Biology subjects

Banerjee, S.

Publications and source records attributed to Banerjee, S..

At least 73 records · Page 4Linked to original sources

bioRxiv2025

Copy number variations in mitochondrial DNA has a potent role in parasitic immunity against Haemonchus contortus-A novel report

Mitochondria is a cellular organelle responsible for a variety of function, apart from energy production through oxidative phosphorylation, TCA cycle, apoptosis, plays a major role in iron and calcium metabolism and immune functions against pathogens (bacterial, viral or parasitic). Unlike nucleus, mitochondria exist in multiple copies, with many copies of mitochondrial DNA. A metabolically active cell possess about 103 and 104 copies of the mitochondrial genome. Lowered mtDNA copy number leads to disorders or disease, in a similar way as mutation in mtDNA causes a wide range of disease or disorders. In this current article, we estimated mtDNA copy number through QPCR analysis of cytochrome B gene and revealed that healthy individuals have better mtDNA copy number compared to that of the infected ones under natural challenge in sheep model against the parasite Haemonchus contortus infection. We diagnosed the infected animals for H. contortus primarily with symptoms, followed by Faecal egg count and final confirmation through molecular diagnosis. We had characterized the cytochrome B gene from abomasum(stomach) of sheep, which is the site of predilection of this parasite. In our lab, earlier we have documented certain immune response nuclear genes to have antiparasitic role. We had reported the mutations in cytochrome B leading to debility and disease in sheep. Quantitative expression profile for cytochrome B is an indication of the copy number of mitochondrial genes and we observed significantly better expression profile of cytochrome B in healthy sheep in comparison to infected one. Thus, mitochondrial copy number is directly associated with antiparasitic immunity, first time reported.

genomics↗

bioRxiv2025

Development of an EMT-related exosomal miRNA signature that can predict prognosis in hepatocellular carcinoma

Chemoresistance and epithelial-mesenchymal transition (EMT) are associated with failure of cancer chemotherapy and poor survival of patients. We have previously shown that chemoresistance and stemness in hepatocellular carcinoma (HCC) cells was accompanied by the development of partial EMT (p-EMT) and identified a number of EMT-associated proteins that are released from exosomes. In this study, we aimed to identify and classify the differentially expressed (DE) exosomal miRNAs from chemoresistant HuH7 cells undergoing p-EMT. Out of the fifty-four miRNAs that were enriched in the exosomes from these cells compared to controls, thirteen were identified in the exosomes isolated from the serum of HCC patients. These miRNAs targeted genes that were associated with cell-cell junctions, extracellular matrix, cytoskeleton, transcription and signal transduction. Univariate Cox regression analysis indicated that 11/13 miRNAs were associated with either favorable (n=4) or worse (n=7) prognosis. A machine learning algorithm indicated that seven miRNAs (miR 215-5p, miR 340-5p, miR 210-3p, miR 19a-3p, miR19b-3p, miR 1266-5p and miR 25-3p) could predict worse prognosis in multiple datasets with 64-68% accuracy. A Bayesian Inference network analysis with the thirteen miRNAs and their key target proteins, along with EMT and survival as the nodes indicated that the common denominator was transcription, suggesting that the exosomal miRNAs released from cells undergoing p-EMT can mediate phenotypic changes in cells through transcriptional regulation.

cancer biology↗

bioRxiv2025

Evidence for hierarchical representations of written and spoken words from an open-science human neuroimaging dataset

Reading and speech recognition rely on multi-level processing that builds from basic visual or sound features to complete word representations, yet details of these processing hierarchies (in particular those for spoken words) are still poorly understood. We re-analyzed the functional magnetic resonance imaging (fMRI) data provided in the Mother Of all Unification Studies (MOUS) open-science dataset by using parametric regressions of word frequency and sublexical unit (bigram or syllable) frequency during reading and speech listening tasks in order to elucidate lexical processing hierarchies in the visual and auditory modalities. We first validated our approach in the written word domain, where the technique identified significant correlations for word frequency in the left mid-fusiform cortex (at the location of the Visual Word Form Area) with a left occipital region tracking bigram frequency, compatible with prior reports. During listening, low-frequency spoken words elicited greater responses in a left mid-superior temporal region consistent with the recently-described Auditory Word Form Area (AWFA), while a more posterior region of the superior temporal gyrus was sensitive to syllable frequency. Activation in the left inferior frontal gyrus correlated with both written and spoken word frequency. These findings demonstrate parallel hierarchical organizations in the anteroventral visual and auditory streams, with modality-specific lexica and upstream sublexical representations that converge in higher-order language areas.

neuroscience↗

bioRxiv2025

Nanoscale Structural and Functional Impacts of Disease-Associated Collagen Mutations

Collagen is the most abundant structural protein in the human body, and its supramolecular organization is central to tissue mechanics and cell-matrix interactions. Integrins, key mediators of these interactions, are essential for important biological processes including adhesion, migration, differentiation, and platelet aggregation. While mutations in collagen are known to cause connective tissue disorders such as Osteogenesis Imperfecta (OI) with phenotypes ranging from mild to perinatal lethal, how these mutations alter fibril level architecture, dynamics, integrin-mediated interactions and their functional consequences at both the protein and cellular level remains poorly understood. Here, we investigated the impact of OI mutations on direct collagen-integrin interactions and on cellular responses to mutant collagen. We generated collagen-rich extra-cellular matrix (ECM) from primary dermal fibroblasts of a healthy donor (WT) and from two OI patients carrying distinct glycine mutations: G610C, associated with moderate disease, and G907D, linked to perinatal lethality. Comparative biophysical studies reveal that both mutants retain the canonical D-banding of collagen I fibrils but differ markedly at the nanoscale. G907D fibrils exhibit greater local structural perturbations and increased molecular mobility relative to the non-lethal G610C. Importantly, while cell surface adhesion and proliferation do not differ between the OI mutants, integrin binding diverges between mutants: G610C displays reduced affinity, whereas G907D exhibits enhanced affinity compared to WT. Together, these findings establish a mechanistic link between single-residue mutations, nanoscale fibril architecture and collagen-receptor interactions, and highlight how genetic or acquired collagen defects can drive ECM dysregulation.

biophysics↗

bioRxiv2025

Copy number of the blaNDM-1 gene (New Delhi metallo-β-lactamase-1) and meropenem susceptibility in Enterobacterales: Consideration for treatment with meropenem?

Some Enterobacterales carrying blaNDM were still susceptible to meropenem, exhibiting meropenem minimum inhibitory concentration (MIC) values below the clinical breakpoint. As this phenomenon is a rare observation, this study investigated the underlying regulatory mechanisms contributing to the low MIC values and evaluated the efficacy of meropenem as a therapeutic preference for such isolates. Six clinical blaNDM-positive Enterobacterales exhibited meropenem MICs between 0.5-2.0 mg/L. Successful transmission of blaNDM into recipient E. coli J53 indicated its presence on plasmids. Conventional Sanger and whole-genome sequencing revealed that no truncation or deletion was observed within blaNDM or its core promoter region up to 120 bp upstream. Quantitative real-time PCR of blaNDM showed significantly lower expression levels of blaNDM, i.e., 0.2-0.5 in study isolates, compared to a clinical blaNDM-possessing isolate (expression=1) exhibiting a high meropenem MIC value (64 mg/L). Droplet digital PCR (ddPCR) further demonstrated that these isolates carried a lower copy number of the blaNDM gene, compared to the blaNDM-possessing isolate with high meropenem MIC (64 mg/L). Furthermore, the in vitro time-kill assay exhibited bactericidal efficacy of meropenem >3 log10 decrease in cfu/mL over the 24 hours from the starting inoculum. Administration of meropenem in in vivo neutropenic mice produced a 4-log cfu reduction compared to untreated controls at the start of dosing. Our data suggest that a reduction in blaNDM gene dosage, reflecting lower expression of blaNDM, correlates with lower meropenem MIC values. Meropenem is effective against these isolates when the meropenem MICs for the isolates are 0.5-2.0 mg/L. ImportanceThe production of NDM by Enterobacterales poses one of the most urgent global public health threats due to its plasmid-mediated spread, leading to treatment failure by exhibiting high MICs against a broad-spectrum of antibiotics. However, in rare instances, blaNDM-1-positive clinical Enterobacterales with unexpectedly low meropenem MICs (0.5-2.0 mg/L) raise a further question of reconsidering meropenem as a potential therapeutic option in these specific cases. This study identified that low MICs were associated with reduced expression and lower copy number of the plasmid-mediated blaNDM gene, despite intact promoter regions. Both in vitro and in vivo assays validated the bactericidal activity of meropenem against these isolates. The study raised an argument about the potential limitations of relying solely on genotypic detection of resistance genes for therapeutic decision-making, which emphasises the need for further investigation. As a safe medication, repurposing meropenem for neonatal treatment may eliminate the need for other toxic drugs.

microbiology↗

bioRxiv2025

Robust antibiotic sensitization of pathogenic Pseudomonas aeruginosa via negative hysteresis in the cell envelope

Antibiotic combination in time and space is a key strategy to combat antimicrobial resistance. The success of such treatment designs requires their robust efficacy across treatment conditions and a pathogens genomic diversity. This study found that an initial treatment with a {beta}-lactam antibiotic causes robust cellular sensitization towards an aminoglycoside antibiotic across the high-risk human pathogen Pseudomonas aeruginosa, including resistant strains. This phenomenon of cellular sensitization, termed negative hysteresis, is modulated by the Cpx envelope stress response system and linked to membrane stress during growth. The increase in efficacy is achieved through a {beta}-lactam induced elevated cellular uptake of the subsequently administered aminoglycoside. Negative hysteresis and the Cpx system are linked in several cases to the expression of synergistic drug interactions, thus enhancing efficacy of antibiotic combinations. Overall, our study identifies the phenomenon of negative hysteresis as a robustly inducible phenotype and thus a unique focus for optimizing antimicrobial therapy.

evolutionary biology↗

bioRxiv2025

Cell Geometry Limits Bacterial Metabolic Efficiency

Bacterial metabolic strategies are fundamentally linked to their physical form, yet a quantitative understanding of how cell size and shape constrain the efficiency of biomass production remains poorly understood. Here, we develop a coarse-grained whole-cell model of bacterial physiology that integrates proteome allocation, metabolic fluxes, and cell geometry with physical limits on cell surface area and intracellular diffusion. Our model shows that the efficiency of cellular growth is not monotonic with nutrient availability; instead, it peaks precisely at the onset of overflow metabolism, framing this metabolic switch as an optimal trade-off between efficient use of imported nutrients and rapid growth. By simulating perturbations to cell morphology, we demonstrate the strong metabolic advantage of a high surface-to-volume ratio, which consistently improves growth efficiency. Finally, we show how geometric limits on growth efficiency result in a hard physical constraint: the maximum sustainable cell size is inversely related to the growth rate. This is due to a fundamental conflict between the proteomic cost of growth speed and the cost of size, which creates a budget crisis in large, fast-growing cells. Our work shows how a few physical rules define the allowable strategies for bacterial metabolism and provides a mechanistic explanation for the observed limits on microbial cell size and growth.

systems biology↗

bioRxiv2025

Exposure to third generation cephalosporin induces L-form transition in Shigella sonnei, potentially acting as a bacterial reservoir for persistent infection

Shigellosis remains a major global health burden, and the increasing prevalence of multidrug-resistant (MDR) Shigella strains is complicating effective antibiotic therapy. Bacteria may survive antibiotics by transitioning into cell wall-deficient L-forms, which are intrinsically resistant to {beta}-lactams and can revert to a virulent state, potentially causing relapsing infections. Here we characterized a clinical MDR isolate Shigella sonnei HK8, a.k.a. PD552A, whose genome contains key resistance (gyrA, PBP3) and virulence (icsA) genes. Exposure to ceftriaxone induced a transition into a viable L-form state that was hyper-adhesive to macrophages in vitro. However, this survival adaptation was linked to a profound loss of pathogenicity. Using murine and guinea pig models, the L-form variant was shown to be profoundly attenuated, failing to cause the keratoconjunctivitis, diarrheal disease, or significant histopathology characteristic of the wild-type strain. These findings reveal a critical virulence-survival trade-off, positioning the L-form as a "stealth" phenotype that enables bacterial persistence at the expense of acute virulence. This offers a potential mechanism for asymptomatic carriage and recurrent infections, highlighting a previously underappreciated mechanism by which antibiotic treatment may resolve acute symptoms while permitting the persistence of a cryptic bacterial reservoir capable of driving recurrent infection. ImportanceOur research provides critical insight into the challenge of antibiotic treatment failure in shigellosis. By integrating experimental validation of reversible L-form transitions with mathematical modelling, we uncover a crucial virulence-survival trade-off. We show that MDR S. sonnei survives ceftriaxone by adopting a "stealth" phenotype, quantified by a high Stealth Index - maintaining bacterial burden while evading host inflammatory detection. These findings imply that standard antibiotics may resolve acute symptoms while inadvertently selecting for a cryptic, persistent reservoir poised for relapse. This work challenges the conventional view of therapeutic success and highlights an urgent need to develop novel diagnostic and therapeutic strategies capable of identifying and eliminating these resilient, "stealth" L-form persisters to achieve true bacterial clearance and prevent chronic infections.

microbiology↗

bioRxiv2025

Engineering Microbial R- and S- β-Hydroxybutyrate Production

Beta-hydroxybutyrate (BHOB) is a therapeutically valuable enantiomeric ketone body that is synthesized by both prokaryotes and eukaryotes. Bacterial synthesis of BHOB has so far mostly been exploited for the synthesis of biofuels and to a lesser extent for the pharmaceutical industry. In this study, we carefully evaluated the expression, induction, selection, and detection elements and identified multigene pathways to direct the synthesis of physiologically relevant amounts of BHOB. Utilizing the reversal of the beta-oxidation pathway that has previously been used for biofuel generation, we engineered E. coli strains with a prebiotic-activated circuit to secrete either (S)-BHOB or (R)-BHOB. Our findings demonstrate high-yield microbial BHOB production with a defined enantiomeric composition and highlight its therapeutic potential for cancer and gut-brain axis involving disorders. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=134 SRC="FIGDIR/small/664879v1_ufig1.gif" ALT="Figure 1"> View larger version (27K): org.highwire.dtl.DTLVardef@8bf92corg.highwire.dtl.DTLVardef@193f067org.highwire.dtl.DTLVardef@18c0e7dorg.highwire.dtl.DTLVardef@b6293_HPS_FORMAT_FIGEXP M_FIG C_FIG

synthetic biology↗

bioRxiv2025

Nuclear Receptor Transcription factors promote axon regeneration in the Adult Corticospinal Tract

Transcription factors are potent levers for neural repair, but which factors govern regenerative capacity in the corticospinal tract remains largely unknown. By intersecting developmental RNA-seq with ATAC-seq footprinting, we identified two nuclear-receptor transcription factors, NR2F1 and NR2F6, neither previously linked to CNS axon growth, whose chromatin occupancy at pro-growth enhancers is progressively lost as neurons mature. Forced expression of either factor significantly increased neurite outgrowth in single-neuron tracing assays, and each drove strong cross-midline sprouting after pyramidotomy and long-tract CST regeneration after complete thoracic crush, with concordant recovery of hip-rise kinematics and grip strength. Parallel multi-omic profiling (CUT&RUN, snRNA-seq and Ribo-seq) of both factors together with NR2F6 Hi-C revealed distinct mechanisms: NR2F1 reactivated chromatin-remodeling and cytoskeletal programs, whereas NR2F6, via a conserved corepressor domain, re-occupied developmental enhancers, reorganized three-dimensional chromatin architecture into new topologically associating domains, and imposed a transient translational down-shift in which growth-relevant modules were selectively preserved through translational buffering. Together, these data identify NR2F nuclear receptors as regulators of corticospinal regeneration, acting through enhancer redeployment, translational reprogramming and three-dimensional genome reorganization.

neuroscience↗

bioRxiv2025

Tumor-Educated-Platelets interact with Breast Cancer-Stem-Cells via P-selectin- PSGL1 and ensure stemness and metastasis through WNT-β-Catenin-VEGF-VEGFR2 intra-cellular signaling: Therapeutic modulation by aspirin

BackgroundProtagonistic role of platelets promote capillary infiltration of tumors for distant metastasis along with immunosurveillance. Despite existing reports highlighting role of platelets in tumorigenesis, its impact on breast cancer stem cells (BCSCs) remain underexplored. Our first ever report on murine and human system, accentuate that, tumor educated platelets (TEPs) of luminal A and TNBC subtypes are distinct from healthy counterparts, collaborating with BCSCs to generate sub-variants that elevate tumor aggressiveness. MethodsImpact of TEPs on BCSCs was evaluated from primary breast tumor and blood samples of luminal A/TNBC patients along with EC/4T1 murine breast tumor models and MCF-7/MDA-MB-231 cell lines. For downstream assays, TEPs were co-cultured with breast tumor samples or cell lines, followed by magnetic sorting of lin-CD44+CD24- BCSCs. TEP induced alterations of BCSCs were evaluated from 3D tumorsphere, colony formation, transwell migration, scratch-wound healing, matrigel invasion, in-vitro tube formation assays. Fluorescence-confocal microscopy, RT-PCR, flow-cytometry, western-blotting was utilized to decipher the role of genes and protein involved in stemness, metastasis along with the transcription factors in the downstream signaling cascade, followed by verifications by RNAi. ResultsTEPs have elevated expression of P-selectin and interacts with BCSCs via P-selectin and PSGL1 on BCSCs surface. Treatment with aspirin had restorative impact on P-selectin level, converting TEPs from active to resting platelet (RP) state. Under TEPs influence, BCSCs were tumorigenic, clonogenic, multidrug resistant, invasive with numerous invadopodia and remained skewed towards mesenchymal phenotype. Administration of RP reduced TEP associated BCSC virulence both in-vivo and in-vitro. P-selectin-PSGL1 interaction results in binding of WNT to FRIZZLED followed by stabilization and nuclear translocation of {beta}-Catenin. Nuclear {beta}-Catenin promotes stemness-EMT (Epithelial to mesenchymal transition)- metastasis, along with stimulation of autocrine VEGF-VEGFR2 cascade. Inhibition of WNT and VEGFR2 by RNAi confirmed the critical role of this axis in regulating TEPs influence on BCSCs. ConclusionThese insights into TEPs-BCSC interplay, acknowledges TEPs, as-well-as unveils novel receptor-ligand signaling cascade between TEPs and BCSCs, that could be a beneficial therapeutic strategy to target cancer metastasis. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/657784v1_ufig1.gif" ALT="Figure 1"> View larger version (50K): org.highwire.dtl.DTLVardef@11db5d0org.highwire.dtl.DTLVardef@18b7270org.highwire.dtl.DTLVardef@64c2borg.highwire.dtl.DTLVardef@172d68f_HPS_FORMAT_FIGEXP M_FIG C_FIG Cellular interaction between TEPs P-selectin and BCSCs PSGL1 to regulate stemness, EMT, metastasis and angiogenesis via WNT-{beta}-Catenin-VEGF-VEGFR2 cascade: Modulation by pharmacological inhibitor and RNAi.

cancer biology↗

bioRxiv2025

Estradiol alters actin and protrusion dynamics in endometriotic epithelial cells

Estradiol (E2), a sex steroid hormone molecule, plays a key role in regulating the actin and shape dynamics of cells in a multitude of normal and pathophysiological conditions. While cytoskeletal rearrangements, membrane dynamics, and cellular protrusions are intimately involved in cell motility and invasiveness, little is known about the impact of E2 on these processes in estrogen-dependent epithelial cells. In this study, we quantified the impact of E2 on cell shape and actin dynamics in 12Z human endometriotic epithelial cells transfected with LifeAct-GFP and observed with lattice lightsheet microscopy, a new imaging technique fast enough to capture 3D dynamics on second timescales. E2, when applied for 24 hours, significantly decreased cell circularity, solidity, and rate of change of circularity, indicating a transition to a more elongated and less variable morphology. 24-hour E2 treatment also induced the formation of large membrane protrusions reminiscent of invadopodia and led to a more disordered flow of actin within those protrusions. However, these effects were not seen after 15 minutes of E2 treatment, suggesting that longer-term signaling is required to drive these structural changes. Together, these results suggest that E2 modulates actin polymerization and membrane protrusion dynamics in endometriotic epithelial cells and may prime them for cell invasion. This work highlights a role for hormonal signaling in mediating cytoskeletal plasticity and migratory cell phenotypes.

biophysics↗

bioRxiv2025

PATZ1 Reinstates a Growth-Permissive Chromatin Landscape in Adult Corticospinal Neurons After Injury

BackgroundThe failure of axon regeneration in the adult central nervous system represents a major barrier to recovery from spinal cord injury and neurodegenerative disease. Pro-growth transcription factors can promote regenerative responses, but their effects remain partial, suggesting that additional restraints must be relieved for these factors to achieve their full potential. The chromatin landscape of adult neurons has emerged as a candidate mechanism, yet we lack a developmental map of when and how this epigenetic restriction occurs, whether injury can reverse it, and how to therapeutically target it. ResultsWe assembled a comprehensive chromatin accessibility atlas spanning mouse forebrain development from embryonic day 11 through adulthood using bulk and single-nucleus ATAC-seq. This revealed progressive restriction of growth-gene promoters and enhancers across postnatal development, leaving over 95% of growth-associated regulatory elements substantially inaccessible in mature neurons. We found that the distance between injury site and neuronal cell body determines the magnitude of chromatin reopening: intracortical lesions proximal to motor cortex soma triggered ten-fold greater enhancer reactivation compared to distal thoracic spinal cord crush. Motif analysis identified PATZ1, a chromatin-remodeling transcription factor, as correlated with this proximity effect. Viral delivery of PATZ1 to adult cortex converted the limited epigenomic response to distal injury into a profile approaching that of proximal injury, selectively reopening enhancers at growth-associated loci and depositing active H3K27ac marks. Hi-C analysis demonstrated that PATZ1 additionally reorganizes higher-order chromatin architecture, inducing compartment switching at growth loci and remodeling topologically associating domain boundaries. Integration with single-nucleus transcriptomics revealed that while PATZ1 selectively opens chromatin at growth genes, transcriptional output and axon regeneration remain modest, indicating that combinatorial approaches pairing epigenetic priming with pro-growth transcription factors may be required for functional repair. ConclusionsThis study provides a developmental timeline of chromatin closure at regeneration-associated genes and identifies PATZ1 as a molecular tool capable of reversing this epigenetic barrier in adult neurons. Our findings indicate that chromatin accessibility functions as a gatekeeping mechanism that must be addressed before transcription factor-based therapies can achieve their full effect, establishing epigenetic priming as a targetable component of CNS repair strategies.

neuroscience↗

bioRxiv2025

Skeletonization of neuronal processes using Discrete Morse techniques from computational topology

To understand biological intelligence we need to map neuronal networks in vertebrate brains. Mapping mesoscale neural circuitry is done using injections of tracers that label groups of neurons whose axons project to different brain regions. Since many neurons are labeled, it is difficult to follow individual axons. Previous approaches have instead quantified the regional projections using the total label intensity within a region. However, such a quantification is not biologically meaningful. We propose a new approach better connected to the underlying neurons by skeletonizing labeled axon fragments and then estimating a volumetric length density. Our approach uses a combination of deep nets and the Discrete Morse (DM) technique from computational topology. This technique takes into account nonlocal connectivity information and therefore provides noise-robustness. We demonstrate the utility and scalability of the approach on whole-brain tracer injected data. We also define and illustrate an information theoretic measure that quantifies the additional information obtained, compared to the skeletonized tracer injection fragments, when individual axon morphologies are available. Our approach is the first application of the DM technique to computational neuroanatomy. It can help bridge between single-axon skeletons and tracer injections, two important data types in mapping neural networks in vertebrates.

neuroscience↗

bioRxiv2025

ARID1A stabilises non-homologous end joining factors at DNA breaks induced by the G4 ligand pyridostatin

ARID1A is a subunit of the BAF chromatin remodelling complex that is frequently mutated in cancer. It is challenging to predict how ARID1A loss impacts cancer therapy response because it participates in many different cellular pathways. G quadruplex (G4) binding ligands, such as pyridostatin, have shown anticancer effects, but the pathways and genetic determinants involved in the response to G4 ligands are still not fully understood. Here, we show that ARID1A deficient cells are selectively sensitive to pyridostatin when compared with isogenic controls. Sensitivity to pyridostatin was apparent in ovarian and colorectal cancer cell line models, and in vivo studies suggest that G4 ligands hold promise for treating ARID1A deficient cancers. While we find that ARID1A impacts on pyridostatin-induced transcriptional responses, we find that pyridostatin-mediated toxicity in ARID1A-deficient cells is driven by defective DNA repair of topoisomerase-induced breaks. We show that ARID1A-deficient cells are unable to efficiently accumulate non-homologous end joining proteins on chromatin following pyridostatin exposure. These data uncover a role for ARID1A in the cellular response to G4 ligands, and link remodelling to G4 ligand-induced transcriptional and DNA damage responses.

molecular biology↗

bioRxiv2025

Insights into gallbladder cancer pathogenesis from a living organoid gallbladder cholangiocyte biorepository

Gallbladder cancer (GBC) while rare worldwide has a high prevalence in India. Pathogenesis is unclear and outcomes poor. Gallbladder cholangiocyte organoids (GCOs) or gallbladder carcinoma organoids (GBCOs) were developed and serially propagated from surgically resected gallbladder tissues with benign or malignant diseases, respectively. Patient derived organoids (PDOs) were derived from 15 normal; 58 inflamed; 12 xanthogranulomatous cholecystitis (XGC); 5 pre-invasive neoplasm and 13 invasive malignant gallbladder pathologies. Protocol optimisation achieved 58% (69/119) success in organoid generation and expansion. Organoids maintained tight junction integrity; P-gp pump and enzymatic activity; preserved tissue-specific gene and protein marker expression; histological features and genetic variations. Cryopreserved organoids from 62 patients with primary tissue and high-quality DNA, RNA and protein derivatives have been banked. In gene expression analyses of tissue, XGC samples clustered with malignant subtypes, separate from benign pathologies. Derived XGC organoids showed a similar clustering. Enriched hallmark pathways in XGC support neoplastic change through chronic inflammation. PDOs generated from different gallbladder pathologies are a promising model to investigate the pathogenesis of GBC. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/651639v1_ufig1.gif" ALT="Figure 1"> View larger version (69K): org.highwire.dtl.DTLVardef@465f3dorg.highwire.dtl.DTLVardef@16c5f0org.highwire.dtl.DTLVardef@11d4807org.highwire.dtl.DTLVardef@163d072_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Cell surface localisation of GPI-anchored receptors in Trypanosoma brucei

Trypanosoma brucei, the causal agent of Human and Animal African trypanosomiasis proliferates in the extracellular milieu of mammals. It acquires host macromolecular nutrients, by receptor mediated endocytosis. The best characterised cell surface receptor is for transferrin (TfR) and it has been reported to be preferentially localised in the flagellar pocket domain of the plasma membrane, the sole site of endocytosis. In this location the TfR may be inaccessible to adaptive immune system effectors. The T. brucei genome encodes [~]15 TfR variants, and here we compared two, the first attached to the plasma membrane by a single glycosylphosphatidylinositol (GPI)-anchor and the other by two. Transferrin uptake kinetics were similar and rapid for both. Unexpectedly, initial binding of transferrin occurred over the whole cell surface suggesting the TfR was not localised solely in the flagellar pocket. This localisation was confirmed by immunofluorescence assays and was independent of the number of GPI-anchors. Two other GPI-anchored receptors were investigated to determine whether localisation to the whole cell surface was a general property of GPI-anchored receptors. Haptoglobin-haemoglobin uptake assays and immunofluorescence localisation of complement factor H receptor showed both were also whole cell surface localised. The mechanisms by which trypanosome receptors are protected from antibody-mediated attack are more complex than hiding in a pocket.

microbiology↗

bioRxiv2025

3D multimodal histological atlas and coordinate framework for the mouse brain and head

Brain reference atlases are essential for neuroscience experiments and data integration. However, histological atlases of the mouse brain, crucial in biomedical research, have not kept pace. Autofluorescence-based volumetric brain atlases are increasingly used but lack microscopic histological contrast, cytoarchitectonic information, corresponding MRI datasets, and often have truncated brainstems. Here, we present a multimodal, multiscale atlas of the laboratory mouse brain and head. The new reference brains include the whole head with consecutive Nissl and myelin serial section histology in three planes of section with 0.46 {micro}m in-plane resolution, including intact brainstem, cranial nerves, and associated sensors and musculature. We provide reassembled histological volumes with 20mu isotropic resolution in stereotactic coordinates, determined using co-registered in vivo MRI and CT. In addition to conventional MRI contrasts, we provide diffusion MRI-based in vivo and ex vivo microstructural information, adding a valuable co-registered contrast modality that bridges MRI with cell-resolution histological data. We shift emphasis from compartmental annotations to stereotactic coordinates in the reference brains, offering a basis for evolving annotations over time and resolving conflicting neuroanatomical judgments by different experts. This new reference atlas facilitates integration of molecular cell type data and regional connectivity, serves as a model for similar atlases in other species, and sets a precedent for preserving extra-cranial nervous system structures.

neuroscience↗