Biology subjects

Dutta, S.

Publications and source records attributed to Dutta, S..

At least 19 recordsLinked to original sources

bioRxiv2026

Surface sensing and metabolic signals drive feedback regulation of long polar fimbriae in enterohemorrhagic Escherichia coli O157

Bacterial colonization requires coordinated regulation of adhesion structures in response to environmental conditions. While metabolic regulation of adhesin expression is well established, how surface sensing contributes to this regulation remains less understood. Here, we investigated the regulation and function of long polar fimbriae (Lpf) in enterohemorrhagic Escherichia coli O157. We show that the lpf1 and lpf2 promoters integrate metabolic and surface-associated signals through distinct regulatory regions. Bile induces both promoters independently of distal regulatory sequences, whereas these regions repress basal transcription and are required for induction following surface association. Surface-dependent activation of both lpf promoters is reduced in mutants lacking the major fimbrial subunits LpfA1 and LpfA2, but is unaffected by deletion of the distal tip adhesins. Lpf structures also promote surface-dependent activation of ler, a positive regulator of lpf expression, supporting a regulatory feedback circuit linking surface sensing to lpf transcription. Loss of the major fimbrial subunits also impairs colonization in zebrafish, whereas deletion of the tip adhesins does not under the conditions tested. Together, these findings show that Lpf integrate environmental signals through surface-dependent regulatory feedback and identify an additional role for the fimbrial structure during colonization that does not require the tip adhesins.

microbiology↗

bioRxiv2026

5-HT1A Antagonist WAY-100635 Prevents Chronic Neurodegeneration and Immune Activation After TBI

Traumatic brain injury (TBI) initiates secondary neurodegeneration that compromises interconnected neural circuits and contributes to persistent visual and neurobehavioral impairment. Pharmacological strategies that preserve vulnerable neurons and synapses while limiting chronic neuroinflammation remain an unmet therapeutic need. We previously identified the serotonin 1A receptor (5-HT1A) antagonist WAY-100635 through screening human stem cell-derived retinal ganglion cells (RGCs) and demonstrated that it promotes neuroprotection through cyclic adenosine monophosphate-dependent mitochondrial biogenesis. Here, we investigated whether post-injury treatment extends this neuroprotective efficacy to cerebral and visual circuitry following TBI. Male C57BL/6J mice aged 2-3 months underwent unilateral controlled cortical impact (CCI) involving the left visual cortex. Mice were randomly assigned to sham, untreated injury or treated injury groups, with 3-10 sham controls and 5-8 mice per injury group across experiments. WAY-100635 was administered intraperitoneally at 5 mg/kg daily, beginning 1 hour after injury and continuing for 6 weeks. Therapeutic efficacy was assessed using motor and psychological-health-relevant risk-taking/behavioral disinhibition by elevated-plus-maze assessment, visual electrophysiology, optokinetic responses, diffusion magnetic resonance imaging, and retinal and cortical histopathology. Unilateral cortical injury produced bilateral RGC dysfunction and loss, with greater degeneration in the eye contralateral to the injured hemisphere, consistent with predominantly crossed murine visual projections. WAY-100635 significantly preserved RGC survival and function, improved visual acuity and contrast sensitivity, and preserved visually evoked cortical responses to contralateral eye stimulation. Diffusion MRI revealed bilateral visual pathway abnormalities, with treatment selectively normalizing fractional anisotropy and radial kurtosis in the optic tract ipsilateral to cortical injury. In perilesional cortex, treatment preserved neuronal cell bodies and synapses detected by synaptophysin immunoreactivity while markedly reducing microglial/macrophage activation and reactive astrogliosis. These effects were accompanied by improved early motor performance and attenuation of injury-associated increases in open-arm exploration in the elevated plus maze. Cortical cavity volume was not significantly reduced, supporting preferential protection of vulnerable circuitry surrounding and connected to the primary lesion. These findings identify post-injury WAY-100635 treatment as a novel therapeutic intervention that combines neuronal and synaptic preservation with reduced chronic glial activation and improved functional outcomes. They support further translational development of serotonin 1A receptor antagonism to limit secondary neurodegeneration and the visual and neurobehavioral consequences of TBI.

neuroscience↗

bioRxiv2026

PySTARC: GPU-accelerated Brownian dynamics for bimolecular association rate constants

Drug-target association and dissociation rates often determine in vivo efficacy more than affinity alone. The association rate constant, however, is computationally challenging to predict since the productive encounter is a rare event in a large translational and orientational search space, which lies beyond the reach of conventional atomistic simulations. We present PySTARC (Python Simulation Toolkit for Association Rate Constants), a GPU-accelerated Brownian dynamics engine for estimating bimolecular association rate constants. PySTARC is a Python reimplementation of the BrownDye engine that converges even small reaction probabilities on a single GPU, at a throughput that would otherwise require a large CPU cluster. The current framework resolves reactions between integration steps with a closed-form Brownian bridge, models the internal flexibility of the solute through a coarse-grained bead chain, distributes trajectories across multiple GPUs, checkpoints long runs, monitors convergence, and automates the entire workflow from input structures to rate estimates. PySTARC is validated against protein-ligand and protein-protein complexes spanning five orders of magnitude in the association rate constant, with most estimates within one order of magnitude of experiment.

biophysics↗

bioRxiv2026

Gasdermin E couples mitochondrial stress to STING-driven neuronal pyroptosis during Chandipura virus encephalitis

Neurotropic RNA viruses are major causes of fatal encephalitis worldwide, yet how infected neurons transition from antiviral defense to inflammatory cell death is not well characterized. Chandipura virus (CHPV), an emerging neurotropic rhabdovirus, causes acute, rapidly progressive encephalitis with high case fatality in children, but the mechanisms underlying its neuropathogenesis remain poorly defined. Here, we demonstrate that CHPV suppresses canonical RNA virus sensing early but subsequently switches to a mitochondria-driven innate immune program that culminates in inflammatory cell death. Early infection of neuronal cells with CHPV was marked by reduced levels of the mitochondrial antiviral adaptor protein, MAVS and attenuation of type I and III interferon responses. As infection progressed, mitochondrial dysfunction promoted accumulation of mtROS, mitochondrial accumulation of cleaved GSDME and cytosolic mtDNA release, triggering STING activation, which coincided with robust neuroinflammation and pyroptotic cell death. Pharmacological inhibition or genetic silencing of STING markedly attenuated inflammatory signaling, prevented pyroptotic membrane rupture and protected neurons from cell death without significantly affecting viral replication. In contrast, GSDME depletion reduced both viral replication and neuronal death. Notably, GSDME depletion markedly attenuated STING phosphorylation, while STING depletion also reduced GSDME activation, revealing functional coupling between these pathways during CHPV-induced neuronal injury. Collectively, our findings identify a mitochondria-GSDME-STING axis linking early immune evasion to neuroinflammation during CHPV infection, revealing a previously unrecognized mechanism of inflammatory neuronal death in viral encephalitis and highlighting STING as a potential therapeutic target in certain CNS viral infections.

immunology↗

bioRxiv2026

KMT2E recruitment by H3 serotonylation regulates neurodevelopmental chromatin dynamics

Histone H3 Gln 5 serotonylation (H3Q5ser) is a recently identified epigenetic modification in brain that modulates reader interactions with adjacent H3 Lys 4 trimethylation (H3K4me3) to promote transcriptional permissiveness. However, whether H3K4me3Q5ser and its associated binding proteins regulate neurodevelopmental gene expression programs remains unknown. Here, we identified the catalytically inactive Lysine methyltransferase 2E (KMT2E) as a reader of combinatorial H3K4me3Q5ser. KMT2E preferentially binds H3K4me3Q5ser over H3K4me3 alone, and enriches at broad chromatin domains marking actively transcribed neurodevelopmental loci. Notably, heterozygous variants in KMT2E have been implicated in ODLURO syndrome, a recently characterized neurodevelopmental disorder (NDD). To identify the molecular mechanisms underlying ODLURO syndrome, we generated a Kmt2e transgenic mouse model that reproduces behavioral, physiological, and cellular endophenotypes associated with this and other NDDs. Furthermore, we observed that KMT2E mediates these effects by recruiting the NCoR/HDAC3 repressor complex to H3K4me3Q5ser-marked loci to restrict spreading of co-localized H3 Lys 9 acetylation (H3K9ac). Inhibition of aberrant H3K9ac spreading was sufficient to rescue transcriptional dysregulation in Kmt2e haploinsufficient neurons. These findings thus establish KMT2E as a critical reader of H3 serotonylation during neurodevelopment and provide mechanistic insights into the pathogenesis of ODLURO syndrome.

neuroscience↗

bioRxiv2026

Integrated in silico identification of fungal-derived dual-target inhibitors for anti-schistosomal drug discovery

Praziquantel, which has limited efficacy against young parasites and reduces susceptibility, is the principal therapy for schistosomiasis, a neglected tropical illness. This work identified fungal-derived compounds with potential dual inhibitory action against Schistosoma mansoni DHODH and cathepsin B1 using an integrated computational method. From 1,831 fungal metabolites, 120 were selected for molecular docking after structure standardisation, drug-likeness evaluation, ADMET, and toxicity screening. Ganoderlactone B (CID_122184973) and Spiroapplanatumine F (CID_132962217) strongly bound to DHODH and CB1, with docking affinities of -10.6 and -10.0 kcal/mol and -9.0 and -8.9, respectively. Docking validation showed good discrimination between active compounds and decoys with area-under-the-curve values of 0.98 for DHODH and 0.96 for CB1. The protein-ligand interaction study showed hydrogen bonding, hydrophobic interactions, and van der Waals contacts at the binding sites. In 100 ns molecular dynamics simulations, protein complexes exhibited modest backbone deviations and maintained compactness, although CID_132962217 showed sustained binding and a constrained conformation. MM-PBSA analysis identified CID_122184973 as the best common ligand for both targets. At the B3LYP/6-31G level, density functional theory calculations showed that CID_139584993 had the lowest HOMO-LUMO energy gap and hardness values of 3.552 and 1.776 eV, respectively, and the highest softness value of 0.282 eV-1, indicating greater electronic reactivity. Electrostatic potential mapping and QSAR predictions supported their interaction and antiparasitic potential. Overall, CID_122184973 and CID_132962217 are promising fungal scaffolds for dual-target anti-schistosomal drug development. Experimental enzyme inhibition, parasite viability, toxicity, and in vivo research are needed to confirm computational findings.

bioinformatics↗

bioRxiv2026

A replicated patient-specific component of tumour telomere length across two pan-cancer cohorts

Bulk telomere length measured from tumour sequencing is routinely interpreted as a property of the cancer cells. However, a tumour specimen is a mixture, and the patient who supplies it has a telomere length of their own. Here I re-analyse published pan-cancer telomere estimates and ask how much of a tumour's telomere length is patient-specific. A calibration step comes first. Whole-genome and low-pass estimates recover the known cross-sectional attrition of leukocyte telomeres with age, at 26.6 bp per year in blood normals, whereas whole-exome estimates do not. After adjustment for cancer type, sequencing centre and sex, the exome slope is minus 0.6 bp per year. In 684 blood-normal aliquots sequenced by both assays, the whole-genome estimate declines at 38.9 bp per year, whereas the exome estimate from the same DNA shows no detectable decline. The difference between assays is 41.5 bp per year, with P = 3 x 10^-10. Because exome data constitute 78.6% of the original resource, downstream analyses use only whole-genome and low-pass libraries. Within those data, tumour telomere length tracks the patient's matched-normal telomere length. The Spearman correlation is 0.395 in TCGA, with positive associations in 22 of 23 cancer types. This finding replicates in PCAWG using a different telomere estimator, with a correlation of 0.472 and positive associations in all 24 histologies examined. Adjustment for cancer type, sequencing centre and library type leaves a regression coefficient of 0.385. The association is also stable after adjustment for age, sex, tumour purity, leukocyte fraction, ploidy, sequencing coverage and continental ancestry, with coefficients ranging from 0.406 to 0.429. Pure normal-cell admixture is rejected as the sole explanation. Under a two-compartment mixture model, the coefficient for host telomere length is expected to equal 1 and the host-by-purity interaction to equal minus 1. These restrictions are jointly rejected with P = 0.001. Tumour purity, leukocyte fraction and age each explain only about 1 to 3% of within-cohort variance and do not alter the cross-cancer ranking. By contrast, the between-cohort coefficient is not directly interpretable. Its apparent near one-to-one relationship with tissue-associated telomere length depends strongly on which tissue supplies the matched-normal reference and on the statistical spread of that predictor, falling to 0.44 when organ-matched solid tissue is used. Bulk tumour telomere length is therefore a composite phenotype containing a replicated patient-specific component. Telomere biomarker studies should include matched-normal telomere length as a covariate rather than treating tumour telomere length as exclusively tumour-intrinsic.

cancer biology↗

bioRxiv2026

Modeling Dynamics of Contact Inhibition of Proliferation and Structural Order in a Confluent Epithelium

Contact inhibition of proliferation (CIP) enables epithelial tissues to self-regulate growth and maintain tissue homeostasis. However, how cell-level mechanical contact, tissue-scale structural order, and proliferation kinetics interplay remains a fundamental open question in living matter physics. Here, we present a particle-based model of a confluent epithelial monolayer governed by overdamped dynamics, where individual cells interact via a two-dimensional hard core- soft shoulder potential. By comparing structural evolution during quasistatic densification with previously reported experimental division kinetics, we find that the dynamics of proliferation arrest mimics the onset of direct steric contacts between the hard cores of the shell. Identifying hard core contacts as the physical driver of CIP, we couple our mechanical model with a stochastic Monte Carlo division scheme in which the instantaneous division rate decreases to zero from an intrinsic value as the number of hard core contact increases to six from zero. We demonstrate that for high intrinsic division rates, the cellular densification outpaces mechanical relaxation. This kinetic mismatch drives premature hard-core contact formation, shifts the onset of jamming and contact inhibition to lower packing fractions, and induces increasingly disordered transient configurations before the tissue universally converges to a hexagonal close-packed limit. Our model's predicted division kinetics and structural order evolution are consistent with epithelial monolayer experiments, both reported and our own. This minimal physical framework links single-cell steric contact mechanics directly to tissue-scale growth regulation and structural evolution.

biophysics↗

bioRxiv2026

Time-Resolved Single-Cell Atlas Reveals Early Endothelial Activation and Stage-Dependent Immune-Stromal Communication in HFpEF

BackgroundHeart failure with preserved ejection fraction (HFpEF) is a heterogeneous syndrome associated with metabolic stress, hypertension, systemic inflammation, and microvascular dysfunction. Early cell-type-specific events and intercellular communication programs that accompany disease onset and progression remain poorly defined. MethodsWe performed a longitudinal study of HFpEF progression in high-fat diet (HFD)+L-NAME mice at control/baseline (0 weeks, 0w/Ctrl), early (1w), intermediate (4w), and established (8w) stages. Metabolic, hemodynamic, exercise, echocardiographic, and single-cardiomyocyte function were assessed. Cardiac non-cardiomyocytes (non-CMs) were profiled by single-cell RNA sequencing (scRNA-seq), with bulk RNA-seq for tissue-level comparison. Endothelial remodeling was assessed in an L-NAME-independent HFD plus mild transverse aortic constriction model (HFD+mTAC) and a published human HFpEF single-nucleus RNA-seq cohort. An endothelial-macrophage adhesion assay tested whether HFpEF-mimic stress promotes endothelial activation and macrophage adhesion. ResultsIn the HFD+L-NAME model, metabolic dysfunction, hypertension, reduced exercise tolerance, abnormal diastolic filling with preserved ejection fraction, and altered cardiomyocyte calcium handling were detected by 1w and persisted through 8w. Bulk RNA-seq showed progressive remodeling, with limited change between 8w and 12w, guiding scRNA-seq timepoint selection. scRNA-seq of 94,848 cardiac non-CMs identified nine major populations with stage-dependent remodeling. Endothelial cells (ECs) were recovered in high proportion and showed an early, pronounced transcriptional response, with inflammatory, adhesion, interferon-response, migratory, and vascular-remodeling programs emerging by 1w. Related EC activation signatures were observed in HFD+mTAC and human HFpEF data. Functionally, HFpEF-mimic stress increased adhesion and chemokine expression in human ECs and enhanced macrophage adhesion. Fibroblast matrix remodeling occurred at later stages, while macrophages progressively shifted toward inflammatory states. CellChat suggested stage-dependent communication remodeling from early endothelial-immune interactions toward later macrophage-fibroblast crosstalk. ConclusionTime-resolved scRNA-seq reveals coordinated, stage-dependent remodeling of the cardiac microvascular and interstitial microenvironment during HFpEF progression. Early endothelial activation emerges before later fibroblast matrix remodeling and inflammatory macrophage remodeling, identifying candidate cell states and signaling pathways for future mechanistic investigation. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSO_LIThis study provides a time-resolved single-cell atlas of the cardiac non-cardiomyocyte compartment across baseline, early, intermediate, and established stages of HFpEF progression, rather than a single late-stage snapshot. C_LIO_LIEndothelial cells exhibit early inflammatory, adhesion, interferon-response, and vascular-remodeling programs within the first week of disease, preceding the later predominance of fibroblast matrix remodeling and inflammatory macrophage remodeling. C_LIO_LIThis endothelial activation signature is supported across two mechanistically distinct HFpEF mouse models and aligns with endothelial inflammatory and vascular-remodeling programs in human HFpEF myocardium, supporting its translational relevance. C_LI What Are the Clinical Implications?O_LIEarly endothelial activation may represent a targetable stage of HFpEF pathogenesis that arises before more established structural and fibrotic remodeling. C_LIO_LITherapeutic strategies aimed at limiting endothelial inflammatory activation or endothelial-immune interactions may help attenuate downstream vascular, immune, and stromal remodeling in HFpEF. C_LIO_LIThese findings provide a preclinical foundation for future longitudinal human studies testing whether early endothelial activation can serve as a biomarker, therapeutic target, or disease-staging feature in HFpEF. C_LI

cell biology↗

bioRxiv2026

Explainable HGT-based framework for predicting human dark kinase protein-pathway associations by leveraging BERT-based embeddings and WGAN-GP

Discovery of pathway associations and druggability can leverage underutililized dark kinase genes for treating complex diseases (proven for cancer and neurodegeneration), boosted with computational methods. Herein, we employ BERT-based embeddings of proteins and pathways (refined via two-stage transformer and heterogeneous graph transformer) and protein-protein and protein-pathway associations-both positive (curated from databases) and negative (generated using Wasserstein Generative Adversarial Networks with gradient penalty) to train XGBoost and lightGBM classifiers for predicting pathways associated to human dark kinase proteins, with important features unveiled through SHAP analysis. All pathways are clustered and proteins related to same pathway clusters are grouped together (via predicted and positive protein-pathway associations). Selected PCOS-related human dark kinase proteins (with high predicted and existent associations to PCOS pathways) are docked with known PCOS drugs for druggability analysis. Our model attains accuracy, F1-score, specificity, MCC, AUROC and AUPRC of 0.9816, 0.9816, 0.9852, 0.9632, 0.9978 and 0.9982 respectively, supersedes existing work, correctly classifies 97.48% of test data, predicts 62225 pathway associations to above proteins, infers functional similarity of 96 such proteins to human protein(s) and traces nine important positive features. Our model can be used to determine varied functionalities and disease relevance of proteins via predicted pathway associations.

bioinformatics↗

bioRxiv2026

Discovery of A Multi-Class Antibiotic Potentiator Against Resistant Klebsiella pneumoniae

The rapid rise of multidrug-resistant (MDR) bacterial infections has severely limited treatment options, particularly for Gram-negative pathogens such as Klebsiella pneumoniae, a leading contributor to pneumonia, bloodstream, urinary tract, and surgical-site infections. One strategy to restore antibiotic efficacy is the use of resistance-mitigating agents (RMAs), compounds that re-sensitize bacteria to existing antibiotics without displaying independent antibacterial activity. Herein, we report the results of a high-throughput screen of a 3,200-compound fragment-based library against an MDR K. pneumoniae isolate in the presence of subinhibitory ciprofloxacin. This screen identified a tetrahydrocarbazole-containing compound, 1, as a ciprofloxacin potentiator. Subsequent structure-activity relationship studies yielded a difluorinated analog, compound 5, which potentiated multiple antibiotic classes in MDR K. pneumoniae, reducing MICs up to [≥]16 fold. Further testing demonstrated synergistic interactions between compound 5 and ciprofloxacin, ceftriaxone, cefoxitin, and tetracycline across four genetically diverse MDR K. pneumoniae strains. These findings suggest that tetrahydrocarbazole-containing compounds constitute a promising new class of RMAs with potential for future development as therapies against MDR K. pneumoniae infections.

microbiology↗

bioRxiv2026

Conformation of the Catalytic Lysine is a Key Determinant of 2-Deoxyribose-5-phosphate Aldolase (DERA) Stereoselectivity

2-Deoxyribose-5-Phosphate Aldolase (DERA) is a key enzyme in the pentose phosphate pathway. Due to its C-C bond formation and stereoselective capabilities, DERA has been widely used for biocatalytic applications including the synthesis of chiral intermediates for antiviral and anticancer drugs. While protein engineering has expanded its substrate pool, improved yield, and enhanced stereoselectivity, the molecular basis of stereoselectivity remains unclear. Here, we determined the crystal structures of wildtype DERA from Geobacillus sp. and two of its variants with opposite stereoselectivity. Using a combination of structural biology, biochemistry, organic synthesis and molecular dynamic simulations, we show that the catalytic Lysine adopts two conformations and the Lysine conformation is a key determinant of DERA stereoselectivity. We also identified a mechanism of regulating stereoselectivity via a key amino acid. Using DERA from E. coli, we show that these findings are most likely conserved among bacteria.

biochemistry↗

bioRxiv2026

Glycocalyx-Directed Enzymatic Hydrogels Unlocks Fibroblast Regeneration to Promote Diabetic Wound Healing

Chronic diabetic wounds remain a major clinical challenge because current therapies address infection or supplement growth factors without correcting the cellular dysfunction that prevents regeneration. We identify pathological glycocalyx thickening in diabetic dermal fibroblasts (DDFs) as a driver of elevated caspase 3, 8, and 9 expression and heightened apoptosis -- deficits that stall wound repair. Cleavage of sialic acid residues by neuraminidase (NMase) reverses this dysfunction, restoring fibroblast migration, proliferation, and contractility. We engineer a photo-crosslinked hybrid hydrogel combining methacrylated gelatin (GelMA) with high-molecular-weight methacrylated chitosan (HMW ChMA). ChMA increases storage modulus 8-12-fold, reduces pore size, and confers antibacterial activity against gram-positive and gram-negative bacteria, addressing infection susceptibility. The fortified HMW hybrid (HMWH) network enables sustained, localized NMase delivery that outperforms GelMA alone in resisting degradation and controlling release kinetics. NMase-loaded HMWH (N-HMWH) gels enhance DDF proliferation and migration in vitro, correlating with reduced focal adhesion size and increased turnover. In a diabetic rat model, N-HMWH patches achieve superior wound closure, outperforming EGF therapy, with robust epidermal regeneration, neovascularization, and collagen deposition. This work establishes glycocalyx-targeting hydrogels as a new class of wound therapeutics addressing the root cause of diabetic fibroblast failure, not just compensating with growth factors.

bioengineering↗

bioRxiv2026

Temporal ordering of migration increments carries directional memory under MYO10 depletion and collagen exposure

A cell track contains not only a set of movements but also an order. We asked whether that order reveals behaviour that speed, endpoint displacement, and conventional persistence measures miss. For each trajectory, we compared the recorded sequence with an exact reference in which the same displacement steps were rearranged; the observed-minus-reference difference quantifies persistence created by step order. In 48,134 MCF10DCIS.com trajectories, most of a reproducible MYO10-collagen interaction in directional persistence disappeared when temporal order was removed. In 131 single MCF10A haptotaxis tracks, widening the fibronectin pattern did not produce a resolved global increase in order; it shifted short- timescale organization from the gradient axis toward lateral movement, with an intrinsic lateral-order difference of 0.2176 (95% hierarchical interval 0.1274-0.3171). In MDA-MB-231 cells migrating toward EGF, PFKL-N702T produced fewer up-gradient steps and shorter up-gradient runs while the mean-speed difference remained unresolved. These directional effects remained after comparisons balanced for measured speed and duration, whereas three cue-independent serial-order measures showed no reduction larger than a locked 0.10-SD margin at the track level. Across independent endothelial, epithelial, and cancer-cell archives, the same calculation distinguished sustained, short-lived, and sign-reversing regimes; a stationary angular hidden-state model failed all eight frozen long-lag targets. Temporal order therefore separates three biological questions: how much a cell moves, whether it continues moving persistently, and whether that persistence remains aligned with an environmental cue. We provide a documented workflow that calculates these readouts from standard x-y tracking tables. Impact statementThe order of otherwise similar migration steps reveals whether cells merely continue moving or sustain commitment to an environmental cue.

biophysics↗

bioRxiv2026

Lateral interactions override nucleotide state in determining FtsZ filament curvature

The bacterial tubulin homolog FtsZ assembles into dynamic filaments that form the cytokinetic Z-ring and drives constriction during cell division. Whether a nucleotide-dependent FtsZ filament curvature plays a role in constriction is often debated. Here, we combine cryo-electron microscopy and molecular dynamics simulations to understand the structural basis of FtsZ filament curvature. Cryo-EM structures of GTP-bound Spiroplasma FtsZ filaments in two curved states emphasize that curvature is an intrinsic property of FtsZ filament, confirming recent models in which GTP hydrolysis does not dictate protofilament bending in the tubulin family. Consistently, molecular dynamics simulations demonstrate that GTP-bound filaments can adopt a range of curved conformations. The preferred intrinsic curvature appears to be such that the C-terminal end of the globular domain faces the convex surface. Structural analyses of the curved conformations identify dynamic and stationary zones at the longitudinal interfaces of the protofilament, suggesting that structural plasticity of the intermonomer interface contributes to filament bending. Furthermore, we demonstrate that lateral interactions between adjacent protofilaments straighten the filaments, overriding their relaxed curved states. Optimal orientations of lateral interactions in the Z-ring assembly could be brought about by other interacting proteins of the divisome machinery. The straighter filament conformation is likely to stimulate a higher GTPase activity. Together, our findings establish lateral association as a primary determinant for straight FtsZ filaments, analogous to the tubulin protofilaments in a microtubule lattice. The snapshots of structural states provide a mechanistic basis for how the intrinsic curvature facilitates association on the membrane and the physiological relevance of transitions between bent and straight conformations of the FtsZ filament during Z-ring assembly and constriction.

biochemistry↗

bioRxiv2026

EZH2 inactivation drives MAPK-dependent vulnerability to MEK inhibition in RAS-mutant CMML

Chronic myelomonocytic leukemia (CMML) is a heterogeneous hematologic malignancy with limited therapeutic options. Although RAS and RAS-modifying mutations (RASmut) are common and associated with poor prognosis, targeting RAS signaling has shown limited clinical success. Here, we define co-occurrence of RASmut and EZH2 inactivation (EZH2inact) as a distinct molecular subgroup of CMML characterized by aggressive disease biology. Mechanistically, RASmutEZH2inact drives selective MAPK/ERK hyperactivation in mature myeloid cells and hematopoietic stem and progenitor compartments. Transcriptomic analysis of a large independent myeloid neoplasm cohort (Beat-AML) further supports this finding, demonstrating selective activation of gene signatures of MAPK/ERK activation in RASmutEZH2inact cases. Functionally, this signaling activation promotes proliferation and myelomonocytic differentiation in human and murine models. Therapeutically, this MAPK/ERK upregulation confers increased sensitivity to MEK inhibition (MEKi). In a murine RasmutEzh2inact-driven CMML model, MEKi suppresses MAPK/ERK activity and reduces leukemic burden by impairing proliferation and myelomonocytic differentiation without inducing cell death. In primary human CMML samples ex vivo, MEKi shows stronger anti-proliferative effects in RASmutEZH2inact specimens compared with RASmut samples. Drug-sensitivity data from the Beat-AML cohort further supported this. Ultimately, these findings were confirmed in a patient-derived xenograft model, where MEKi reduced the leukemic burden by selectively inhibiting the proliferation of transplanted human RASmutEZH2inact leukemic cells. In summary, our data define RASmutEZH2inact CMML as a clinically relevant subgroup with selective MAPK/ERK hyperactivation and increased sensitivity to MEKi. They provide a mechanistic explanation for the limited efficacy of MEK inhibitors in unselected CMML and support molecularly guided use of MEK-targeted therapy in this patient population.

molecular biology↗

bioRxiv2026

Transcriptome-inferred CIN-like fields mark antigen-presentation-low, immune-cold spatial neighborhoods

Cancer immune escape is usually interpreted as either a tumor-cell-intrinsic antigen-presentation defect or an immune-cold microenvironment. How these states are spatially arranged relative to chromosomal-instability-like genotype states remains unresolved. Here, spatial transcriptomic, single-cell and clinical transcriptomic analyses show that transcriptome-inferred CIN-like fields mark antigen-presentation-low, immune-cold neighborhoods. Across 14 melanoma tissue sections, the interaction between inferred copy-number-like burden and chromosome-expression deviation was associated with reduced MHC-I antigen-presentation activity after adjustment for tumor state, immune inflammation, technical covariates and spatial coordinates. CIN-high/AP-low spots formed coherent neighborhoods enriched for AP-low neighbors but depleted of immune-high and IFN-high neighbors under block-preserving spatial nulls. Two breast cancer Visium sections reproduced AP-low neighborhood topology, while malignant melanoma single-cell RNA-seq supported a tumor-intrinsic CNA-by-chromosome-deviation association with AP repression. Patient-level TCGA analyses linked the adverse genotype-ecotype score to poor melanoma survival. These results define transcriptome-inferred CIN-like fields as spatial correlates of immune-cold antigen-presentation failure.

cancer biology↗

bioRxiv2026

Sustained presence of metabolically active mesophiles in the boiling vent-water of a low-salinity, slightly-alkaline, sulfate-rich geothermal spring characterized by an inequitable ecology of hyperthermophiles and thermophiles

Geothermal vent-heads exclusively support the proliferation of (hyper)thermophilic microorganisms. However, diverse mesophiles are stochastically thrust into these ecosystems by local geodynamic forces, and their population-level responses to the unfamiliar stressor hold critical implications for lifes intrinsic resilience to biophysical adversities. Here, we report a time-course exploration of the boiling vent-water of a Trans-Himalayan geothermal spring to determine the population dynamics, in situ functionalities, and potential ecological roles of mesophilic incomers in the context of indigenous (hyper)thermophiles. The temporally-consistent (hyper)thermophilic core-community, predominated in turn by a few Aquificia and Thermoproteota, was delineated as metagenome-assembled genomes. Mesophiles/moderate-thermophiles were identified as MAGs and/or pure-cultures, and whether temporally-consistent/inconsistent, had far lower prevalence. Overall, in situ transcriptional activity and prevalence had significant positive correlation; but many species exhibited high activity despite low prevalence and vice versa, implicating the decoupling of global metabolism from growth/proliferation. Bulked metatranscriptomic signatures identified the (hyper)thermophiles as primary producers of the ecosystem. Populations of mesophiles and moderate-thermophiles were apparently active, but not growing, in situ, with some being engaged in environment detoxification, and production of nutrients, metabolites and protective-biomolecules wanting in the (hyper)thermophiles. The findings engender an unprecedented portrayal of geothermal-vents as multi-community ecosystems where unfamiliar immigrants provide critical metabolic services.

microbiology↗