Biology subjects

Deng, L.

Publications and source records attributed to Deng, L..

At least 19 recordsLinked to original sources

bioRxiv2026

Efficient recovery of transgene-free edited tobacco using the transgene self-elimination system via de novo regeneration

Elimination of integrated editing constructs remains a major challenge for generating transgene-free progeny in plant genome editing based on Agrobacterium-mediated regeneration. Here, we adapted the Transgene Killer CRISPR (TKC) concept to tobacco and established the transgene self-elimination system, in which CRISPR/Cas9 is coupled with developmentally regulated BARNASE cassettes. Three pU3TR-derived vectors carrying DLL-, OsRP3- or PHAS-driven Barnase regenerated normally after leaf-disc transformation. The DLL construct pEB138 showed the highest T editing frequency, with 56 of 69 independent T plants (81.16%) carrying mutations at one or both NtDFR target loci. Under a stringent lineage-level screen in which up to 48 T progeny were tested per T line, 36 of 43 pEB138 lineages (83.72%) yielded uniformly marker-negative progeny for the three assayed T-DNA markers, compared with 0 of 7 lineages transformed with the parental pU3TR vector. The platform also supported recovery of dfr mutants with altered flower pigmentation and NtA622-edited lines with reduced nicotine accumulation. Moreover, introduction of DLL-iBarnase into the independent pDC45 editing backbone did not impair shoot regeneration, and representative NtBBL progeny showed markedly reduced nicotine content together with loss of the selectable cassette. These results demonstrate that BARNASE-assisted transgene elimination can be integrated with Agrobacterium-mediated de novo regeneration in a dicot, enabling one-step recovery of transgene-free edited tobacco progeny.

molecular biology↗

bioRxiv2026

A FIT2-BLTP1 module sustains lipid droplet phosphatidic acid and restrains overgrowth

Lipid droplets (LDs) are assembled at discrete endoplasmic reticulum (ER) subdomains whose local phospholipid composition, rather than their protein content alone, determines whether a LD nucleates and how large it grows. Phosphatidic acid (PA) is the pivotal lipid of this environment, yet how PA reaches a forming LD has remained unknown. Here we show that the bridge-like lipid transfer protein BLTP1 is required to maintain PA in LD-associated membranes. BLTP1 depletion impaired LD formation and produced fewer but enlarged LDs across mammalian cell types, and lowered LD accumulation during adipogenic differentiation. At the ER, BLTP1 engaged the LD emergence factor FIT2 through its N-terminal transmembrane segment, an interaction that strengthened upon induction of LD formation and was strongly reduced by the disease-associated FIT2 G232R substitution. Co-depletion of FIT2 relieved the LD overgrowth caused by loss of BLTP1. Wild-type BLTP1, but neither a FIT2-binding-defective chimera nor a lipid-transfer-groove mutant, rescued LD formation in BLTP1-depleted cells. Lipidomics of purified LDs showed that BLTP1 loss most strongly lowered PA, most prominently the species PA 36:2, whereas PA and the major phospholipid classes of bulk ER membranes were unchanged. Collectively, we propose that local PA supply by BLTP1 coordinates LD assembly and growth.

cell biology↗

bioRxiv2026

AI-Guided Multi-Objective Engineering of Glucoamylase Enables Acidification-Free Starch Saccharification

Glucoamylase is essential for industrial starch saccharification, but the limited thermostability and near-neutral pH tolerance of fungal glucoamylases necessitate cooling and acidification of liquefied starch. Here, we developed an artificial intelligence-guided strategy to simultaneously improve the thermostability, pH tolerance, and catalytic activity of glucoamylase from Penicillium oxalicum (PoGA). Two property-specific machine-learning models, CASPE-T and CASPE-A, identified substitutions associated with thermostability and pH tolerance, respectively. Experimental screening identified beneficial substitutions in 11 of 21 CASPE-T and 12 of 22 CASPE-A candidates. Folding-energy-guided recombination integrated the two traits while maintaining structural compatibility. The optimal variant, PoGA T513E/Q305N, exhibited 2.21-fold higher specific activity than the wild type, with half-life extended from 22.3 to 57.9 min at 60 degrees C and from 16.6 to 64.7 min at pH 8.0. Molecular dynamics simulations attributed these improvements to reinforcement of high-occupancy hydrogen-bonding networks, suppression of conformational fluctuations in the linker and carbohydrate-binding module, enhanced long-range dynamic coordination, and preservation of a compact catalytic architecture. At 60 degrees C and pH 6.5 without acidification, PoGA T513E/Q305N produced 219.9 g/L glucose and achieved 89.1% starch conversion, 31.4% higher than the wild type. This work provides an efficient framework for multi-objective enzyme engineering and sustainable starch biorefining.

synthetic biology↗

bioRxiv2026

Adaptive introgression in Tibetans spans focal and distributed architectures

The Denisovan-derived EPAS1 haplotype is a paradigmatic example of adaptive introgression, but whether archaic ancestry contributed beyond such large-effect loci remains unclear. We analyzed genomes from 1,039 Tibetans, Han Chinese, archaic hominins and ancient Tibetan Plateau individuals. Denisovan-derived adaptive variation was highly localized around EPAS1, whereas Neanderthal-derived variation was distributed across the genome; temporal and elevational patterns reinforced this contrast. Despite individual-level heterogeneity, Neanderthal-introgressed gene repertoires repeatedly converged on immune, metabolic and signal-transduction pathways. A Tibetan-enriched Neanderthal PPARGC1A haplotype was associated with lower fasting glucose and showed concordant support from an independent East Asian type 2 diabetes GWAS. These findings reveal that adaptive introgression can contribute to complex human adaptation through functionally convergent combinations of archaic variants, rather than only through shared large-effect haplotypes.

evolutionary biology↗

bioRxiv2026

A bipolar disorder-associated ultra-rare AKAP11 protein-truncating variant attenuates stimulus-dependent PKA activation and induces anxiety- and depression-related behaviors in mice

Rare genetic variants associated with psychiatric disorders are thought to have larger individual effect sizes and direct biological roles, offering a unique opportunity for understanding causal relationships between genetic architecture and disease phenotypes. A recent whole-exome sequencing meta-analysis identified an increased burden of ultra-rare protein-truncating variants (PTVs) in AKAP11 in patients with bipolar disorder and schizophrenia. AKAP11 encodes an A-kinase anchoring protein that mediates the association of protein kinase A (PKA) and its substrates. How ultra-rare AKAP11 variants contribute to psychiatric disorder pathogenesis remains unknown. Here, using CRISPR-Cas9 genome editing, we introduced into the mouse Akap11 locus an ultra-rare PTV identified in a human patient with bipolar disorder. This ultra-rare PTV reduced Akap11 mRNA and protein levels without producing stable novel mRNA isoforms, leading to Akap11 haploinsufficiency. Male heterozygous mice exhibited behavioral abnormalities consistent with anxiety- and depression-like phenotypes. Transcriptomic and proteomic profiling of the neocortex revealed molecular changes involving synaptic organization, synaptic signaling, and neurite morphogenesis. Notably, the heterozygous mutant showed selective elevation in type I, but not type II, PKA regulatory subunits, as well as PKA catalytic subunits, in the neocortex. Functionally, these changes were accompanied by reduced phosphorylation of PKA substrates, attenuated stimulus-dependent PKA activity in cortical excitatory neurons, and impaired nascent dendritic development in cortical neurons. Together, our study presents a clinically relevant and genetically precise mouse model that provides mechanistic insight into how ultra-rare PTVs may contribute to psychiatric disorder pathogenesis, and a platform for testing rational therapeutics.

neuroscience↗

bioRxiv2026

mBaoJin-labeled pangolin coronavirus for evaluating population cross-neutralizing antibodies and the entry-inhibitory activity of cepharanthine

Replication-competent coronaviruses carrying fluorescent protein-tagged structural proteins remain scarce. Using the highly attenuated pangolin coronavirus GX_P2V(short_3UTR) as a backbone, we generated GX_P2V-mBJ-N, a recombinant coronavirus in which the bright green fluorescent protein mBaoJin is fused to the nucleocapsid (N) protein. The reporter virus is attenuated and genetically unstable in normal Vero cells but can be amplified to high titers in cells expressing wild-type N, and its fluorescence directly reports N protein expression. Using this authentic-virus platform, we show that high-titer GX_P2V cross-neutralizing antibodies persist in most healthy individuals and that cepharanthine potently blocks viral entry. GX_P2V-mBJ-N thus provides a simple and reliable tool for coronavirus tracing, immune surveillance, and antiviral drug evaluation.

microbiology↗

bioRxiv2026

LIFU-Responsive Nanocomplexes Deliver PDGF-BB mRNA for Plaques Stabilization via Neovascularization Modulation

BackgroundPathological intraplaque neovascularization, vascular leakage, and fibrous cap thinning contribute to vulnerable atherosclerotic plaque rupture. Platelet- derived growth factor-BB (PDGF-BB) has been shown to promote pericyte recruitment, thereby stabilizing the microvascular structure, and to induce phenotypic modulation of vascular smooth muscle cells (VSMCs), which enhances fibrous cap thickness and reinforces plaque stability. Nevertheless, systemic protein delivery is limited by rapid clearance and potential off-target effects. MethodsWe developed PDGF-BB mRNA-loaded lipid nanoparticle-poly(lactic-co- glycolic acid) nanobubble complexes (LNPmRNA@PLGA) and used low-intensity focused ultrasound (LIFU) to enhance plaque-targeted delivery. Cellular uptake, PDGF- BB expression, vascular mural-cell responses, plaque histology, hemodynamics, and proteomic changes were evaluated in vitro and in ApoE-/-Fbn1C1041G+/- mice. ResultsLIFU enhanced nanocomplex uptake and PDGF-BB expression, promoted vascular smooth muscle cell proliferation, migration, and phenotypic switching, and increased pericyte coverage. In vivo, LIFU plus LNPmRNA@PLGA reduced the plaque vulnerability index by 78.2% and the neovascularization area by 67.3% compared with controls, while increasing collagen deposition and improving carotid hemodynamics. ConclusionsLIFU-responsive delivery of PDGF-BB mRNA stabilized vulnerable plaques by promoting neovessel maturation and strengthening the fibrous cap. This strategy provides a spatially controlled framework for therapeutic remodeling of high-risk atherosclerotic plaques. Research Perspective What New Question Does This Study Raise?O_LICan spatially controlled PDGF-BB mRNA delivery simultaneously mature intraplaque neovessels and reinforce the fibrous cap without the systemic effects associated with recombinant PDGF-BB? C_LI What Question Should Be Addressed Next?O_LIFuture studies should define the therapeutic window, durability, and long-term safety of LIFU-triggered PDGF-BB mRNA delivery in large-animal models that more closely reproduce human plaque rupture. C_LI

pharmacology and toxicology↗

bioRxiv2026

Tracing the Evolutionary Origin of Interferon to Basal Chordates and Unveiling Its Antiviral Functionality in Jawless Vertebrates

Interferons (IFNs) are essential mediators of antiviral defense in vertebrates, having gradually replaced the RNA interference (RNAi) antiviral mechanism that predominates in invertebrates and plants. To date, IFNs have been identified exclusively in jawed vertebrates, leaving the origin of IFN-based antiviral mechanisms largely mysterious. In this study, by conducting a genome-wide screening of IFN homologs accross various species, we successfully identified seveal IFN homologs from agnatha and lancelet, but not other invertebrates. Notably, both agnatha and lancelet IFN homologs have ability to induce a set of interferon-stimulated genes (ISGs)-like genes, thus tracing the origin of IFN to basal chordate. Using VSV infected peripheral blood mononuclear cells (PBMCs) of Japanese lampreys, we found that lamprey IFNs have antiviral functionality by inducing the expression of hundreds of ISGs through interacting with a heterodimeric complex composed of CRFB7 and CRFB14. In addition to robustly mediating antiviral responses in monocytes, lamprey IFNs exert their effects on variable lymphocyte receptor B (VLRB)+ cells by remodeling the cytokine/chemokine networks to orchestrate antiviral innate and adaptive immunity. Furthermore, cross-species functional comparison of Dicer revealed that changes in residues essential for dsRNA processing occurred concurrently with the evolution of the IFN system. Collectively, these findings uncover the evolutionary origin of IFN and underscore its ancient roles in antiviral response and immune regulation, especially in the takeover of the RNAi antiviral mechanism during the early evolution of vertebrates. Significance StatementInterferons (IFNs) represent a hallmark of vertebrate antiviral immunity, yet their origin has remained elusive. Here, we reported bona fide IFN ligands and cognate receptors in both lamprey and lancelet, two key species placed at the transition from invertebrates to vertebrates. Using the VSV infection model, we further demonstrated the roles of lamprey IFN in antiviral defense and immune regulation. We also found that substitutions in residues essential for Dicer mediated dsRNA processing coincided with the emergence of the IFN system. Collectively, our findings provide key insights into the evolutionary origin of IFN-based immunity and its gradual replacement of RNAi as the dominant antiviral strategy in vertebrates.

evolutionary biology↗

bioRxiv2026

Physiological trade-offs drive the archaeal dominance and carbon turnover in deep subsurface

Marine sediments host a vast deep biosphere, yet how microorganisms persist under severe energy limitation and govern long-term organic carbon (OC) preservation remains poorly understood. Here we show that archaea, primarily Bathyarchaeia, systematically displace bacteria with depth and form net growth zones across East China Sea shelf deep sediments. Multi-omics analyses and bioenergetic modelling reveal that this transition is driven by sustained archaeal metabolism of diverse recalcitrant OC compounds, and a physiological trade-off that prioritizes cellular maintenance over growth, minimizing mortality in deep sediments. This strategy triggers a fundamental shift in sedimentary carbon turnover: from rapid bacterial degradation of labile OC near the surface to persistent archaea-driven turnover of recalcitrant OC at depth. We estimate that Bathyarchaeia mediate [~]77% of total OC degradation after 1,000 years of burial, corresponding to [~]18% ([~]11.4 Pg C) of millennial OC degradation in global shelf sediments. These findings identify subsurface archaea as key microbial regulators of long-term OC preservation and reveal how physiological trade-offs sustain life and carbon turnover in the energy-limited deep biosphere.

microbiology↗

bioRxiv2026

Postnatal Reprogramming Shapes Human Intestinal Epithelial Immune Competency

At birth, the intestine must rapidly adapt to enable nutritional function and immune microbial tolerance. Here, integrating single-cell multi-omics and spatial transcriptomics we define the circuits underpinning this process. We identify asynchronous developmental trajectories with postnatal epithelial reprogramming characterised by coordinated changes in metabolism, junctional structure and innate defence. At birth epithelial stem cells demonstrate dynamic enhancer remodelling, with accessibility often preceding transcription. Fetal stemness elements remain accessible despite reduced transcription across epithelial lineages, retaining plasticity potential. Post-natal epithelia experience sequential homing of myeloid cells followed by innate T cells with peri-epithelial B cells localising later in infancy. Using developmentally staged organoids, we show that epithelial responses to inflammatory stimuli are age-dependent and constrained in early life. We identify BHLHE40 as an early-life regulator that attenuates the impact of interferon- and NF-{kappa}B-driven signalling. Altogether we define the events driving epithelial licensing and barrier adaptation at birth and through infancy.

cell biology↗

bioRxiv2026

Serine Stabilizes SLC7A11 and Enhances Cystine Influx to Protect Against Acute Pancreatitis

Lethal sterile inflammatory diseases are linked to amino acid metabolism, but the role of serine remains unclear. Here, we show that dysregulated serine metabolism and reduced plasma serine levels correlate with disease severity of acute pancreatitis (AP) in patients and mouse models. Elevating serine levels via exogenous serine supplementation or pancreatic phosphoglycerate dehydrogenase (PHGDH) overexpression mitigates pancreatic injury, whereas a serine deprivation diet or pancreatic PHGDH knockdown exacerbates AP. Serine prevents cell death and oxidative stress in pancreatic acinar cells, human induced pluripotent stem cells-derived pancreatic organoids and mouse pancreatic tissue. Serine enhances cysteine and glutathione biosynthesis primarily by promoting solute carrier family 7 member 11 (SLC7A11)-dependent cystine uptake rather than by serving as a direct substrate. Mechanistically, the E3 ubiquitin ligase NEDD4 mediates ubiquitination and degradation of SLC7A11, whereas serine binds to NEDD4 and thereby inhibits SLC7A11 degradation. Similarly to serine, pharmacological inhibition of NEDD4 alleviates lipid peroxidation and pancreatic injury. These findings identify serine as a critical signaling regulator of SLC7A11 stability and oxidative stress, and provides a new therapeutic strategy for AP and associated sterile inflammatory disorders. HighlightsAcute pancreatitis (AP) is linked to abnormal serine metabolism and serine depletion. Serine prevents cell death in AP acinar cells, human pancreatic organoids and mice. Serine promotes SLC7A11-dependent cystine uptake and glutathione levels in acinar cells. Serine reduces NEDD4-mediated ubiquitination of SLC7A11. In briefSerine protects against cell death and pancreatic injury in acute pancreatitis by stabilizing SLC7A11 through disruption of NEDD4-mediated ubiquitination in acinar cells.

pharmacology and toxicology↗

bioRxiv2026

E3 ubiquitin ligase HUWE1 mediates K6-linked polyubiquitylation and stabilization of Nrf2 in an HBx-dependent manner, thereby inhibit ing hepatitis B virus replication

Hepatitis B virus (HBV) infection remains a major global health burden, and HBV X protein (HBx) plays a central role in modulating host pathways that influence viral replication. We previously reported that the oxidative stress sensor Kelch-like ECH-associated protein 1 (Keap1) recognizes HBx to activate the NF-E2-related factor 2 (Nrf2) signaling pathway to suppress HBV replication. Although canonical K48-linked ubiquitylation is known to control Nrf2 turnover, the contribution of non-canonical ubiquitin linkages to Nrf2 regulation during HBV infection remains unclear. Here, we investigated the role of HECT, UBA, and WWE domain-containing E3 ubiquitin ligase 1 (HUWE1) in the regulation of Nrf2 in the context of HBV replication. Cell-based ubiquitylation assays demonstrated that HUWE1 knockdown reduced HBx-mediated K6-linked polyubiquitylation of Nrf2, while overexpression of wild-type HUWE1, but not the catalytically inactive HUWE1(C4341A) mutant, enhanced it. Coimmunoprecipitation and proximity ligation assays demonstrated that HUWE1 interacts with HBx in the cytoplasm and binds Nrf2 only in the presence of HBx, suggesting that HBx promotes the interaction between HUWE1 and Nrf2. Cycloheximide chase assays demonstrated that HUWE1 knockdown destabilized Nrf2 in HBx-expressing cells. Furthermore, depletion or pharmacological inhibition of HUWE1 increased intracellular HBV RNA and pgRNA levels as well as extracellular HBV DNA and HBsAg levels in HBV-infected cells. Collectively, these results support a model in which HUWE1 mediates HBx-dependent K6-linked polyubiquitylation and stabilization of Nrf2 to restrict HBV replication. This study expands current understanding of non-canonical ubiquitin signaling in HBV-host interactions. DATA SUMMARYAll data are presented in the main figures. The data that support the findings of this study is available at bioRxiv (https://doi.org/10.64898/2026.04.20.719611). Raw sequencing data, microscopy images, materials, and sequence information are available upon request. Correspondence and requests for materials should be addressed to Professor Ikuo Shoji. IMPACT STATEMENTHepatitis B virus (HBV) chronically infects approximately 254 million people worldwide, yet host mechanisms that restrict viral replication remain incompletely understood. The Keap1/ Nrf2 signaling pathway is a central defense against oxidative stress. Under basal conditions, Nrf2 is targeted for degradation via Keap1/Cullin3-mediated K48-linked polyubiquitylation. Here, we provide evidence that the E3 ubiquitin ligase HUWE1 contributes to HBx-dependent K6-linked polyubiquitylation and stabilization of Nrf2. Our findings support a model in which non-canonical ubiquitin signaling helps shape the HBV-host interactions and contributes to suppression of viral replication. This study extends current understanding of the ubiquitin code in HBV infection and highlights HUWE1 as a candidate component of an anti-HBV regulatory pathway.

microbiology↗

bioRxiv2026

Therapeutic Stress-induced Activation of PGCC Life Cycle Drives the Resistance Acquisition and Structured Tissue Differentiation

To elucidate how cancer cells generate resistance and defined forms of tissue structure in response to therapeutic stress, we tracked the temporal dynamics of life cycle of polyploid giant cancer cells (PGCCs) induced by the mitotic destabilizer vincristine (VCR). Live-cell fluorescence imaging revealed that VCR activated a distinct endoreplication-based life cycle, which replaced canonical mitosis. PGCCs exhibited reduced proliferative activity, enhanced epithelial-mesenchymal transition (EMT), progressive acquisition of blastomere-like features, and broad multilineage differentiation potential. Both PGCC populations and single PGCC-derived progeny displayed time- and dose-dependent acquisition of malignant traits in vitro and tumorigenic capacity in vivo. PGCC-derived spheroids exhibited ability to differentiate into the cells of origin from three germ layers. Importantly, pre-budding PGCCs induced by higher VCR concentrations exhibited enhanced ability for glandular structure formation and tissue differentiation. Morphologically, the nuclei of PGCC-derived spheroids underwent growth in size, formation of luminal structure, and followed by maturation of lumen. Mechanistically, PGCCs entered a senescent state characterized by elevated senescence-associated secretory phenotype (SASP)-manifested by rich proinflammatory cytokines. Notably, silencing IL1{beta}, IL6, or IL8, or pharmacological inhibition of their receptors, suppressed PGCC formation, budding, EMT, and blastomere-like reprogramming into structured tissue. Our studies provide novel mechanistic insights into early embryogenesis and tumorigenesis at the tissue structural developmental level.

cancer biology↗

bioRxiv2026

White-matter connectivity shapes visual and semantic representations in the aging brain

Multiple lines of evidence indicate that aging is associated with a reduction in the quality of sensory information coupled with increased reliance on semantic information. Consistent with this evidence, functional MRI studies have repeatedly found that, compared to younger adults, older adults show weaker visual representations but stronger semantic representations. However, the factors that engender this visuo-semantic representational shift (VSRS) remain unclear. Here, we test whether structural connectivity within the representational network predicts these shifts. In the face of typical age-related declines in visual memory and structural connectivity, we find that structural connectivity (i) mediates age-related decline in perceptual representation, and (ii) supports semantic and perceptual mnemonic representations in older adults. These findings outline a potential mechanism of age-related perceptual processing declines and highlight the adaptability of the memory system with age.

neuroscience↗

bioRxiv2026

EmbryoTempoFormer: clip-based developmental tempo inference from zebrafish brightfield time-lapse microscopy

Nominal hours post fertilization (hpf) are widely used to index zebrafish embryogenesis, yet under condition shifts--such as temperature change, genetic perturbation, or environmental stress--nominal time can decouple from true developmental progression. In such settings, biologically meaningful variation is better described as a systematic change in developmental tempo rather than a simple temporal offset. Here we introduce an embryo-resolved framework that treats developmental tempo as the primary quantity of interest in brightfield time-lapse imaging. We present EmbryoTempoFormer (ETF), a clip-based CNN-Transformer that predicts developmental progression from short time-lapse clips and is trained with a within-embryo temporal-difference consistency regularizer to promote temporally coherent trajectories. Crucially, we couple model predictions with an embryo-level inference and statistical workflow: temporally correlated clip-level outputs are aggregated into interpretable embryo-level tempo and stability readouts, and cross-condition effects are quantified using embryo-bootstrap confidence intervals with embryos--rather than frames or clips--as independent units, avoiding pseudo-replication. Using temperature perturbation as a representative domain shift, we robustly quantify condition-induced changes in global developmental dynamics and show that developmental delay predominantly manifests as reduced developmental tempo. This framework enables statistically principled, high-throughput phenotyping for perturbation screens, drug assays, and environmental stress studies. HIGHLIGHTSO_LIClip-based CNN-Transformer predicts developmental time from brightfield time-lapse microscopy. C_LIO_LIWithin-embryo temporal-difference consistency improves trajectory self-consistency. C_LIO_LIEmbryo-level anchored tempo slopes enable interpretable cross-condition comparisons. C_LIO_LIReproducible pipeline via code, scripts, and a Zenodo bundle with embryo-level inference C_LI Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=80 SRC="FIGDIR/small/710433v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@ddbf01org.highwire.dtl.DTLVardef@26e975org.highwire.dtl.DTLVardef@a911d7org.highwire.dtl.DTLVardef@1d24f1b_HPS_FORMAT_FIGEXP M_FIG C_FIG

developmental biology↗

bioRxiv2026

TACE reprograms RANKL-mediated differentiation of macrophages by activating the non-canonical pathway of IRF3

Inflammation is associated with an influx of inflammatory macrophages and increased activation and differentiation of osteoclasts. Receptor activator of NF-kB ligand (RANKL) is a key driver for osteoclast differentiation. However, the pathogenic mechanisms augmenting RANKL-induced osteoclast differentiation in inflammatory conditions are not fully elucidated. Here, we show that TNF- converting enzyme (TACE) plays a critical role in pathological bone erosion and enhances osteoclast differentiation in inflammatory conditions. Myeloid cell-specific TACE deletion in a murine arthritis model attenuates joint inflammation and bone destruction. TACE deficiency suppresses distal RANKL signaling in macrophages by increasing IRF3 activation, while enhancing proximal RANKL signaling, leading to the suppression of osteoclast differentiation. Mechanistically, IRF3 activation limits macrophage reprogramming by suppressing NFATc1 and HB-EGF in response to RANKL through a non-canonical pathway. HB-EGF, a TACE substrate, activates EGFR signaling and promotes osteoclastogenesis by inhibiting IRF3 activation. TACE regulates the reciprocal inhibition of the IRF3-HBEGF axis. Our study highlights a role for TACE as a rheostat, balancing both pro- and anti-osteoclastogenic signals.

cell biology↗

bioRxiv2026

A Parallel Accumulation-Mobility Aligned Fragmentation Strategy Utilizing High-Resolution Ion Mobility for High Performance Proteomics Analysis

Here we present a novel data independent acquisition (DIA) mass spectrometry (MS) operating mode termed parallel accumulation-mobility aligned fragmentation (PAMAF) that offers enhanced speed and sensitivity of ion fragmentation analysis for nontargeted discovery workflows such as bottom-up proteomics. This mode of operation leverages high-resolution ion mobility (HRIM) separation capabilities of the structures for lossless ion manipulation (SLIM) technology to achieve HRIM-based precursor isolation in place of traditional quadrupole filtering approaches. This PAMAF mode of operation increases the number of features that can be identified per MS1/MS2 acquisition cycle by employing mobility-based time alignment to associate fragment ions with their corresponding precursor ions. By using a high-speed, lossless separation technique for precursor isolation instead of the comparatively slow and wasteful quadrupole filtering method, we can avoid ion losses up to 99% while simultaneously increasing the rate at which precursor ions are sequentially fragmented and detected. Additionally, by storing ions in a trapping region while the previous packet of ions is being analyzed, the PAMAF mode achieves [~]100% ion utilization efficiency. Benchmarking results of LC-PAMAF-MS analysis of a whole cell protein digest showed approximately 6x more protein group identifications compared to a standard data-dependent acquisition (DDA) analysis without HRIM on the same QTOF instrument, and to over 100x improvement for low-load workflows. Quantitative evaluations demonstrated that PAMAF mode could quantify low abundance peptides, including those undetectable by DDA. Additionally, since precursor isolation in PAMAF mode is size-based rather than m/z-based, many coeluting isobars and isomers can be resolved prior to fragmentation to eliminate chimeric spectra that compromise identification accuracy. In this work we also explored the benefits of combining HRIM and quadrupole isolation to achieve improved specificity. This approach, known as DIA-PAMAF mode, further reduces the frequency of chimeric fragmentation spectra, and enabled the detection of over 8,000 protein groups from a HeLa digest analysis. PAMAF mode brings a powerful new technique to the field of proteomics that has the potential to improve the sensitivity and selectivity of mass spectrometry-based proteomics. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/704896v1_ufig1.gif" ALT="Figure 1"> View larger version (114K): org.highwire.dtl.DTLVardef@7984c3org.highwire.dtl.DTLVardef@1fb2fe3org.highwire.dtl.DTLVardef@50d35org.highwire.dtl.DTLVardef@1a62926_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2026

Basal ppGpp regulation by SpoT coordinates metabolic homeostasis and acid resistance

Bacteria maintain low basal levels of the alarmone ppGpp during steady-state growth, yet how this basal state is established and why it matters physiologically remain poorly understood. Here, we show that basal ppGpp represents an actively maintained regulatory state that coordinates metabolic homeostasis with stress resistance. Using a targeted perturbation of SpoT regulation in Escherichia coli, we uncover a sharp requirement for a sub-basal yet non-zero ppGpp pool to sustain growth in minimal medium and survival under extreme acid stress. Disruption of this basal state leads to misallocation of metabolic flux into arginine biosynthesis, depletion of glutamate, and collapse of the glutamate-dependent Gad acid resistance system. Through intragenic suppressor analysis, enzymatic perturbations, and protein-level feedback measurements, we further demonstrate that SpoT intrinsically tunes basal ppGpp through a distributed intramolecular regulatory network coupled to negative feedback control of SpoT abundance. This regulatory logic stabilizes ppGpp within a narrow physiological window, below the threshold of canonical stringent response activation. The requirement for SpoT-dependent basal ppGpp regulation is conserved in pathogenic Salmonella and Shigella. Together, our findings establish basal ppGpp as a distinct and actively regulated signaling regime that integrates metabolism and stress preparedness beyond acute starvation responses.

microbiology↗