Biology subjects

Mahapatra, S.

Publications and source records attributed to Mahapatra, S..

At least 19 recordsLinked to original sources

bioRxiv2026

ProcessNets: Towards an efficient approach for ensemble analysis of biological networks

Integrative analysis of the properties of multiple networks pertaining to a biological system is a key problem in systems biology. But computing the properties of thousands of large networks poses a challenge. Most techniques that partially address this challenge, such as parallelism and optimized algorithms, treat the analysis of each network as an independent task. However, the networks arising from the same biological system are often similar to each other, and can we harness this similarity to achieve speedup? Towards this end, we propose a phylogeny-like data structure, nc-tree, to compactly represent an ensemble of related biological networks; and a versatile framework, ProcessNets, that runs incremental algorithms over the nc-tree to speedup property computations on the input networks. Our asymptotic analysis of space and time complexity, coupled with empirical evaluations of diverse ensembles of simulated and real-world GTEx gene coexpression networks, demonstrate that ProcessNets leads to significant space and time advantages when computing different network science measures on ensembles of similar networks. For instance, we achieve a compression factor of 2.1x and 8.1x in storing two representative ensembles of GTEx Muscle Skeletal networks with 1000 nodes/genes, and a time speedup of 2.86x to 3.97x over the fastest baseline for computing degree centrality in ensembles of networks with at least 14,500 nodes derived from subsampled GTEx datasets of ten tissues. These results are promising and encourage application of ProcessNets to analyze biological network ensembles derived from rapidly accumulating consortium/biobank-based datasets.

bioinformatics↗

bioRxiv2026

A druggable chromatin vulnerability in suppressive neutrophils restores antitumor immunity

Many cancers evade immunity by converting neutrophils into polymorphonuclear myeloid-derived suppressor cells (PMN-MDSCs), but the chromatin mechanisms that maintain this pathological state remain unclear. Here we show that tumor-induced suppressive neutrophils depend on mSWI/SNF chromatin remodeling. Two orally bioavailable mSWI/SNF ATPase antagonists, a degrader and a catalytic inhibitor, produced immune-dependent tumor control across syngeneic models, including tumors resistant to PD-1 blockade, and enhanced checkpoint therapy without overt toxicity. Treatment rapidly depleted intratumoral PMN-MDSCs, restored functional CD8+ T cells, and blocked tumor explant-induced expansion and suppressive activity of mouse and human PMN-MDSCs. mSWI/SNF antagonism collapsed chromatin accessibility and PU.1/C/EBP{beta} occupancy at regulatory elements that sustain PMN-MDSC identity. Thus, suppressive neutrophils harbor a druggable chromatin vulnerability that can be exploited to restore cancer immunity.

cancer biology↗

bioRxiv2026

Coxiella burnetii type IVB secretion system modulates TLR3/TRIF-dependent NF-κB and IRF responses during infection

Coxiella burnetii ( Cb ), the causative agent of Q fever, replicates within host macrophages by modulating innate immune responses through its type IVB secretion system (T4SS). Host cells sense pathogens via Pattern recognition receptors (PRRs), including Toll-like receptors (TLRs), to recognize pathogen-associated molecular patterns (PAMPs) and initiate signaling pathways that drive pro-inflammatory cytokine and interferon responses. Toll-like receptor 3 (TLR3) triggers the nuclear translocation of nuclear factor kappa-light-chain-enhancer of activated B cells (NF-{kappa}B) and Interferon regulatory factors (IRFs) resulting in pro-inflammatory cytokine production and type I interferon (IFN-I) induction. Here we demonstrate that Cb requires T4SS to suppress TLR3-induced NF-{kappa}B and IRF transcriptional responses. Furthermore, RNA purified from both virulent and avirulent Cb is sufficient to activate TLR3, identifying pathogen RNA as a relevant PAMP in this context. Using a pulmonary infection model with virulent Cb, we found that TLR3/ Toll-Interleukin-1 Receptor Domain-Containing Adapter Protein Inducing Interferon Beta (TRIF)-dependent innate immune pathway inhibits cachexia. In contrast, signaling through the interferon-/{beta} receptor (IFNAR) restricts bacterial dissemination, indicating that these pathways play distinct but complementary roles in host defense. Mechanistically, Cb suppresses TLR3/TRIF signaling in a T4SS-dependent manner by preventing host TLR3 recruitment to the Coxiella-containing vacuole (CCV) and disrupting TRIF-TNF Receptor-Associated Factor 6 (TRAF6) interactions, thereby selectively inhibiting impairing NF-{kappa}B activation. Consistent with this, we identify five T4SS effector proteins that attenuate TLR3-induced NF-{kappa}B signaling, including CBU1292, which suppresses both NF-{kappa}B and IRF-dependent responses downstream of TLR3.

microbiology↗

bioRxiv2026

Solvent-Isotope Effects in Biomolecular Phase Separation and Fibrillation of Disordered Proteins and Peptides

Heavy water (D2O) is widely used in biomolecular spectroscopy and imaging, often under the assumption that it is an inert replacement for H2O. However, D2O differs subtly in hydrogen-bonding, viscosity, and dielectric properties, which can alter biomolecular interactions and self-assembly. Here, we test how solvent isotope substitution modulates protein/peptide phase separation and amyloid formation in multiple intrinsically disordered systems. Using turbidity-based phase diagrams and microscopy, we quantify how D2O shifts protein-RNA complex coacervation boundaries and alters condensate morphology. Droplet recovery measurements indicate significant solvent-dependent changes in condensate material properties. We further evaluate amyloid formation kinetics, in the presence or absence of a cofactor, supported by orthogonal structural characterization, and assess the functional consequences of tau fibrils using a tau biosensor seeding assay with explicitly defined seed delivery conditions. Together, these results show that D2O can systematically bias liquid-liquid phase separation and aggregation readouts and should be treated as an active experimental variable rather than a neutral solvent substitute.

biophysics↗

bioRxiv2026

Genetic mapping of Citrullus amarus for resistance to gummy stem blight in watermelon

Gummy stem blight affects several cucurbit crops and has emerged as a serious production constraint of watermelon cultivation globally. However, no commercial varieties are available possessing resistance against this disease. Identification of genetic determinants and underlying QTLs are prerequisites for resistant variety development. In this direction, an attempt was made to understand genetics and identify responsible loci using two resistant accessions viz., PI 482276 and IIHR 82. Inheritance analysis indicated that resistance to GSB is governed by polygenes in both accessions. Four QTLs were identified for the population derived from PI 482276 x Arka Manik, while six were observed in the cross IIHR 82 x Arka Manik employing QTL-seq approach. The QTL regions contained important genes putatively involved in resistance reaction such as NAC domain-containing protein 17-like, chitinase 2- like, Pectinesterase, Coiled-coil domain-containing protein 18, Kinase family protein expansin-like B1 protein etc. Our results offer further insight into the disease resistance genetics and its utilization in resistance breeding for gummy stem blight in watermelon.

genomics↗

bioRxiv2026

A Stress-Adaptive Lipid Kinase Axis Defines Metabolic Vulnerabilities in Neuroendocrine Prostate Cancer

Neuroendocrine prostate cancer (NEPC) persists in a profoundly hypoxic microenvironment, yet the mechanisms enabling tumor adaptation to this metabolically challenging niche remain undefined. Here, we identify the lipid kinase PIKfyve as overexpressed in NEPC, functioning as a central node in a stress-lipid kinase axis that drives adaptation to persistent endoplasmic reticulum (ER) stress. Mechanistically, NEPC requires PIKfyve-mediated lysosomal degradation and lipid recycling to maintain metabolic homeostasis under hypoxia. PIKfyve inhibition disrupts lysosomal function, leading to ER stress accumulation and activation of a compensatory, sterol regulatory element-binding protein (SREBP)-dependent de novo lipogenesis program essential for NEPC survival. This stress-lipid axis creates a synthetic vulnerability between PIKfyve and fatty acid synthase (FASN), where dual inhibition synergistically amplifies ER stress, triggers the terminal unfolded protein response, and induces tumor cell death. These findings reveal a metabolic adaptation in NEPC and provide preclinical evidence that co-targeting PIKfyve and FASN can overcome hypoxia-associated stress adaptation.

cancer biology↗

bioRxiv2026

Intranasal Delivery of Hypoxia Primed Whartons Jelly MSC Derived sEVs Reprograms Neuroimmune Signalling and Ameliorates Behavioural Deficits in a Valproic Acid Induced Mouse Model of Autism Spectrum Disorder

BackgroundBeyond disrupted neurodevelopment, autism spectrum disorder (ASD) encompasses progressive neurodegenerative alterations that remain refractory to standard of care behavioral therapies, highlighting the need for biologically targeted adjunctive interventions. Although, Mesenchymal stem cell (MSC) derived small extracellular vesicles (sEVs) have emerged as potent neuroprotective agents; however, the optimal MSC tissue source and strategies enhancing their efficacy for clinical translation remain undefined. Hypoxic preconditioning potentiates their therapeutic effects, however its specific impact on ASD-related impairments is yet to be established. This study conducts a head to head evaluation of sEVs from bone marrow (BM) and Whartons jelly (WJ) MSCs under normoxic and hypoxic conditions to delineate their comparative neuroregenerative efficacy in ASD. MethodsWe investigated the neuroprotective efficacy of sEVs derived from human tissue-specific mesenchymal stem cells (BM/WJ) cultured under normoxic (21% O2) and hypoxic (1% O2) conditions. In vitro assays evaluated sEV uptake, cell proliferation, neurodifferentiation, mitochondrial health, and immunomodulatory effects using neural stem cell (C17.2) and microglial (N9) cell lines. For in vivo studies, ASD-like phenotypes were induced in C57BL/6 mice via prenatal exposure to valproic acid (600 mg/kg), followed by the biodistribution of fluorescently labeled hypoxia-primed WJ MSCs sEVs (WJ-H-sEVs) following intranasal administration was assessed using IVIS imaging. Behavioural outcomes after intranasal treatment were evaluated. Additionally, post-mortem brain tissues were analyzed for neuroinflammation, oxidative stress, synaptic integrity, and downstream signalling pathways using immunofluorescence, Western blotting, and qRT-PCR, while systemic cytokine pro-inflammatory and anti-inflammatory levels were quantified by ELISA. Mechanistic involvement of Nrf2 and NF-{kappa}B signaling pathways was examined using pharmacological inhibitors. ResultsComparative analyses revealed that hypoxic priming significantly enhanced sEV yield and enriched neuroprotective miRNAs, with WJ-H-sEVs exhibiting elevated levels of miR-125b-5p, miR-21a-5p, and miR-145a-5p. Consistent with this enrichment, WJ-H-sEVs demonstrated superior cellular uptake as observed in neural stem cells and microglia, enhanced neurodifferentiation, robust antioxidant activity, effective immunomodulation, and improved mitochondrial health, thereby outperforming their normoxic and BM-derived counterparts. Intranasally administered WJ-H-sEVs efficiently localized to the brain within 12 h and significantly improved anxiety-like behavior, recognition memory, and spatial learning in ASD mice. These effects were accompanied by reduced neuroinflammation and oxidative damage, enhanced neuronal survival, decreased serum IL-6 levels, and increased IL-10 and TGF-{beta}. Mechanistically, therapeutic benefits were mediated through activation of the Nrf2 antioxidant pathway and suppression of NF-{kappa}B and JAK-STAT signaling. ConclusionIn this study, hypoxia emerges as a clinically exploitable priming strategy to enhance the neuroregenerative performance of tissue-specific MSC-derived sEVs, with potential applicability across MSC sources and other neurological disorders. Moreover, intranasal delivery of WJ-H-sEVs demonstrates translational feasibility, reinforcing their potential as an adjunctive, cell-free, pediatric-friendly neurotherapeutic modality for ASD management. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=103 SRC="FIGDIR/small/721255v1_ufig1.gif" ALT="Figure 1"> View larger version (21K): org.highwire.dtl.DTLVardef@dd0f7forg.highwire.dtl.DTLVardef@1247d24org.highwire.dtl.DTLVardef@93e6deorg.highwire.dtl.DTLVardef@1a349d_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Deciphering the Acetaldehyde Signaling Network Underlying Bacterial Escape from Protozoan Predators

Entamoeba histolytica (Eh) is a formidable intestinal pathogen, yet the ecological principles governing its invasion of the gut microbiome remain elusive. Upon colonization, Eh encounters resident bacteria typically sequestered within aggregates and biofilms. While Eh utilizes cysteine proteinases to degrade biofilm matrices and access bacterial prey, the strategies bacteria employ to sense and evade this predation are largely unknown. Here, we identify a metabolic signalling axis that allows the probiotic bacterium Bacillus subtilis to perceive and respond to predatory Eh. In the absence of mitochondria, Eh relies on fermentative glycolysis, using alcohol dehydrogenase to produce distinct metabolic byproducts. Using quantitative proteomics and single-cell imaging, we demonstrate that B. subtilis detects the Eh-derived metabolite acetaldehyde as a proxy for predator presence. By mapping the acetaldehyde-responsive regulatory network, we show how this metabolic input is transduced to control the motility machinery, while our data suggest that the broader predatory secretome acts as a multi-modal signal influencing multiple bacterial physiological programs. This chemical cue triggers a rapid phenotypic switch in B. subtilis, driving a transition towards a motile, planktonic "flight" response. Our findings reveal that commensal bacteria exploit the unique metabolic signature of anaerobic parasites to coordinate defensive behaviours, highlighting how inter-kingdom signalling shapes microbiome architecture during infection.

microbiology↗

bioRxiv2026

Rewiring Oncogenic Transcriptional Complexes with Domain-ALTeration Chimeras (DALTACs) in Prostate Cancer

Transcriptional addiction to the androgen receptor (AR) underlies metastatic castration-resistant prostate cancer (mCRPC), where AR maintains oncogenic programs through domain-specific interactions with the acetyltransferases p300/CBP. Here, we describe a distinct therapeutic modality, Domain-ALTerAtion Chimeras (DALTACs), that rewire endogenous protein complexes by enforcing non-native domain-domain interactions. Our first-in-class AR-p300/CBP DALTAC-1 induces synthetic proximity between the AR ligand-binding domain and p300/CBP-bromodomain, misconfiguring their native interface and locking the complex in a non-productive state. DALTAC-1 triggers a super-inhibitory effect, suppressing AR-driven transcription and proliferation more potently than combined AR and p300/CBP inhibition. Mechanistically, DALTAC-1 reprograms p300/CBP substrate engagement, abolishing the histone mark H2B N-terminal acetylation (H2BNTac) while inducing neomorphic acetylation of AR and coactivators, ultimately collapsing the AR neo-enhanceosome. Chromatin profiling revealed redistribution of AR and p300/CBP toward palindromic AREs, accompanied by disruption of cofactor and transcriptional machinery recruitment at oncogenic AR/ERG neo-enhancers. DALTAC-1 exhibits exquisite lineage selectivity, displaying potent activity in AR-p300/CBP dual-dependent cells while sparing AR-negative cells. In multiple in vivo models, DALTAC-1 induces deep and durable tumor regressions. Together, these findings establish DALTACs as a broadly applicable strategy to rewire disease-defining complexes through domain-topology alteration, expanding induced-proximity therapeutics, while DALTAC-1's precise lineage-selectivity supports its translational potential in AR-driven prostate cancer.

cancer biology↗

bioRxiv2026

Piezoelectric Response of Lysozyme-PVA Composite Films for Flexible and Biocompatible Applications

Flexible and biocompatible piezoelectric materials are crucial for next-generation wearable and bio-integrated electronics. In this work, we report a sustainable bio-composite film by incorporating lysozyme, a naturally abundant protein, into a polyvinyl alcohol matrix to achieve efficient electromechanical conversion. The composite exploits the intrinsic molecular dipoles of lysozyme, which are effectively stabilized and aligned within the polymer network. Under applied bending strain and vertical pressure, the film exhibits a pronounced piezoelectric response, as evidenced by time-dependent electrical measurements under forward and reverse bias conditions. The deformation of -helices and other helical structures within lysozyme induces dipole reorientation and charge separation, generating a measurable electrical output. In contrast, pure polyvinyl alcohol films show no detectable response, confirming the essential role of lysozyme in the observed piezoelectricity. Furthermore, the device enables real-time human motion sensing, highlighting its potential for flexible, eco-friendly, and biocompatible electronic applications.

biophysics↗

bioRxiv2025

Uncertainty-Aware Gene Rankings Reveal Key Players in Coexpression Networks

MotivationKey genes of a biological system are often prioritized by computing network science measures on a coexpression network inferred from transcriptomic data. But human population heterogeneity and modest sample sizes introduce uncertainty in the inferred coexpression network. Earlier studies have estimated this uncertainty using bootstrap resampling or similar approaches, but fewer have investigated how it propagates to downstream network analyses and affects gene prioritization. Methods and ResultsWe present a systematic workflow to propagate network uncertainty to downstream measures such as degree/PageRank centrality, with the goal of producing robust gene scorings/rankings. We specifically propose uncertainty-aware scorings, BooNS and BPNS, which utilize the spread of a centrality measure across bootstrapped coexpression networks to prioritize stable central genes. Across several (semi-)simulated and real-world (GTEx) datasets, BooNS and BPNS recover reference or tissue-specific genes significantly better than other traditional centrality rankings. This performance gap highlights the long-overdue adoption of uncertainty-aware gene ranking for stable biological inference. Availability and ImplementationCode and supplemental data are available at https://github.com/BIRDSgroup/Bootstrap-based_Node_Scorings_BNS, and https://tinyurl.com/BNS-suppl-data respectively.

bioinformatics↗

bioRxiv2025

The gut microbiota-derived metabolite indole regulates cytoskeletal functions and virulence in Entamoeba histolytica

Entamoeba histolytica is a pathogenic amoeba that inhabits the human large intestine and causes amoebiasis. E. histolytica interacts with both the intestinal microbiota and the metabolites they produce. These bacterial metabolites play a crucial role in shaping the virulence and stress resistance of E. histolytica. One such metabolite, indole, is synthesized by bacteria from tryptophan and functions as a key signaling molecule. In this study, we investigated the impact of indole on E. histolytica by incubating trophozoites with the metabolite and performing proteomic analyses under various conditions, including trophozoites adapted to indole. Our results show that indole is toxic to E. histolytica, with an inhibitory concentration (IC) of 1.2 mM; however, the parasite can adapt to this concentration. Proteomic analyses reveal that indole-adapted trophozoites display enhanced resistance to oxidative stress (OS), upregulation of cytoskeletal proteins, and increased virulence. These trophozoites exhibit increased F-actin formation, smaller cell size, stronger adhesion to HeLa cells, enhanced migratory capacity, and more effective colonization of the mouse cecum compared to non-adapted trophozoites. Thus, indole exerts a dual effect on E. histolytica physiology. While indole is initially toxic to the parasite, adaptation to indole confers enhanced resistance to OS and promotes a more virulent phenotype. This duality underscores the complex role of microbiota-derived metabolites in modulating parasite behavior and highlights indole as a key microbial signal. Author summaryEntamoeba histolytica is a unicellular parasite living in the human large intestine and can cause a disease called amoebiasis. Inside the intestine, E. histolytica interacts with the microbiota and with the metabolites they produce. One such metabolite is indole, which is produced by gut bacteria from tryptophan and used by human cells and trophozoites. In this study, we explored how indole affects E. histolytica. We found that indole is toxic to the parasite at first, but over time, the amoeba can adapt and survive in its presence. Using protein analysis techniques, we discovered that indole-adapted amoebas become more resistant to stress and more virulent. They produce more F-actin, leading to improved mobility, degrade more HeLa cells, and colonize the gut of mice more efficiently than wild-type amoebas (WT). These results show that, while indole initially harms the parasite, it also triggers changes that make it more resistant to stress and more virulent. Our work highlights how metabolites produced by bacteria in the large intestine can influence the behavior of E. histolytica.

microbiology↗

bioRxiv2025

Quantification of small molecule partitioning in a biomolecular condensate with 2D NMR spectroscopy

Several intrinsically disordered proteins have been shown to undergo phase separation into a dense and dilute phase and this process is intimately linked with the regulation of cellular processes. It is therefore highly relevant to know how metabolites partition between these phases. We show here that the partitioning of components in a complex mixture can be robustly obtained from a single set of 2D NMR spectra recorded on the dilute and dense phases separately using a so-called "time zero extrapolated approach" known as HSQC0. The spectral separation power of 2D NMR spectroscopy circumvents the need for physical isolation or workup of the mixture components in the two samples. Using quantitative 1D 1H NMR, it is validated that the HSQC0 approach effectively removes all the undermining effects that plague quantification in common 2D NMR experiments, including differential attenuation due to relaxation in the two phases, pulse imperfections, partial decoupling, off-resonance effects, and incomplete coherence transfer in the case of scalar coupling variation. These results should be of widespread interest as partitioning into biomolecular condensates is crucial for the calibration of computational physicochemical models of phase separation and key to the further understanding of cellular biochemistry involving membraneless organelles.

biophysics↗

bioRxiv2025

Label-Free Quantification of Apoptosis and Necrosis Using Stimulated Raman Scattering Microscopy

Recombinant proteins are critical for modern therapeutics and diagnostics, with Chinese hamster ovary (CHO) cells serving as the primary production platform. However, environmental and chemical stressors in bioreactors often trigger cell death, particularly apoptosis, posing a significant challenge to recombinant protein manufacturing. Rapid, label-free methods to monitor cell death are essential for ensuring better production quality. Stimulated Raman scattering (SRS) microscopy offers a powerful, label-free approach to measure lipid and protein compositions in live cells. We demonstrate that SRS microscopy enables rapid and reagent-free analysis of apoptotic and necrotic transitions. Our results show that apoptotic cells exhibit higher protein concentrations, while necrotic cells show an opposite trend. To enhance analysis, we developed a quantitative single-cell analysis pipeline that extracts chemotypic and phenotypic signatures of apoptosis and necrosis, enabling the identification of subpopulations with varied responses to stressors or treatments. Furthermore, the cell death analysis was successfully generalized to other stressors and cell types. This study highlights SRS microscopy as a robust and non-invasive tool for rapid monitoring of live cell apoptotic and necrotic transitions. Our method and findings hold potential for improving quality control in CHO cell-based biopharmaceutical production and for evaluating cell death in diverse biological contexts.

cell biology↗

bioRxiv2025

Real-Time and Site-Specific Perturbation of Dynamic Subcellular Compartments Using Femtosecond Pulses

Understanding laser interactions with subcellular compartments is crucial for advancing optical microscopy, phototherapy, and optogenetics. While continuous-wave (CW) lasers rely on linear absorption, femtosecond (fs) lasers enable nonlinear multiphoton absorption confined to the laser focus, offering high axial precision. However, current fs laser delivery methods lack the ability to target dynamic molecular entities and automate target selection, limiting real-time perturbation of biomolecules with mobility or complex distribution. Additionally, existing technologies separate fs pulse delivery and imaging, preventing simultaneous recording of cellular responses. To overcome these challenges, we introduce fs real-time precision opto-control (fs-RPOC), which integrates a laser scanning microscope with a closed-loop feedback mechanism for automated, chemically selective subcellular perturbation. fs-RPOC achieves superior spatial precision and fast response time, enabling single- and sub-organelle microsurgery of dynamic targets and localized molecular modulation. By applying a pulse-picking method, fs-RPOC independently controls laser average and peak power at any desired subcellular compartment. Targeting mitochondria, fs-RPOC reveals site-specific molecular responses resulting from fs-laser-induced ROS formation, H2O2 diffusion, and low-density plasma generation. These findings offer new insights into fs laser interactions with subcellular compartments and demonstrate fs-RPOCs potential for precise molecular and organelle regulation.

bioengineering↗

bioRxiv2025

Clostridium novyi type B causes fatal hemorrhagic disease in wild Asian elephants

The population of Asian elephants, an endangered species, is decreasing significantly due to anthropogenic interference in India. Research on Asian elephant disease is largely confined to observations reported from captive populations. The present study explored 11 disease investigation cases whose clinicopathological changes were similar to those of fatal hemorrhagic disease caused by Bacillus anthracis. We used molecular diagnostic approaches such as PCR (polymerase chain reaction), quantitative PCR, 16S metagenomics analysis and whole-metagenome sequencing for identification of the etiological agent responsible for these wild elephant mortalities. 16S metagenomics analysis revealed the presence of Clostridium hemolyticum as the dominant bacteria in all the mortality events. In contrast, flagellin gene-specific identification of all the samples and whole metagenomics analysis of blood samples collected from the ear pinna of a freshly deceased elephant revealed Clostridium novyi type B as the sole pathogenic agent responsible for the death of elephants. This study provides the first evidence of the involvement of Clostridium novyi type B in the death of wild elephants with similar clinical manifestations to anthrax. The current study also provides ample evidence of the need to explore investigations of emerging diseases of wild elephants to conserve these large mammals.

microbiology↗

bioRxiv2024

Cellular cartography reveals mouse prostate organization and determinants of castration resistance

Inadequate response to androgen deprivation therapy (ADT) frequently arises in prostate cancer, driven by cellular mechanisms that remain poorly understood. Here, we integrated single-cell RNA sequencing, single-cell multiomics, and spatial transcriptomics to define the transcriptional, epigenetic, and spatial basis of cell identity and castration response in the mouse prostate. Leveraging these data along with a meta-analysis of human prostates and prostate cancer, we identified cellular orthologs and key determinants of ADT response and resistance. Our findings reveal that mouse prostates harbor lobe-specific luminal epithelial cell types distinguished by unique gene regulatory modules and anatomically defined androgen-responsive transcriptional programs, indicative of divergent developmental origins. Androgen-insensitive, stem-like epithelial populations - resembling human club and hillock cells - are notably enriched in the urethra and ventral prostate but are rare in other lobes. Within the ventral prostate, we also uncovered two additional androgen-responsive luminal epithelial cell types, marked by Pbsn or Spink1 expression, which align with human luminal subsets and may define the origin of distinct prostate cancer subtypes. Castration profoundly reshaped luminal epithelial transcriptomes, with castration-resistant luminal epithelial cells activating stress-responsive and stemness programs. These transcriptional signatures are enriched in tumor cells from ADT-treated and castration-resistant prostate cancer patients, underscoring their likely role in driving treatment resistance. Collectively, our comprehensive cellular atlas of the mouse prostate illuminates the importance of lobe-specific contexts for prostate cancer modeling and reveals potential therapeutic targets to counter castration resistance. Significance StatementAndrogen deprivation therapy is a mainstay in prostate cancer treatment, yet many patients eventually develop castration-resistant disease--a lethal progression driven by poorly understood cellular mechanisms. Our study provides a comprehensive cellular map of the prostate, identifying key determinants of normal organization and castration-induced remodeling. By pinpointing the cell types and molecular programs that confer ADT responsiveness or resistance, our findings offer new directions for prostate cancer modeling and pave the way toward novel therapeutic strategies aimed at enhancing ADT efficacy and preventing the emergence of castration-resistant prostate cancer.

cancer biology↗

bioRxiv2024

p300/CBP degradation is required to disable the active AR enhanceosome in prostate cancer

Prostate cancer is an exemplar of an enhancer-binding transcription factor-driven disease. The androgen receptor (AR) enhanceosome complex comprised of chromatin and epigenetic coregulators assembles at enhancer elements to drive disease progression. The paralog lysine acetyltransferases p300 and CBP deposit histone marks that are associated with enhancer activation. Here, we demonstrate that p300/CBP are determinant cofactors of the active AR enhanceosome in prostate cancer. Histone H2B N-terminus multisite lysine acetylation (H2BNTac), which is exclusively reliant on p300/CBP catalytic function, marked active enhancers and was notably elevated in prostate cancer lesions relative to the adjacent benign epithelia. Degradation of p300/CBP rapidly depleted acetylation marks associated with the active AR enhanceosome, which was only partially phenocopied by inhibition of their reader bromodomains. Notably, H2BNTac was effectively abrogated only upon p300/CBP degradation, which led to a stronger suppression of p300/CBP-dependent oncogenic gene programs relative to bromodomain inhibition or the inhibition of its catalytic domain. In vivo experiments using an orally active p300/CBP proteolysis targeting chimera (PROTAC) degrader (CBPD-409) showed that p300/CBP degradation potently inhibited tumor growth in preclinical models of castration-resistant prostate cancer and synergized with AR antagonists. While mouse p300/CBP orthologs were effectively degraded in host tissues, prolonged treatment with the PROTAC degrader was well tolerated with no significant signs of toxicity. Taken together, our study highlights the pivotal role of p300/CBP in maintaining the active AR enhanceosome and demonstrates how target degradation may have functionally distinct effects relative to target inhibition, thus supporting the development of p300/CBP degraders for the treatment of advanced prostate cancer.

cancer biology↗