Biology subjects

Garg, A.

Publications and source records attributed to Garg, A..

At least 19 recordsLinked to original sources

bioRxiv2026

Filament assembly confers the mechanical resilience of the IFI16 restrictosome

Interferon-inducible protein 16 (IFI16) is a mammalian innate immune sensor composed of a filament-forming pyrin domain (PYD) followed by tandem HIN200 domains that bind nucleic acids. First recognized as a major regulator of inflammatory responses against cytosolic double-stranded (ds)DNA, IFI16 filaments have been implicated in several key mechanical processes involving both host and pathogens, including viral replication restriction, latency regulation, replication-stress responses, and DNA-damage responses. Moreover, IFI16 filaments are ultra-stable, a key trait believed to drive its autoantigenicity. Although recent studies reported that IFI16 undergoes liquid-liquid phase separation (LLPS) via disordered linkers and multivalent protein-dsDNA interactions, whether such a metastable entity provides a framework for the mechanical activities of IFI16 remains unknown. Here, we show that PYD-driven filament assembly confers the mechanical stability of IFI16 condensates by compacting DNA into ultra-stable tangles capable of withstanding forces sufficient to induce duplex deformation. By contrast, HIN200-dsDNA complexes are much more sensitive to ionic perturbation, DNA pretension, and mechanical interference. Together, we demonstrate that filament assembly allows IFI16 to act as a mechano-sensitive restrictor.

biophysics↗

bioRxiv2026

One-carbon metabolism sustains effector T cell function through cell-surface glycosylation

Folate is a driver of one-carbon metabolism that is essential in T cells. The cellular consequences of its deprivation in CD8+ T cells and impact on anti-tumor function are unknown. Single cell RNA-seq analysis of primary central nervous system lymphoma (PCNSL) patients' tumor samples revealed exhaustion in T cells with high folate metabolism gene expression signature. Functional genomics, metabolite profiling, and glycomics identified disrupted cell surface glycosylation as a major consequence of folate deprivation in CD8+ T cells. Mechanistically, folate deprivation reduced nucleotide sugar levels, perturbed glycosylation, and triggered the apoptotic unfolded protein response. Overexpressing folate transporters in adoptively transferred CD8+ T cells increased intratumoral T cell numbers and reduced exhaustion. Therefore, our data draw a mechanistic line between one-carbon metabolism, cell-surface glycosylation, and anti-tumor T cell function, and support a hypothesis that increased folate uptake can enhance CD8+ T cell function including ex vivo and in vivo CAR-T cells.

cell biology↗

bioRxiv2026

Surface Functionality and pH Govern Structural Dynamics and Drug Binding in PETIM and PAMAM Dendrimers

1.Surface functionality and pH play a decisive role in governing the structural dynamics, hydration, and drug-binding behaviour of dendrimers. Here, all-atom molecular dynamics (MD) simulations were performed on five generations of PAMAM (G1-G5) and PETIM (G2-G6) dendrimers with O-core and N-core architectures, functionalized with amine, carboxylic acid, or sugar terminal groups under different protonation states. Protonation of the tertiary branch-point amines expands the dendrimer structure, increases internal porosity and hydration, and enhances structural fluctuations across both families. In contrast, non-protonated amine -NH2 (NP) and carboxylic acid -COOH (NP) terminated dendrimers, together with deprotonated carboxylate-COO- (DeP) systems, retain comparatively compact conformations. Sugar-functionalized dendrimers ({beta}-galactose-terminated PETIM and D-glucose-terminated PAMAM) are most hydrated and structurally rigid, whereas amine-terminated dendrimers exhibit the greatest conformational dynamics. PAMAM dendrimers with -NH2, -NH3+, and -COO- terminal groups are generally more hydrated than their PETIM counterparts. However, {beta}-galactose-terminated PETIM dendrimers are more hydrophilic than D-glucose-terminated PAMAM dendrimers. N-core PETIM dendrimers also adopt more compact and spherical conformations than equivalent O-core PETIM dendrimers. Drug-binding MD simulations show that curcumin binding is dominated by van der Waals (vdW) interactions, whereas doxorubicin complexation is primarily driven by electrostatic interactions. Among the investigated surface functionalities, -NH2 (NP), -NH3+ (P), -COOH (NP), and -COO- (DeP) terminations exhibit the most favourable drug-binding characteristics. Except for deprotonated carboxylate systems, curcumin binds more strongly than doxorubicin. Overall, these findings establish molecular-level relationships between surface functionality, protonation state, dendrimer architecture, and drug-binding behaviour, providing design principles for pH-responsive dendrimer nanocarriers with enhanced drug-loading and controlled-release performance. TOC O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=75 SRC="FIGDIR/small/742721v1_ufig1.gif" ALT="Figure 1"> View larger version (35K): org.highwire.dtl.DTLVardef@1b63094org.highwire.dtl.DTLVardef@2f81f2org.highwire.dtl.DTLVardef@fc651forg.highwire.dtl.DTLVardef@530a04_HPS_FORMAT_FIGEXP M_FIG C_FIG

biophysics↗

bioRxiv2026

Deep Brain Stimulation Microelectrodes as a Source of Human Subcortical RNA: Validation of a Low-Input Transcriptomic Protocol

BackgroundUnderstanding the molecular basis of Parkinsons disease (PD) phenotypic heterogeneity maybe improved by in vivo access to deep brain tissue. Deep brain stimulation (DBS) surgery offers a unique opportunity: microelectrodes traversing the subthalamic nucleus (STN) carry adherent brain tissue upon withdrawal, providing a source of RNA from subcortical regions in living patients without additional invasive procedures. AimTo develop and validate a low-input RNA extraction and transcriptomic profiling protocol using DBS microelectrodes in post-mortem human brain, to confirm that recovered RNA is of brain rather than blood origin, and to characterise its sub-regional and cellular identity. MethodologyDBS microelectrodes were inserted without image guidance or guide tube into three unfixed post-mortem human brains targeting the STN trajectory. In clinical practice, a guide tube shields the electrode from cortical tissue; its absence here means tissue from the full insertion trajectory may contribute to recovered RNA. Thirty-eight microelectrodes were evaluated across single and pooled strategies. RNA was extracted using a modified RNeasy Micro low-input protocol; libraries prepared using NEBNext Single Cell/Low Input RNA Library Kit and sequenced on Illumina NovaSeq 6000 (paired-end, 2x150 bp). Tissue identity was validated against GTEx v10 (54 tissues) and Allen Human Brain Atlas (ABA, 19 subcortical regions including STN) using Pearson correlation with permutation testing (1,000 permutations) and BH-FDR correction. Transcriptional overlap between subcortical and cortical reference regions was quantified and subcortical-enriched gene filtering performed. ResultsTwenty-five RNA isolates were obtained from 38 microelectrodes; 54.5% of Bioanalyzer-assessed samples achieved RIN [≥]5 (median 7.1; range: 5.9-7.8). Fifteen libraries passed sequencing QC (mean depth 43.0 {+/-} 14.1 million read pairs; mean Q30 83.2 {+/-} 5.6 %). PCA of rlog transformed expression data resolved samples by donor identity. All samples confirmed brain tissue origin by GTEx {tau}-index tissue specificity correlation (n=996 brain and blood specific markers). Brain correlations were highest for frontal cortex (mean r= 0.683 {+/-} 0.072), anterior cingulate cortex (mean r= 0.658 {+/-} 0.069), amygdala (mean r= 0.615 {+/-} 0.068), and basal ganglia including caudate (mean r= 0.553 {+/-} 0.059), putamen (mean r= 0.546 {+/-} 0.059), and nucleus accumbens (mean r= 0.544 {+/-} 0.057); all BH-FDR < 0.05. Cerebellum showed the lowest brain correlations (cerebellar hemisphere: mean r = 0.327 {+/-} 0.039; cerebellum: mean r = 0.314 {+/-} 0.037). Whole blood correlation was strongly negative (mean r= -0.250 {+/-} 0.079), confirming non-haematological origin. ABA genome-wide analysis confirmed positive STN correlation (r=0.54-0.62; permutation p<0.001). MuSiC cell-type deconvolution against the Allen Brain Atlas HMBA-BG snRNA-seq reference identified oligodendrocytes (33.5 {+/-} 17.2%), frontal cortical neurons (9.1 {+/-} 7.0%), STR D1 MSNs (6.0 {+/-} 4.9%), and dopaminergic neurons (1.1{+/-} 2.7%) as the principal cell types, independently corroborating bulk transcriptomic findings at single-cell resolution. ConclusionThis study validates a low-input RNA extraction protocol for DBS microelectrodes, confirming brain-specific transcriptomic profiles consistent with STN-adjacent subcortical sampling. The 96% transcriptional overlap between cortical and subcortical regions, combined with absence of a guide tube in this post-mortem model, limits sub-regional specificity; clinical application with a guide tube would enrich the subcortical signal. These findings provide the methodological framework for in vivo molecular profiling of the human basal ganglia during DBS surgery in PD patients.

genetics↗

bioRxiv2026

Mechanistically informed adaptive dosing for cancer immunotherapy using AI-guided decision making

Optimizing dose and schedule remains a central challenge in oncology drug development, particularly for immunotherapies where fixed dosing regimens often fail to account for patient specific heterogeneity in tumor-immune dynamics. Here, we present a hybrid quantitative systems pharmacology-reinforcement learning-Monte Carlo Tree Search (QSP-RL-MCTS) framework for personalized immunotherapy dosing that formulates dose selection as a sequential decision-making problem. The approach integrates a mechanistic QSP model of prostate cancer immunotherapy, transcriptomics informed virtual patient populations and data driven AI system comprising reinforcement learning and Monte Carlo tree search. Reinforcement learning is used to learn adaptive generalized dosing policies that optimize treatment outcomes across the population, while Monte Carlo Tree Search provides forward-looking evaluation of RL predicted dosing trajectories to refine patient-specific decisions. On benchmarking against fixed dosing regimens of ipilimumab, the remission rate of the proposed model (95.2%) was comparable to the highest fixed dosing regimen of 10 mg/kg per dose while the median total dose (72 mg/kg) of the proposed model designed regimen was comparable to the lowest fixed dosing regimen of 3 mg/kg per dose. The model is generalizable across different dosing protocols and can be extended to predict optimal dose under different therapeutic scenarios. Analysis of the learned dosing trajectories enables stratification of patients into distinct response groups and identifies drug activity rate as the dominant determinant of long-term treatment outcome. These results demonstrate how mechanistically guided artificial intelligence can transform population-level dose optimization into patient-specific, biologically interpretable treatment strategies for precision immuno-oncology.

systems biology↗

bioRxiv2026

Curcumin - Gold Nanocomposites for Enhanced Doxorubicin Delivery: Molecular Mechanisms of Loading and Membrane Interactions

Curcumin-functionalized gold nanoclusters are promising platforms for catalysis and drug delivery, however, the molecular determinants governing their stability, morphology, and solvent response remain poorly understood. Here, microsecond all-atom molecular dynamics simulations were employed to investigate a 2 nm gold nanoparticle noncovalently coated with different curcumin forms, including the neutral enol and trans-keto tautomers, the deprotonated enolate, and their mixtures in water-ethanol and water-methanol solvents. Region-resolved analyses of the radius of gyration, density profiles, and surface coverage reveal that neutral enol and trans forms generate compact assemblies with near-complete surface coverage, whereas enolate-rich systems adopt more expanded conformations with greater solvent exposure. Mixed systems preserve these intrinsic packing characteristics while improving overall surface coverage. Solvent substitution from ethanol to methanol reduces {pi}-{pi} stacking, strengthens Au-curcumin interactions, and increases surface coverage, yielding more compact nanostructures. Free energy and potential of mean force calculations further indicate that deprotonated curcumin most effectively screens Au-Au interactions and promotes nanoparticle dispersion, whereas the neutral tautomers provide moderate stabilization. Curcumin functionalization also enhances the loading of the anticancer drugs doxorubicin (DOX) and niraparib (NIR) onto Au nanoparticles. Membrane interaction with AuDOX/NIR-Curcumin simulations show that Enolate(An)-containing systems form more extended structures and interact more weakly with both negatively charged and neutral DMPC membranes. In contrast, neutral curcumin complexes form compact, positively charged assemblies with stronger interactions with the negatively charged model membrane. Furthermore, these interactions are predominantly driven by electrostatic attraction and are substantially weaker with the neutral DMPC membrane. Overall, these findings demonstrate how curcumin tautomeric state and solvent environment cooperatively govern interfacial organization and colloidal stability, drug-loading, and membrane interactions. This provides molecular-level design principles for curcumin-based gold nanocarriers for catalysis, sensing, and drug delivery applications.

biophysics↗

bioRxiv2026

Structural dynamics between Argonaute-2 and CK1α promote target RNA release in microRNA-mediated silencing

Argonaute (Ago) proteins associate with 20-22 nucleotide (nt) long microRNAs (miRNAs) to constitute the functional RISC core and downregulate mRNAs containing complementarity to the seed sequence1-3. Target RNA engagement in RISC stimulates CK1-mediated phosphorylation of the conserved eukaryotic insertion (EI) in Ago, releasing the target and enabling the RISC complex to suppress additional target sites for efficient miRNA-mediated silencing4-6. Here, we provide a complete structural view of miRNA guide and target binding to human Ago2, showing Ago2 holding the double-stranded guide-target RNA in an untwisted conformation at its center. We visualize the dynamic changes that RISC undergoes as the guide supplementary region progressively base pairs with the target, enabling CK1 binding. Following seed-helix assembly, initial supplementary pairing restricts RISC to a "closed" form, while with half-supplementary pairing, the PAZ domain moves to open RISC to become receptive to CK1, exhibiting an initial increase in Ago2 phosphorylation. Complete supplementary pairing supports a full PAZ-CK1 interface, allowing for hierarchical phosphorylation of the EI. The combination of target repulsion by EI phosphorylation with an unwound guide-target enables efficient target release to promote RISC turnover.

biochemistry↗

bioRxiv2026

Sequence determinants of the hypomobility of intrinsically disordered proteins in SDS-PAGE

Proteins with intrinsically disordered regions (IDRs) migrate at a higher apparent molecular weight in sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) complicating their analysis and identification. Here, we investigate the sequence determinants of the hypomobility of IDRs using a series of synthetic low complexity domains. We find that negative charge increases the apparent molecular weight, but neutral polar tracts also have abnormally slow migration. Positive charge and hydrophobic residues decrease the apparent molecular weight, although lysine residues show a biphasic effect with decreased migration at high fractional contents. Combinations of residues show that different sequence contributions to the apparent molecular weight are not additive. The results can be rationalized by the protein-decorated micelle model by considering both SDS binding and the compaction of protein SDS-complexes.

biophysics↗

bioRxiv2026

Nanoneedle-Enabled Quantification of rAAV9 Capsid and Genome Integrity Reveals a Truncation Hotspot Locus in a 4.5 kb Transgene

BackgroundAdeno-associated virus (AAV) vectors are foundational to gene therapy but remain difficult to manufacture at high quality. Vector preparations frequently contain empty capsids and truncated genomes, diminishing potency and increasing immunogenic and production burdens. Conventional assays such as qPCR and ddPCR quantify only short regions, overestimating functional genomes and failing to resolve truncation patterns. MethodsWe applied the NanoMosaic Tessie nanoneedle platform to quantify AAV9 capsid and genome titers, directly distinguishing full-length (>4 kb) and truncated genomes. A 4.5 kb CAG- Luciferase-WPRE-bGH transgene packaged in AAV9 was analyzed using (i) nanoneedle "Probe Walk" assays to map truncations, (ii) PacBio SMRT long-read sequencing for orthogonal validation, and (iii) sedimentation velocity analytical ultracentrifugation (SV-AUC) to assess particle heterogeneity. ResultsProbe-walk mapping revealed asymmetric packaging with a [~]570 bp truncation hotspot 0.44-1.01 kb from the left inverted terminal repeat (ITR). PacBio sequencing confirmed positional concordance, identifying left partial reads clustering within the same region. SV-AUC resolved four major populations--empty (1.8%), partial (4.6%), full-length (70.4%), and high-molecular-weight (HMW) species (18.5%)--suggesting dimeric or multimeric capsids co-sedimenting with full-genome particles. Discussion and ConclusionsThe nanoneedle platform provided quantitative, region-specific insights into genome integrity that aligned with sequencing data while requiring minimal sample and processing time. The disproportion between molecular and AUC estimates indicates that apparent "full" species may contain long partial genomes or multimeric capsids bearing partial genomes. Together, these results establish the NanoMosaic Tessie system as a critical quality attribute (CQA) tool for assessing genome integrity and guiding process optimization. Integrating nanoneedle-based analytics early in development enables detection of truncation hotspots, improvement of vector fidelity, and acceleration of scalable, high-quality AAV manufacturing.

molecular biology↗

bioRxiv2026

Systemic hypoxia suppresses solid tumor growth

Local hypoxia is a hallmark of solid tumors and a negative prognostic factor in the progression and treatment of cancer. Here, we showed that systemic hypoxia, in contrast to localized tumor hypoxia, decreases tumor growth in vivo across multiple cancer types and preclinical models. The reduced tumor growth in systemic hypoxia was not explained by hypoglycemia, hypoinsulinemia, or HIF activation. Instead, metabolite profiling in tumors and tumor interstitial fluid revealed extensive perturbations in purine-related metabolites. Stable isotope tracing demonstrated that systemic hypoxia caused tumors to suppress de novo purine synthesis. Furthermore, tumors did not develop resistance to systemic hypoxia therapy, and when used in combination with chemotherapy or immunotherapy, systemic hypoxia dramatically suppressed tumor growth. Finally, we showed that systemic hypoxia can be achieved pharmacologically with the small molecule HypoxyStat. These findings challenge the long-held paradigm of hypoxia as a negative prognostic factor in cancer progression, and they suggest a potential therapeutic role for systemic hypoxia in suppressing solid tumor growth.

cancer biology↗

bioRxiv2026

Slow diffusion limits phosphorylation in a biomolecular condensate

Biomolecular condensates form dynamic compartments that regulate biochemical reactions in cells. Condensates recruit many kinases and regulate their enzymatic activity. Condensates alter the rate of enzymatic reactions through several opposing effects, so it is unclear whether these mostly enhance or retard phosphorylation. Here, we use a synthetic condensate formed by intrinsically disordered proteins to show that slow diffusion in the condensate controls phosphorylation kinetics in the dense phase. We vary the length of substrates by appending phase-separating repeat proteins of different lengths, in order to study how phosphorylation depends on partitioning, diffusion and volume fraction across substrate motifs with different intrinsic kinetics. The condensate environment is generally inhibitory to phosphorylation, although the enzyme remains intact. This inhibition is partially offset by an enhanced reaction rate in the dilute phase, likely due to soluble nanoclusters. Phosphorylation rates are strongly correlated to diffusion coefficients of substrates in the condensate, suggesting mass-transport limitation. Our results suggest that condensates can modify the substrate usage of a kinase via different trade-offs between diffusion and partitioning. We suggest that diffusion limitations are likely a common feature of many macromolecular reactions in condensates, and that high fluidity is crucial for condensates to act as reaction crucibles.

biophysics↗

bioRxiv2025

Coevolutionary constraints of Zika virus nonstructural protein 5 replication and interferon antagonism activities

The flavivirus nonstructural protein 5 performs multiple functions during infection, including RNA replication and type I interferon signaling antagonism. Although flavivirus NS5 proteins inhibit IFN signaling through distinct mechanisms, which suggests evolutionary flexibility, the evolutionary constraints for these activities to coexist within a single protein remain to be determined. Here, we mapped the Zika virus NS5 STAT2 antagonism determinants and compared them with replication constraints defined by deep mutational scanning. Antagonism and replication determinant extensively overlapped, and no single amino acid substitution eliminated antagonism without impairing replication. Resolving these fitness landscapes in parallel identified specific combinations of partially functional substitutions that retained replication capacity while markedly reducing antagonism. These viruses were profoundly attenuated in human STAT2 knock-in mice. Our results uncover a fundamental evolutionary constraint linking replication and immune evasion activities in NS5, highlight that STAT2 antagonism is essential for ZIKV pathogenesis and provide new avenues for attenuated ZIKV vaccines.

microbiology↗

bioRxiv2025

Construction of a CMV promoter-driven Langat virus cDNA clone and reporter viruses

Langat virus (LGTV) is a tick-borne member of the Flaviviridae family and a biosafety level 2 surrogate for studying tick-borne encephalitis virus (TBEV) replication and pathogenesis. Here, we report the construction of a plasmid encoding a cytomegalovirus (CMV) promoter-driven LGTV cDNA that initiates infection following direct transfection of mammalian cells. Incorporation of three introns eliminated viral cDNA-associated toxicity in bacteria, enabling stable propagation of the full-length plasmid. Transfection of this construct resulted in high-level production of infectious LGTV, which exhibited robust replication kinetics, though slightly slower growth compared to a patient-derived isolate. We further engineered mCherry and Gaussia luciferase reporter versions of the clone, which yielded viruses expressing high levels of their respective reporters while retaining efficient replication. These LGTV infectious clones provide versatile tools for investigating viral replication, gene function, and pathogenesis, and may facilitate screening for antiviral inhibitors. HighlightsO_LISingle-plasmid CMV-driven system launches infectious Langat virus (LGTV) C_LIO_LIThree introns stabilize full-length LGTV cDNA in E. coli C_LIO_LIDNA transfection yields high-titer infectious virus in mammalian cells C_LIO_LIReporter LGTVs enable fluorescent and luminescent infection readouts C_LIO_LIProvides a versatile platform for LGTV genetics and pathogenesis studies C_LI

microbiology↗

bioRxiv2025

NOVEL SMALL-MOLECULE INHIBITORS OF THE PROTEIN KINASE DYRK: POTENTIAL THERAPEUTIC CANDIDATES IN CANCER

Dual-specificity tyrosine-regulated kinase 1A (DYRK1A) is crucial for normal brain development and its disruption has been linked to various cancers. DYRK1A drives glioblastoma (GBM) progression via stabilization of epidermal growth factor receptor (EGFR). Here we describe two, selective, benzothiazole-derived DYRK inhibitors, FC-2 and FC-3, obtained by structure-activity optimization of a natural product lead. Both compounds inhibit DYRK1A with nanomolar potency and display high selectivity across a kinase panel. The co-crystal structure of FC-3 with DYRK1A revealed ATP-competitive binding, with interactions at the hinge region and the DYRK-specific phenylalanine gatekeeper residue explaining target selectivity. Generation of inhibitor-resistant mutants confirmed DYRK1A as the primary cellular target. In GBM cell-models, FC-2 and FC-3 impaired neurosphere self-renewal, cell invasion, and EGFR stability, phenocopying DYRK1A loss. Both compounds crossed the blood-brain barrier and suppressed tumor growth, to prolong survival in intracranial xenografts. These findings identify FC-2 and FC-3 as selective small-molecule inhibitors of DYRK1A with potential therapeutic utility in GBM.

cancer biology↗

bioRxiv2025

Identification and Validation of an inhibitor of the protein kinases PIM and DYRK

Fermented wheat germ extract (FWGE), a nutraceutical with reported anticancer properties, contains numerous biologically active molecules, but its precise therapeutic constituents remain unclear. In this study, we identify and characterize a novel small-molecule inhibitor, CSH-4044, isolated from FWGE. Through preparative HPLC and structural elucidation via X-ray crystallography, CSH-4044 was revealed to be a unique benzothiazole compound. Kinase profiling demonstrated its high specificity toward the PIM and DYRK families of protein kinases. We determined the co-crystal structure of CSH-4044 bound to PIM1, revealing ATP-competitive binding, and critical hydrophobic and hydrogen-bonding interactions. A chemically synthesized version of CSH-4044 mirrored the activity of the natural product, confirming structural integrity and biological equivalence. Functionally, CSH-4044 suppressed PIM3-driven BAD phosphorylation in pancreatic cancer cells and reduced DYRK1A-mediated Tau phosphorylation in neuronal cells. Our findings position CSH-4044 as a promising lead for targeting PIM and DYRK families of kinases and highlight FWGE as a source of potential therapeutic compounds.

biochemistry↗

bioRxiv2025

Integrins pattern the Drosophila embryonic neuroepithelium by influencing progenitor morphodynamics, division and position

Gene regulatory networks that confer cell fate and intracellular force generation mechanisms that drive cellular morphodynamics guide the patterning of tissues, but the nature of their interplay is poorly understood. We explore this during Drosophila embryonic neurogenesis whose first step, the delamination of a neuroblast from the surface epithelium, resembles an epithelial to mesenchymal transition (EMT). Using real-time, 3D confocal microscopy combined with quantitative morphometry, we identify robust morphometric state transitions that culminate in the basal delamination of the neuroblast (NB) from an equipotent epidermal proneural cluster, and find that mitotic rounding occurs concomitantly with delamination. We uncover marked heterogeneity and reduced collectivity in the morphodynamics of the NB and its nearest neighbours, and suggest their origins in the morphogenetic activity in the extending germband. We show that the appearance and distribution of the NB and GMC fate determinants Deadpan/dpn and Prospero/pros respectively correlate temporally with distinct morphometric states. We identify changes in cell-cell and cell-substrate adhesion that accompany neuroblast delamination and division and show that the adhesive microenvironment provided by integrin-ECM interactions patterns the neuroepithelium by influencing the spatiotemporal control of cell shape, division and position.

cell biology↗

bioRxiv2025

Structural and mechanistic insights into Dis3L2 mediated degradation of structured RNA

The RNase II/RNB family of exoribonucleases is present in all domains of life and includes three main eukaryotic members, the Dis3-like proteins (Dis3, Dis3L1, Dis3L2). At the cellular level, Dis3L2 is distinguished by the unique preference for uridylated RNA substrates and the highest efficiency in degrading double-stranded RNA. Defects in these enzymes have been linked to some types of cancers and overgrowth disorders in humans. In this work, we used the Dis3L2 protein from the model organism Schizosaccharomyces pombe (SpDis3L2) to better understand the mechanism of action of Dis3-like exoribonucleases, and to elucidate how single amino acid substitutions in these proteins can affect the biochemical properties of the enzymes, potentially contributing to the molecular basis of the related human diseases. We determined the crystal structure of SpDis3L2 bound to a U13 RNA, in which the protein displays a typical vase-like conformation, accommodating 6 nucleotides of the RNA 3-end. Furthermore, we constructed two SpDis3L2 protein variants, harbouring single amino acid substitutions mimicking the ones already found in human patients, to test their catalytic activity in vitro. We highlight the A756R SpDis3L2 variant, which loses the ability to degrade double-stranded RNA substrates and accumulates intermediary degradation products when degrading single-stranded RNA substrates. As such, A756 seems to be a key residue responsible for the normal cellular function of Dis3L2, specifically regarding its important role in the degradation of structured RNA substrates.

biochemistry↗

bioRxiv2025

circEPSTI1 Enables Dengue Innate Immune Evasion by Sponging miR-942-5p, a Repressor of AKT1 and the Viral Genome

Circular RNAs (circRNAs) have recently been identified as crucial regulators of gene expression in various diseases. Their role in dengue remains unexplored. In this study, circEPSTI1 induction was observed in peripheral blood mononuclear cells (PBMCs) and plasma of dengue patients. The induction of circEPSTI1 is interferon-dependent and enhances DENV infection by sponging the expression of miR-942-5p. The antiviral role of miR-942-5p is mediated by bidirectional inhibition through targeting conserved genomic sequences of the DENV genome of different subtypes across NS1, NS3, and NS5 and the host AKT1 signaling pathway. RNA-seq analysis of DENV-infected circEPSTI1 knockdown A549 cells identified SERPINE1 and AKT1 signaling pathways to be dysregulated significantly. circEPSTI1 relieves the inhibition of miR-942-5p over DENV genomic RNA and the host SERPINE1 to activate AKT1 signaling. The activation of AKT1 signaling facilitates cell survival and enhances DENV replication. The expression of SERPINE1 and circEPSTI1 was upregulated in Dengue patients, and pharmaceutical inhibition of SERPINE1 through Tiplaxtinin inhibits the DENV replication by reducing the expression of circEPSTI1. Overall, our result demonstrates the therapeutic potential of Tiplaxtinin by targeting the circ-EPSTI1-miR-942-5p-SERPINE1-AKT axis in dengue treatment.

immunology↗