Biology subjects

Zhang, C.

Publications and source records attributed to Zhang, C..

At least 217 records · Page 12Linked to original sources

bioRxiv2025

CircRNA-based, non-integrated, in vivo panCAR-mediated B cell immune resetting in mouse models and non-human primates

B cell immune resetting, defined as the comprehensive depletion and subsequent reconstitution of B cells, represents a pivotal therapeutic approach for B cell-associated disorders. Recently, chimeric antigen receptor T cell (CAR-T) therapy has demonstrated substantial clinical efficacy in treating B cell malignancies and autoimmune diseases. However, this approach remains constrained by its reliance on lymphodepleting conditioning regimens, high invasiveness, high costs, and the risk of severe cytokine release syndrome (CRS). Antibody-based therapies, including monoclonal antibodies and T cell-engager (TCE) bispecific antibodies, suffer from suboptimal tissue penetration, resulting in inadequate B cell depletion in lymphoid and peripheral tissues, and subsequent rapid resurgence of pathogenic B cells. Here, we engineered highly stable circular RNAs (circRNAs) encoding anti-CD19 CAR (circRNA-CAR), which demonstrated prolonged and enhanced CAR protein expression compared to conventional linear mRNAs. By employing immune cell-tropic lipid nanoparticles (LNPs) for in vivo delivery, circRNA-CAR facilitated the generation of panCAR immune cells (including CAR-T, CAR-NK, and CAR-macrophages) in both murine models and cynomolgus monkeys. Compared to rituximab or teclistamab, in vivo panCAR induced more extensive B cell depletion across multiple tissue compartments in mice. Moreover, in vivo panCAR mediated robust B cell depletion, eliminated autoreactive antibodies, and restored renal function by alleviating proteinuria in a systemic lupus erythematosus (SLE) murine model. It also effectively reduced IgE antibody levels, decreased eosinophil activity, and improved lung pathology in an asthma murine model. Notably, in vivo panCAR-mediated B cell depletion significantly attenuated aging-associated phenotypes in 17- month-old aging mice, remarkably outperforming both rituximab and teclistamab. In cynomolgus monkeys, in vivo panCAR achieved sustained B cell depletion lasting approximately 40 to 50 days, followed by reconstitution of a naive B cell repertoire. Collectively, circRNA-based in vivo panCAR enables complete B cell immune resetting, offering a versatile and promising therapeutic platform for a broad spectrum of B cell- and antibody-mediated disorders.

immunology↗

bioRxiv2025

Genetic mechanisms of resistance to targeted KRAS inhibition

KRAS mutations are among the most prevalent oncogenic drivers in non-small cell lung cancer (NSCLC), yet the mechanisms of therapeutic resistance to KRAS inhibitors in these cancers remains poorly understood. Here, we deploy high-throughput CRISPR base editing screens to systematically map resistance mutations to three mechanistically distinct KRAS-targeted therapies, including KRAS-G12C(OFF) inhibitor (adagrasib), RAS(ON) G12C-selective tri-complex inhibitor (RMC-4998), and RAS(ON) multi-selective tri-complex inhibitor (RMC-7977). Using both a saturation Kras tiling approach and cancer-associated mutation library, we identify common and compound-selective second-site resistance mutations in Kras, as well as gain-of-function and loss-of-function variants across cancer-associated genes that rewire signaling networks in a context-dependent manner. Notably, we identify a recurrent missense mutation in capicua (Cic), that promotes resistance to RMC-7977 in vitro and in vivo. Moreover, we show that targeting NF{kappa}B signaling in CIC-mutant cells can resensitize them to RAS pathway inhibition and overcome resistance.

cancer biology↗

bioRxiv2025

Pathogenic DVL frameshifting variants in Robinow syndrome disrupt WNT signaling and cellular dynamics

Robinow syndrome (RS) is a genetically heterogeneous rare disorder involving six genes in the WNT/planar cell polarity (PCP) signaling pathway. Frameshifting variants in DVL genes that introduce a novel basic C-terminus are a common cause of autosomal dominant RS, accounting for [~]33% of individuals without ROR2 variants. Here, we review ClinVar and literature variants affecting DVL paralogs resulting in RS and investigate the cellular effects of pathogenic DVL frameshift variants with mutant tails replacing at least 82 amino acids. In silico analysis of the new C-termini revealed altered intrinsically disordered regions (IDRs), charge distribution, and predicted protein structures. To explore potential altered biological mechanisms caused by novel C-termini, we generated wild-type (WT), frameshift, and truncated constructs of DVL1-3, and analyzed their behavior in a transfection-based in vitro systems. DVL proteins normally polymerize into cytoplasmic puncta that redistribute upon WNT stimulation. Immunocytochemistry showed that mutant DVL proteins failed to change their localization in response to WNT ligands, in contrast to WT alleles--a consistent observation across all three DVLs. In line with this, TOPFlash reporter assays demonstrated that mutant DVL1 and DVL3 failed to activate canonical WNT signaling, while WT proteins induced strong activation. Additionally, the mutant C-terminal tail interfered with CSNK1E-induced phosphorylation, offering a potential mechanism underlying the impaired WNT response. Our results provide further understanding of the cellular consequences of pathogenic DVL frameshifting variants and offers insights into the effects of such alleles on WNT signaling, and the perturbations thereof, that may lead to developmental phenotypes observed in RS.

genetics↗

bioRxiv2025

Steric control of signaling bias in the immunometabolic receptor GPR84

Biased signaling in G protein-coupled receptors offers therapeutic promise, yet rational design of biased ligands remains challenging due to limited mechanistic understanding. Here, we report a molecular framework for controlling signaling bias at the immunometabolic receptor GPR84. We identified three structurally-matched ligands (OX04529, OX04954, and OX04539) with varying steric profiles that exhibit comparable Gi protein activation but dramatically different {beta}-arrestin recruitment capacities. A high- resolution cryo-EM structure of GPR84-Gi in complex with OX04529, complemented by molecular dynamics simulations and targeted mutagenesis, revealed that steric interactions between ligand substituents and Leu3366.52 and Phe1875.47 indirectly disrupt a critical polar network involving Tyr3326.48, Asn1043.36 and Asn3627.45 essential for {beta}-arrestin recruitment. Based on these insights, we developed a steric-dependent model that enabled rational design of G protein-biased agonists with predictable {beta}-arrestin recruitment profiles. This mechanistic framework provides a blueprint for designing biased agonists with customized signaling profiles at GPR84 and potentially other class A GPCRs.

pharmacology and toxicology↗

bioRxiv2025

Vacuolar Phosphatidylinositol 3,4,5-trisphosphate controls fusion through binding Vam7, and membrane microdomain assembly

Membrane trafficking is regulated by the spatiotemporal distribution of phosphoinositides. The endolysosomal pathway is controlled by PI3P, PI(4,5)P2 and PI(3,5)P2, whereas a role for PI(3,4,5)P3 is less clear. We report that yeast produce PI(3,4,5)P3 through Vps34 activity. In vitro assays showed that dioctanoyl (C8) PI(3,4,5)P3, the PI(3,4,5)P3-binding domain Grp1-PH and the phosphatase PTEN blocked vacuole fusion. Fluorescence microscopy showed that PI(3,4,5)P3 was present at the plasma membrane and vacuoles, and that its detection was blocked by PTEN, C8-PI(3,4,5)P3, the Vps34 inhibitor SAR405 and a VPS34 temperature sensitive mutation. In addition, minimizing PI(4,5)P2 as a substrate for Vps34 with a MSS4 temperature sensitive mutation reduced PI(3,4,5)P3 levels. Importantly, PI(3,4,5)P3 was required for the vertex enrichment of Ypt7 and the HOPS subunit Vps33. Finally, we showed that the soluble SNARE Vam7 was retained in a PI(3,4,5)P3-dependent manner and that its displacement from membranes blocked trans-SNARE pairing. These results demonstrate that vacuolar PI(3,4,5)P3 coordinates vertex assembly and SNARE function. SummarySaccharomyces cerevisiae produces PI(3,4,5)P3 via Vps34 activity on vacuoles to regulate homotypic fusion. PI(3,4,5)P3 functions through controlling vertex microdomain assembly and retaining the soluble SNARE Vam7 on membranes to drive fusion.

biochemistry↗

bioRxiv2025

Grassland Ecological Compensation Policy On Pastoral Production Efficiency--Evidence From Pastoral China

Grassland Ecological Compensation Policy(GECP) in the protection of grassland ecological environment at the same time also promote the transformation and upgrading of animal husbandry, pastoral production efficiency is one of the important indicators to evaluate the sustainable development of animal husbandry, but also has a direct impact on the economic benefits of the herders. Based on field questionnaire data from 468 herding households in the pastoral areas of Inner Mongolia Autonomous Region of China, this study used two-stage semi-parametric DEA model and mediated effect model to measure herding households pastoral production efficiency and analyze the effect and influence mechanism of GECP on herding households pastoral production efficiency, respectively.The results of the study show that: (1) the overall pastoral production efficiency of herding households in Inner Mongolia is low, with a mean value of 0.43, which is mainly caused by low pure technical efficiency. (2) GECP, the number of years of education of the household head, whether or not the head of the household receives technical training, the percentage of income from herding, the number of herding machines, the evaluation of the herding socialized services and whether or not to rent pasture have a significant positive effect on the herding efficiency of herding households. (3) the realization of appropriate scale management by herding households plays a part of the mediating effect in the process of affecting herding households pastoral production efficiency. The realization of moderate scale operation by herders plays a partial intermediary effect in the process of GECP affecting herders pastoral production efficiency, and the direct effect of this policy on the pastoral production efficiency of large-scale herders is significantly larger than that of small-scale herders. Based on the above conclusions, this paper puts forward the suggestions of improving the supporting policies of ecological bonus, demonstrating and popularizing the breeding technology, and guiding the moderate scale management.

ecology↗

bioRxiv2025

Clathrin-mediated endocytosis of ERECTA family receptors is essential for proper stomatal development in Arabidopsis

Stomata, specialized structures of plant epidermis, are crucial for gas (e.g. CO2, O2 and H2O) exchange between plants and the environment. Stomatal density and pattern are governed by ERECTA Family (ERf) receptor-like kinases (RLKs)-controlled signaling. Clathrin-mediated endocytosis (CME) is a new mechanism for the internalization of receptor to activate the downstream signaling in animals. Here, we found that mutation of CME components resulted in formation of stomatal clusters and thus increased stomatal index. The adaptor protein 2 {sigma} (AP2{sigma}) subunit of CME interacted with ERf. ERf receptor internalization required CME. Furthermore, the ERf receptor motifs were identified to be recognized by AP2{sigma}. Genetic analysis showed that CME components CHC2, CLC2, and CLC3 acted downstream of EPIDERMAL PATTERNING FACTOR 1/2 (EPF1/2) while upstream of YODA, and worked together with ERf to regulate stomatal development. Consistently, EPF2-induced MAPK activation was significantly reduced in chc2-2 clc2 clc3 and ap2 clc2 clc3 mutants or when the ERf endocytic motifs were mutated, leading to stabilized SPEECHLESS protein and misregulated stomatal lineage progression. Overall, our findings demonstrate that activation of the ERf receptors via internalization is essential for stomatal development, establishing a novel mechanism of CME-mediated receptor internalization activation in plants. Significance StatementStomatal development in Arabidopsis is well characterized, but how EPF-ERf signals activate the MAPK cascade remains unclear. While animals employ clathrin-mediated endocytosis (CME) for receptor internalization and signaling, this mechanism was unknown in plants. We identified CME as a novel regulator of stomatal development. The ERf receptors represent the first identified cargo proteins for AP2{sigma} in plants, undergoing internalization through CME. Clathrin acts downstream of EPF but upstream of YODA, and blocking ERf internalization impairs MAPK activation. Thus, ERf internalization is essential for downstream signaling, revealing a novel CME-dependent activation mechanism in plants.

cell biology↗

bioRxiv2025

The Role of Primate-Specific Genes and Network Dynamics in Cancer Evolution

The atavistic evolutionary theory of cancer evolution highlights the role of ancient and unicell-originated genes, and comprehensive research demonstrated the evolutionary inference. Comparably, very few reports linked young genes with cancer development and maintenance. Here, we found that in cancer cell lines a higher proportion of core essential genes was present among primate-specific genes (PSG) than early metazoan-originated genes (Wilcoxon rank-sum test, p-value = 4.67e-12) and mammal-originated genes (Wilcoxon rank-sum test, p-value = 1.22e-16). Additionally, we found that the loss of many co-expression gene pairs in pan-cancer leads to their network becoming looser compared with normal tissue. However, PSGs particularly those being essential, exhibit a dynamic increase in co-expression, explaining their enhanced role in maintaining cancers. Furthermore, clustering of the gene co-expressions brings a cancer-exclusive module, which contains a large number of PSG connections. We also demonstrate the divergence between essential genes in healthy individuals and those in cancer cells. Our findings complement the atavistic theory in elucidating the evolutionary process of cancer.

evolutionary biology↗

bioRxiv2025

AlphaGEM Enables Precise Genome-Scale Metabolic Modelling by Integrating Protein Structure Alignment with deep-learning-based Dark Metabolism Mining

Constructing high-quality genome-scale metabolic models (GEMs) for less-studied species remains challenging. To address this, we developed AlphaGEM, a versatile toolbox leveraging proteome-scale structural alignment and deep-learning-based predictions for efficient genomic mining to generate GEMs ready for applications. Our findings show that the structural alignment or protein-language-model-based prediction (i.e., PLMSearch), could identify more homologous protein relationships than sequence-blast-based alignment, contributing to the accurate profiling of metabolism from target organisms. Additionally, AlphaGEM encompasses an ensemble procedure empowered by multiple deep learning toolboxes to effectively mine the dark metabolic functions encoded by nonhomologous proteins, significantly expanding species-specific metabolic networks. We demonstrate AlphaGEMs accuracy by building GEMs for eukaryotes (e.g., S. pombe, C. albicans) and prokaryotes (e.g., K. pneumoniae, B. subtilis), achieving predictions comparable to manually curated models while outperforming existing tools. AlphaGEM also successfully reconstructs GEMs for M. musculus and C. griseus, showcasing its great potential for uncovering dark metabolism in complex mammals. Lastly, we demonstrate that AlphaGEM could facilitate the automatic GEMs reconstruction for 332 distinct yeast species with high prediction fidelity. In conclusion, AlphaGEM provides unprecedented opportunities for the precise, rapid construction of GEMs across diverse domains, which sets a solid foundation for universal functional analysis of non-model organisms having genome sequences available.

bioinformatics↗

bioRxiv2025

Remodeling of the immune-metabolic landscape triggered by long-term high-altitude exposure

Growing evidence indicates that immunological and metabolic outcomes are key mediators of long-term high-altitude exposure (LTHAE) adaption, but the underlying mechanisms remain poorly understood. This study employs plasma metabolomics and peripheral blood single-cell transcriptomic sequencing to analyze the metabolic and immune dynamic regulation in 46 young male lowlanders following a 90-day adaptation period at high altitude. Single-cell analysis shows a pattern of "innate immune activation and adaptive immune suppression" under LTHAE, characterized by facilitated maturation of neutrophils, enhanced cytotoxicity of CD56dim NK cells, and increased immune responsiveness of cDC2 and pDC, while inhibited maturation of plasmablasts and suppressed immune responsiveness of CD8{square}TEM and CD4+ T cells. Plasma metabolic analysis reveals significant alterations, involving enhanced steroid hormone synthesis, unsaturated fatty acid and amino acid metabolism under LTHAE, which in turn are associated with immune remodeling. Moreover, transcriptomic-metabolic integration analysis indicates the molecular mechanisms of enhanced aerobic oxidation efficiency under LTHAE. Collectively, these findings provide integrated insights into immune-metabolic landscape remodeling and suggest potential mutual regulatory relationship between immune and metabolic state following LTHAE, offering a molecular foundation for high-altitude adaptation research.

genomics↗

bioRxiv2025

The Calcium Pump ATP2B1/PMCA1 Regulates CNS Vascular Development by Facilitating Norrin- and WNT7A/B-induced Frizzled4 signaling

Frizzled4 (FZD4) is a receptor for Norrin and WNT7A/B ligands, is expressed in endothelial cells (ECs), is required for endothelial blood-central nervous system (CNS) barrier function as well as CNS angiogenesis, and transduces {beta}-catenin-dependent signaling. Despite its fundamental importance in neurovascular biology, including as a drug target, the molecular mechanisms governing FZD4 regulation remain poorly understood. Here, we employed proximity biotinylation to identify proteins that regulate FZD4. We identified ATPase Plasma Membrane Ca{superscript 2} Transporting 1 (ATP2B1, also known as PMCA1) as a FZD4 proximity interactor. Functional analyses revealed that ATP2B1 depletion increased EC Ca2+, activated NFAT, and significantly attenuated Norrin/Frizzled4 signaling. Endothelial-specific Atp2b1 deletion caused CNS vascular phenotypes consistent with compromised Norrin/Frizzled4 signaling. This study identifies ATP2B1 as a novel regulator of Norrin- and WNT7A/B-induced FZD4 signaling and suggests that in pathological contexts with elevated EC Ca2+-levels, EC function may be modulated by suppression of {beta}-catenin-dependent signaling.

developmental biology↗

bioRxiv2025

Self-Reactive B Cells in Artery Tertiary Lymphoid Organs Encode Pathogenic High Affinity Autoantibody in Atherosclerosis

Artery tertiary lymphoid organs (ATLOs) emerge in atherosclerosis which is a chronic inflammatory artery disease with an autoimmune component. However, whether disease-relevant autoimmune B cells emerge in ATLOs and their impacts remains unknown. To map atherosclerosis-specific humoral autoimmunity and define its roles, we isolated germinal-center (GC) B cells from ATLOs and lymph-nodes, expression-cloned 60 autoantibodies and screened them for arterial wall reactivity. ATLO-derived autoantibodies markedly skewed to atherosclerosis-relevant autoantigens versus those of lymph-nodes. One ATLO GC-derived autoantibody bound to histone 2B (H2B) with high-affinity ([~]25 nM). Moreover, vaccination with H2B or adoptive transfer of its cognate autoantibody markedly accelerated atherosclerosis suggesting that ATLOs fail to delete pathogenic high-affinity self-reactive B cells. In a human cohort, total circulating anti H2B antibody titers positively correlated with aortic and coronary artery calcification. We conclude that ATLOs harbor a dysregulated immune tolerance environment permissive for autoreactive B cells that express pathogenic autoantibodies driving atherosclerosis.

immunology↗

bioRxiv2025

EZpred: improving deep learning-based enzyme function prediction using unlabeled sequence homologs

Features extracted from sequence homologs significantly enhance the accuracy of deep learning-based protein structure prediction. Indeed, models such as AlphaFold, which extracts features from sequence homologs, generally produce more accurate protein structures compared to single sequence-based methods like ESMfold. In contrast, features from sequence homologs are seldom employed for deep learning-based protein function prediction. Although a small number of models also incorporate function labels from sequence homologs, they cannot utilize features extracted from sequence homologs that lack function labels. To address this gap, we propose EZpred, which is the first deep learning model to use unlabeled sequence homologs for protein function prediction. Starting with the target sequence and homologs identified by MMseqs2, EZpred extracts sequence features using the ESMC protein language model. These features are then fed into a deep learning model to predict the Enzyme Commission (EC) numbers of the target protein. For 753 enzymes, the F1-score of EZpred EC number prediction is 4% higher than a similar model that does not use sequence homologs and at least 10% higher that state-of-the-art EC number prediction models. These results demonstrate the strong positive impact of sequence homologs in deep learning-based enzyme function prediction. Significance StatementMultiple sequence alignment (MSA) of homologous sequences is the most important source of input feature for deep learning-based protein structure prediction. Yet, this kind of feature is rarely used for protein function prediction. We propose the first deep learning model that significantly improves protein function prediction using features from sequence homologs without functional labels. This shows the utility of an important set of features that are often overlooked by previous studies.

bioinformatics↗

bioRxiv2025

Expanding the repertoire of chemically induced covalent neoantigens

The ubiquitin-proteasome system generates peptide fragments that are displayed on MHC-I molecules. Recent studies revealed that covalent small molecules can hijack this process, leading to the presentation of hapten-modified peptide fragments, or covalent neoantigens. Here, we report a chemical proteomics platform to systematically investigate this process and harness covalent neoantigens for immune cell recruitment and activation. Using a bioorthogonal cysteine-reactive probe (IA-mTz), we demonstrate that diverse intracellular proteins can be modified, processed, and presented as covalent neoantigens across multiple cell lines. Mass spectrometry confirmed the presence of IA-mTz-modified peptides within the MHC-I immunopeptidome, and structural modeling revealed stable peptide-MHC-I interactions. We further integrated a bioorthogonal strategy that enables immune engagement: IA-mTz-modified cells conjugated with trans-cyclooctene (TCO)-IgG elicited Fc receptor activation in a reporter assay, supporting immune recruitment via antibody-dependent cellular phagocytosis. This approach was extended to additional cysteine-reactive probes and to 2,4-dinitrochlorobenzene (DNCB), a common skin sensitizer, which we show induces covalent neoantigen formation in a cell- and HLA-dependent manner. These findings reveal a previously underappreciated breadth of covalent neoantigen formation and provide a generalizable strategy for immune targeting of covalent neoantigens.

biochemistry↗

bioRxiv2025

Pluripotent stem cell-derived siTNK cells attack tumors via a synthetic CD8-CD28 TCR complex

Tumor-associated antigen-specific T cell receptor (TCR)-engineered T cells offer a promising strategy for cancer therapy. Natural killer (NK) cells exhibit broad anti-tumor activity with low side effects but lack the capacity to recognize intracellular antigens. Here, we found that the human pluripotent stem cell (hPSC)-derived iNK cells, unlike tissue-isolated NK cells, expressed all four CD3 subunits at the transcriptome level. We introduced a synthetic gene-expressing complex (SCOTR), encoding a tumor antigen- specific TCR, CD8 coreceptor, and CD28 costimulatory molecule, into hPSCs to generate SCOTR-hPSCs. The SCOTR-hPSCs gave rise to abundant synthetic TCR complex-expressing iNK (siTNK) cells via an organoid induction method. These siTNK cells showed HLA-dependent, antigen-specific cytotoxicity against tumor cells and significantly suppressed tumor growth in tumor xenograft animal models, while also preserving universal non-specific tumor-killing activity. Collectively, siTNK cells, as hPSC-derived hybrid cells with dual features of adaptive T and inherent NK cells, offer an artificial cell source for human immunotherapies.

immunology↗

bioRxiv2025

BrainBeacon: A Cross-Species Foundation Model for Single-cell Resolved Brain Spatial Transcriptomics

The brains functional complexity emerges from spatiotemporal heterogeneity in molecular, cellular, and circuit organization, shaped by evolution, aging, and disease. Single-cell spatial transcriptomics provides a transformative framework to decode this complexity, resolving cell-type-specific expression patterns, region-specific regulation, evolutionary divergence, and disease-associated disruptions. Despite recent advances in spatial transcriptomics, a unified foundation model capturing cross-species, whole-brain cellular architecture remains lacking. Here, we introduce BrainBeacon, the first cross-species foundation model for whole-brain spatial transcriptomics. Trained on 133 million spatially resolved cells covering a total area of 210194 mm2 from human, macaque, marmoset and mouse brains profiled across five major platforms, BrainBeacon integrates gene expression rankings, spatial cellular organization, and evolutionarily conserved genetic relationships into a unified transformer-based architecture. A two-stage training strategy captures both intra-cellular transcriptional dependencies and inter-cellular spatial interactions, yielding biologically grounded and interpretable representations of brain structure. Subsequently, BrainBeacon enables cross-species alignment of brain cell types and anatomical regions, facilitating integrative analyses of conserved and divergent cellular architectures. Moreover, it uncovers spatial regulatory mechanisms of aging by predicting bidirectional perturbation responses between cells and their local niche. Together, BrainBeacon serves as a foundational cross-species model for whole-brain spatial transcriptomics, enabling virtual brain atlas construction, systematic in silico perturbation studies, and mechanistic insights into brain disease pathogenesis.

bioinformatics↗

bioRxiv2025

Rapid Identification of Metal Resistance Genes Using an Enhanced ResNet Deep Learning Model Trained on a largely Expanded BacMet-Based Database

Heavy metal pollution poses significant risks to both the environment and public health. Effective management requires not only reducing contaminants but also understanding microbial adaptation, which could be achieved through the comprehensive identification and classification of metal resistance genes. This study expanded the existing BacMet database by incorporating 1,219,137 unique amino acid sequences through BLASTp analysis, thereby increasing the number of metal resistance-related acid sequences by more than 1,600-fold compared to the 753 sequences included in the previous version. We employed various deep learning models for our proposed multi-label framework which could effectively overcome the well-recognized challenging issue of strict classification among metal translocating proteins such as CopA, ZntA, SilA, CadA, and CzcA due to their high sequence similarity and overlapping metal specificities, including AlexNet, VGG, GoogleNet, ResNet, BERT, ViT, and Mamba2, with ResNet demonstrating superior performance in terms of accuracy, robustness, and computational efficiency. The ResNet model achieved a Jaccard score of 98.91%, significantly higher than BLASTp (98.19%) and DIAMOND (98.16%), and was approximately 6,500 times faster in inference speed than these traditional alignment-based methods. Furthermore, the predictive performance of the model and the reliability of the expanded gene library were experimentally validated through overexpression and metal resistance assays of selected genes. Additionally, we developed the Predicting Metal Resistance Amino Acid Sequences (PMRAAS, https://s3.v100.vip:16165) website, facilitating online predictions of gene metal resistance. Our findings provided deeper insights into microbial adaptation mechanisms in metal-polluted environments and offered a robust tool for advancing heavy metal pollution management through enhanced bioremediation strategies.

genomics↗

bioRxiv2025

Human induced pluripotent stem cell-derived microglia with a CX3CR1-V249I genetic variant exhibit dysfunctional phenotypes and modulate neuronal growth and function

The involvement of microglia in neurodegenerative diseases has drawn increasing attention, as many genetic risk factors are preferentially expressed in microglia. Microglial fractalkine receptor (CX3CR1) signaling regulates many key microglial functions, and the CX3CR1-V249I single nucleotide polymorphism (SNP) has been associated with increased risk for multiple neurodegenerative conditions, including Alzheimers disease, yet its functional consequences in human microglia remain unexplored. In this study, we generated iPSC-derived human microglia-like cells (hMGLs) and found that the CX3CR1-V249I variant increased susceptibility to starvation-induced cell death, reduced amyloid-beta uptake, altered microglial morphology, and impaired migration, with more pronounced effects in homozygous cells. Co-culture with neurons demonstrated that hMGLs with the CX3CR1-V249I variant misregulated neuronal properties, including abnormal neuronal growth as well as an induction of neuronal hyperexcitability. These findings highlight the critical role of CX3CR1 in regulating microglial function and implicate the V249I variant in driving pathogenic microglial states relevant to neurodegeneration.

neuroscience↗