Biology subjects

Sharma, A.

Publications and source records attributed to Sharma, A..

At least 109 records · Page 6Linked to original sources

bioRxiv2025

Human AUTS2 regulates neurodevelopmental pathways via dual DNA/RNA binding.

The AUTS2 gene is implicated in neurodevelopmental and psychiatric disorders, with patient mutations leading to intellectual disability, microcephaly, and autistic behavior. While AUTS2s chromatin-and RNA-related functions are recognized, its direct binding to RNA in human neural progenitors has not been previously demonstrated. Here, we used ChIP-seq and eCLIP-seq in human neural progenitor cells (NPCs) to map AUTS2s chromatin targets and, for the first time, its direct RNA interactome. AUTS2 knockdown in NPCs led to widespread gene expression changes and impaired cell proliferation, migration, and neurite outgrowth. Integrated analysis revealed downregulation of Wnt pathway genes, notably WNT7A, among targets directly bound by AUTS2 at both chromatin and RNA levels. Supplementation with WNT7A rescued cellular phenotypes in AUTS2-deficient NPCs, underscoring the significance of Wnt signaling. These findings highlight AUTS2s central role in human neurodevelopment and provide mechanistic insight into how its disruption may contribute to the pathology of neurodevelopmental disorders.

neuroscience↗

bioRxiv2025

The 9-1-1 complex protects ssDNA gaps in BRCA2-deficient cancer

Single-stranded DNA (ssDNA) gaps are a hallmark of BRCA-deficient cells, yet the mechanisms that safeguard these lesions remain unclear. Through a genome-wide CRISPR screen, we identified the RAD9A-HUS1-RAD1 (9-1-1) complex as essential for the survival of BRCA2-deficient cells through an ATR-independent mechanism. Loss of 9-1-1 in this context leads to the accumulation of PRIMPOL-dependent gaps that fail to undergo post-replicat ive repair, resulting in pathological expansion and increased DNA damage. This instability is driven by excessive EXO1-mediated degradation, as EXO1 depletion rescues the phenotype. We further demonstrate that the 9-1-1 complex is required for POL{zeta}-dependent gap filling. We propose a model in which ssDNA gaps, when extended beyond a critical length, become inaccessible to TLS-mediated repair and are fully reliant on homologous recombination. These findings establish the 9-1-1 complex as key regulator of ssDNA gap stability and a promising therapeutic target in BRCA2-deficient cancers. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=200 SRC="FIGDIR/small/680950v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@56516aorg.highwire.dtl.DTLVardef@fb1ce3org.highwire.dtl.DTLVardef@25a7b2org.highwire.dtl.DTLVardef@249731_HPS_FORMAT_FIGEXP M_FIG C_FIG

molecular biology↗

bioRxiv2025

Molecular attributes of intrinsically disordered regions in secretomes influence fungal pathogenesis

Secretory proteins are crucial for establishing fungal infection through biomolecular interactions with the host. Accumulating evidence suggest that intrinsically disordered regions (IDRs) in proteins facilitate molecular interactions. How do IDRs of secretory proteins influence fungal pathogenesis? By analyzing 195,359 secretory proteins of 73 fungal species, we find that IDRs in plant pathogen extracellular non-effectors are enriched for weak polyampholytes and polyelectrolytes. These could adopt beads-on-string conformation effectively promoting assembly of diverse enzymes aiding swift degradation of host cell wall. Both animal pathogen secretory proteins and intracellular plant pathogen effectors show enrichment for strong polyampholytes, potentially aiding phase-separation and organizing intracellular biological matter to hijack or suppress host machinery. Importantly, IDRs of plant pathogen effectors which mimic host IDRs could have emerged through convergent evolution, while those of non-effectors might have evolved de novo. Thus, specific molecular attributes of fungal secretome IDRs can influence initiation, establishment and long-term persistence of infection.

systems biology↗

bioRxiv2025

A novel approach for the extraction of nucleic acids using a hybrid paper-plastic device

Nucleic acid-based diagnostics play a crucial role in early and accurate disease detection. However, conventional extraction approaches are expensive, time-consuming, and require complex instrumentation and skilled personnel, which restricts their use in resource-limited settings. To develop and evaluate a simple, low-cost, and equipment-free paper-based microfluidic cassette device for rapid extraction of nucleic acids (DNA and RNA) from biological samples. A paper-plastic cassette was fabricated by laminating filter paper or glass fiber substrates between thermally bonded plastic sheets. The system was tested using Klebsiella pneumoniae (DNA) and HeLa cells (RNA) with different lysis buffer formulations. Extracted nucleic acids were quantified using a Qubit fluorimeter and assessed by gel electrophoresis and PCR amplification. Results were compared with standard commercial extraction kits. Among tested substrates, LF1 combined with lysis buffers 2, 4, and 5 yielded the highest quality DNA and RNA with 260/280 absorbance ratios of approximately 1.8 (DNA) and 2.0 (RNA). The nucleic acid yields were comparable to commercial kits, and the extracted material was suitable for direct downstream applications, including PCR. The developed paper-plastic cassette enables rapid, affordable, and equipment-free extraction of nucleic acids. This platform shows strong potential for point-of-care molecular diagnostics, particularly in low-resource and decentralized healthcare settings.

molecular biology↗

bioRxiv2025

NTX250: A Modular mRNA-Based Immunotherapy Platform for HPV-Associated Cancers with Broad Applicability.

Infection with high-risk human papillomavirus (HPV) is a key driver of multiple HPV-associated malignancies, including cervical intraepithelial neoplasia (CIN), oropharyngeal, head and neck, and anogenital cancers. Despite the high efficacy of prophylactic HPV vaccines, a substantial population remains at ongoing risk due to issues related to vaccine accessibility, awareness, or personal choice. Current treatments, such as the loop electrosurgical excision procedure (LEEP), address lesions but do not eliminate persistent HPV infection and are associated with potential complications. Moreover, individuals treated for HPV-related disease are at increased risk for subsequent HPV-associated malignancies. These factors underscore an urgent need for effective, non-invasive therapeutic strategies capable of targeting and eradicating persistent HPV infections. Here we introduce NTX250, an innovative mRNA-based therapeutic platform designed to deliver HPV type 16 (HPV16) E6-E7 antigens, combined with immunomodulators human interleukin-12 (IL-12) p70 and engineered human LIGHT (LIGHT). The mRNAs are co-delivered via lipid and ionizable peptoid nanoparticles referred to as Nutshell formulation for intralesional administration. Our preclinical evaluation demonstrates that localized delivery of NTX250 in HPV16-transformed tumor-bearing models results in complete tumor regression and the induction of durable, antigen-specific immune memory. Moreover, this modular mRNA nanoparticle approach combining tumor-specific antigens and immunomodulators is adaptable beyond HPV, with potential applications targeting neoepitopes or other tumor-associated antigens, thus offering a versatile platform for immunotherapy across a broad range of indications. These findings highlight the potential of this strategy as a broadly applicable, non-surgical immunotherapeutic capable of inducing robust and specific anti-tumor responses.

immunology↗

bioRxiv2025

In silico prediction of cellular organelles from computationally super-resolved (SR) phase-modulated optical micrographs

Differential interference contrast (DIC) & phase contrast microscopy (PCM) represent 2 widely-assimilated optical microscopical imaging modalities often employed for live cell imaging (LCI) applications. Although both of these approaches have marked advantages over traditional brightfield (BF) microscopy (they dont require staining and provide real time visualization of cellular dynamics & metabolomics), there is a need to often supplement these modalities with epifluorescent microscopical imaging for the detection of specific organelles and structures in vivo (a process known as fluorescence combination/colocalization microscopy). Nonetheless, epifluorescent microscopy (both widefield and confocal) rely on the use of fluorophores (specialized fluorescent molecules and/or fluorescent proteins) for labelling key structures and features in the cell, which are prone to several issues, including photobleaching or cross-talk (amongst others). In this context, we seek to develop a novel deep neural network (DNN)-based approach aimed at predicting the location of 3 specific organelles (the cell nucleus, mitochondria & Golgi Apparatus) from acquired PCM & DIC images which have been super-resolved (SR) using our previously developed (& published) O-Net & {Theta}-Net model architectures. The model-generated images depict relatively close correlation with the ground truth images, implying that the O-Net & {Theta}-Net model architectures serve as viable frameworks for DNN model sculpting and training for both the purposes of image SR in optical microscopy as well as feature localization in these SR micrographs. We thus surmise on the potentiality of our proposed O-Net & {Theta}-Net DNN architectures for the development of models to be deployed in fully-automated image analysis pipelines in biomedical and healthcare diagnostics in the near future.

bioinformatics↗

bioRxiv2025

mRNA-1273.251 and mRNA-1283.251 vaccines expressing SARS-CoV-2 variant LP.8.1 antigens broadly neutralize contemporary JN.1-lineage viruses

The continued evolution of the SARS-CoV-2 Omicron JN.1 lineage has led to the emergence of antigenically distinct subvariants including KP.2, KP.3, XEC, and LP.8.1, which became the dominant strains in the Americas and Europe by mid-2025. LP.8.1 was designated a Variant Under Monitoring by the WHO in January 2025 due to its potential to displace prior circulating variants. Informed by early growth modeling and antigenic analysis, we selected LP.8.1 as a candidate strain for the 2025-2026 vaccine season. Here, we describe the development of updated LP.8.1-matched mRNA vaccine compositions encoding either the full-length spike protein for mRNA-1273 (monovalent) or the membrane-anchored receptor-binding and N-terminal domains for the mRNA-1283 vaccine. Initial in vitro characterization, including structural analysis, demonstrated robust antigen expression and intact antigenic features. Immunogenicity of both vaccines were evaluated in murine models following immunization as either a primary series in naive animals or as a booster dose. LP.8.1-matched vaccines elicited strong neutralizing antibody responses against the homologous LP.8.1 strain and more recently emerging JN.1-lineage subvariants, including XFG and NB.1.8.1. Notably, the mRNA-1283 vaccine expressing LP.8.1 induced higher mean neutralization titers than the mRNA-1273 version across multiple variants. These data demonstrate the immunogenicity and breadth of both LP.8.1-based mRNA-1273 and mRNA-1283 vaccines in the context of ongoing JN.1 lineage evolution and support the selection of LP.8.1 as the updated vaccine antigen for the 2025-2026 season.

immunology↗

bioRxiv2025

BenchIDPs: Evaluation of Conformational Preferences Molecular Mechanics and Solvent Interactions of IDPs across popular Force Fields and Water Models

Intrinsically disordered proteins (IDPs), unlike globular proteins, lack stable secondary structure and exist as dynamic ensembles of conformations in physiological conditions. These conformations allow them to adapt to many roles while interacting with other proteins, forming partially folded soluble oligomers or insoluble plaques rich in {beta}-sheet, and are responsible for different pathological diseases. The dynamic nature of IDPs and the lack of well-defined binding sites make drug discovery and development both challenging. Although computational protocols, predominantly involving molecular dynamics (MD) simulations studies, have been complementing in understanding the structure and dynamics of IDPs, the choice of force fields become important in reproducing experimental observations. We herewith provide a systematic study to investigate the structural propensity of four IDPs (A{beta}42, Tau43, amylin and S), using 13 combinations of force field-water models (FF-wm). In addition to validating with NMR observables, we also examine the water dynamics surrounding the chosen IDPs to underscore the generalizability of chosen FF-wms. C36-IDPSFF with amber99sb-dispersion water model (A99SB-disp) is found to perform optimal in simulating IDPs in comparison with other FF-wm combination based on structural propensity and comparison with experimental NMR 3JHN-H-Coupling data as well as dynamical observables.

biophysics↗

bioRxiv2025

Hemoglobin in the diet modulates post-blood feeding behavioral rhythms and gene expression in Aedes aegypti

Female Aedes aegypti mosquitoes rely on blood meals to acquire nutrients essential for egg development. However, blood ingestion also introduces physiological stressors--including thermal, osmotic, and oxidative stress--particularly during the digestion of heme-containing proteins. In Drosophila melanogaster, oxidative stress response genes are regulated by the circadian clock, and core circadian transcription factors are redox-sensitive. Additionally, sufficient iron ingestion is necessary to maintain normal circadian behaviors, as iron metabolism genes influence circadian behaviors, and flies lacking iron storage and transport are arrhythmic. However, whether similar interactions between iron metabolism and circadian rhythms exist in mosquitoes remains unclear. Here, we leverage the known alteration of mosquitoes activity rhythms following a bloodmeal to investigate whether dietary hemoglobin contributes to post-feeding activity suppression and gene regulation in the female Ae. aegypti. Using vertebrate blood and artificial blood mimic diets of equal nutritional values but with and without hemoglobin, we compared mosquito egg production, locomotor activity, sleep profiles, and transcript abundance of genes involved in circadian regulation and host-seeking behavior. Hemoglobin intake significantly reduced post-feeding activity, increased sleep amounts, and suppressed transcription of the core circadian gene period in mosquito heads. Short periods of sleep deprivation during the post-blood feeding period of inactivity did not alter egg production, timing of deposition, or viability. Our findings reveal that hemoglobin-derived heme influences behavioral and molecular responses in Ae. aegypti after a blood meal, pointing to a complex regulatory network linking heme acquisition, oxidative stress, daily rhythms, and behavior.

animal behavior and cognition↗

bioRxiv2025

Generation of uniform-sized spheroids using PDMS-based microwell devices as 3D cancer models for pharmacological profiling of drugs

Cancer researchers now consider spheroids a valuable in vitro model for cancer research and personalized medicine. They are used to studying cancer development, testing drug effectiveness, and potentially guiding treatment decisions for individual patients. Spheroids represent the simplest form of three-dimensional (3D) cellular arrangement and encapsulate the essential tumor microenvironment. These characteristics are crucial for studying processes such as tumor invasion, metastasis, angiogenesis, and cell cycle kinetics. In particular, spheroids excel in chemo-response assays where traditional monolayer cell cultures often fall short. A PDMS microwell device was developed to generate uniform-sized cancer spheroids. This device is user-friendly and capable of producing a large number of spheroids. The device measures 13 mm in diameter (1200 microwells per well if the device has microwells 400 m in size, and 300 microwells per well if the device has microwells 800 m in size). It advances 3D cultures by requiring only a small volume of cell culture supplements and is easy to manage. The hydrophobic nature of the PDMS device prevents cells from adhering to it, thereby promoting spheroid formation. Spheroids can be created on microwell devices, and subsequent experiments may either be conducted on the device or transferred to cell culture dishes for additional 3D biological assays. Seeding cells is notably easier compared to other 3D cell culture techniques, and the number of cells in each spheroid can be adjusted according to specific requirements. Overall, the PDMS-based microwell device offers a simple and efficient means to produce large quantities of uniform-sized spheroids for 3D cell culture studies, showcasing high throughput, short generation times, long-term effectiveness, and ease of handling.

bioengineering↗

bioRxiv2025

SynGlue: AI-Driven Designer for Clinically Actionable Multi-Target Therapeutics

The rational design of protein degraders, such as proteolysis-targeting chimeras (PROTACs), requires the simultaneous optimization of multiple molecular properties, a complex challenge that limits efficient discovery. Here, we introduce SynGlue, a generative artificial intelligence (AI) framework that addresses this challenge through two core modules: data-driven, leveraging large-scale protein-ligand intelligence, and structure-guided, for physics-aware molecular design. SynGlue harness MagnetDB, a curated database of 6.37 million experimental protein-ligand interactions, and couples it with deep learning models that quantitatively predict degradation potency (DC50), maximal degradation (Dmax), and guide ternary-complex-compatible linker design. Benchmarked against 6,935 compounds, SynGlue demonstrates superior performance in relevant pharmacology prediction. To validate SynGlue, we engineered degraders for BRD4 and GSPT1. Our data-driven design for BRD4 yielded compounds with novel warhead scaffolds (<50% warhead similarity with known PROTACs), which proved to be potent degraders in vitro (DC50 = 0.19 nM) and efficacious in vivo in mouse models. Independently, our structure-guided de novo design for GSPT1 produced ultrapotent degraders (DC50 {approx} 0.0011 M) that are also effective both in vitro and in vivo, uncovering a new oncogenic dependency. By unifying data-driven and physics-aware design, SynGlue establishes a generalizable AI framework for the rapid development of clinically relevant protein degraders, with principled extension to other multi-target modalities.

bioinformatics↗

bioRxiv2025

A dual-localized geraniol synthase and a previously unreported cytosolic geranyl pyrophosphatase contribute to geraniol formation in lemongrass

Geraniol, a major constituent of many essential oils and precursor for geraniol-derived aldehydes and acetates, is produced in plants through the action of a terpene synthase encoding geraniol synthase or via terpene synthase-independent non-canonical pathway involving a Nudix hydrolase and a yet to be discovered pyrophosphatase. Here, we identify a geraniol synthase (Cymbopogon flexuosus geraniol synthase; CfGES) that catalyzes the conversion of geranyl pyrophosphate (GPP) (also known as geranly diphosphate) to geraniol, as well as a previously unreported geranyl pyrophosphatase (CfG(P)Pase) that acts on both GPP and geranyl monophosphate (GP), albeit with different efficiencies, to generate geraniol. Virus-induced gene silencing of CfGES or CfG(P)Pase resulted in a substantial reduction in geraniol and its immediate product citral in lemongrass leaves. Conversely, transient overexpression of CfGES or CfG(P)Pase resulted in enhanced production of geraniol and citral in lemon balm (Melissa officinalis) leaves, as well as geraniol, citronellol, and citral in rose (Rosa damascena) flower petals. Subcellular localization studies revealed that while CfGES exhibited dual cytosolic/plastidial localization, CfG(P)Pase was localized to the cytosol. This localization pattern was further supported by the significantly higher geraniol-forming activity observed in the purified cytosolic protein fraction compared to the chloroplast fraction. Our study uncovers the missing step in cytosolic geraniol formation via a TPS-independent non-canonical route and demonstrates that geraniol, required for citral production in lemongrass, is synthesized by cytosolic CfG(P)Pase and cytosol-/plastid-localized CfGES.

plant biology↗

bioRxiv2025

Dynamic neural states underpin bradykinesia severity in Parkinsons disease

BackgroundBradykinesia in Parkinsons disease (PD) may arise due to transient, network-wide neural dynamics that extend beyond beta-band oscillatory activity within the motor cortical-subthalamic nucleus (STN) circuit. MethodsWe address this question by using Hidden Markov Models (HMMs) to identify neural states from chronic motor cortical and STN recordings in five PD patients (1,046 hours from 10 hemispheres), with concurrent measurements of bradykinesia using wearable sensors. FindingsWe identified four neural states with distinct spectral and temporal features. Two states exhibited spectral signatures--particularly STN low and high gamma, STN delta/alpha, cortical beta, and cortico-STN beta coherence--that predicted worsening bradykinesia. However, STN beta power alone was not consistently predictive, challenging traditional beta-centric views. These states also displayed compensatory features associated with bradykinesia amelioration, including cortical delta/alpha activity, cortical high gamma, and cortico-STN high gamma coherence. Two additional states affected bradykinesia through temporal rather than spectral properties. Prolonged lifetimes of one of these state worsened symptoms, whereas increased occurrences of another, marked by local beta without cortico-STN beta coherence, improved motor function. InterpretationOur findings highlight the multidimensional nature of bradykinesia and suggest that state-aware, adaptive interventions targeting state features--rather than single frequency bands--may offer new opportunities for improved deep brain stimulation in PD. FundingAO is supported by an MRC Clinician Scientist Fellowship (MR/W024810/1) and a Rosetrees Trust/Race Against Dementia Team award. BA and AO acknowledge funding support from the Oxford University Hospitals Charity and Jon Moulton Trust. TL acknowledges funding support from the China Scholarship Council. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSPrevious work has demonstrated that subthalamic nucleus oscillatory activity at beta (15-30 Hz) frequencies correlates positively with motor symptoms in Parkinsons disease. This has led to beta activity being used as a biomarker for adaptive Deep Brain Stimulation. It remains unclear however whether other oscillatory features within the broader motor cortical-subthalamic nucleus network could provide improved biomarkers for tracking symptom severity. Added value of this studyWe address this by performing chronic motor cortical and subthalamic nucleus recordings in Parkinsons disease patients during activities of daily living. Simultaneous measurements of symptom severity were captured using wearable sensors. We used Hidden Markov Models to identify transient states of neural activity and related these to symptom severity. Although cortical beta and cortico-STN beta coherence predicted worsening motor symptoms, STN beta activity alone was not a consistent predictor. Interestingly, we identified spectral features associated with motor symptom improvements, including cortical delta/alpha activity, cortical high gamma, and cortico-STN high gamma coherence. Additionally, there was a compensatory state characterised by short-lived cortical and subthalamic nucleus beta activity, whose increased occurrence was associated with symptomatic improvements. Implications of all the available evidenceOur findings highlight the importance of prolonged, high temporal resolution measurements of both neural activity and symptom severity for discovering adaptive Deep Brain Stimulation biomarkers. Crucially, we identify new target states and spectral features for improving motor symptoms in Parkinsons disease.

neuroscience↗

bioRxiv2025

MutAIverse: An AI-Powered, Mechanism-backed Platform for Discovering Novel DNA Adducts and their precursor Genotoxins

Genotoxin exposure leads to DNA adduct formation, potentially causing mutations if unrepaired. Current DNA adductomics platforms or analytical workflows are limited by incomplete spectral libraries, reliance on experimentally validated adducts, limited cellular contexts, and inefficient computational methodologies. We introduce MutAIverse, an advanced AI-driven DNA adductomics analysis platform that overcomes these limitations by leveraging intracellular mechanistic modeling of genotoxin bioactivation to construct a comprehensive DNA adduct library and offers advanced spectral mapping. MutAIverse integrates experimentally validated and chemically valid putative DNA adducts, enabling interpretable retrograde tracking to parental genotoxins. Validation of MutAIverse against experimental MS/MS datasets demonstrated the detection of both known and novel adducts. Furthermore, application to in-house generated DNA adductomics data from tissue biopsies of smokeless tobacco-induced head and neck cancer patients revealed selective enrichment of both novel and known DNA adducts; a subset of them was validated using MS/MS analysis. Collectively, MutAIverse provides a robust, end-to-end, and interpretable platform for advanced DNA adductomics analysis.

bioinformatics↗

bioRxiv2025

Arg80 Orchestrates a Metabolic-Translational Proteostasis Network in S. cerevisiae

Proteostasis or protein homeostasis is essential for cellular function and organismal health. While many models of cytosolic proteostasis emphasize heat shock response as critical for regulating cellular protein folding, a comprehensive understanding of transcriptional modules that may regulate cytosolic protein folding is lacking. Through a focused screening for transcription factors, we provide evidence that a number of transcriptional programs unlinked to canonical proteotoxic response are involved in maintaining cellular homeostasis of protein folding. Among these, Arg80, a regulator of arginine metabolism, was activated during proteotoxic stress and found essential for mitigating it. We show that proteostasis imbalance in arg80{Delta} cells is caused by excess arginine accumulation, which is sufficient to impair protein folding. We reveal a complex interplay between arginine repression (Arg80), trehalose biosynthesis (Tps2), and the integrated stress response (Gcn2) in combating proteotoxic insults. We posit that multiple metabolic pathways integrate with classical protein quality control networks to regulate the protein folding environment. Harnessing these metabolic circuits may offer new avenues to modulate proteostasis when needed.

systems biology↗

bioRxiv2025

Clustering within a single-component biomolecular condensate

Biomolecular condensates (BMCs) are assemblies of hundreds to many thousands of macromolecules within cells that are organized without physical barriers. Condensate function is dictated not only by its molecular composition, but also by substructural organization and molecular mobility. One hypothesis for the onset of multiple protein aggregation diseases is that the increased densities of specific proteins within BMCs promotes the formation of solid inclusions. However, deciphering the internal structural and functional properties of BMCs at the nanoscale and identifying the initiating events of inclusion formation requires tools with high spatiotemporal precision. Here we show using single molecule and other microscopy approaches that single component Fused in Sarcoma (FUS) condensates exhibit confinement and contain clusters with higher FUS density even at early timepoints. Upon aging, condensates displayed altered physical properties and reduced monomer mobility, and yet most FUS monomers diffused throughout the condensate within seconds. While an increase in connectivity over time explains reduced mobility, the large fraction of molecules retaining high mobility suggests a sponge-like structure rather than a system-spanning network. These findings indicate that a pseudo-equilibrium between distinct structural connectivities can exist within simple condensates, suggesting the potential for substantial structural and functional complexity of BMCs at the nanoscale.

biophysics↗

bioRxiv2025

CerS2 is a druggable target in triple-negative breast cancer

Triple-negative breast cancer (TNBC) remains a significant clinical challenge due to its aggressive nature and lack of effective targeted therapies. The enzyme ceramide synthase 2 (CerS2), which synthesizes pro-apoptotic very long-chain ceramides (VLCCs), represents a promising therapeutic target. Here, we identify and characterize DH20931, a novel, first-in-class small-molecule agonist of CerS2. We demonstrate that DH20931 directly activates CerS2 with nanomolar potency, leading to significant VLCC accumulation in breast cancer cells. This lipotoxic event induces endoplasmic reticulum (ER) stress and triggers apoptosis via the canonical ATF4/CHOP/PUMA signaling pathway. Mechanistically, we uncover a novel interaction between CerS2 and the ER calcium channel, Inositol 1,4,5-trisphosphate receptor 1 (IP3R1). We demonstrate that DH20931 promotes this interaction, enhancing ER-mitochondria proximity and facilitating a CerS2-dependent flux of calcium (Ca{superscript 2}) from the ER into mitochondria. This subsequent mitochondrial Ca{superscript 2} overload serves as a critical trigger for apoptosis. In preclinical evaluations, DH20931 potently inhibited the growth of TNBC cells in 2D and 3D cultures and significantly suppressed tumor progression in orthotopic and patient-derived xenograft (PDX) models, all while exhibiting a favorable safety profile. Our findings validate CerS2 as a druggable target in TNBC and establish a novel therapeutic strategy that leverages a coordinated attack on cancer cells through ER stress and calcium-mediated mitochondrial dysfunction. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=100 SRC="FIGDIR/small/670525v1_ufig1.gif" ALT="Figure 1"> View larger version (33K): org.highwire.dtl.DTLVardef@2db377org.highwire.dtl.DTLVardef@6175d4org.highwire.dtl.DTLVardef@7edb8corg.highwire.dtl.DTLVardef@80042e_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIDH20931 is a first-in-class, potent agonist of Ceramide Synthase 2 (CerS2). C_LIO_LICerS2 activation induces ER stress and engages the ATF4/CHOP/PUMA apoptotic pathway. C_LIO_LIDH20931 promotes a novel CerS2-IP3R1 interaction, causing lethal mitochondrial calcium overload. C_LIO_LITargeting CerS2 shows significant preclinical efficacy against triple-negative breast cancer. C_LI

cancer biology↗

bioRxiv2025

A new species of Polyrhachis Smith from Garbhanga Reserve Forest, Assam, India, with a key to the Indian species of Polyrhachis mucronata group (Hymenoptera: Formicidae)

Polyrhachis Smith, 1857 is a genus of ants, found widely across the Old-World tropics, with significant diversity across South Asia. Known to have diverse nesting habits, ranging from subterranean to arboreal, the genus is arguably one of the most taxonomically and ecologically diverse ant genera globally. The genus is, however, characterised by a unique morphology that includes prominent spines on the mesosoma and petiole, thick integuments, and brightly coloured pubescence in some species. With over 700 described species and 82 valid subspecies, Polyrhachis is also the second most diverse ant genus in India, with 71 identified species. In the state of Assam in northeastern India, the genus is the second-most diverse after Camponotus. Field sampling in the Garbhanga Reserve Forest, near the city of Guwahati in Assam, revealed a new species of Polyrhachis, which is described and named here as Polyrhachis garbhangaensis or the "Assamese Spiny Ant." The discovery of this species, which belongs to the Polyrhachis mucronata group, and its subsequent characterisation made evident the urgent need for a reassessment of the classification key of the genus, which we additionally provide here. This finding, we believe, contributes to a deeper understanding of the taxonomic diversity of Polyrhachis but, at the same time, highlights the importance of urban and fragmented forest areas in sustaining tropical ant biodiversity.

zoology↗