Biology subjects

Lu, X.

Publications and source records attributed to Lu, X..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

Causal Modeling Reveals Cell-Cell Communication Dynamics in the Tumor Microenvironment During Anti-PD-1 Therapy in Breast Cancer Patients

BackgroundImmune checkpoint blockade (ICB) targeting PD-1/PD-L1 plays a crucial role in breast cancer treatment. Despite clinical success, how ICB reshapes the tumor microenvironment (TME) to enhance anti-tumor activity remains unclear. Anti-PD-1 therapy alters TME cells beyond PD-1+ T cells, with extensive cell-cell communication (CCC) playing a key role. Understanding the dynamic CCC changes upon anti-PD-1 treatment can illuminate ICB mechanisms of action and TME dynamics. MethodsWe analyzed single-cell RNA-seq data from 31 breast cancer patients before and after anti-PD-1 (pembrolizumab) treatment (Bassez et al., 2021). We identified differentially expressed genes (DEGs) induced by treatment in major cell types. We then applied an instrumental variable approach to uncover causal relationships between T-cell and non-T-cell DEGs. We further mapped ligand-receptor interactions mediating signal transduction between cells and constructed a CCC network from T to non-T cells. ResultsAnti-PD-1 therapy induced widespread transcriptional changes across multiple cell populations. Key pathways modulated in T cells included NF-{kappa}B, interferon-{gamma}, and interleukin signaling. CD4+ and CD8+ exhausted T cells engaged in distinct ligand-receptor interactions with tumor-associated macrophages (TAMs) and other types of cells, reshaping the TME. Our results indicated CD4+ exhausted T cells activated M1-like TAMs via TNF-TNFRSF1A and TNFSF14-LTBR, while CD8+ exhausted T cells engaged M1-like TAMs through ICAM1-ITGAL/ITGB2 and CCL8-CCR2, promoting anti-tumor immunity. Conversely, immunosuppressive interactions were also observed, such as TNF-TNFRSF1B (TNFR2) and TNFSF14-TNFRSF14 (HVEM) from CD4 T cells, as well as CSF1-CSF1R and RPS19-C5AR1 from CD8 T cells, which likely promote M2-like tumor-associated macrophage (TAM) polarization and contribute to pro-tumor immune regulation and resistance to therapy. Notably, key receptors in the causal CCC networks, such as C5AR1, TNFR2, and CSF1R, emerged as potential targets to enhance anti-PD-1 efficacy. ConclusionsThese findings elucidate TME remodeling during anti-PD-1 therapy and underscore the pivotal role of CCC in treatment response. Our study identifies critical communication networks that may be biomarkers for immunotherapy responsiveness and highlights novel therapeutic targets, including C5AR1 and HVEM. Furthermore, our application of causal inference methodologies provides a robust framework for dissecting CCC mechanisms in immunotherapy.

bioinformatics↗

bioRxiv2025

Inferring Personalized Cell-Cell Communication Networks in Colorectal Cancer with Individualized Causal Discovery

Understanding tumor heterogeneity at the resolution of individualized cell-cell communication networks (CCCNs) remains a major computational challenge in precision oncology. Existing inference methods largely rely on population-level correlation and thus fail to capture patient-specific signaling patterns across diverse cell types. To address this limitation, we developed an integrative computational framework combining the nested hierarchical Dirichlet process (nHDP) model for identifying hierarchically structured gene expression modules, with instance-specific Greedy Fast Causal Inference (iGFCI) for inferring individualized CCCNs (iCCCNs) in colorectal cancer (CRC). Applied to large-scale single-cell RNA-seq data from over 625,000 cells, our model successfully decomposed complex gene expression modules GEMs, potentially representing the cell lineage and cellular signaling states, and uncovered iCCCNs across detailed cell subtypes. We further used TCGA bulk RNA-seq data with survival data to validate the clinical relevance of these individualized gene expression module causal interactions, demonstrating their potential as robust prognostic signatures in CRC. Finally, we used principled causal inference methods to search for ligand-receptor pairs that mediate cell-cell communication. This framework enables mechanistic insights into immune evasion. Our computational method represents a significant advance toward realizing personalized oncology, enabling precise patient stratification and identification of actionable biomarkers for improved therapeutic targeting in cancers.

bioinformatics↗

bioRxiv2025

Hepatitis E ORF2 blocks trophoblast autophagy to induce miscarriage via LC3B binding rather than PI3K/Akt/mTOR pathway suppression

Hepatitis E virus (HEV) is a zoonotic pathogen that can infect pregnant women and cause adverse pregnancy outcomes, including miscarriage and preterm delivery. The previous study demonstrated that HEV genotype 3 (HEV-3) inhibits complete autophagic flux in both mouse placental tissue and human trophoblast cells (JEG-3), evidenced by reduced expression of ATG proteins (including LC3, Beclin1, ATG4B, ATG5, and ATG9A) and accumulation of p62. However, the specific regulatory pathway involved remains unclear. Thus, eukaryotic expression vectors for HEV open reading frames (ORFs) were constructed, and ORF2 and ORF3 proteins were transiently overexpressed in JEG-3 cells via liposome transfection.. While both ORF2 and ORF3 significantly reduced LC3B protein levels (p < 0.01), only ORF2 induced p62 accumulation (p < 0.01), indicative of autophagic inhibition, which indicates that ORF2 was the key viral protein mediating autophagy suppression in JEG-3. The results of WB and RT-qPCR show that ORF2 suppressed the PI3K/Akt/mTOR pathway while enhancing nuclear translocation of TFEB (p < 0.01) and AMPK phosphorylation (p < 0.01), suggesting paradoxical activation of upstream autophagy regulators. Through co-transfection of mCherry-LC3 with ORF2, co-localization studies, and AlphaFold 3-based intermolecular interaction predictions, we proposed that ORF2 directly binds LC3B to block autophagosome formation. Finally, co-immunoprecipitation confirmed physical interaction between HEV ORF2 and LC3B, elucidating the molecular mechanism of HEV-induced autophagy suppression in trophoblasts. These findings reveal the molecular mechanism by which HEV inhibits autophagy leading to miscarriage in mice, providing new insights into HEV-induced reproductive damage.

pathology↗

bioRxiv2025

Critical phenomenon underlies de novo luminogenesis during mammalian follicle development

A key process during mammalian folliculogenesis is the formation of a fluid-filled antrum around the oocyte. While it is known that the antrum is critical for oocyte maturation and the eventual ovulation, the detailed process underlying de novo luminogenesis remains poorly understood. In this study, we investigated the spatiotemporal dynamics of lumen growth and the cellular mechanism driving this process, using advanced microscopy, molecular perturbations and computational modelling. We found that in secondary follicles, the interstitial gaps exist in a near-critical regime, characterised by a highly dynamic and interconnected fluid network with gap size obeying a power-law distribution. Above a critical size of 180 m, we observed an onset of cell death and the emergence of a stably growing dominant fluid cavity resembling phase separation. By modelling the granulosa cells and the interstitial fluid as a binary fluid, we reproduced the near-critical and phase-separated regimes and found that a spatial gradient of cell-fluid interfacial tension, as observed experimentally, is sufficient to robustly maintain the secondary follicles in a near-critical state. Reducing cell-fluid interfacial tension globally by weakening the cell-cell adhesion between granulosa cells leads to fragmentation of fluid and growth arrest of the dominant cavity, as predicted by the model. Importantly, perturbing the critical state in secondary follicles leads to impaired follicle growth. Altogether, our study reveals how collective spatiotemporal regulation of cell junction mechanics and cell death can contribute to the effective transition between distinct regimes of fluids, which are indispensable for functional maturation of follicles.

developmental biology↗

bioRxiv2025

Crosslinking of Lipid Nanoparticles Enhances the Delivery Efficiency and Efficacy of mRNA Vaccines

Lipid nanoparticles (LNPs) have enabled the effective delivery of RNA therapeutics and mRNA vaccines. However, their broader applications are limited by the suboptimal stability and endosomal escape efficiency. Here, we present an easy-to-adopt post-assembly crosslinking approach to enhance the structural and functional stability of mRNA LNPs. By leveraging a series of cholesterol derivatives and crosslinking methods, we induce crosslinks of the lipid components following mRNA LNP assembly to form the crosslinked LNPs (cLNPs). We systematically evaluated crosslinking parameters and identified optimal conditions that enhance both the physical stability and transfection efficiency of cLNPs. Our findings demonstrate that cLNPs exhibit improved structural integrity under storage and lyophilization conditions, as well as increased extracellular stability and endosomal escape efficiency, resulting in improved performance of mRNA LNPs both in vitro and in vivo. This crosslinking strategy represents a critical advance in LNP engineering, enabling more resilient LNPs and broadening the applicability of LNP-based therapies for gene therapy and vaccine delivery. Our work lays the foundation for developing next-generation LNPs with superior stability and delivery efficiency, broadening the impact of RNA therapeutics and vaccines.

bioengineering↗

bioRxiv2025

GSDME unlocks astrocyte-driven neurotoxicity in Alzheimer's Disease

Astrocytic calcium dysregulation and reactivity precede A{beta} deposition in amyloid-{beta} deposition in Alzheimers disease (AD) but the neurotoxic mechanisms remain unclear. We show that GSDME acts as a switch, linking MAM-mediated calcium release to astrocyte-driven neurotoxicity. Specifically, A{beta}-activated microglial signals activate astrocytic GSDME, releasing its N-terminal fragment, which targets MAMs and triggers ER calcium efflux. This induces biphasic CaMKII phosphorylation, initially boosting NRF2 defenses, then activating NF-{kappa}B-driven inflammation, shifting astrocytes from protective to toxic states. GSDME activation also drives astrocyte-derived exosomes (ADEs) to carry neurotoxic tau, proinflammatory miRNAs, and toxic lipids, propagating toxicity. GSDME deletion in AD mice reduces A{beta} burden, restores NF-{kappa}B/NRF2 balance, reprograms astrocytes and ADEs to protective states, and rescues cognition. Multi-omics profiling of serum ADEs from AD patients reveals a disease-specific signature with central neurotoxicity and peripheral immune regulation. These findings position GSDME as a promising dual diagnostic and therapeutic target for early AD invention.

neuroscience↗

bioRxiv2025

Identification and characterization of a novel exo-glycosidase activity of NGLY1 on ENGase-digested N-GlcNAc proteins in vitro

N-Glycanase 1 (NGLY1) is known for its activity to completely remove conjugated N-glycans from glycoproteins. Early studies illustrated that NGLY1 defects were associated with a rare disease named NGLY1-related congenital disorder of deglycosylation (NGLY1-CDDG). Although extensive research has been conducted over the past decade on the biological impact of NGLY1s endo-(N-)glycanase activity in cells and on disease, whether NGLY1 also exhibits an exo-(N-)glycanase activity remains open. In this study, an exo-(N-)glycanase activity of NGLY1 on the N-GlcNAc proteins was firstly reported and characterized in vitro. To distinguish for the conventional endo-(N-)glycanase activity and the newly reported exo-(N-)glycanase activity of NGLY1, the active sites of exo-NGLY1 were predicted and compared with those of endo-NGLY1. In addition, the correlation between NGLY1s exo-(N-)glycanase activity in vitro and NGLY1-CDDGs clinical characterization was investigated and discussed. The observation of NGLY1s novel exo-(N-)glycanase activity expanded the functional repertoire of NGLY1 beyond canonical endo-(N-)glycanase-mediated deglycosylation, and may provide a new framework to explain the clinical heterogeneity of NGLY1-CDDG.

biochemistry↗

bioRxiv2025

MSF-CPMP: A Novel Multi-Source Feature Fusion Model for Prediction of Cyclic Peptide Membrane Permeability

Cyclic peptides are becoming attractive molecules for drug discovery because of their properties with inherent stability and structural diversity. However, the high potential of cyclic peptide drugs is challenged by the limited membrane permeability cross cell membrane. To predict cyclic peptide membrane permeability (CPMP), an increased number of computational models or tools are designed and used. But these existing algorithms or models do not appropriately capture feature diversity of cyclic peptides. In this study, we introduce a novel multi-source feature fusion model called MSF-CPMP, which aims to increase the accuracy of predicted CPMP. The MSF-CPMP model incorporates three features extracted from SMILES sequences, graph-based molecular structures, and physicochemical properties of cyclic peptides. By benchmarking with other machine learning and deep learning-based methods, MSF-CPMP achieved the highest levels of the evaluation metrics such as accuracy of 0.9062 and AUROC of 0.9546, and further validated MSF-CPMP robustness in learning capabilities and efficacy of its multi-source fusion. Our result demonstrates that MSF-CPMP outperforms other methods in predicting CPMP, that provides also exemplifies the power of advanced deep learning methods in tackling complex biological challenges, offering contributions to computational biology and clinical treatment. Code is available at https://github.com/wanglabhku/MSF-CPMP Author summaryWe have recognized that cyclic peptides are one type of main macro-molecular drugs useful for treatment of human diseases. However, the structural diversity of cyclic peptides results in limited permeability across cell membranes which is challenging drug research or industrial development. Previously some computational models or tools including machine learning or deep learning ones tried to solve this problem, but they still are not efficient. There are urgent requirement for more effective methodologies. Thus, we introduce a novel multi-source feature fusion model called MSF-CPMP. Our aim is to enhance accuracy and efficiency of predicted CPMP. We carried out evaluation of performance metrics by comparative analysis between MSF-CPMP and other machine learning or deep learning methods. Our result demonstrates that MSF-CPMP outperforms other models in predicting CPMP. We further validated MSF-CPMP robustness in learning capabilities and efficacy of its multi-source feature fusion. In the future we would further improve our methods that can integrate broader biomedicine and biomedical information and provide guide for drug diversity in clinically treating complex human diseases.

bioinformatics↗

bioRxiv2025

Buffer Valency Engineering Enables High-concentration and Shelf-stable DNA Transfection Particles for Viral Vector Production

Cost-effective and scalable production is critical for advancing the clinical translation of adeno-associated virus (AAV)-mediated gene therapy. The widely used transient transfection method using plasmid DNA (pDNA)-loaded transfection particles for AAV production faces technical challenges due to instability of the particles and the concentration limits for particle preparation, hindering reproducibility and scalability. Here, we report a streamlined and scalable strategy to generate shelf-stable, highly concentrated pDNA/poly(ethylenimine) (PEI) transfection particles. By incorporating trivalent citrate ions in the dilution buffers, we kinetically modulate electrostatic complexation to achieve uniform nanoparticle assembly and prevent aggregation at high concentrations. This enables a tenfold increase in pDNA concentration in stabilized transfection particles from a typical range of 10-20 g/mL to 200 g/mL, while reducing the required dosing volume from 5-10% to 0.5% of the cell culture medium. The particle assembly process is robust to changes in mixing scale and timing and is compatible with standard workflows. We demonstrate equivalent AAV production efficiencies to standard methods and consistent performance in various production scales, which confirms the practical utility of this assembly method in developing robust, scalable, and cost-effective AAV manufacturing processes.

biochemistry↗

bioRxiv2025

Inactivating a β1 subunit of SnRK1 promotes broad-spectrum disease resistance in rice

Rice is a staple crop for over half of the worlds population, and its sustainable production is vital to ensure global food security. However, rice is highly susceptible to several devastating fungal diseases1, including blast disease caused by Magnaporthe oryzae, sheath blight by Rhizoctonia solani, false smut by Ustilaginoidea virens, brown spot by Bipolaris oryzae, bakanae by Fusarium fujikuroi, and head blight by F. graminearum. The mechanisms underlying the susceptibility of rice to these fungal diseases remain unclear. Here, we report that the {beta} subunit of SnRK1, SnRK1{beta}1A, confers broad-spectrum susceptibility to these fungal diseases. Our findings reveal that diverse rice fungal pathogens have convergently evolved an effector, Gas2, which interacts with SnRK1{beta}1A to prevent its ubiquitination-mediated degradation and promotes its nuclear translocation. While SnRK1{beta}1A is expressed at low levels in healthy plants, its expression is markedly induced upon fungal infections, facilitating susceptibility by inhibiting SnRK11, the subunit of SnRK1, whose overexpression has been shown to enhance broad-spectrum resistance in rice2. Notably, rice lines with disrupted SnRK1{beta}1A are resistant to multiple fungal diseases without compromising growth and yield in the field. Together, this study demonstrates that broad-spectrum disease resistance in crops can be achieved by disrupting inducible susceptibility genes whose encoded proteins are targeted by effectors conserved in multiple pathogens.

plant biology↗

bioRxiv2025

MF-ProtDisMap: protein real-valued distance prediction with fusion of sequence and coevolutionary features

The precise estimation of protein inter-residue distances is essential for high-accuracy protein structure modeling. Currently, the prediction methods are predominantly based on MSA-derived coevolutionary features or language model-based sequence features. To effectively leverage the strengths of both methods, this study developed MF-ProtDisMap (Multi-Feature Protein Distance Map), an integrative framework that effectively combines both feature types to achieve superior real-valued distance prediction. Briefly, MSA Transformer is employed to extract the coevolutionary features from protein multiple sequence alignments, whereas ESM2 is used to capture long-range interactions and sequence-level features. To reduce the computational cost while maximumly represent fused feature information, we implement group pooling for feature dimensionality reduction and introduce Diff-former--a novel module combining a diffusion model with a triangular attention mechanism to enhance representation learning. MF-ProtDisMap achieved a MAE of 2.20 [A] and an RMSE of 3.40 [A] in the protein real-valued distance prediction task. The predicted distances can be converted into contact results, achieving ROC and PR values of 84.56% and 81.01%, respectively. These results demonstrate that MF-ProtDisMap outperforms state-of-the-art real-valued protein distance methods.

bioinformatics↗

bioRxiv2025

Rational design of respiratory syncytial virus dimeric F-subunit vaccines in protein and mRNA forms

BackgroundRespiratory syncytial virus (RSV) poses a significant public health threat, particularly to children and the elderly. Two protein-based vaccines and one mRNA vaccine have been approved, all targeting the prefusion conformation of the fusion (F) glycoprotein. However, it has been reported that the F protein transitions to the post-fusion state during storage, resulting in a reduction of the vaccines immunogenicity. MethodsIn this study, we engineered novel pre-F-based antigens to preserve pre-F-specific immunodominant epitopes while eliminating sub-potent ones. Based on this, we constructed a series of single-chain dimers and selected the one with the highest expression yield and melting temperature (Tm). Next, we created a heterodimer, scDimer AB. Structural and protein characterization analyses were conducted to verify our design. All monomeric and scDimer antigens were used to immunize rodent models. Additionally, we prepared the antigens in mRNA form and immunized BALB/c mice. Finally, we combined both antigen forms, administering intramuscular mRNA priming followed by intranasal protein delivery in mice. In all immunization strategies, viral challenges were performed in animals to evaluate the immunologic protective effects. FindingsThrough rational design, we developed a monomeric and two single-chain dimeric (scDimer) proteins with the expected characteristics, including complete II, V, and O epitopes and a partial III epitope. The scDimers elicited stronger binding and neutralizing antibody responses in rodent models compared to the monomer, and they also boosted T cell responses when combined with appropriate adjuvants. After three doses of scDimer immunization, live RSV was barely detectable in the tissues of infected animals. The copies of RNA encoding N-gene were significantly reduced in the immunized groups compared to the PBS-injected control groups. We also engineered mRNA versions of the antigens and verified their protective efficacy in mice. Notably, there were no significant differences between intranasal boost and intramuscular two doses after RSV challenged, suggesting that intranasal boost provided equivalent protection to intramuscular vaccination and could reduce the risk of vaccine-enhanced disease (VED) potentially. InterpretationThe scDimer-based RSV vaccines effectively protected rodents from RSV infections, highlighting their clinical potential. Our antigen design removed certain suboptimal epitope regions, enhancing the efficiency of antigen presentation and increasing the proportion of the most potent pre-F-specific neutralizing antibodies. This approach provides a novel perspective for future vaccine design. FundingNational Key R&D Program of China, National Science Foundation of China, Young Scientists in Basic Research, Chinese Academy of Sciences, and Special Program of China National Tobacco Corporation. RESEARCH IN CONTEXTO_ST_ABSEvidence before this studyC_ST_ABSThe licensed respiratory syncytial virus (RSV) vaccines were based on RSV pre-F structure. We conducted a PubMed search for articles published in English from databases inception to March 31, 2025, using the search terms "RSV" (interchanged with "respiratory syncytial virus"), "pre-F" (interchanged with "prefusion F") and "vaccine". Our search revealed that most of the articles focus on combining pre-F with RSV G protein or other proteins to form viral-like particles (VLPs) or nanoparticles. The second-largest category of articles examined the antibodies level elicited by the pre-F antigens in animal model or some special cohorts. Other studies addressed topics such as optimization of injection dosage and immunization strategies, methodologies for detecting pre-F-specific antibodies, and the development of mRNA-LNP vaccines. Notably, only 4 articles described novel designs of RSV pre-F antigens, all of which were trimeric and based exclusively on the RSV A subtype F protein sequence. Added value of this studyTo our knowledge, our design is the first single-chain dimer version of RSV pre-F antigen. The engineered antigens demonstrated high yield, thermostability, and immunogenicity comparable to that of DS-Cav1. Additionally, we developed the first chimeric RSV-antigen covering both subtype A and B, thereby broadening the potential protective spectrum. We further validated the immunogenicity of our designs in mRNA form and as a protein-mRNA combination. This research emphasizes the potential of constructing and combining minimized, stable antigen modules, offering a novel approach for future vaccine development. Implications of all the available evidenceIn this study, we present a novel approach for constructing and combining minimized, stable antigen modules for future vaccine design. The strong immunogenicity of our antigens underscores their potential for clinical application. Furthermore, given the structural similarities between the RSV antigen and those of other Pneumoviruses, such as human metapneumovirus (hMPV), our design strategy could be extended to the development of multivalent vaccines.

immunology↗

bioRxiv2025

Synthetic essentiality of TRAIL/TNFSF10 in VHL-deficient renal cell carcinoma

Clear cell renal cell carcinoma (ccRCC) is the most common and aggressive subtype of kidney cancer. Loss of von Hippel-Lindau (VHL) and the consequent activation of hypoxia-inducible factor- (HIF, especially HIF2) plays an essential role in ccRCC initiation and progression. The approved HIF2 inhibitor belzutifan faces the challenge of resistance, presenting an opportunity of co-targeting HIF2 and another vulnerability. This study elucidates the synthetic essentiality of TRAIL (tumor necrosis factor-related apoptosis-inducing ligand) in VHL-deficient ccRCC, uncovering a novel reciprocal regulation between HIF2 and TRAIL. TRAIL was identified as a direct transcriptional target of HIF2 and paradoxically found to be crucial for cell proliferation, primarily by activating the p38 MAPK pathway and facilitating G1/S phase transition. Depletion of endogenous TRAIL or inhibition of HIF2 with belzutifan sensitizes ccRCC cells to recombinant TRAIL, presenting a promising avenue for combination therapy to overcome both TRAIL resistance and belzutifan resistance in treating ccRCC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=162 SRC="FIGDIR/small/621197v1_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@1d603b9org.highwire.dtl.DTLVardef@18e6dc7org.highwire.dtl.DTLVardef@1c953cdorg.highwire.dtl.DTLVardef@9cd144_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Fish remain high in selenium long after mountaintop coal mines close

Mountaintop removal (MTR) coal mining generates large volumes of waste rock. Weathering of this waste rock releases selenium, which can bioaccumulate to levels that can harm, and even extirpate, downstream fish communities. This is well demonstrated in ecosystems impacted by active MTR operations; however, less is known about the long-term impacts after coal mines close. Here we show that MTR coal mines still present an acute threat to downstream fish populations, decades after mining ends. Crowsnest Lake (Alberta, Canada) receives runoff from the Tent Mountain Coal Mine, which closed in the 1980s and part of which was certified reclaimed. Fish in Crowsnest Lake contain tissue selenium concentrations (5-26 {micro}g/g dry weight) that exceed guidelines and rival fish selenium levels downstream of active MTR operations. This is despite lake water selenium concentrations ([≤]2 {micro}g/L) that are below water quality guidelines intended to protect fish. The clinical signs of selenium poisoning in fish are similar to the symptoms of Whirling Disease, which was first detected in the Crowsnest basin in 2016 making this the first aquatic system to be impacted by both stressors. This finding demonstrates that the biological impacts of MTR coal mining can persist long after mining operations end, and it suggests that any further coal mine development may well push the Crowsnest fishery beyond sustainability. SynopsisFish in Crowsnest Lake, Alberta, are high in selenium sourced from an abandoned mountaintop removal coal mine.

ecology↗

bioRxiv2025

Structural basis of auxin binding and transport by Arabidopsis thaliana AUX1

Indole-3-acetic acid (IAA), the major form of auxin, is essential for plant growth. Auxin-resistant 1 (AUX1), the first identified auxin importer, plays a crucial role in polar auxin transport (PAT). Here we present cryo-EM structures of Arabidopsis thaliana AUX1 in the IAA-free and IAA-bound states. AUX1 exists as a monomer that contains 11 transmembrane helixes (TMs). TMs 1-5 and 6-10 constitute the two halves of a classic LeuT-fold, and TM11 interacts with both halves at the interface. In the IAA-bound state, IAA is specifically recognized in a central pocket formed by TM1, TM3, TM6, and TM8. In the presence of IAA, TM1 and TM6 undergo marked conformational changes that are critical for IAA transport. His249 stands out to be a key residue for substrate uptake and release. Our structures reveal the molecular basis for AUX1-mediated IAA binding and transport. SignificanceAuxin-resistant 1 (AUX1) is a major auxin influx transporter, playing critical regulatory roles in callus growth, vascular patterning, leaf phyllotactic patterning, root aerial development, and apical hook formation. However, its working mechanism remains unclear. In this study, we report two structures of IAA-bound and IAA-free AUX1, elucidating its substrate recognition mechanism and proposing a potential substrate release model for AUX1. These findings offer important insights into the molecular mechanisms of AUX1-mediated IAA binding and transport, and lay the foundation for future structure-based functional studies of the AUX1/LAX family and the application of auxin analogs in agriculture.

molecular biology↗

bioRxiv2025

IL-17A-driven Macrophage Disorder Promotes Plaque Instability in Psoriatic Atherosclerosis

Psoriasis is a common chronic inflammatory skin disease that predisposes individuals to cardiovascular diseases such as atherosclerosis. However, the underlying mechanisms linking these conditions have not yet been fully elucidated. Recent studies have indicated that the inflammatory cytokine IL-17A plays a significant role in both diseases. The aim of this study was to investigate how psoriasis affects the stability of atherosclerotic plaques via the IL-17A/IL-17RA pathway. We performed single-cell sequencing on patients with both psoriasis and atherosclerosis to analyze changes in the immune microenvironment within their carotid plaques and psoriatic lesions. We found that IL-17A significantly upregulated the expression of pro-inflammatory factors (e.g., CXCL8) in macrophages of psoriatic atherosclerosis patients, leading to weakening of the fibrous cap structure of plaques. Additionally, IL-17A further exacerbated plaque instability by interfering with macrophage lipid metabolism, particularly sphingolipid metabolism. Finally, using in vitro experiments and animal models, we demonstrated that IL-17A enhances pro-inflammatory and metabolic abnormalities in macrophages by downregulating PPAR{gamma}. Therapeutic strategies targeting IL-17A may contribute to the simultaneous mitigation of psoriasis and atherosclerosis-associated cardiovascular risk, providing new directions for clinical intervention.

cell biology↗

bioRxiv2025

Leukocyte-type 12/15-lipoxygenase is essential for timely inflammation-resolution and effective tissue regeneration following skeletal muscle injury

Unlike traditional anti-inflammatory therapies which may interfere with musculoskeletal tissue repair, pharmacological administration of specialized pro-resolving lipid mediators (SPMs) can promote timely resolution of inflammation while stimulating skeletal muscle regeneration. Despite this, the potential role of endogenous inflammation-resolution circuits in skeletal muscle injury and repair remains unknown. Here, we investigated the effect of whole-body knockout of leukocyte-type 12/15-lipoxygenase (12/15-LOX) on acute inflammation and regeneration following skeletal muscle injury in mice. Prior to muscle injury, Alox15-/- mice displayed lower intramuscular concentrations of 12/15-LOX-derived lipid mediators than wild type (WT) mice, and this was associated with chronic low-grade muscle inflammation. Alox15-/- mice mounted an exaggerated acute immune response to sterile skeletal muscle injury which was associated with a local imbalance of pro-inflammatory vs. pro-resolving lipid mediators. During the regenerative phase, Alox15-/- mice displayed defects in myogenic gene expression, myofiber size, and myonuclear accretion. Mechanistically, bone marrow-derived macrophages (M[FE]) obtained from Alox15-/- mice produced less 12/15-LOX-derived lipid mediators and this was associated with impaired M2 polarization. Isolated myogenic progenitor cells also produced many LOX metabolites in response to long chain polyunsaturated fatty acid (LC-PUFA) supplementation, including bioactive SPMs. Alox15-/- myoblasts were both impaired in their ability to produce SPMs and were insensitive to the stimulatory effect of LC-PUFAs on in vitro myogenesis. These data show that the 12/15-LOX pathway is essential for timely resolution of acute inflammation and direct determination of myogenic progenitor cell fate following skeletal muscle injury.

developmental biology↗

bioRxiv2025

FASN Inactivation-induced Progranulin (GRN) Expression Promotes Lysosome-dependent Cell Death to Suppress Leukemogenesis

Cancer cells rely on lipogenesis in addition to exogenous lipid uptake, and fatty acid synthase (FASN) is aberrantly overexpressed in myeloid leukemia. However, the precise role of FASN in leukemogenesis in vivo remains elusive. Here, we demonstrated that FASN is essential for leukemogenesis. Ablation of FASN impeded leukemic cell growth, survival, clonogenicity in vitro, and the leukemic burden in vivo. Conditional knockout of FASN barely affected hematopoiesis but significantly attenuated the leukemic progression of MLL-AF9 transplants. By screening a library of platensimycin derivatives, we identified compound MS-C19 as a potent FASN inhibitor. Pharmacological targeting of FASN by MS-C19 suppressed leukemic cell growth and clonogenicity in clinical AML blasts. Mechanistically, both MS-C19 treatment and FASN deficiency triggered the activation of lysosomal and inflammatory gene expression. Loss of FASN led to lysosomal membrane permeabilization and subsequent lysosome-associated cell death, but not lysosome biogenesis. We further identified that GRN, a lysosomal and neuroinflammatory gene, was potently transcribed by TFEB upon FASN loss. Depletion of GRN significantly reversed the inhibitory effects caused by FASN knockdown. Our work demonstrates that FASN is a therapeutic target for myeloid leukemia, and inactivation of FASN by the lead compound MS-C19 provides an alternative approach for leukemic intervention. Key PointsO_LIGenetic ablation of FASN induces apoptosis, impedes leukemia cell growth, and improves the survival of leukemic xenografts. C_LIO_LITargeting FASN by the compound MS-C19, a derivative of the natural microbe antibiotic platensimycin, reduces the cell survival of leukemic cell lines, the clinical leukemic blasts, and MLL-AF9 transformed murine leukemic cells. C_LIO_LIFASN inhibition induces lysosome-dependent cell death that relies on Progranulin (GRN) expression. C_LI

cancer biology↗