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Ghosh, P.

Publications and source records attributed to Ghosh, P..

At least 19 recordsLinked to original sources

Discovery of a Small-Molecule mTORC1 Pathway Activator that Enhances Adoptive T-Cell Therapy via Immuno-metabolic Reprogramming of CD8+ T Cells

Adoptive cell therapy (ACT) has transformed cancer immunotherapy; however, its clinical efficacy remains limited by progressive T cell dysfunction and inadequate metabolic fitness acquired during ex vivo expansion and within the tumor microenvironment. Here, we report the discovery of AS-3, a first-in-class small-molecule activator that enhances the therapeutic competence of CD8 T cells through RAPTOR-dependent mTORC1 activation. Identified by phenotypic screening of an in-house library of pharmacologically relevant scaffolds and subsequent medicinal chemistry optimization, AS-3 markedly increased effector cytokine production while preserving T cell viability. Mechanistically, AS-3 enhanced phosphorylation of mTORC1 downstream effectors, promoted glycolytic and mitochondrial metabolism, and sustained pathway activity under rapamycin-mediated inhibition. Transcriptomic profiling of activated human CD8 T cells revealed coordinated enrichment of mTORC1 signalling, oxidative phosphorylation, glycolysis, proliferative programs, and cytotoxic effector gene networks, consistent with comprehensive immunometabolic reprogramming. Genetic silencing of RAPTOR attenuated both mTORC1 signalling and cytokine induction, establishing pathway dependency. Ex vivo conditioning with AS-3 significantly improved antitumor efficacy in two independent adoptive T-cell therapy models, accompanied by enhanced persistence, reduced exhaustion, and superior effector function. Together, these findings establish pharmacological activation of the RAPTOR-mTORC1 axis as a strategy to generate metabolically resilient T cells and provide a clinically translatable approach to improving the durability and efficacy of next-generation ACT.

immunology↗

Comparative transcriptomic analysis reveals conserved injury responses and divergent molecular responses underlying early regenerative competence following traumatic brain injury

Abstract Background: Traumatic brain injury (TBI) is a leading cause of mortality and long term neurological disability worldwide. Adult mammals have limited regenerative capacity following central nervous system (CNS) injury, but zebrafish have a remarkable regenerative potential, providing an opportunity to identify molecular mechanisms associated with successful CNS repair. Methods: We have integrated publicly available acute phase TBI transcriptomic datasets from human, mouse, rat, and zebrafish studies published up to April 2026. Differential expression data were combined using restricted maximum likelihood (REML) based random effects meta analysis to account for biological and technical heterogeneity. Following ortholog mapping, we compared conserved injury responses with transcriptional programmes preferentially enhanced in zebrafish. Results: The acute molecular response to TBI is largely conserved across vertebrate species with predominant activation of cell cycle regulation, chromosome segregation, and interferon-mediated immune signalling genes. A conserved injury-responsive gene set further highlighted enrichment of mitotic and JAK-STAT signalling. In contrast, 54 zebrafish-enhanced genes displayed preferential activation of wound healing, extracellular matrix remodelling, integrin mediated signalling, and regulated immune responses. Protein protein interaction analysis identified STAT1, STAT3, FN1, CD44, ANXA2, and AXL as central hub genes connecting these injury and repair associated responses. Conclusions: Our study suggest that successful CNS regeneration is not driven by unique injury pathways but rather by coordinated modulation of conserved injury responses and additional molecular programmes that promote tissue remodelling and repair. These regeneration associated networks provide potential targets for future functional studies and may contribute to the development of regenerative therapeutic strategies for traumatic brain injury.

neuroscience↗

Peripheral nerve-derived extracellular vesicles are dynamically regulated in chemotherapy-induced painful peripheral neuropathy

Communication between Schwann cells (SCs) and other cells in the peripheral nerve remains incompletely understood. Extracellular vesicles (EVs) are important mediators of cell-cell communication, however, understanding the function of EVs in vivo is challenging in part because of difficulty in determining the cell type from which EVs originate. To identify SC EVs in vivo, we created a novel P0-Cre-turbo-GFP/human-CD9-EV reporter mouse. EVs were isolated from sciatic nerves without disrupting cell integrity. SC-derived EVs were identified by high-resolution microscopy and fluorescence nanoparticle tracking analyses. To test whether sciatic nerve EV (snEV) populations are regulated under neuropathological conditions, we treated mice with the chemotherapy agent, paclitaxel, which induces neuropathic pain. Proteomes of healthy and neuropathic snEVs differed as determined by LC-MS/MS. Proteins essential for maintenance of axonal integrity and SC myelination were identified selectively in healthy snEVs, whereas neuropathic snEVs contained increased levels of metabolic enzymes and receptors associated with neuronal excitability. Neuropathic snEVs contained diminished levels of EVs derived from SCs. These EVs differed in size from normal snEVs and triggered altered cell-signaling responses in sensory neurons. The appearance of neuropathic EVs correlated with the development of pain-related behaviors. Our findings demonstrate that peripheral nerve EV physiology is dynamically regulated in peripheral neuropathy.

neuroscience↗

Unbiased and Epicardial-Specific Lineage Tracing Reveal Epicardial Contribution to Vascular Endothelial Cells in Heart Development

Controversy surrounds the lineage potential of cardiac cells, particularly epicardial cells, during heart development, largely due to the non-specific expression of epicardial marker genes and the resulting non-specific labeling in Cre-loxP mouse models. Using DARLIN mice, a CRISPR/Cas9-based lineage-tracing system independent of the Cre-loxP system, we analyzed the lineage development of embryonic cardiac cells in an unbiased manner and identified lineages shared among different cell types, such as epicardial cells and vascular endothelial cells (Vas_ECs). To further confirm the lineage potential of epicardial cells, we identified an epicardial cell-specific marker gene, Lrrn4, through analysis of a multi-staged single-cell mRNA-sequencing (scRNA-seq) dataset, and generated a corresponding Lrrn4-CreER mouse line. We then bred this line with a reporter mouse to confirm its specificity for labeling epicardial cells, and subsequently performed prolonged lineage tracing, which revealed specification of the labeled epicardial cells into Vas_ECs. Finally, Using this mouse line, we investigated epicardial cell function by selectively ablating these cells and by expressing TGF{beta} in epicardial cells to convert their lineage from Vas_ECs to fibroblasts. Both approaches resulted in significant developmental defects in embryonic hearts. Together, these results indicate that epicardial cells can give rise to Vas_ECs, and that the Lrrn4-CreER mouse model is a valuable tool for elucidating the role of the epicardium in heart development.

developmental biology↗

An extended N-terminus restrains the plant cell death-inducing ability of the catalytically competent ribonuclease domain in a pea powdery mildew RALPH effector

RALPH (RNase-like proteins associated with haustoria) effectors, which are preferentially expressed in haustoria and structurally resemble fungal T1/F1 RNases, constitute one of the largest effector families in powdery mildew (PM) fungi, yet their functions in dicot-adapted PM species remain poorly understood. Unlike cereal PM RALPHs, which lack the catalytic residues required for RNase activity, some dicot PM RALPHs retain these residues. Here, we performed a comprehensive structural and expression-based characterization of the pea PM Erysiphe pisi RALPH (EpRALPH) repertoire and functionally characterized EpRALPH11, a RALPH effector with partial conservation of the catalytic residues of T1/F1 fungal RNases. Comparative analyses identified multi-RNase-domain RALPHs as a conserved feature of the Erysiphe lineage, while expression profiling showed that many EpRALPHs are preferentially expressed in haustoria during early host colonization. AlphaFold 3-based structural analyses revealed a conserved T1/F1 RNase-like fold despite substantial sequence and surface charge divergence, indicating functional diversification among EpRALPHs. EpRALPH11 enhanced susceptibility to E. pisi in Medicago truncatula, localized to the nucleolus, and induced nucleolar fragmentation when heterologously expressed in Nicotiana benthamiana leaves. Its RNase domain exhibited T1 RNase activity in vitro, supporting the retention of a catalytically competent RNase domain and, together with its nucleolar localization, suggesting that EpRALPH11 targets plant rRNA and disrupts nucleolar functions. The RNase domain induced cell death in N. benthamiana, whereas the full-length protein and catalytic mutants did not. Cell death induction required exclusive nucleolar localization of the RNase domain, and an extended N-terminal intrinsically disordered region suppressed this activity in the full-length protein. Together, our findings reveal a previously unrecognized mechanis regulating RNase activity in a dicot PM RALPH effector and provide new insights into the functional diversification of RALPHs and their adaptation to obligate biotrophy.

plant biology↗

A minimal thermodynamic theory for re-entrant liquid-liquid phase separation regulated by small molecules

Small molecules regulate biomolecular condensates in a biphasic manner, promoting liquid-liquid phase separation (LLPS) at low concentrations while suppressing it at higher concentrations. Despite increasing experimental evidence for such re-entrant behavior, a unified physical description remains lacking. Here, we identify a minimal thermodynamic mechanism for re-entrant LLPS by coupling Cahn-Hilliard dynamics to a concentration-dependent Flory interaction parameter containing competing LLPS-promoting and inhibitory contributions. The resulting model reproduces experimentally observed nonmonotonic condensate formation in Tau-tannic acid and TDP-43-bis-ANS systems, including the concentration-dependent emergence and dissolution of protein-rich domains. Spinodal analysis reveals finite concentration windows for phase instability and demonstrates that re-entrant mixing is encoded directly in the free-energy landscape. The framework further captures morphology transitions and diffusive coarsening within the phase-separated regime. These results establish a general mesoscale description of chemically regulated condensates and provide design principles for controlling phase separation through small-molecule modulators.

biophysics↗

Breaking the bottleneck: self-supervised deep learning framework for fully automated fossil CT segmentation

Semantic segmentation of domain-specific imaging data where labelled training examples are scarce and foreground-background contrast is low remains an open challenge in deep learning applied to science. Palaeontological computed tomography (CT) exemplifies this problem: digitally isolating fossilised bone from surrounding rock matrix is labour-intensive ([≥]100 hrs/dataset), subjective, and often reliant on expensive proprietary software, creating a "segmentation bottleneck" that prevents large-scale and rapid processing of CT data collections. Here we present a self-supervised, end-to-end framework combining SimCLR v1 contrastive pretraining with deterministic pseudo-label generation and U-Net refinement to fully automate fossil CT segmentation without manual annotation. Using 50,626 CT images from the Middle Jurassic Kilmaluag Formation spanning amphibians, reptiles, dinosaurs, and early mammals, the framework achieved a Dice coefficient of 93.66% and IoU of 82.42% on a held-out specimen not seen during training, comparable to the highest Dice and IoU values reported in recent Deep Learning-based fossil CT segmentation studies. Cross-taxon generalisation was validated geometrically on six fully external specimens, achieving sub-voxel mesh agreement with manually thresholded references. By eliminating the annotation requirement that has limited prior deep learning approaches in palaeontology, this framework reduces per-specimen processing from [~]100 person-hours to 6 hrs (one-time UNet training) +1-3 minutes (mesh generation per specimen), an essential first step towards batch processing and analysis of CT data for large-scale comparative and quantitative analyses.

paleontology↗

Stromal state plasticity defines risk and therapeutic opportunity in recalcitrant inflammatory bowel disease

Inflammatory bowel diseases (IBD) remain a relapsing, treatment-refractory disorder marked by progressive tissue injury and inflammation despite expanding immune-targeted therapies. We established a prospective cohort integrating stromal biobanking, functional phenotyping, cross-cohort benchmarking, and outcome modeling to define disease-anchored cellular states. Colonic myofibroblasts from 34 individuals spanning health, ulcerative colitis, and Crohns disease resolved into two dominant states: inflammatory (IMFs) and quiescent (QMFs) myofibroblasts. QMF predominance forecasted remission, whereas IMF predominance increased the odds of worsening endoscopic severity despite therapy escalation during follow-up by [~]4.6-fold, linking early stromal biology to clinical outcomes. Unlike QMFs, IMFs exhibited a senescence-associated secretory phenotype that impaired epithelial stemness, barrier integrity, and innate immune fitness. State-guided prioritization identified EDNRB-antagonism as a high-confidence stromal intervention, reversing pathogenic phenotypes across orthogonal assays and species. Outcome simulation positioned stromal-state reversibility by EDNRB-antagonism as a precision axis, reducing odds of recalcitrance by [~]96.4% and reframing treatment resistance as a reversible stromal state. Graphic Abstract O_FIG O_LINKSMALLFIG WIDTH=185 HEIGHT=200 SRC="FIGDIR/small/720931v2_ufig1.gif" ALT="Figure 1"> View larger version (88K): org.highwire.dtl.DTLVardef@3b2c50org.highwire.dtl.DTLVardef@da5400org.highwire.dtl.DTLVardef@1c100c1org.highwire.dtl.DTLVardef@1882e1_HPS_FORMAT_FIGEXP M_FIG C_FIG In this work, Tindle et al. identify reversible stromal states that govern remission vs. recalcitrant outcomes in IBD and nominate precision reprogramming of pathogenic myofibroblasts as a new therapeutic strategy.

physiology↗

An Endocytic Checkpoint Controls Macrophage PD-1 Function and Immunotherapy Fate

Responses to PD1 blockade span durable tumor control to hyperprogressive disease (HPD), yet innate immune mechanisms governing these extremes remain undefined. Here we integrate a macrophage systems atlas (>12,500 transcriptomes) with single-cell profiles from >1,000 anti-PD1 treated patients, to identify CCDC88A (GIV) as a macrophage-intrinsic determinant of durable response versus HPD. GIV loss increases PD1 surface retention, suppresses phagocytosis, and accelerates tumor growth across murine models, human macrophages, and patient-derived organoids. Myeloid-specific GIV deletion converts PD1 blockade from tumor-restraining to tumor-accelerating by reprogramming macrophages toward HPD-like states. Mechanistically, GIV engages a conserved TIR-like [TILL] motif within the PD1 cytoplasmic tail to drive dynamin-dependent endocytosis, coupling innate immune signaling logic to checkpoint receptor trafficking. Pharmacologic disruption of this axis phenocopies GIV loss, revealing an endocytic vulnerability that undermines checkpoint efficacy and triggers accelerated growth at relapse. These findings define PD1 routing, rather than ligand-binding, as a macrophage-encoded checkpoint governing antitumor immunity. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/718292v1_ufig1.gif" ALT="Figure 1"> View larger version (65K): org.highwire.dtl.DTLVardef@a8f83aorg.highwire.dtl.DTLVardef@140dc7dorg.highwire.dtl.DTLVardef@14bc366org.highwire.dtl.DTLVardef@1096b8a_HPS_FORMAT_FIGEXP M_FIG GRAPHIC ABSTRACT C_FIG In briefMullick et al. show that PD1 trafficking in tumor associated macrophages (TAMs), controlled by the endocytic adaptor GIV/Girdin, determines the durability of immunotherapy. Disrupting this pathway traps PD1 at the surface, converts checkpoint blockade into hyperprogressive disease, and abolishes therapeutic benefit, revealing PD1 routing as a macrophage-encoded checkpoint of immunotherapy outcome. HighlightsO_LIGIV defines macrophage states that stratify durable response vs hyperprogressive disease C_LIO_LIGIV limits surface checkpoint accumulation by facilitating PD1 endocytosis C_LIO_LILoss of GIV traps PD1 at the membrane and drives hyperprogressive disease C_LIO_LIEndocytic blockade phenocopies GIV loss and abolishes checkpoint efficacy C_LIO_LIPsychotropic drugs disrupt PD1 trafficking and accelerate tumor growth C_LI

cancer biology↗

A NOD2-Encoded Toggle Switch Resolves the Host-Microbe Battle Over Cyclic AMP Control

Pathogens hijack macrophages by triggering pathological cAMP surges that block phagolysosomal killing--a defect mirrored in phagocytes from refractory colitis. We identify a host-encoded, pathogen-specific surge-protector comprised of a three-protein toggle: The innate sensor NOD2 binds and masks an evolutionarily conserved motif in GIV that activates trimeric-GTPase Gi, enforcing a biphasic surge-to-plunge cAMP-program: early, NOD2*GIV assembly permits a brief, tolerogenic cAMP rise, whereas subsequent GIV*Gi engagement collapses cAMP to drive phagolysosomal fusion and microbial clearance. Structural, biochemical, and ultrastructural analyses reveal how molecular toggling imposes precise spatial and temporal control. Pharmacogenomic perturbations pinpoint cAMP-PKA hyperactivation as the defining lesion in GIV-deficient macrophages. Functional studies in primary macrophages and human gut organoid co-cultures show that toggling the NOD2*GIV*Gi-axis is necessary and sufficient to convert tolerant macrophages into microbicidal machines that preserve mucosal barrier integrity. These findings uncover a druggable cAMP-control pathway with therapeutic promise in colitis. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/715116v1_ufig1.gif" ALT="Figure 1"> View larger version (70K): org.highwire.dtl.DTLVardef@53cd40org.highwire.dtl.DTLVardef@1c83c82org.highwire.dtl.DTLVardef@fcbc58org.highwire.dtl.DTLVardef@b14f8e_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC BlurbPathogens hijack macrophages by inducing cAMP surges that help them evade clearance. Anandachar et al. identify a host "toggle switch" in which NOD2 and G proteins compete for GIV, driving a rapid and robust surge-to-plunge transition in cAMP. This temporal switch limits tolerogenic signaling, restores microbial clearance and barrier integrity, and unveils a targetable host pathway in infection and IBD. HighlightsO_LIPathogens exploit cAMP surges in macrophages to block phagolysosomal killing of microbes C_LIO_LIGIV acts as a molecular "toggle" linking NOD2 sensing to Gi-mediated cAMP control C_LIO_LIStructural and mutagenesis studies reveal mutually exclusive binding of NOD2 and Gi to GIV C_LIO_LIPharmacogenomic perturbations pinpoint PKA, not EPAC, as the critical downstream effector C_LIO_LIOrganoid co-cultures show NOD2-GIV-PKA crosstalk safeguards microbial clearance and gut barrier integrity C_LI

immunology↗

High Resolution Solvated Models Reveal Mechanisms of Allosteric Activation of mTORC1 by RHEB

The mechanistic target of rapamycin complex 1 (mTORC1) is a [~]1.2 MDa dimeric assembly comprising mTOR, mLST8, and RAPTOR that integrates nutrient, energy, and stress signals to regulate cell growth. While Cryo-EM structures have provided insights into allosteric activation of the complex by the small GTPase RHEB, their limited resolution has constrained a full mechanistic understanding. Here, we combine deep learning-based AlphaFold-3 models with Molecular Dynamics Flexible Fitting and simulations to generate refined, atomistic solvated models of mTORC1{+/-}ATP{+/-}RHEB. Simulations reveal a global remodelling of the complex by RHEB, which strengthens mTOR-RAPTOR interactions while weakening mTOR-mLST8 contacts. These drive the reorganization of Kinase N- and C-lobes into a catalytically competent state in which ATP binding is stabilized enthalpically with improved Mg{superscript 2} coordination. Our studies present structural, energetic and dynamic changes induced by RHEB binding which collectively cause allosteric preorganization of mTORC1 for catalysis prior to substrate binding.

bioinformatics↗

A Druggable G Protein Checkpoint in Cholesterol Efflux

Immunometabolic diseases such as obesity, fatty liver, and atherosclerosis arise when lipid-associated macrophages (LAMs) fail to resolve lipid overload via reverse cholesterol transport (RCT), the bodys sole pathway for lipid disposal. How RCT is restrained in disease remains unknown. Integrating systems modeling with human plaque transcriptomes, we identify LAM subpopulations associated with plaque progression and uncover CCDC88A (GIV) as a macrophage-intrinsic checkpoint on RCT. Myeloid-specific GIV deletion in mice reduces aortic plaque burden, mobilizes hepatic and adipose lipid stores and promotes fecal sterol disposal. Mechanistically, GIV sequesters the cholesterol transporter ABCA1 within endomembranes and activates Gi[bullet]{beta}{gamma} signaling to suppress cAMP/PKA-CREB-dependent efflux programs. Pharmacogenomic disruption of this checkpoint reactivates efflux programs. In human plaque-in-a-dish models targeting this pathway restored efflux where statins and {beta}-blockers failed, translating to an estimated [~]98% reduction in plaque-progression risk in outcome modeling. Thus, RCT-restoration represents a macrophage-intrinsic therapeutic paradigm for immunometabolic disease. GRAPHIC ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/705962v2_ufig1.gif" ALT="Figure 1"> View larger version (64K): org.highwire.dtl.DTLVardef@50dd10org.highwire.dtl.DTLVardef@e16d9borg.highwire.dtl.DTLVardef@1e2eaf3org.highwire.dtl.DTLVardef@af29b9_HPS_FORMAT_FIGEXP M_FIG C_FIG eTOC blurbLipid-associated macrophages drive immunometabolic disease. Katkar et al. show that disabling a GIV-dependent G-protein brake restores cholesterol efflux, reverses plaque lipid accumulation, and establishes reverse cholesterol transport as a druggable therapeutic axis. HighlightsO_LIStatins slow but rarely reverse plaque burden, leaving residual risk driven by LAM dysfunction C_LIO_LIGIV (CCDC88A) non-canonically modulates Gi to suppress macrophage cholesterol efflux C_LIO_LIGIV loss or inhibition restores ABCA1 activity via transcriptional and post-translational control C_LIO_LIBlocking GIV[bullet]Gi checkpoint defats LAMs, regresses plaques, and relieves systemic lipid overload C_LIO_LISIdentifies a druggable node that redefines RCT restoration as a therapeutic paradigm in immunometabolic disease C_LI

immunology↗

Dysregulation of xenobiotic metabolism and mitochondrial dysfunction exacerbate acetaminophen-induced hepatotoxicity in human antigen R-deficient male mice

Acetaminophen (APAP) overdose is a leading cause of acute liver failure worldwide. The RNA-binding protein Human antigen R (HuR) is a multifunctional post-transcriptional regulator that plays a pivotal role in cellular stress responses, including those triggered by APAP toxicity. This study investigated the mechanisms by which HuR protects against APAP-induced hepatotoxicity in male mice. Hepatocyte-specific HuR-deficient (HuRHep-/-) male mice on a C57BL/6N background and wild-type (WT) littermates were treated with 200 mg/kg APAP, and liver tissues were collected at 2, 6, and 24 hours post-treatment. APAP administration increased hepatic HuR mRNA expression and induced HuR cleavage and the formation of a higher-molecular weight HuR-immunoreactive band, with the latter two correlating with injury severity. Compared with WT controls, HuRHep-/- mice exhibited markedly increased susceptibility to hepatotoxicity at both 2 and 6 hours. Metabolite profiling revealed altered APAP metabolism and reduced glutathione S-transferase (Gst) expression in HuRHep-/- livers, consistent with impaired APAP detoxification and increased APAP-protein adduct formation. Fourier-transform infrared (FTIR) spectroscopy further identified early biochemical differences between WT and HuRHep-/- livers as early as 2 hours after APAP exposure. Additionally, HuR deficiency resulted in pronounced mitochondrial structural abnormalities and dysfunction at 2 and 6 hours, accompanied by reduced expression of the mitochondrial fission and fusion proteins Drp1 and Mfn2, increased mitochondrial protein release, and enhanced hepatocyte death. Although pro-inflammatory cytokine levels were elevated in HuRHep-/- mice relative to WT controls at 24 hours, hepatocyte proliferation was similarly blunted in both genotypes, consistent with severe liver injury and delayed recovery. Collectively, these findings identify hepatocyte HuR as a critical regulator of xenobiotic metabolism and mitochondrial integrity and establish its essential role in early protection against APAP-induced hepatotoxicity in male mice.

pharmacology and toxicology↗

DDX3X syndrome mutations lock DDX3X-RNA conformational states to drive persistent pathological condensation and neuronal death

DDX3X is a highly conserved RNA helicase associated with RNA metabolism, translation initiation, and deciding cell fate choices. Spontaneous mutations in DDX3X cause a rare genetic human disorder called DDX3X syndrome, showing a spectrum of neurodevelopmental and intellectual abnormalities. How missense mutations in DDX3X lead to aberrant cellular functions and pathological consequences is unclear. Here, we demonstrate that specific DDX3X syndrome missense mutations induce the formation of persistent, solid-like DDX3X stress granules by structurally altering the conformation of the DDX3X-RNA complex. Structural interrogation of DDX3X syndrome missense mutations revealed critical mutations that perturb the DDX3X-RNA complex, exhibit high clinical pathogenicity scores, and are associated with cancers. N and C-terminal mutations adjacent to the helicase domain of the DDX3X (F182V, I190S, T198P, L556S, and L559H) showed augmented stress granule (SG) assembly, and formation of persistent DDX3X-SGs in neuronal and non-neuronal cells. Intriguingly, these mutations altered the liquid-like properties of DDX3X-SGs, forming solid-like SGs. Mechanistically, these mutations drive the persistent DDX3X-SGs by either locking DDX3X in an open, RNA-bound conformation or by increasing the rigidity of the DDX3X-RNA complex (I190S; T198P), thereby conferring a loss of liquid-like properties. The persistent solid-like DDX3X-SGs preferentially promoted neuronal lytic cell death and did not affect translation. Also, the C-terminal L556S and L559H mutations, which form persistent granules, promoted the DDX3X-driven {beta}-amyloid aggregation. Our observations indicate that DDX3X syndrome mutations near the N- and C-termini promote the formation of solid-like DDX3X condensates, neuropathological aggregation, and neuronal cell death, which might underlie the disease pathogenesis in humans. GRAPHICAL ABSTRACT O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/702492v1_ufig1.gif" ALT="Figure 1"> View larger version (37K): org.highwire.dtl.DTLVardef@164b436org.highwire.dtl.DTLVardef@73741aorg.highwire.dtl.DTLVardef@1cb6fcforg.highwire.dtl.DTLVardef@119b652_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

Spatio-temporal coordination of virulence, metabolism, and stress responses shapes infection dynamics of Xanthomonas perforans

Plants provide distinct ecological niches for diverse microbial communities, with each member adopting strategies tailored to the specific ecological niche it inhabits. Two foliar niches, the leaf surface (epiphytic environment) and the apoplast, impose distinct physiological constraints on microbial fitness, particularly for hemibiotrophic pathogens. In this study, we investigated how these environments shape the transcriptional responses of Xanthomonas perforans (Xp), a tomato pathogen, and how its virulence factors, metabolic pathways, and regulatory networks are spatially and temporally coordinated during disease progression. Transcriptome profiling of a pathogen recovered from the leaf surface and apoplast revealed pronounced niche-specific and colonization stage-specific gene expression patterns. Early epiphytic colonization was characterized by activation of chemosensing, and motility pathways that facilitate pathogen relocation and acquisition of limiting nutrients such as iron and phosphate. This stage also featured induction of DNA and protein repair systems, quorum sensing pathways, phenylalanine degradation and tyrosine conversion to counter phenylpropanoid defenses, genes involved in mitigating osmotic and oxidative stress, active DNA exchange machinery, and type VI secretion system-mediated microbial competition. Upon entry into the apoplast, Xp shifted toward active metabolism and replication, accompanied by investment in type II and III secreted virulence factor expression. Genes involved in evasion of plant immunity and overcoming of host-mediated nutrient sequestration were also upregulated, including those involved in quinone detoxification, phosphate and sulfur uptake, and fatty acid, xanthan, and LPS biosynthesis. During late apoplastic colonization, the pathogen transitioned again towards strong stress response activation, followed by renewed expression of flagellar motility and chemotaxis genes, suggesting preparation for dissemination. Notably, genes associated with oxidative and nutrient stress were enriched across both niches, although specific components differed. Type IV pili, conjugation genes, and plasmid-borne type III effectors were induced early in both niches, suggesting their niche-independent role in initial establishment. Together, these findings reveal a coordinated spatio-temporal regulatory strategy during the transition from the leaf surface to the apoplast. Author SummaryXanthomonas perforans is a foliar bacterial pathogen that infects tomato plants and leads to severe yield losses. To establish a successful infection, the pathogen must overcome a series of environmental and host-imposed challenges. This study characterizes the traits activated at distinct stages of infection, during both early and late pathogenesis, and across different niches, including the leaf surface and its interior (apoplastic) space. On the leaf surface Xanthomonas mainly focuses on movement, communication, and survival against stress and starvation with the major functions related to motility, nutrient uptake, and DNA transfer during early stages. Once inside the leaf, the bacteria switches tactics to focus primarily on reproduction, defense against the plant immune response, production of factors that weaken the plants defenses and gaining access to nutrients the plant normally restricts. Understanding the different stages of infection may inform how the crosstalk among host and pathogen unfolds during pathogenesis allowing us to understand the host environment. These findings can help us discover pathogen weaknesses that could be targeted for disease management.

microbiology↗

HSF1-dependent, long-range directional HSPA1 gene motion to nuclear speckles is coupled to DDX39B condensate dynamics

Approximately 5-10% of the genome, enriched [~]10-fold in the most highly active genes, positions near deterministically within several hundred nm of nuclear speckles (NS). This includes the HSPA1 locus, among the most strongly NS-associated genes. Here we address how HSPA1 endogenous genes and transgenes stably position adjacent to the nuclear speckle periphery, facilitating their gene expression amplification. Live-cell imaging demonstrates a transcription-dependent speckle-anchoring of HSPA1 genes. Removal of this anchoring reveals sustained, long-range, curvilinear oscillations of the HSPA1 genes away from and back to nuclear speckles or between nuclear speckles. Curvilinear transgene movements are dependent on the transcription factor HSF1, largely independent of nuclear actin or cohesin, but unexpectedly spatially and temporally correlated with DDX39B condensate dynamics and dependent on DDX39B protein levels. We propose that stable nuclear speckle association of HSPA1 results from combining metastable speckle anchoring with constitutive, restorative long-range chromosome movements driven by DDX39B condensate dynamics.

cell biology↗

Mettl3-catalyzed m6A methylation determines CD8+ T cell differentiation fate in tumor

The heterogeneity in patient responses to immune checkpoint blockade (ICB) is dictated by the relative abundance of exhausted CD8 T cell (Tex) subsets with distinct therapeutic responsiveness. Progenitor exhausted (pTex) cells remain sensitive to ICB, whereas terminally exhausted (tTex) cells are refractory; however, the molecular cues that bias differentiation toward these divergent fates remain poorly defined. Here, we identify the RNA methyltransferase Mettl3 as a central regulator of Tex fate. Across murine tumor models, human T cells, and adoptive transfer systems, Mettl3 expression is selectively enriched in tTex cells and inversely correlated with TCF1 pTex populations. Mechanistically, Mettl3 drives terminal exhaustion by stabilizing DNMT3B transcripts via mA modification, enforcing CpG methylation and chromatin compaction at memory-associated loci. Inhibition of the Mettl3-Dnmt3b axis reprograms chromatin accessibility toward memory-like states, thereby preserving progenitor potential and effector function. Consequently, T cells lacking Mettl3-Dnmt3b activity persist longer, mount robust recall responses, and achieve superior tumor control with enhanced responsiveness to PD-1 blockade. These findings establish the Mettl3-mA-Dnmt3b axis as a molecular rheostat of CD8 T cell fate, coupling epitranscriptomic regulation to epigenetic remodeling, and reveal a tractable pathway to improve the durability of cancer immunotherapy.

immunology↗

Eco-friendly approach to indenodiazepinones from o-formylynones and o-phenylenediamines: Novel pharmacophoric constructs and their anti-bacterial activity

We have conceptualised and executed an efficient, eco-friendly, one-flask, synthetic approach of general applicability to functionally enriched and potentially pharmacophoric tetracyclic indenodiazepinones through a base-mediated reaction cascade between a multifunctional o-formylynones and commercial o-phenylenediamines. The pertinence of this operationally simple, no-waste protocol, embodying many green and sustainable features, has been scoped with 26 variegated examples. This controlled one-pot assembly of novel tetracyclic indenodiazepinones with an unusual placement of an olefin through a reaction cascade involving Schiff base formation, intramolecular aza-Michael addition and a Mannich reaction between o-formylynones and o-phenylenediamines rapidly generates a diverse library poised for exploring their therapeutic potential and medicinal chemistry applications. The newly accessed indenodiazepinones exhibit promising antibacterial activities against many microorganisms and are non-cytotoxic even at higher concentrations. Interestingly, one of the compounds, 3v did not develop resistance in Salmonella Typhimurium (STM) upon repeated exposure to sub-lethal doses up to the 160th cycle, whereas resistance against clinically used antibacterial ciprofloxacin was attained at the 128th cycle. These preliminary findings open avenues towards the development of novel antimicrobial agents with enhanced durability against drug resistance and these efforts are disclosed in this report. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=133 SRC="FIGDIR/small/697289v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1d1d9beorg.highwire.dtl.DTLVardef@2e8560org.highwire.dtl.DTLVardef@36742eorg.highwire.dtl.DTLVardef@105ae7c_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗