Biology subjects

Das, D.

Publications and source records attributed to Das, D..

At least 19 recordsLinked to original sources

bioRxiv2026

Deciphering the dynamical origin of the Adipogenic commitment during stress-induced disruption of the circadian rhythm

Obesity is a major health concern worldwide and is caused by an excessive fat accumulation in the body due to adipogenesis. Recent studies suggest that excessive stress or disruption of circadian rhythms can enhance adipogenic commitment and lead to obesity. Moreover, this adipogenic commitment occurs at a specific time of day, highlighting a correlation with the circadian rhythm. However, the dynamical nature of this kind of stress-induced adipogenic differentiation remains an unresolved puzzle. Herein, we proposed a mathematical model centred on the key transcription factor PPAR{gamma}, associated with adipogenic differentiation, and demonstrated that adipogenic commitment is a bistable, irreversible differentiation process in which slow positive feedback regulation of PPAR{gamma} primarily controls the differentiation commitment threshold. The model reproduced the experimental observations regarding the extent of adipogenesis induced by constant and pulsatile stress input signals and explained the correlation between adipogenic differentiation time and circadian phase. It further predicts how to control the adipogenic commitment even under stressful conditions. Overall, our study elucidates how stress signalling dynamically governs adipogenesis.

systems biology↗

bioRxiv2026

HeartVar: An LLM-Assisted Tool for Clinical Classification of Variants in Cardiovascular Disease Cohorts

Manual clinical DNA variant classification is the bottleneck of every clinical and research rare disease workflow. The process typically requires a curator to assemble evidence from numerous databases, weigh 28 criteria, reconcile competing evidence, and produce a defensible case for the final classification. Additionally, the framework used to assess variants is not static and successive addenda have revised individual criteria. The most complete and current evidence aggregators available are commercial platforms, which can limit researcher access. We present HeartVar, an open-source web tool that automates the evidence-gathering and interpretation steps of variant classification associated with cardiovascular disease. Given a gene, a variant, and clinical context, HeartVar queries 20 public databases in parallel and assigns ACMG/AMP criteria through a hybrid rule-based/large language model (LLM) approach. Criteria that can be resolved from structured data are computed programmatically, and only those requiring interpretation of unstructured evidence are passed to the LLM. HeartVar returns a classification, point score, per-criterion breakdown, clinical-narrative summary, and database annotations. Benchmarking of 106 expert-curated ClinGen variants showed HeartVar outperformed other curation tools, assigning the correct ACMG tier in 72% of cases. HeartVar demonstrates that an LLM constrained by a domain-specific prompt and grounded in structured evidence can produce variant interpretations of first-pass quality for a cardiovascular disease cohort; however, it is not intended to replace manual assessment by a qualified variant curator. The tool is freely available to use and hosted at www.heartvar.victorchang.edu.au.

bioinformatics↗

bioRxiv2026

A Microneurosurgical Survival Platform for Elucidating Mechanisms of Brain Tumor Recurrence and Metastasis

Brain tumor recurrence remains the leading cause of mortality in neuro-oncology, and there is a lack of preclinical models replicating the clinical cycle of surgical resection and relapse. To bridge this gap, we developed a novel microneurosurgical survival platform in mice using the NICO Myriad system. We orthotopically implanted pediatric medulloblastoma cells into the mouse cerebral cortex or cerebellum, followed by longitudinal microneurosurgical resection. Bioluminescence imaging and gross fluorescence verified successful resection, local and distal recurrence and metastasis. Comparative bulk RNA sequencing revealed extensive stage-specific transcriptomic divergence alongside conserved core gene sets (2,702 genes in the cerebral cortex and 3,240 genes in the cerebellum) across primary, locally recurrent, and distally recurrent stages. Pathway analysis shows activation of cellular growth, second messenger signaling, and cellular stress adaptation pathways. Targeted qPCR validation demonstrated that post-surgical relapse is driven by a distinct molecular program: recurrent tumors downregulate primary developmental drivers (PTCH1, MYCBP2), canonical suppressors (FOS, PTEN), and chromatin regulators (HDAC2), while selectively upregulating post-transcriptional machinery (RBM8A), endosomal trafficking regulators (RAB5C), acetyltransferases (NAA15), and the m6A RNA demethylase ALKBH5. These findings reveal that medulloblastoma shifts from a primary oncogenic state toward post-transcriptional and transcriptomic survival mechanisms following surgery. Identifying persistent candidates within this conserved core framework provides a roadmap for next-generation precision immunotherapies.

cancer biology↗

bioRxiv2026

Distributions of threshold crossing times of messenger RNA

Within the studies of stochastic gene expression, apart from the variability of copy number of gene products, the problems of threshold crossing of those products are biologically important as they often lead to terminal cellular events. Here, we study the threshold crossing problem of the messenger ribonucleic acid (mRNA) and present an exact probability distribution of first passage times in Laplace space. The function furnishes moments of any order and also predicts the characteristic time of the exponential tail of the distribution, which we match against Gillespie simulations. We find that all the measures of relative fluctuations of the threshold crossing times show U-shapes within this simple model of mRNA, as was found earlier in more mathematically involved models of threshold crossing time statistics of proteins. Furthermore, we extend the exact formula to include the phenomenon of DNA duplication and the corresponding doubling of transcription rate. As expected, the distribution varies considerably depending on the onset of the duplication stage within the cell cycle.

biophysics↗

bioRxiv2026

Differential Impact of Isoflurane and Propofol on Apoptotic Regulation of Helper T cells

BackgroundAnesthetic agents administered during surgery are one of the key perioperative factors affecting immune modulation in cancer patients. This comparative study elucidated the mechanisms by which the volatile anesthetic, isoflurane and the intravenous anesthetic, propofol impacted apoptosis signaling in CD4+ helper T (Th) cells. MethodsFlow cytometry was used to analyze apoptosis, mitochondrial function and reactive oxygen species (ROS) generation, while Western blotting, ELISA and RT-qPCR were employed to study protein/gene expression in sorted CD4{square} Th cells from perioperative breast cancer female patients (anesthetized with isoflurane or propofol, n=15 per group) and Jurkat T cells. ResultsPatient-derived CD4{square} Th cells and Jurkat T cells exhibited that isoflurane at clinically relevant concentrations triggered apoptosis through mitochondrial depolarization, ROS generation, DNA damage, and activation of caspase-3/7. Specific use of caspase-3/7 inhibitor, Z-DEVD-FMK and antioxidant N-acetyl cysteine rescued isoflurane-induced apoptosis. Further, isoflurane relative to propofol, activated p38 mitogen-activated protein kinase (MAPK), and use of p38 inhibitor, SB203580 suppressed isoflurane-induced apoptosis. Collectively, these findings validated the involvement of the ROS-p38-caspase-3/7 axis in isoflurane-associated apoptosis signaling. On the other hand, propofol conserved mitochondrial integrity, reduced oxidative stress, and maintained higher proliferative capacity. Interestingly, isoflurane-associated apoptosis was transient, with postoperative recovery in patients and similar rescue from apoptosis was evident in Jurkat T cells within 24-48 h of drug removal. ConclusionsBy integrating analyses of patient-derived CD4+ Th cells with mechanistic validations in Jurkat T cells, this study identified the ROS-p38-caspase-3/7 signaling axis and the reversible nature of isoflurane-induced apoptosis.

cancer biology↗

bioRxiv2026

Target-Specific Discovery of BMM_1567 Restores Aminoglycoside Activity Against Multidrug-Resistant Gram-Negative ESKAPE Pathogens

The global emergence of multidrug-resistant (MDR) ESKAPE pathogens has significantly reduced the effectiveness of existing antibiotics, highlighting the urgent need for new strategies to restore antimicrobial susceptibility. Here, we report the discovery and mechanism of BMM_1567, a peptide potentiator that enhances aminoglycoside efficacy against MDR pathogens. A genetically defined reporter-based screen identified BMM_1567 as a potent inhibitor of aminoglycoside resistance, potentiating spectinomycin activity against MDR Gram-negative ESKAPE isolates at low micromolar concentrations. Structural modeling and molecular dynamics simulations indicated that BMM_1567 interacts with residues lining the antibiotic-binding groove of aminoglycoside-modifying enzymes (ANT, APH, AAC), with highest affinity for ANT ({Delta}G_bind = -62.25 kcal/mol), suggesting competitive inhibition of substrate binding. Site-directed mutagenesis of key ANT residues identified critical amino acids involved in BMM_1567 binding, confirming their role in mediating spectinomycin potentiation. In murine abscess model using XDR E. coli, BMM_1567 in combination with spectinomycin significantly reduced bacterial burden and pro-inflammatory cytokine levels, comparable to colistin. Collectively, these findings establish BMM_1567 as a promising aminoglycoside potentiator that restores antibiotic activity against MDR pathogens through direct inhibition of resistance enzymes, while exhibiting in vivo efficacy and a remarkably low propensity for resistance development.

microbiology↗

bioRxiv2026

Learning the spatial cell-cell communication network to decode multi-channel signaling and predict network-hub vulnerabilities with MOSANIC

Intercellular signaling governs the central decisions of tissue biology, from proliferation and immune recruitment to metabolic adaptation and cell death, and its dysregulation is a hallmark of disease. What matters most are properties of the signaling network as a whole rather than of individual interactions: the hubs that hold the network together and mark rational points of intervention, the relays through which a signal propagates across intermediate cells to reach partners it does not directly contact, the response of tissue-wide communication to the loss of a single node, and the metabolite-mediated axis that operates alongside secreted-protein signalling. Scoring known ligand-receptor pairs yields a ranked interaction list that captures none of these and excludes metabolite signalling. We present MOSANIC (Multi-mOdal Self-Attention Network for Intercellular Communication), which learns a tissues communication network directly from spatial transcriptomics. MOSANIC represents each tissue as a single heterogeneous graph of cells, genes and metabolites, initialises every node with a frozen foundation-model representation (scVI, ESM-2 and ChemBERTa), and propagates these representations through a self-attention network over biologically typed edges. Supervision is restricted to spatial gene-expression prediction and excludes ligand-receptor annotation, rendering the inferred communication statistically independent of the reference databases used for evaluation. Across five spatial datasets spanning three platforms and two species, MOSANIC attains the highest accuracy on all eight independent ligand-receptor benchmarks (mean AUROC 0.756) against nine established methods, resolves a metabolite-receptor channel statistically orthogonal to the peptide channel, and reconstructs multi-step signal relays that concentrate within a compact rich-core of load-bearing hub genes and cells whose removal fragments the network far beyond a degree-preserving null. In-silico knockout of these hubs recovers experimentally reported phenotypes, and, given no prior oncological input, MOSANIC nominates SCARF1 as a previously unrecognised communication hub in breast cancer whose elevated expression predicts significantly worse survival in an independent cohort after adjustment for tumour stage and age (hazard ratio 1.17, P = 0.043). MOSANIC is released as an open-source Python package (mosanic-ccc).

bioinformatics↗

bioRxiv2026

Spatially confined niches support hypoxia-associated transcriptional plasticity contributing to malignant progression in IDH-mutant gliomas

BackgroundWhile hypoxia is a well-established driver of glioblastoma progression, its role in IDH-mutant gliomas, characterized by localized hypoxic microenvironments rather than overt necrosis, remains poorly understood. Here, we investigate how hypoxia and microenvironmental-adaptations shape cellular heterogeneity and transcriptional plasticity in these tumors. MethodsWe integrated bulk, single-cell, and spatial-transcriptomics datasets from IDH-mutant glioma patients (Astrocytomas and Oligodendrogliomas) to characterize cellular-states and map the localization of hypoxic niches. To uncover tumor microenvironment effects, we established co-culture models using primary IDH-mutant glioma cells with human microglia and astrocytes, maintained under hypoxic and normoxic conditions, followed by bulk RNA-sequencing. ResultsWe identified a hypoxia-associated astrocyte-like (AC-like) program that defines a quiescent, non-cycling population with a distinct transcription factor profile indicative of functional plasticity in IDH-mutant gliomas. These cells harbor glioma stem cell (GSC)-like features and are poised for a quiescent-to-activated (Q-to-A) transition that drives tumor progression. Mechanistically, co-culture models reveal that microglia promote this Q-to-A transition by enhancing HBEGF/EGFR paracrine signaling. Spatial transcriptomics uncovers the co-localization of hypoxic niches within quiescent AC-like cells, whereby the activated subpopulation forms discrete niches defined by localized HBEGF/EGFR communication gradients. Notably, tumors exhibiting elevated EGFR-driven activation signatures correlate with higher histological grade and poorer patient survival, implicating the Q-to-A transition as a critical driver of malignant progression. ConclusionQ-to-A transition within the hypoxic niche represents a critical driver of malignant progression in IDH-mutant gliomas, providing a microenvironment-driven mechanism for the transition to higher-grade disease and identifying targetable-vulnerabilities for therapeutic intervention. Key pointsO_LIHypoxic niches spatially confine quiescent, astrocyte-like cellular state characterized by glioma stem cell features in IDH-mutant gliomas. C_LIO_LIMicroglia triggers the quiescent-to-activated (Q-to-A) transition via paracrine EGFR signaling crosstalk. C_LIO_LIEGFR-driven Q-to-A plasticity serves as a microenvironmentally-regulated driver of malignant progression and adverse patient survival. C_LI Importance of the studyWhile high-grade glioblastomas feature well-defined hypoxic and necrotic regions that drive tumor progression and therapy resistance, IDH-mutant gliomas lack these distinct hallmarks, instead exhibiting disorganized hypoxic niches. Consequently, the functional contribution of these niches to tumor progression has remained poorly understood. Although genetic and epigenetic alterations are established drivers of progression in IDH-mutant gliomas, we provide an additional, essential layer of complexity: microenvironment-driven transcriptional plasticity. By uncovering the relationship between tumor hypoxia and heterogeneous glioma cell states, we uncover that these niches are essential for such plasticity. We also show that the tumor microenvironment provides critical molecular cues necessary to initiate a transcriptional shift enabling glioma cells to transition from a quiescent reservoir into an activated state primed for rapid proliferation. By identifying this paracrine mechanism, our work uncovers a targetable vulnerability that dictates how dormant cell reservoirs are mobilized to fuel malignant transformation.

cancer biology↗

bioRxiv2026

GraphTox: A Semi-Supervised Pre-Trained Framework for Peptide Toxicity Prediction using Geometric Graph Transformer and LORA-Based Finetuning

Peptides are widely used as potential therapeutic agents in drug discovery and biotechnology because they are specific, effective, and relatively inexpensive to produce. They are used in drug development, vaccines, and antimicrobial treatments. However, peptide toxicity remains a major concern as it offers unwanted toxic consequences, such as membrane rupture, haemolysis, tissue damage and adverse immunological response. Early detection of toxic peptide candidates is vital for the development of safe and effective therapies. Current computational methods for predicting peptide toxicity are largely based on hand-crafted sequence descriptors or sequence-only deep learning architectures that may not fully account for the underlying 3-dimensional structural determinants of peptide toxicity. We introduce GraphTox, a structure-aware geometric deep learning framework which combines self-supervised graph representation learning with hierarchical structural modelling to accurately predict peptide toxicity. Our framework learns geometry-aware embeddings from peptide structural graphs via self-supervised masked residue reconstruction, based on a Masked Graph Autoencoder (MGAE) built on a Geometric Graph Transformer (GGT) encoder. The pretrained structural representations are cross fused via a multi-scale U-Net architecture to capture both local residue-level interactions and global conformational patterns associated with peptide toxicity. GraphTox explicitly models spatial relationships between residues, thereby efficiently capturing structural aspects that are generally neglected by sequence-based predictors, such as residue clustering, hydrophobic interactions and electrostatic organization. On benchmark datasets our framework shows superior performance and interpretability over the existing state-of-the-art methods. Our hybrid hierarchical structural modelling framework is a superior computational platform to improve the prediction of peptide toxicity and expedite the creation of safer peptide therapies. https://github.com/debraj-55555/GraphTox

bioinformatics↗

bioRxiv2026

Distinct and shared synergistic effects of high-fat and high-iron diets on liver tumorigenesis and transcriptomic remodeling in mice

Background and AimsThe incidence of hepatocellular carcinoma (HCC) is increasingly driven by metabolic risk factors, including obesity and iron overload. Although high-fat and high-iron diets independently promote hepatocarcinogenesis, their shared and distinct molecular effects remain unclear. We sought to define how dietary fat and iron differentially shape HCC development. ApproachMale C3HeB/FeJ mice were exposed to long-term high-fat (HFD), high-iron (HID), or combined (HFD+HID) diets for 16.5 months. Tumor burden, hepatic iron distribution, mTOR signaling, oxidized phospholipid (OxPL) accumulation, and transcriptomic alterations across normal, adjacent non-tumor, and tumor liver tissues were analyzed using biochemical, histological, and RNA sequencing approaches. ResultsAll diets induced HCC with comparable tumor burden. HID increased iron levels in non-tumor liver tissue but resulted in relative iron depletion within tumors, indicating tumor-specific iron utilization. Tumors from all diet groups showed robust mTOR activation and increased OxPL accumulation, with stronger oxidative stress signatures in HFD and HFD+HID tumors. Transcriptomic analyses revealed conserved oncogenic programs alongside diet-specific signatures, with HFD exerting a dominant effect on metabolic reprogramming and gene dysregulation, whereas HID preferentially enhanced immune and inflammatory signaling. Progressive, monotonic changes in gene expression were observed across disease stages. Cross-species analyses linked diet-induced mouse tumors to immunologically "hot" human HCC subtypes. ConclusionsDietary fat and iron promote HCC through overlapping yet distinct molecular pathways, highlighting metabolic and immune mechanisms as key targets in diet-associated liver cancer.

cancer biology↗

bioRxiv2026

Non-canonical role of a PHOSPHATE1 HOMOLOG 2 in suppressing seedling photomorphogenesis via the TOC1-PIF4 module

Photomorphogenesis, the light-driven development of seedlings, is governed by a complex network of transcription factors and circadian regulators. While the TIMING OF CAB EXPRESSION 1 (TOC1) is known to link circadian rhythms with light-responsive growth, the mechanisms fine-tuning its activity remain poorly understood. Here, we identify PHOSPHATE 1 HOMOLOG 2 (PHO1;H2) as a novel negative regulator of seedling photomorphogenesis in Arabidopsis. Loss-of-function pho1;h2 mutants exhibit hypersensitivity to light, characterized by markedly shorter hypocotyls and increased photopigment accumulation, whereas overexpression lines display reduced photomorphogenic response. We demonstrate that the N-terminal SPX domain of PHO1;H2 is both necessary and sufficient to repress seedling photomorphogenic growth. Mechanistically, in vitro and in vivo interaction assays reveal that the SPX domain physically binds and sequesters TOC1, inhibiting its regulatory function. This PHO1;H2-mediated sequestration of TOC1 alleviates the repression of PHYTOCHROME INTERACTING FACTOR 4 (PIF4), thereby promoting the expression of downstream genes involved in cell elongation and hormone signaling. Collectively, our findings reveal a competitive binding mechanism by which PHO1;H2 modulates the TOC1-PIF4 signaling axis, providing a crucial checkpoint for seedling growth in dynamic light environments.

plant biology↗

bioRxiv2026

Herbivory-induced alterations in cytosolic proteins of pigeon pea (Cajanus cajan) leaves

Insect herbivory triggers cytosolic proteome reprogramming by activating defense pathways and modulating key metabolic processes. We found that simulated herbivory in pigeon pea (Cajanus cajan) induced reactive oxygen species (ROS) production and molecular alterations within 12 hours (h) of post treatment. We compared the leaf proteome profiles of two cultivated genotypes, ICPL 332 (moderately resistant) and ICPL 87 (susceptible), using two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) coupled with mass spectrometry (MS). More than 220 protein spots were detected in ICPL 332 and over 200 in ICPL 87. Comparative analysis revealed 75 differentially accumulated proteins (DAPs), of which 40 were consistently reproducible across biological replicates. These included 11 unique to ICPL 87, 9 unique to ICPL 332, and 10 common to both genotypes. Among the shared DAPs, ICPL 332 showed five upregulated and five downregulated, whereas ICPL 87 exhibited only two upregulated and eight downregulated. Functional categorization grouped DAPs into primary metabolism, stress response, and growth and development. Proteins related to primary metabolism were largely downregulated in both genotypes, while stress-associated proteins exhibited substantial downregulation in ICPL 87 compared to ICPL 332. Overall, the results demonstrate proteomic adjustments underlying defense responses in pigeon pea genotypes.

plant biology↗

bioRxiv2026

Chromosome 2q31.2 Deletion Impairs Neuronal Plasticity through Integrated Stress Response Activation

Rare genomic deletions disrupt gene networks essential for neural development and synaptic plasticity, yet their mechanistic effects remain poorly understood. Here, we investigated the impact of a chromosome 2q31.2 deletion using induced pluripotent stem cell (iPSC)-derived neural models from an affected individual and a genetically matched parental control. Differentiation into neural precursor cells and glial lineages was maintained, with subtle changes in cytoskeletal and lineage-associated gene expression. Transcriptomic analysis showed activation of oxidative stress, mitochondrial dysfunction, and degeneration-linked pathways, consistent with engagement of the integrated stress response (ISR). Pharmacologic inhibition of the ISR with ISRIB reduced ATF4 expression in neural precursors and mature neurons and increased CREB phosphorylation throughout development. Functionally, ISRIB improved neuronal network activity in cortical organoids, increasing calcium burst amplitude and synchronization after NMDA and AMPA stimulation. These results identify ISR dysregulation as a mechanistic link between chromosome 2q31.2 deletion and impaired neuronal plasticity, highlighting ISR modulation via ISRIB as a potential therapeutic approach.

neuroscience↗

bioRxiv2026

Impact of variability in cell generation times on cell-to-cell variability of protein concentrations

The influence of arbitrary randomness in cell division times on the variability of protein copy numbers within a lineage ensemble has been recently studied, going beyond the contributions of noisy gene expression and partitioning error. However, variability of protein concentrations need separate study, since cell size growth between cell divisions dilute protein concentrations at the same rate as size growth, which also determines mean division times. Here for a model of bursty protein production, we present exact moments (of all orders) of protein concentrations in the cyclo-stationary state, comparing: (i) population and lineage cell ensembles, and (ii) statistics at different cell ages. Two interesting results emerge. While the variance of protein concentration changes with the degree of division time heterogeneity at any cell age, the age-averaged variance is independent of it within lineage ensemble but stays dependent within population ensemble. The skewness within population ensemble is higher in younger cells than within lineage ensemble, and this behavior reverses at older ages. Such a feature vanishes for the age-averaged distribution, with population based skewness always dominating over that of lineage. We also show that mother-daughter correlations in generation times, do not add any significant difference to the results.

systems biology↗

bioRxiv2026

A novel lipid-triggered allosteric site modulates LC3-LIR receptor binding activity

Membrane recruitment is a fundamental regulator of protein function. However, the allosteric mechanisms by which lipid binding controls protein activity remain poorly understood. In autophagy, the ubiquitin-like protein LC3 is lipid-anchored to autophagosomes, where it is essential for receptor recruitment and vesicle formation. While LC3-receptor interactions are structurally well defined, how membrane engagement governs LC3 functional dynamics has remained enigmatic. Here, we uncover that membrane binding triggers a major conformational transition in LC3, exposing functional pockets that are occluded in its cytosolic form. We demonstrate that this shift is mediated by dynamic coupling between the allosteric site (3- loop5-{beta}3-loop6) and the functional binding pockets. To conclusively test this mechanism, we utilised an ensemble-based protein design strategy guided by molecular dynamics to engineer the allosteric site. From a series of mutants, two variants emerged that stabilized LC3 conformation in either active or inactive state on the membrane. X-ray crystal structures of mutant LC3, biophysical assays, super-resolution microscopy, and TEM confirmed that the activated allosteric site mutant facilitates receptor binding and cargo capture. In contrast, the inactive variant is functionally inert on the membrane. Our work identifies a fundamental lipid-triggered allosteric site in LC3 that is critical for autophagy regulation and broader implication of membrane-dependent reprogrammable protein activities.

biophysics↗

bioRxiv2026

Ex vivo drug testing in metastatic biopsies reveals patient-specific vulnerabilities to cancer targeting and immune activating drugs

Biomarker-guided therapies in oncology often fail to induce considerable responses in patients with advanced cancer. As a complementary approach, direct drug testing on individual patient samples is highly attractive yet is currently hampered by the lack of assays that combine (i) fast reporting, (ii) the ability to inform about immune-mediated responses, (iii) robust quantification, and (iv) scalability for parallel assessment of multiple drugs. Here, we introduce our patient-derived ex vivo drug response assay (PEDRA) that fulfills all these requirements. Using malignant pleural effusions (MPEs) from five non-small cell lung cancer (NSCLC) patients with detailed clinical treatment histories, we tested 52 guideline-recommended therapies and eight investigational antibody-drug conjugates (ADCs). In all patients, PEDRA identified treatment options that outperformed the therapies the patients had received. The results reflected clinical observations as well as expectations derived from mutational profiling and disease courses. To extend the applicability of PEDRA beyond MPEs to other metastatic lesions, we generated a protocol starting from core needle biopsies. Owing to its reproducible and quantitative nature, PEDRA may provide a valuable diagnostic tool to guide time-sensitive clinical therapy decisions. Additionally, PEDRA has great potential for preclinical testing of investigational drugs, thereby reducing the need for animal experiments.

cancer biology↗

bioRxiv2026

Impact of competition between precursor and mature microRNAs on stochastic gene expression

MicroRNAs (miRNAs) are key post-transcriptional regulators, processed from precursor miRNAs (pre-miRNAs) into mature miRNAs through nuclear and cytoplasmic proteins. Recent evidence shows that pre-miRNAs and mature miRNAs can compete for the same target mRNAs, yet the impact of this miRNA maturation-driven competition on gene expression noise remains unknown. We address this in widespread feedback motifs where both pre- and mature miRNAs degrade a proteins transcripts, and the protein itself either activates or represses miRNA transcription. Using a mathematical model, we show that miRNA maturation tunes the behavior of positive or negative feedback loops, which function as bistable switches or oscillators at the mean-field level, respectively. The relative degradation of mature versus pre-miRNAs and the mRNA-miRNA co-degradation rates can jointly modulate the parameter regions of bistability or oscillations. Moreover, for positive feedback, stochastic simulations reveal that bimodal mRNA distributions emerge near the saddle-node bifurcation boundaries, but not always within the bistable regions. Bimodal mRNA distributions also appear for negative feedback, but outside the region of limit cycles. Importantly, in both feedback types, such noise-induced bimodality emerges in regions where mean-field analysis predicts no bistability or limit cycles. These results demonstrate that noise-induced phenotypic variability cannot necessarily be linked to underlying deterministic bifurcations and elucidate how miRNA maturation shapes stochastic gene expression in regulatory motifs relevant to development and disease.

biophysics↗

bioRxiv2025

Chromosome-associated spot formation by human cytomegalovirus immediate early 1 (IE1) protein

HCMV is associated with severe disease in immunocompromised patients and is a cause of congenital disease. Already more than 30 years ago, IE1 was described to bind to mitotic chromosomes, however the implications of this finding have yet to be determined. HCMV can infect a wide range of cell types and was also detected in different tumours; however, the majority of molecular studies relating to this virus are performed in fibroblasts or monocytic cells. We examined the localization of HCMV IE1 across multiple cell types, including tumour cell lines, to better understand how the protein behaves in these cellular contexts. IE1 is one of the first HCMV genes expressed after lytic infection of the cell and it was observed to distribute evenly over the chromosomes in so-called "chromosome painting" pattern. In leukemia and glioblastoma cells we detected a novel mitotic localization pattern of IE1 - in chromosome-associated spots (CAS), in addition to "painting the chromosomes", as reported before. We demonstrate that the IE1 core domain mediates CAS localization and that the distribution pattern of IE1 on mitotic chromosomes is influenced by both the cell type being infected and the level of IE1 expression. The novel CAS localization of IE1 suggests a new, possibly cell-type specific function of this protein, distinct from its role in transcriptional regulation.

microbiology↗