Biology subjects

Yuan, X.

Publications and source records attributed to Yuan, X..

At least 19 recordsLinked to original sources

bioRxiv2026

Reconstructing human gene regulatory evolution using deep learning

Understanding the genetic changes that drove the evolution of human-specific traits is a central goal in biology. Changes in gene expression are thought to be a major source of phenotypic innovations, but identifying the underlying changes in cis-regulatory elements (CREs) along the human lineage has been difficult: functional data from great apes are scarce and unobtainable for extinct hominins, and pinpointing causal substitutions requires knowing which sequences determine CRE activity. Here, we used AlphaGenome, a sequence-to-function deep-learning model, to predict the cis-regulatory effects of ~17 million single-nucleotide substitutions specific to the human lineage and traced their consequences for gene expression evolution across 305 tissues and cell types. The 71,345 predicted cis-regulatory gains lie mostly outside human accelerated regions and arose either through creation of new CREs or, more often, through co-option of CREs ancestrally accessible in other tissues. They are also enriched for distal enhancers and for target gene functions characteristic of the corresponding tissues, suggesting that they contributed to the evolution of tissue-specific biology in humans. Genes linked to more gains were more likely to be upregulated in humans, and in silico reversion to ancestral alleles traced such upregulations to individual substitutions creating transcription factor binding motifs. Comparison with Neandertal and Denisovan genomes revealed that nearly all gains now fixed in humans predate the split from archaic hominins, yet a few modern-human-specific gains contribute substantially to gene upregulation. Our study provides a genome-wide, tissue-resolved map of cis-regulatory changes and their contribution to gene expression evolution along the human lineage.

evolutionary biology↗

bioRxiv2026

Ketogenic diet is protective during endotoxin-induced lung injury through the elevation of BHB

Acute respiratory distress syndrome (ARDS) is marked by severe pulmonary edema and concomitant hypoxia, affecting hundreds of thousands of people a year, especially those in critical care conditions or suffering from septic shock. Previous studies have implicated that the ketogenic diet, a high-fat and low-carbohydrate diet, modulates inflammatory responses. However, the impact of the ketogenic diet on septic ARDS outcomes is unknown. Here, we demonstrated that mice on a ketogenic diet showed strikingly reduced lung injury and inflammation compared to those on a control diet during a murine model of endotoxin-induced lung injury, induced by intratracheal lipopolysaccharide (LPS) injection. Immune mass cytometry studies on lung tissue indicated that the ketogenic diet reduces immune cell infiltration. Treating mice with beta-hydroxybutyrate (BHB), the primary metabolite of ketogenesis, after the onset of ARDS reduced pulmonary edema and lung inflammation, as well as NF-kB activity, suggesting strong therapeutic potential. By multiplex analysis in bronchial alveolar lavage fluid, we observed that the ketogenic diet or BHB administration attenuates the chemotaxis and activation of immune cells. Altogether, our findings reveal that the ketogenic diet provides lung protection during endotoxin-induced lung injury through BHB.

physiology↗

bioRxiv2026

A conserved vesicular circuit enables metabolic adaptation and maintains systemic heme homeostasis

Metabolic homeostasis depends on adaptive control of intracellular metabolite flux, yet how such control is reconfigured when canonical transport pathways fail is unknown. Here we define a conserved vesicular circuit that preserves systemic heme balance by rerouting intracellular heme flux. We show that loss of the intestinal heme exporter MRP-5 in Caenorhabditis elegans causes lethal heme sequestration within endolysosomal compartments. This defect is bypassed by disabling the vesicular adaptor AP-3, which stabilizes and reroutes the heme importer HRG-1, restoring heme export without increasing cytosolic heme. Unbiased genetics and transcriptomics identify two previously uncharacterized SLC49A family members, HRG-13 and HRG-14, as heme exporters with distinct affinities that engage in a vesicular importer-exporter handoff. Live imaging reveals heme-enhanced contacts between HRG-1 and SLC49A-containing vesicles, consistent with direct vesicular transfer. This circuitry extends to vertebrates as disruption of the SLC49A3 homolog impairs erythropoiesis in zebrafish and causes intracellular heme overload, premature hemoglobinization and apoptosis in differentiating human erythroid cells. Together, these findings establish SLC49A3 proteins as conserved heme exporters and uncover a general principle of metabolic adaptation in which reprogramming intracellular compartmentalization, rather than increasing nutrient supply, restores systemic homeostasis.

cell biology↗

bioRxiv2026

Host cell identity shapes the replication and evolution of Drosophila C virus

RNA viruses encounter diverse cellular environments within their hosts, yet how different host cell types influence viral evolution remains poorly understood. Here, we investigated the replication and experimental evolution of Drosophila C virus (DCV) in glial, mesodermal, and hemocyte-derived S2 cells. Mesodermal cells supported substantially higher viral RNA accumulation, viral protein production, and infectivity than glial or S2 cells, demonstrating pronounced cell type-dependent permissiveness. Comparative transcriptomic and proteomic analyses revealed distinct host responses to DCV infection despite the common mesodermal origin of mesodermal and S2 cells. Functional analyses showed that RNA interference, cGAS-STING signaling, viral binding and entry, and cellular ATP abundance could not account for the enhanced replication of DCV in mesodermal cells, whereas S2 cells displayed stronger cGAS-STING and JAK- STAT responses. Serial passage of DCV for 15 generations in mesodermal or S2 cells resulted in rapid phenotypic adaptation, with evolved viruses exhibiting improved replication in the corresponding cell type without altering infectivity in adult flies. Genome sequencing revealed distinct evolutionary patterns between nonstructural and structural protein-coding regions. Nonstructural proteins remained highly conserved with limited evidence of parallel evolution, whereas structural proteins accumulated more mutations and exhibited broader signatures of positive selection. A recurrent VP3 mutation (G8089A; R270H) independently emerged in three S2-passaged lineages, representing the only mutation consistently associated with adaptation to a specific cell type. Structural modeling suggested that this substitution is unlikely to substantially alter VP2-VP3 interactions, implying more subtle effects on capsid function. Together, our findings demonstrate that different Drosophila cell types impose distinct intracellular selective pressures that shape DCV replication and evolutionary trajectories, highlighting host cell identity as an important determinant of RNA virus evolution.

microbiology↗

bioRxiv2026

The endosomal trafficking protein Myopic differentially regulates Drosophila C virus infection in cultured cells and adult flies

Positive-sense RNA viruses extensively exploit host membrane trafficking pathways to establish intracellular replication organelles required for efficient viral replication. However, the contribution of endosomal trafficking proteins to infection by Drosophila C virus (DCV), a natural dicistrovirus of Drosophila melanogaster, remains poorly understood. Here, we investigated the role of Myopic (Mop), a conserved ESCRT-associated endosomal trafficking protein, during DCV infection. Knockdown of mop in cultured S2 cells significantly increased DCV RNA and viral protein accumulation without affecting viral binding or entry, indicating that Mop restricts DCV replication at a post-entry stage. In addition, depletion of mop altered the intracellular distribution of viral proteins, suggesting that Mop may influence the organization of DCV-associated intracellular membrane compartments. Unexpectedly, fat body-specific knockdown of mop in adult flies produced the opposite phenotype, resulting in reduced viral accumulation and prolonged survival following systemic DCV infection. This antiviral phenotype was not associated with enhanced activation of the STING or JAK-STAT pathways. Instead, transcriptomic and proteomic analyses revealed extensive remodeling of gene and protein expression, including altered abundance of proteins associated with autophagy and RNA interference. Together, our findings identify Mop as a previously unrecognized regulator of DCV infection and reveal distinct cell-autonomous and systemic functions of this conserved trafficking protein. These results highlight the importance of endosomal trafficking in antiviral defense and demonstrate that host membrane trafficking factors can exert fundamentally different effects on virus infection at the cellular and organismal levels.

microbiology↗

bioRxiv2026

Systematic functional annotation of thousands of BAHD acyltransferases in plant genomes using Protein Language Model and phylogenomic tools

The functional annotation of plant genes lags significantly behind their genomic annotation. Closing this gap requires thorough cataloging of reported protein activities alongside predictive methods that scale beyond sequence-similarity inference. Focusing on the BAHD acyltransferase enzyme family as a model, we assembled FuncZymeDB-BAHD, a large database of 2,705 LLM-retrieved and curated enzyme-acceptor-donor activities covering 336 BAHDs from 156 plant species, a 2-to-6-fold expansion over Swiss-Prot and prior compilations. We further developed FuncPred-OG, which maps queries to orthologous groups and previously characterized enzymes in FuncZymeDB-BAHD, returning hits with high evidence provenance. FuncPred-OG enabled functional prediction of over half of BAHDs across 85 plant proteomes, of which five novel predictions were validated via in vitro assays and recent studies. For the remaining BAHDs without FuncPred-OG annotation, we developed FuncPred-AI, where logistic-regression classifiers trained on protein language model embeddings achieved high Area-Under-the-Precision-Recall-curve (AUPR) scores and correct-hit rates up to 93%. FuncPred-AI yielded [≥]1 probable donor/acceptor annotation for 99.9% (8894/8897) of BAHDs in our pan-plant dataset. Finally, the FuncPred workflow and datasets were deployed on a web portal for broader utilization, potentially reducing experimentalists efforts for selecting candidates from days to minutes. Overall, this framework provides a generalizable template for functional annotation of entire enzyme families.

bioinformatics↗

bioRxiv2026

Comparative Proteomics Across Tissues and Crop Agroecosystems Reveals Agricultural Stressor Responses in the Western Honey Bee

Maintaining honey bee health in crop production systems is increasingly difficult because worker bees encounter multiple chemical and biological pressures from pesticides and pathogens. How these field-realistic pressures affect molecular physiology across functionally distinct tissues remains poorly understood. Here, we tested whether tissue-resolved proteomics could separate stable tissue-specific patterns from crop-associated molecular changes. To do this, we profiled abdomen, gut, and head proteomes from honey bees collected across four Canadian crop ecosystems over two consecutive years, and integrated these data with pesticide-residue and pathogen-load measurements. Proteomic variation was structured by both tissue identity and crop environment. Tissue-specific proteomic profiles were characterized across samples, whereas crop-associated effects were detected in both years and were stronger in 2021, the second year of the study. Tissue-specific enrichment and network analyses linked the abdomen to lipid catabolism and ubiquitin-proteasome proteostasis, the gut to central carbon metabolism, membrane transport, vesicle trafficking, and cytoskeletal organization, and the head to neurosensory and mitochondrial functions, together with amino-sugar metabolism and vesicle-associated quality-control modules. Among the measured pesticide residues, boscalid was the most reproducible chemical correlate of proteomic variation, with the strongest signal in the gut. Cross-year validation associated boscalid exposure with reduced abundance of gut proteins involved in mitochondrial metabolism, protein quality control, vesicle trafficking, nutrient transport, and biosynthetic pathways. Additionally, integrated proteome-transcriptome-microbiome factor analysis further identified gut-centered components associated with measured stressor variables and linked protein-level variation to coordinated transcriptomic and microbial shifts. Independent-year validation showed that compact crop-associated protein signatures detected in 2020 were also present in 2021. Together, these results show that honey bee tissues maintain stable proteomic identities while showing tissue- and year-specific responses to pesticide and pathogen pressures encountered in crop ecosystems. The gut proteome may specifically provide a sensitive molecular indicator of pesticide-associated perturbation under field conditions.

bioinformatics↗

bioRxiv2026

Repurposing of the assembly chaperone PAC1-PAC2 defines a specialized proteasome landscape in mature mammalian sperm

Mature mammalian sperm rely on active proteasomes containing the testis-specific subunit 4s for capacitation, acrosomal exocytosis and fertilization, but how these proteasomes are structurally specialized remains unclear. We determine the endogenous proteasome landscape of mature bovine spermatozoa and testis using cryo-electron microscopy. We resolve five sperm proteasome assemblies: PA200-20S, free 20S, a previously unrecognized PA200-20S-PAC1/2 hybrid, and PAC1/2-20S complexes capped at one or both ends. Unexpectedly, the PAC1/2-bound complexes are mature and POMP-free, selectively incorporated for 4s, lack 2, and adopt a PAC1/2 orientation and gate configuration distinct from known assembly intermediates. Together with elevated proteolytic activity, these features indicate that PAC1/2 is repurposed from a transient assembly chaperone into a stable post-assembly regulator in mature sperm. 4s-containing proteasomes assemble through the canonical PAC1-PAC4/POMP pathway yet may follow {beta}2-{beta}3-{beta}1 incorporation ordering; functionally, 4s incorporation remodels the sCP surface and enhances peptidase activities, definining the spermatoproteasomes as a hyperactive 20S variant. PAC1/2-bound proteasomes are absent from testis, where PA200-20S and 26S proteasomes are present, while 26S proteasomes are nearly lost in mature sperm. Our findings define a sperm-specific, ATP-independent proteasome landscape, expand the functional repertoires of 4s and PAC1/2, and provide a structural framework for proteasome specialization in male fertility.

cell biology↗

bioRxiv2026

Ultra-efficient High Resolution 3D Reconstruction of Spatial Omics Data with Neural Transcriptomic Field

Biological tissues are inherently three-dimensional (3D) ecosystems where spatial architecture dictates cellular function. While spatial omics technologies have revolutionized molecular profiling, they are largely restricted to isolated two-dimensional (2D) tissue sections. Existing computational methods attempting to reconstruct 3D volumes from sparse slices rely heavily on local slice-to-slice interpolation, struggling to balance high-fidelity reconstruction, noise reduction, and atlas-scale efficiency. Here, we present Neural Transcriptomic Field (NTF), a deep learning framework employing multi-resolution hash-grid encoding and implicit neural representations. Unlike interpolation-based approaches that merely bridge adjacent observations, NTF learns a global, continuous 3D representation of the tissue. By modeling the underlying latent biological patterns, NTF intrinsically decouples true molecular signals from technical artifacts, naturally enabling robust denoising and high-fidelity reconstructions. This global field paradigm shatters traditional scalability limits: NTF achieves up to a 1,000x speedup over existing methods, notably reconstructing a 100-million-cell scale 3D whole-mouse embryo atlas in under 15 minutes. Furthermore, NTF can generate super-resolved volumes from sparse input (e.g., utilizing only 10% of slices) and robustly extrapolating into unseen tissue regions. We demonstrate NTFs versatility across diverse transcriptomic and proteomic datasets, capturing complex spatiotemporal dynamics in Drosophila and mouse embryogenesis, and mapping intra-tumoral functional gradients in human breast cancer. Ultimately, NTF provides an unprecedentedly fast, scalable, and robust computational engine for constructing the next generation of comprehensive 3D tissue atlases.

bioinformatics↗

bioRxiv2026

A shared neural code for gender across faces, bodies, and objects in the human brain

Humans can readily infer gender from diverse visual categories, including faces, bodies, and objects, yet it remains unclear whether the brain constructs a shared, category-general representation of gender. To fill the gap, we measured neural responses using fMRI while participants viewed female and male stimuli across these three categories. Multivoxel pattern analyses revealed that gender information was encoded throughout distributed occipitotemporal regions for all categories. Critically, cross-category decoding and regression-based representational similarity analyses converged on a region of the right middle temporal gyrus (rMTG) that encoded gender independently of stimulus category. This region also carried category information, indicating mixed selectivity. Comparisons between neural representational dissimilarity matrices and those from a fine-tuned convolutional neural network (CNN) showed that rMTG activity most closely resembled intermediate CNN layers, suggesting that shared gender representations rely on mid-level visual features. Finally, functional connectivity analyses revealed that gender-related interactions among occipitotemporal regions were similar for faces and bodies but not for objects. Together, these findings identify a category-general neural hub for gender perception and illuminate how mid-level visual features and distributed networks support the abstraction of gender across heterogeneous visual inputs.

neuroscience↗

bioRxiv2026

Survivin inhibition induces PD-L1 expression through cGAS stabilization and attenuates antitumor immunity

BackgroundSurvivin is a mitotic regulator frequently overexpressed in human cancers and an attractive therapeutic target. However, how Survivin inhibition influences tumor immune regulation remains incompletely understood. This study aimed to investigate whether Survivin inhibition modulates antitumor immunity and to elucidate the underlying mechanisms. MethodsProgrammed death-ligand 1 (PD-L1) expression was evaluated in multiple tumor cell lines following pharmacological or genetic inhibition of Survivin. Mechanistic studies included RNA sequencing, immunoblotting, flow cytometry, cGAS knockdown, and NF-{kappa}B inhibition. Immune profiling was performed using CD8 T-cell cytotoxicity assays, mass cytometry, flow cytometry, immunofluorescence and single-cell RNA sequencing. Clinical relevance was assessed using patient tumor specimens and public immunotherapy cohorts. ResultsSurvivin inhibition, either by YM155 treatment or genetic depletion, increased PD-L1 expression at both mRNA and protein levels in tumor cells. Mechanistically, Survivin inhibition stabilized cyclic GMP - AMP synthase (cGAS) by reducing its ubiquitination and activated NF-{kappa}B signaling, thereby promoting transcriptional upregulation of PD-L1. Functionally, the induced PD-L1 enhanced PD-1 engagement and suppressed CD8 T-cell cytotoxicity, promoting immune evasion. In immunocompetent ovarian cancer models, pharmacological inhibition of Survivin increased PD-L1 expression in tumor and immune compartments and attenuated cytotoxic immune activity. PD-L1 blockade restored antitumor immunity and significantly enhanced the therapeutic efficacy of Survivin inhibition. In addition, analyses of patient samples and public single-cell datasets revealed an inverse association between Survivin and PD-L1 expression, and high Survivin expression was associated with reduced benefit from PD-1/PD-L1 blockade. ConclusionsThese findings identify a Survivin-cGAS-PD-L1 axis linking mitotic stress to immune suppression and provide a mechanistic rationale for combining Survivin-targeted therapy with immune checkpoint blockade.

cancer biology↗

bioRxiv2026

LGTM: Gaussian Process Modulated Neural Topic Modeling for Longitudinal Microbiome

Longitudinal microbiome data are key to understanding the dynamics of microbial communities and their relationships with the host and environment. However, analysis of such data is challenging due to high dimensionality, compositionality, irregular sampling and temporal dependencies on external covariates. Existing analytical approaches typically address only subsets of these challenges, limiting their ability to yield biologically interpretable insights. We introduce LGTM, a probabilistic modeling framework that combines flexible non-linear longitudinal modeling with interpretable topic-based representations of the microbiome. LGTM simultaneously identifies microbial co-abundance patterns ("topics") and models how their proportions change over time and in relation to host and environmental covariates. Using multiple longitudinal human gut microbiome datasets, we demonstrate that LGTM identifies diverse microbial topics whose major patterns are reproducible across runs, while achieving competitive performance in imputation and forecasting tasks. A key strength of the framework is its interpretability: LGTM yields microbial topics with biologically interpretable taxonomic compositions and directly quantifies associations between covariates and microbial dynamics. LGTM is available at https://github.com/yuanx749/lgtm.

microbiology↗

bioRxiv2026

CDKL5 phosphorylates neuronal ELAVL proteins to promote mRNA binding, protein synthesis and visual cortex development

Loss-of-function mutations in the X-linked CDKL5 gene lead to a severe neurodevelopmental disorder characterized by early-onset epilepsy, known as CDKL5 Deficiency Disorder (CDD). Despite its clinical significance, the physiological substrates of the serine/threonine kinase CDKL5 and its roles in neuronal development remain poorly understood. To address this, we performed quantitative phosphoproteomics analysis in Cdkl5 knockout (KO) mouse brains, identifying 22 CDKL5 substrates involved in diverse cellular functions. Among these, we focused on the neuronal RNA-binding proteins (nELAVLs) ELAVL2, ELAVL3, and ELAVL4, as these represented the only evolutionarily conserved phosphorylation and are known regulators of neuronal differentiation. Through kinase assays and individual-nucleotide resolution crosslinking and immunoprecipitation (iCLIP), we found that CDKL5 phosphorylates S119/131 in ELAVL2/3/4, promoting their cytoplasmic localization and enhancing their binding to target mRNAs at 3UTRs. Loss of CDKL5 activity in neurons caused reduced new protein synthesis, as measured by puromycin incorporation; this phenotype was rescued by knockdown of the nELAVL inhibitor long non-coding RNA, RNY3, revealing an essential function of CDKL5 in enhancing protein synthesis via nELAVL phosphorylation. To investigate the in vivo functions of nELAVL phosphorylations, we generated Elavl2/3/4 phosphomutant mice and found that collectively nELAVL phosphorylations are required for viability. Proteomic and transcriptomic analyses of Elavl2/3 homozygous phosphomutants, which exhibited sub-viability, revealed compensatory upregulation of ELAVL4 and synaptic proteins. Functionally, in Elavl2/3/4 triple heterozygous mice Neuropixels recordings in the primary visual cortex showed deficits in receptive field properties and orientation tuning, revealing the role of nELAVL phosphorylation for accurate cortical circuit formation. Our study uncovers a crucial role for CDKL5 in regulating nELAVL-mediated protein synthesis and the development of cortical circuits.

neuroscience↗

bioRxiv2026

Metformin Stabilizes the Abdominal Aorta in Aneurysm by Restoring VSMC Mitochondrial Homeostasis via the AMPK-SIRT1-PGC-1α Axis

BACKGROUNDAbdominal aortic aneurysm (AAA) is a life-threatening condition with >80% mortality upon rupture and no effective pharmacotherapy available. Despite epidemiological evidence linking metformin use to reduced AAA progression, its mechanism remains elusive. Notably, peroxisome proliferator-activated receptor {gamma} coactivator 1 (PGC-1, encoded by Ppargc1a) is downregulated in human AAA, yet its functional role in metformins protection is unknown. METHODSWe employed porcine pancreatic elastase (PPE)-induced murine AAA, VSMC-specific Ppargc1a knockout (Ppargc1aVSMC-KO), primary VSMC senescence models, and pharmacological inhibition (Compound C for AMPK; Ex-527 for SIRT1) to define the AMPK-SIRT1-PGC-1 axis. RESULTSMetformin significantly inhibited AAA expansion, suppressed VSMC senescence (p53/p21{downarrow}, SA-{beta}-gal{downarrow}), and preserved contractile phenotype (SMTN{uparrow}, IL-6/TNF-{downarrow}). Crucially, all benefits were abrogated in Ppargc1aVSMC-KO mice, which exhibited accelerated aneurysm growth, mitochondrial fragmentation, ATP depletion, and ROS accumulation. Mechanistically, metformin activated AMPK/SIRT1 to upregulate PGC-1; AMPK or SIRT1 inhibition blocked this cascade and reversed protection. CONCLUSIONMetformin restrains AAA by restoring VSMC mitochondrial homeostasis via the AMPK/SIRT1[->]PGC-1 axis, positioning PGC-1 as a non-redundant, cell-autonomous guardian against vascular degeneration. These findings provide a mechanistic foundation for repurposing metformin and developing PGC-1-targeted therapies in AAA.

cell biology↗

bioRxiv2026

A cell-nonautonomous heme acquisition pathway enables erythroid hemoglobinization under stress

Heme, an iron-containing cofactor, is synthesized in mitochondria by an eight-enzyme pathway. Although cells were thought to manage heme autonomously, over 1,000 proteins contribute to its production, transport, and regulation. During terminal erythroid differentiation, mitochondria are discarded yet hemoglobin production continues, implying a cell-nonautonomous heme supply. We show that, under stress, erythroblasts import heme through the permease Heme Responsive Gene 1 (HRG1), which localizes to the plasma membrane and accumulates during stress erythropoiesis, the emergency program that expands red cell output. HRG1 loss impaired heme uptake, inhibited terminal erythroid differentiation, and caused anemia. In {beta}-thalassemic mice, partial HRG1 loss reduces ineffective erythropoiesis, underscoring the importance of balanced heme import. These findings reveal intercellular heme sharing and identify HRG1 as a potential therapeutic target in hemoglobinopathies.

cell biology↗

bioRxiv2026

Salmonella exploits metal-responsive UMPylation to enable intracellular biphasic growth and antibiotic tolerance

Salmonella develops profound antibiotic tolerance during in vivo infection, directly contributing to antimicrobial treatment failure. Although phenotypic heterogeneity in bacterial growth rates underlies this tolerance, the exact mechanisms remain elusive. Here, we reveal that Salmonella exhibits a biphasic growth pattern within macrophages, with initial antibiotic levels modulating lag phase duration. Crucially, this growth plasticity is orchestrated by metal ion homeostasis and a reversible PTM-mediated protein phase transitions. Mechanistically, under stress conditions, enhanced Mn2+ uptake activates the UMPylator YdiU, which modifies critical translational machinery components such as elongation factor TufA. These modifications induce protein aggregation, leading to translational arrest and growth stasis. Conversely, upon stress alleviation, Salmonella accumulates Mg2+ and effluxes Mn2+, then the de-UMPylase YdiV is activated, which resolves protein aggregates to enable rapid bacterial resuscitation and proliferation. This metal-responsive proteostatic switch represents an evolutionarily conserved strategy for bacterial stress adaptation, with broad implications for combating antimicrobial tolerance. SIGNIFICANCE STATEMENTAntibiotic tolerance, a key cause of treatment failure in chronic infections, is often linked to bacterial phenotypic heterogeneity, yet the underlying regulatory mechanisms remain largely understood. This study uncovers a fundamental survival strategy employed by intracellular pathogen Salmonella, where host-derived manganese acts as a critical signal to induce a reversible, dormant state. We demonstrate that stress-induced Mn2+ influx activates widespread protein UMPylation, which functions as a molecular glue to drive the aggregation of essential proteins, thereby halting bacterial growth and conferring antibiotic tolerance. Crucially, this state is reversible upon stress relief through Mn2+ efflux and subsequent de-UMPylation, enabling rapid bacterial resuscitation. As an evolutionarily conserved mechanism of adaptive tolerance, this metal-ion-responsive switch, mediated by reversible protein UMPylation, identifies a key target for developing therapeutics against persistent bacterial infections.

microbiology↗

bioRxiv2026

MERTK inhibition cooperates with immunomodulatory cyclophosphamide to induce CXCL9⁺ monocyte-macrophage programming and durable anti-tumor immunity in triple negative breast cancer

Triple-negative breast cancer (TNBC) has high rates of recurrence despite chemotherapy and immune checkpoint blockade (ICB). Tumor-associated macrophages (TAMs) can either suppress or support anti-tumor immunity, but the mechanisms governing these states and therapeutic targets remain unclear. Here, integrating public scRNAseq datasets with TNBC cohorts, we identify a prognostic myeloid signature defined by CXCL9hi/C1Qlow TAM programs, associated with improved survival and increased lymphocyte activation pathways. Using immunocompetent p53-null syngeneic TNBC models spanning basal-like (2153L) and claudin-low (T12) subtypes, we show that immunomodulatory cyclophosphamide (CTX) reprograms hematopoiesis toward the monocytic lineage and induces an interferon (IFN) conditioned tumor milieu that supports CXCL9 monocyte-derived macrophages (Mo.Macs) in basal-like disease. Combining CTX with the next generation MERTK-selective inhibitor UNC2371 (MRX-2843) drives complete remissions in both models, but durable long-term responses occurred selectively in the basal-like subtype model. The expansion of antigen-presenting CXCL9 Mo.Macs and reduction of C1q phagocytic TAMs are observed in responding tumors. Mechanistically, MERTK inhibition relieves MAPK/SOCS1 mediated restraint of IFN signaling driving a positive feedback loop of IRF7/STAT1/IRF1 driven CXCL9 induction. Functionally, tumor control requires CXCL9-CXCR3 dependent CD4 T cell recruitment, accumulation of stem-like memory CD4 T cells, and germinal center like immune organization in tumor-draining lymph nodes. PD-1 blockade further increases durability, preventing recurrence in most treated basal-like tumors. Together, these findings define an IFN licensed, MERTK regulated myeloid checkpoint that can be therapeutically targeted to convert suppressive TNBC microenvironments into durable adaptive immunity, supporting clinical translation of CTX + MRX-2843 based combinations in basal-like TNBC. SignificanceSuppressive myeloid programing limits effective adaptive immune engagement in TNBC usually resulting in ICB treatment resistance and tumor recurrence. This study identifies a therapeutically actionable myeloid interferon checkpoint in which MERTK inhibition stabilizes CXCL9 monocyte-macrophage programming to promote CD4 T cell dependent immune memory and durable tumor control in basal-like TNBC.

cancer biology↗

bioRxiv2026

Diet-Driven Gut Microbiome Differences Between Cohabiting Han and Yi Ethnic Groups in Liangshan, China

BackgroundWhile ethnic variations in gut microbiota are well-documented, their persistence in genetically distinct populations sharing the same geographic environment remains poorly understood. This study investigates the Han and Yi ethnic groups cohabiting rural Southwest China, where contrasting dietary traditions persist under identical environmental conditions. MethodsWe analyzed fecal samples from 100 healthy adults (50 Yi/50 Han) using 16S rRNA gene sequencing (V3-V4 region). Dietary intake was quantified via three 24-hour recalls validated with plasma biomarkers. Multivariate analyses (DESeq2, PERMANOVA) controlled for age, sex, and BMI covariates. ResultsYi individuals exhibited significantly higher Prevotellaceae (log2FC=1.82, padj=0.028) and Succinivibrionaceae (log2FC=2.15, padj=0.013) abundances, corresponding to their buckwheat-rich diet (58.5 {+/-} 12.3% vs Han 3.3{+/-}1.8%, p<0.001) Han microbiota showed enriched Bacteroidaceae (log2FC=1.24, padj=0.041), associated with higher animal fat intake (23.6% vs Yi 1.8%, p<0.001) Dietary factors (buckwheat/animal fat intake) explained greater microbiota variation than ethnic genetic ancestry (PERMANOVA R{superscript 2}=0.10 vs 0.07, p < 0.05) ConclusionCohabiting Han and Yi populations maintain distinct gut microbiota compositions primarily driven by dietary differences. These findings highlight diet as a stronger determinant than genetic ancestry in shaping microbial communities under shared environments. Future studies should validate these observations with metagenomic sequencing.

microbiology↗