealed the relationship between LRG1 and atherosclerosis. MethodWe evaluated the impact of LRG1 on atherosclerosis progression by analyzing atherosclerotic tissue and serum samples from patients with coronary artery disease (CAD) and healthy individuals and analyzed its role in such a process using two types of mice models: Apoe knock-out mice (Apoe-/-) and Apoe and Lrg1 double knock-out mice (Apoe-/-/Lrg1-/-). These mice were fed with a high-fat diet for 16 to 32 weeks to simulate conditions exacerbating atherosclerosis. To examine the effects of inhibiting LRG1 on atherogenesis, we administered intraperitoneal injections of LRG1 neutralizing antibody (50g/kg) weekly to Apoe-/- mice for 8 weeks. We conducted in vitro assays using bone marrow-derived macrophages isolated from wild-type mice and analyzed transcriptional signatures using RNA sequencing. Additionally, we utilized small molecular inhibitors to validate the signaling pathway through which LRG1 promotes macrophage-driven inflammation. ResultsLRG1 levels were found to be elevated in patients with atherosclerosis and correlated with higher levels of a plasma pro-inflammatory biomarker high-sensitive C-reactive protein (hsCRP), and several macrophage-related pro-inflammatory markers including CD68, VE-Cadherin and VCAM-1. In a high fat diet induced Apoe-/- mouse atherosclerosis model, the deletion of LRG1 gene significantly delayed atherogenesis progression and reduced levels of macrophage-related pro-inflammatory cytokines. Addition of purified LRG1 to cultured macrophages stimulated those macrophages to pro-inflammatory M1-like polarization regulated by the activation of ERK and JNK pathways. An anti-LRG1 neutralizing antibody effectively blocked LRG1-induced macrophage M1-like polarization in vitro and conferred therapeutic benefits to animals with ApoE deficiency-induced atherosclerosis. ConclusionLRG1 plays an important pro-inflammatory role in atherosclerosis by influencing macrophage polarization towards a pro-inflammatory state. The inhibition of LRG1 with neutralizing antibodies may offer a potential therapeutic strategy for patients with atherosclerosis by mitigating the pro-inflammatory response and delaying disease progression, offering a novel therapy in atherosclerosis management. Translational PerspectiveAtherosclerosis, a persistent inflammatory condition affecting the arterial wall, serves as the underlying pathophysiological basis for acute ischemic cardiovascular events. The involvement of macrophages is crucial in the advancement of atherosclerosis. In this investigation, heightened levels of plasma LRG1 were observed in individuals with coronary artery disease. Moreover, this study presents initial evidence highlighting LRG1 as a pivotal activator of macrophages, instigating a pro-inflammatory M1 polarization during atherogenesis through the activation of ERK1/2 and JNK pathways. The use of an anti-LRG1 neutralizing antibody demonstrated a delay in atherosclerosis progression in an animal model, suggesting a potential therapeutic target for atherosclerosis treatment. Suppression of LRG1 production could impede atherosclerosis advancement and enhance plaque stability. Utilizing neutralizing antibodies against LRG1 emerges as a promising therapeutic approach for treating atherosclerosis.

pathology↗

bioRxiv2024

CACIMAR: Cross-species Analysis of Cell Identities, Markers, Regulations and Interactions Using Single-cell RNA Sequencing Data

Transcriptomic analysis across species is increasingly used to reveal conserved gene regulations which implicate crucial regulators. Cross-species analysis of single-cell RNA sequencing (scRNA-seq) data provides new opportunities to identify the cellular and molecular conservations especially for cell types and cell type-specific gene regulations. However, few methods have been developed to analyze cross-species scRNA-seq data to uncover both molecular and cellular conservation patterns. Here, we built a tool called CACIMAR, which can perform cross-species analysis of cell identities, markers, regulations and interactions using scRNA-seq profiles. Based on the weighted sum models of the conserved features, we developed different conservation scores to measure the conservation of cell types, regulatory networks and intercellular interactions. Using publicly available scRNA-seq data on retinal regeneration in mice and zebrafish, we demonstrated four main functions of CACIMAR. First, CACIMAR allows to identify evolutionarily conserved cell types, including poorly conserved cell types. Second, the tool facilitates the identification of evolutionarily conserved or species-specific marker genes. Third, CACIMAR enables the identification of conserved intracellular regulations, including cell type-specific regulatory subnetworks and regulators. Lastly, CACIMAR provides a unique feature on the identification of conserved intercellular interactions. Overall, CACIMAR facilitates the identification of evolutionarily conserved cell types, marker genes, intracellular regulations and intercellular interactions, providing insights on the cellular and molecular mechanisms of species evolution.

bioinformatics↗

bioRxiv2024

Declining reservoir elevations following a two-decade drought increase water temperatures and non-native fish passage facilitating a downstream invasion

River ecosystems are threatened by interactions among river regulation, non-native species, and climate change. Water use has exceeded supply for two decades in the USAs Colorado River basin draining its two largest storage reservoirs (Lake Powell and Lake Mead). In 2022, after more than two decades of declining reservoir levels and warming downstream river water temperatures, Lake Powell began releasing water from its lower epilimnion into the Grand Canyon segment of the Colorado River. While managers were concerned about the risk of non-native, predatory smallmouth bass (Micropterus dolomieu) entrainment and reproduction, they lacked a quantitative tool to understand entrainment rates and population growth potential under different reservoir management strategies. To fill this void, we developed models in spring 2022 that: 1) predicted propagule pressure at different reservoir elevations, and 2) linked reservoir storage/operations, water temperatures, and smallmouth bass population dynamics to forecast population growth rates under different hydrologic and management scenarios. In the summers of 2022 and 2023, smallmouth bass were documented reproducing in the lower Colorado River for the first time. Our models accurately forecasted adult catch of smallmouth bass in 2022 and 2023 and forecasted that reproduction would occur in both years for the first time in the history of this river segment. Above average runoff in 2023 increased reservoir elevations, however the potential for smallmouth bass establishment remains high because of long-term forecasts of reduced reservoir inflows and lake levels significantly below full pool. Maintaining Lake Powell elevations above 1,088 m (3,570 ft) would likely minimize propagule pressure from the reservoir and would likely create downstream conditions that minimize smallmouth bass population growth.

ecology↗

bioRxiv2024

NeuralTE: an accurate approach for Transposable Element superfamily classification with multi-feature fusion

MotivationClassifying Transposable Elements (TEs) at the superfamily level offers deeper insights into species variation and evolution. Recent advancements in third-generation sequencing technologies have made a large number of genomes from non-model species becoming available. However, existing TE classification methods suffer from several limitations, including the necessity to train multiple hierarchical classification models, the incapacity to perform classification at the superfamily level, and deficiencies in both accuracy and robustness. Therefore, there is an urgent need for an accurate TE classification method to improve genome annotation. ResultsIn this study, we develop NeuralTE, a deep learning method designed to classify transposons at the superfamily level. To achieve accurate TE classification, we identify various structural features of transposons, and use different combinations of k-mers for terminal repeats and internal sequences to uncover distinct patterns. Evaluation on all transposons from Repbase shows that NeuralTE outperforms existing deep learning, machine learning, and homology-based methods in classifying TEs. Testing on the transposons from novel species highlights the superior performance of NeuralTE compared to existing methods. We also conduct TE annotation experiments on rice using different classification tools, and the results show that NeuralTE achieves annotations nearly identical to the gold standard, highlighting its robustness and accuracy in classifying transposons. AvailabilityNeuralTE is publicly available at https://github.com/CSU-KangHu/NeuralTE.

bioinformatics↗

bioRxiv2024

CryoCycle your grids: Plunge vitrifying and reusing clipped grids to advance cryoEM democratization

CryoEM democratization is hampered by access to costly plunge-freezing supplies. We introduce methods, called CryoCycle, for reliably blotting, vitrifying, and reusing clipped cryoEM grids. We demonstrate that vitreous ice may be produced by plunging clipped grids with purified proteins into liquid ethane and that clipped grids may be reused several times for different protein samples. Furthermore, we demonstrate the vitrification of thin areas of cells prepared on gold-coated, pre-clipped grids.

molecular biology↗

bioRxiv2024

Tmc7 deficiency causes acrosome biogenesis defects and male infertility in mice

Transmembrane channel-like (TMC) proteins are a highly conserved ion channel family consisting of eight members (TMC1-TMC8) in mammals. TMC1/2 are components of the mechanotransduction channel in hair cells, and mutations of TMC1/2 cause deafness in humans and mice. However, the physiological roles of other TMC proteins remain largely unknown. Here, we show that Tmc7 is specifically expressed in the testis and that it is required for acrosome biogenesis during spermatogenesis. Tmc7-/- mice exhibited abnormal sperm head, disorganized mitochondrial sheaths, and reduced number of elongating spermatids, similar to human oligo-astheno-teratozoospermia. We further demonstrate that TMC7 is colocalized with GM130 at the cis-Golgi region in round spermatids. TMC7 deficiency leads to aberrant Golgi morphology and impaired fusion of Golgi-derived vesicles to the developing acrosome. Moreover, upon loss of TMC7 intracellular ion homeostasis is impaired and ROS levels are increased, which in turn causes Golgi and endoplasmic reticulum (ER) stress. Taken together, these results suggest that TMC7 is required to maintain pH and ion homeostasis, which is needed for acrosome biogenesis. Our findings unveil a novel role for TMC7 in acrosome biogenesis during spermiogenesis.

developmental biology↗

bioRxiv2024

Copper drives remodeling of metabolic state and progression of clear cell renal cell carcinoma

Copper (Cu) is an essential trace element required for mitochondrial respiration. Late-stage clear cell renal cell carcinoma (ccRCC) accumulates Cu and allocates it to mitochondrial cytochrome c oxidase. We show that Cu drives coordinated metabolic remodeling of bioenergy, biosynthesis and redox homeostasis, promoting tumor growth and progression of ccRCC. Specifically, Cu induces TCA cycle-dependent oxidation of glucose and its utilization for glutathione biosynthesis to protect against H2O2 generated during mitochondrial respiration, therefore coordinating bioenergy production with redox protection. scRNA-seq determined that ccRCC progression involves increased expression of subunits of respiratory complexes, genes in glutathione and Cu metabolism, and NRF2 targets, alongside a decrease in HIF activity, a hallmark of ccRCC. Spatial transcriptomics identified that proliferating cancer cells are embedded in clusters of cells with oxidative metabolism supporting effects of metabolic states on ccRCC progression. Our work establishes novel vulnerabilities with potential for therapeutic interventions in ccRCC. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/575895v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@14e1b89org.highwire.dtl.DTLVardef@f1c83forg.highwire.dtl.DTLVardef@191aff8org.highwire.dtl.DTLVardef@1b7ccd1_HPS_FORMAT_FIGEXP M_FIG C_FIG O_LIAccumulation of copper is associated with progression and relapse of ccRCC and drives tumor growth. C_LIO_LICu accumulation and allocation to cytochrome c oxidase (CuCOX) remodels metabolism coupling energy production and nucleotide biosynthesis with maintenance of redox homeostasis. C_LIO_LICu induces oxidative phosphorylation via alterations in the mitochondrial proteome and lipidome necessary for the formation of the respiratory supercomplexes. C_LIO_LICu stimulates glutathione biosynthesis and glutathione derived specifically from glucose is necessary for survival of CuHi cells. Biosynthesis of glucose-derived glutathione requires activity of glutamyl pyruvate transaminase 2, entry of glucose-derived pyruvate to mitochondria via alanine, and the glutamate exporter, SLC25A22. Glutathione derived from glucose maintains redox homeostasis in Cu-treated cells, reducing Cu-H2O2 Fenton-like reaction mediated cell death. C_LIO_LIProgression of human ccRCC is associated with gene expression signature characterized by induction of ETC/OxPhos/GSH/Cu-related genes and decrease in HIF/glycolytic genes in subpopulations of cancer cells. Enhanced, concordant expression of genes related to ETC/OxPhos, GSH, and Cu characterizes metabolically active subpopulations of ccRCC cells in regions adjacent to proliferative subpopulations of ccRCC cells, implicating oxidative metabolism in supporting tumor growth. C_LI

cancer biology↗

bioRxiv2024

The lateral habenula integrates age and experience to promote social transitions in developing rats

Social behavior deficits are an early-emerging marker of psychopathology and are linked with early caregiving quality. However, the infant neural substrates linking early care to social development are poorly understood. Here, we focused on the infant lateral habenula (LHb), a highly-conserved brain region at the nexus between forebrain and monoaminergic circuits. Despite its consistent links to adult psychopathology, this brain region has been understudied in development when the brain is most vulnerable to environmental impacts. In a task combining social and threat cues, suppressing LHb principal neurons had opposing effects in infants versus juveniles, suggesting the LHb promotes a developmental switch in social approach behavior under threat. We observed that early caregiving adversity (ECA) disrupts typical growth curves of LHb baseline structure and function, including volume, firing patterns, neuromodulatory receptor expression, and functional connectivity with cortical regions. Further, we observed that suppressing cortical projections to the LHb rescued social approach deficits following ECA, identifying this microcircuit as a substrate for disrupted social behavior. Together, these results identify immediate biomarkers of ECA in the LHb and highlight this region as a site of early social processing and behavior control.

neuroscience↗

bioRxiv2024

Chromosome-level de novo genome unveils the evolution of Gleditsia sinensis and thorns development

Gleditsia Linn is widely distributed in the world and Gleditsia sinensis as an important Leguminosae specie, especially its thorns, has been used in the Chinese medicine as a chief ingredient for centuries. While the lack of genome database limits its in-depth research, especially genetic regulation and molecular developmental mechanism. In this investigation, a chromosome-level de novo genome of G. sinensis was assembled through PacBio HiFi, Illumina sequencing as well as those from Hi-C, genetic mapping and K-mer analysis. The G. sinensis harbors 786.13 Mb sized genome (contig N50=1.58 Mb, scaffold N50=51.53 Mb, 2n=28) with 36, 408 protein-coding genes. The full-length transcriptome sequencing of diverse tissues was performed to assist genome functional annotation. The comparative and evolutionary analysis unveiled that G. sinensis diverged from the Cretaceous period approximately 76.31 million years ago (Mya) and the close relationship between G. sinensis and other 8 Leguminosae species. The whole-genome duplication (WGD) analysis indicated G. sinensis underwent three WGD events and might go through another WGD event after differentiating from other Leguminosae plants. The Weighted Gene Coexpression Network Analysis based on phenotype and differentially expressed genes further demonstrated that GsinMYB should be involved in the development of thorns via regulating late thorn differentiation. This investigation provides a high level genome of Gleditsia for Leguminosae species evolution comparison and functional elucidation and also key insights for further study on the molecular regulation mechanisms of the thorns development as a special abnormal stem organ in plants and the molecular breeding of G. sinensis.

genomics↗

bioRxiv2024

Sequence-Dependent Conformational Transitions of Disordered Proteins During Condensation

Intrinsically disordered proteins (IDPs) can form biomolecular condensates through phase separation. It is recognized that the conformation of IDPs in the dense and dilute phases as well as at the interfaces of condensates can critically impact the resulting properties associated with their functionality. However, a comprehensive understanding of the conformational transitions of IDPs during condensation remains elusive. In this study, we employ a coarse-grained polyampholyte model, comprising an equal number of oppositely charged residues--glutamic acid and lysine--whereby conformations and phase behavior can be readily tuned by altering the protein sequence. By manipulating the sequence patterns from perfectly alternating to block-like, we obtain chains with ideal-like conformations to semi-compact structures in the dilute phase, while in the dense phase, the chain conformation is approximately that of an ideal chain, irrespective of the protein sequence. By performing simulations at different concentrations, we find that the chains assemble from the dilute phase through small oligomeric clusters to the dense phase, accompanied by a gradual swelling of the individual chains. We further demonstrate that these findings are applicable to several naturally occurring proteins involved in the formation of biological condensates. Concurrently, we delve deeper into the chain conformations within the condensate, revealing that chains at the interface show a strong sequence dependence, but remain more collapsed than those in the bulk-like dense phase. This study addresses critical gaps in our knowledge of IDP conformations within condensates as a function of protein sequence. TOC graphics O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=151 SRC="FIGDIR/small/575294v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@cd06e3org.highwire.dtl.DTLVardef@7f58e3org.highwire.dtl.DTLVardef@a4a370org.highwire.dtl.DTLVardef@e63fa1_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2024

Spatial transcriptomic analysis drives PET imaging of tight junction protein expression in pancreatic cancer theranostics

We apply spatial transcriptomics and proteomics to select pancreatic cancer surface receptor targets for molecular imaging and theranostics using an approach that can be applied to many cancers. Selected cancer surfaceome epithelial markers were spatially correlated and provided specific cancer localization, whereas the spatial correlation between cancer markers and immune- cell or fibroblast markers was low. While molecular imaging of cancer-associated fibroblasts and integrins has been proposed for pancreatic cancer, our data point to the tight junction protein claudin-4 as a theranostic target. Claudin-4 expression increased [~]16 fold in cancer as compared with normal pancreas, and the tight junction localization conferred low background for imaging in normal tissue. We developed a peptide-based molecular imaging agent targeted to claudin-4 with accumulation to [~]25% injected activity per cc (IA/cc) in metastases and [~]18% IA/cc in tumors. Our work motivates a new approach for data-driven selection of molecular targets.

bioengineering↗

bioRxiv2024

BLADE-ON-PETIOLE interacts with CYCLOIDEA to fine-tune CYCLOIDEA-mediated flower symmetry in Monkeyflowers (Mimulus)

AbstractMorphological novelties, or key innovations, are instrumental to the diversification of the organisms. In plants, one such innovation is the evolution of zygomorphic flowers, which is thought to promote outcrossing and increases flower morphological diversity. We isolated three allelic mutants from two Mimulus species displaying altered floral symmetry and identified the causal gene as the orthologue of Arabidopsis BLADE-ON-PETIOLE. We found that MlBOP and MlCYC2a physically interact and this BOP-CYC interaction module is highly conserved across the angiosperms. Furthermore, MlBOP self-ubiquitinates and suppresses MlCYC2a self- activation. MlCYC2a, in turn, impedes MlBOP ubiquitination. Thus, this molecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression of MlCYC2a, contributing to the formation of bilateral symmetry flowers, a key trait in angiosperm evolution. One Sentence SummaryMolecular tug-of-war between MlBOP and MlCYC2a fine-tunes the expression of MlCYC2a, contributing to the bilateral flower symmetry formation.

developmental biology↗

bioRxiv2024

CRISPR-repressed toxin-antitoxin provides population-level immunity against diverse anti-CRISPR elements

Prokaryotic CRISPR-Cas systems are highly vulnerable to phage-encoded anti-CRISPR (Acr) factors. How CRISPR-Cas systems protect themselves remains unclear. Here, we uncovered a broad-spectrum anti-anti-CRISPR strategy involving a phage-derived toxic protein. Transcription of this toxin is normally reppressed by the CRISPR-Cas effector, but is activated to halt cell division when the effector is inhibited by any anti-CRISPR proteins or RNAs. We showed that this abortive infection-like effect efficiently expels Acr elements from bacterial population. Furthermore, we exploited this anti-anti-CRISPR mechanism to develop a screening method for specific Acr candidates for a CRISPR-Cas system, and successfully identified two distinct Acr proteins that enhance the binding of CRISPR effector to non-target DNA. Our data highlight the broad-spectrum role of CRISPR-repressed toxins in counteracting various types of Acr factors, which illuminates that the regulatory function of CRISPR-Cas confers host cells herd immunity against Acr-encoding genetic invaders, no matter they are CRISPR-targeted or not.

microbiology↗

bioRxiv2024

Fish Blood Response to Ash-Induced Environmental Alkalinization, and their Implications to Wildfire-Scarred Watersheds

Changes in land use, warming climate and increased drought have amplified wildfire frequency and magnitude globally. Ash mixing into aquatic systems after wildfires rapidly increases water pH, creating an additional threat to wildlife, especially species that are already threatened, endangered and/or migratory. Here, Chinook salmon (Oncorhynchus tshawytscha) yearlings acclimated to 15 or 20{degrees}C were exposed to an environmentally relevant concentration of ash (0.25% w/v) which caused water pH to rapidly rise from [~]8.1 to [~]9.2. Mortalities occurred within the first 12 hours, and was higher at the higher temperature (33 versus 20 %). The greatest differences in blood chemistry between the two temperatures were dramatically greater ([~]7.5-fold) and very rapid (within 1 hour) spikes in both plasma total ammonia (to [~]1200 {micro}M) and lactate (to [~]6 mM) in warm-acclimated salmon, whereas cold-acclimated salmon experienced a much smaller and gradual rise in plasma total ammonia. Salmon at both temperatures experienced extracellular and intracellular alkalosis within 1 hour that recovered within 24 hours, but the alkalosis was smaller in magnitude in fish at warmer temperature. Impacts on plasma ion concentrations were relatively mild and plasma glucose increased by 2- to 4-fold at both temperatures. Notably, the increase in plasma total ammonia in fish at the warmer temperature was far faster and much greater than those reported in previous studies exposing fish despite higher water pH (9.4-10.5) induced without using ash. This suggests that ash has physiological impacts that cannot be explained by high water pH alone which may relate to the complex mixture of metals and organic compounds also released from ash. This demonstrates post-wildfire ash input can induce lethal yet previously unexplored physiological disturbances in fish and highlights the complex interaction with warmer temperatures typical of wildfire-scarred landscapes.

physiology↗

bioRxiv2024

The Nrf2/Id2 Axis in Vascular Smooth Muscle Cells: Novel Insights into the Interplay between Vascular Calcification and Aging

OBJECTIVEVascular calcification (VC) significantly contributes to cardiovascular morbidity and mortality and escalates with age. However, effective pharmaceutical interventions are lacking, and the molecular mechanisms linking aging to VC remain elusive. This study explores the role of nuclear factor erythroid 2-related factor 2 (NRF2) in VC, specifically focusing on the interplay between vascular senescence and oxidative stress (OS). APPROACH AND RESULTSUsing a chronological aging mouse model, we noted a significant decline in the expression and activity of Nrf2 in the aortas of aged mice, coinciding with increased medial VC. Administering NRF2 activators effectively reduced this calcification. In the vascular smooth muscle cell (VSMC)-specific Nrf2 knockout (Nrf2SMCKO) models, created using adenine and Vitamin D, there was an increase in calcium deposition within the aortic medial layer, alongside heightened VSMC senescence and OS. Furthermore, NRF2 knockout exacerbated VC in aortic rings and primary VSMCs in high-phosphate conditions, while Nrf2 overexpression in VSMCs inhibited calcium deposition by alleviating cell senescence and OS. RNAseq analysis of the aortas from Nrf2SMCKO and control mice highlighted a significant downstream regulator of Inhibitor of DNA Binding 2 (ID2). Our results show that reduced NRF2 levels lead to increased VSMC senescence, characterized by heightened p16 expression and diminished ID2 expression. Inhibiting ID2 negated NRF2s protective effects against VSMC senescence and VC. CONCLUSIONThis study emphasizes the critical role of NRF2 dysfunction in the nexus of vascular senescence, OS, and VC. It proposes the NRF2-ID2 axis in VSMCs as a promising therapeutic target for reducing VC and mitigating age-related cardiovascular diseases. HighlightsO_LIDecline in NRF2 activity is linked to increased vascular calcification (VC) and aging. C_LIO_LIVSMC-specific Nrf2 knockout causes a remarkable exacerbation of arterial calcification. C_LIO_LINRF2 alleviates VC by inhibiting oxidative stress and VSMC senescence. C_LIO_LIID2 contributes to the protective role of NRF2 in VSMC senescence and VC. C_LI

molecular biology↗

bioRxiv2024

Metabolomics unveiled the impact of alterations in nucleotide glucose metabolism on palmitic acid-induced TLR4 activation in THP-1 macrophages

OBJECTIVEThe association of palmitic acid with macrophage inflammation and its promotion of the expression of inflammatory factors through TLR4 have been demonstrated. It has been observed that immature TLR4 localizes to the endoplasmic reticulum and Golgi apparatus, necessitating glycosylation for migration to the cell membrane. The objective of this study was to identify potential biomarkers associated with N-glycosylation subsequent to the activation of TLR4 inflammatory signaling in human macrophages by palmitic acid. APPROACH AND RESULTSThe co-cultivation of palmitic acid with THP-1 macrophages was conducted for a duration of 24 hours, followed by the collection of cell extracts for subsequent metabolomic and lipidomic analyses using high performance liquid chromatography-tandem mass spectrometry. Multivariate and univariate statistical analyses were conducted to identify potential biomarkers, in accordance with established scientific protocols. The impact of palmitic acid on the TLR4 signaling pathway and macrophage N-glycosylation was assessed at various time points using Western blot analysis, immunofluorescence staining, Elisa assays, and chemical labeling techniques. The TLR4 inflammatory signaling pathway was examined in macrophages at different time points, revealing that PA induced the upregulation of MyD88 and TRAF6 expression as well as NF-{kappa}B phosphorylation, indicating the activation of classical NF-{kappa}B signaling. After 24 hours, TLR4 translocated from the cell membrane to the cytoplasm and initiated internalization, accompanied by significant colocalization with GalAz in the cytosol. In addition, the metabolites in the cell extract were found to be altered in both the control and model groups. Significantly alterations in two N-glycosylation related metabolites were observed in the model group, including guanosine diphosphate-L-fucose and uridine diphosphate-N-acetylglucosamine/uridine diphosphate-N-acetylgalactosamine. CONCLUSIONSTHP-1 macrophages incubated with palmitic acid exhibited a distinct metabolomic profile compared to the control group. Our findings suggest that metabolomics analysis holds promise in identifying disease-specific biomarkers for diagnosing fatty acid-induced inflammatory responses in macrophages.

immunology↗

bioRxiv2024

STING Licensing of Type I Dendritic Cells Potentiates Antitumor Immunity

Stimulator of interferon genes (STING) is an immune adaptor protein that senses cyclic GMP-AMP (cGAMP) in response to self or microbial cytosolic DNA as a danger signal. STING is ubiquitously expressed in diverse cell populations including cancer cells with distinct cellular functions such as activation of type I interferons, autophagy induction, or triggering apoptosis. It is not well understood whether and which subsets of immune cells, stromal cells, or cancer cells are particularly important for STING-mediated antitumor immunity. Here using a polymeric STING-activating nanoparticle (PolySTING) with a "shock-and-lock" dual activation mechanism, we show type 1 conventional dendritic cell (cDC1) is essential for STING-mediated rejection of multiple established and metastatic murine tumors. STING status in the host but not in the cancer cells (Tmem173-/-) is important for antitumor efficacy. Specific depletion of cDC1 (Batf3-/-) or STING deficiency in cDC1 (XCR1creSTINGfl/fl) abolished PolySTING efficacy, whereas depletion of other myeloid cells had little effect. Adoptive transfer of wildtype cDC1 in Batf3-/- mice restored antitumor efficacy while transfer of cDC1 with STING or IRF3 deficiency failed to rescue. PolySTING induced a specific chemokine signature in wildtype but not Batf3-/- mice. Multiplexed immunohistochemistry analysis of STING-activating cDC1s in resected tumors correlates with patient survival while also showing increased expressions after neoadjuvant pembrolizumab therapy in non-small cell lung cancer patients. Therefore, we have defined that a subset of myeloid cells is essential for STING-mediated antitumor immunity with associated biomarkers for prognosis. One Sentence SummaryA "shock-and-lock" nanoparticle agonist induces direct STING signaling in type 1 conventional dendritic cells to drive antitumor immunity with defined biomarkers

immunology↗