Biology subjects

Ahmed, M.

Publications and source records attributed to Ahmed, M..

At least 19 recordsLinked to original sources

bioRxiv2026

BRCA2 loss drives a PKM1-dominant glycolytic state that is selectively lethal to pyruvate kinase activation

Homologous recombination deficiency (HRD), most commonly arising from BRCA1/2 loss, is accompanied by metabolic remodeling whose contours and therapeutic implications remain poorly defined. Through pan-cancer analysis of 10,619 tumors from The Cancer Genome Atlas (TCGA) and isogenic BRCA1/2-deficient models, we show that HRD tumors display broad metabolic rewiring, with consistent alterations in glucose metabolism. Unexpectedly, BRCA1/2 loss is associated with selective upregulation of the constitutively active glycolytic enzyme Pyruvate Kinase M1 (PKM1) isoform, contrasting with the PKM2-dominant state of most cancers, and produces an elevated pyruvate kinase activity state. Overactivating PKM, with small molecules activators, including the FDA-approved drug mitapivat, triggers superoxide accumulation, disrupts PINK1-dependent mitochondrial quality control, induces DNA damage, and selectively kills BRCA2-deficient tumors in vivo, while sparing BRCA2-proficient counterparts. These findings recast HRD as a metabolic state and identify PKM activation as a candidate therapeutic strategy for biomarker-selected HR-deficient cancers.

cancer biology↗

bioRxiv2026

Translation elongation factor EF-P drives susceptibility to fluoroquinolone antibiotics in Bacillus subtilis

The emergence of antimicrobial resistance restricts the clinical efficacy of therapeutic antibiotic drugs. Elucidating the molecular mechanisms by which bacteria evade antibiotic activities will lead to novel therapeutic approaches. Therefore, it is critical to understand the mechanisms that govern susceptibility to antibiotics. Fluoroquinolones are a class of antibiotics widely used to treat both Gram-positive and Gram-negative bacterial infections. Resistance to fluoroquinolones is widespread in multiple pathogenic bacteria, limiting their therapeutic usefulness. Resistance to fluoroquinolones is well-known to be mediated by Point mutations in the genes encoding the cellular targets of fluoroquinolones, type-II topoisomerases, leads to clinically relevant resistance. However, several recent studies have revealed that dysregulation of translation influences fitness during fluoroquinolone exposure. For example, several screens have identified insertions in gene that encodes elongation factor P (EF-P) increases survival to fluoroquinolones. Here, we sought to understand the impact of EF-P on fluoroquinolone survival using the Gram-positive model organism Bacillus subtilis. We found that loss of EF-P increases the survival of B. subtilis exposed to fluoroquinolones by several orders of magnitude. Furthermore, we demonstrate that fluoroquinolone sensitivity is dependent on post-translational modification of EF-P, indicating that it is dependent on EF-P activity. Remarkably, loss of EF-P increases survival of cells lacking RecA, a key DNA repair protein, which is crucial for the survival of fluoroquinolone drugs. Using transcriptomics, we identify key cellular response pathways differentially regulated in cells lacking EF-P during fluoroquinolone treatment. We conclude that EF-P regulates diverse mechanisms that drive the susceptibility to fluoroquinolones.

microbiology↗

bioRxiv2026

DNMT1-Mediated Epigenetic Reprogramming Drives KMT2A Amplifications and Rearrangements

MLL/KMT2A amplifications and rearrangements are prevalent in infant, adult, and therapy-induced leukemia; however, the molecular contributors controlling these alterations remain elusive. Here, we reveal that rapid CTCF degradation generates local genome structure alterations at KMT2A and copy gains and rearrangements. We then established a conserved, coordinated interplay between DNA and histone methylation pathways that control CTCF occupancy, and in turn, KMT2A locus stability. For example, DNMT1 overexpression promotes increased H3K9 methylation, reduced CTCF occupancy, and causes KMT2A alterations. However, DNMT1 inhibition suppresses these events and KMT2A alterations caused by topoisomerase II inhibition. Locus-specific epigenome targeting demonstrated that DNA or H3K9 methylation promotes KMT2A copy gains and rearrangement, whereas targeted TET activity suppresses these events upon methylation perturbation or doxorubicin treatment. These findings identify a conserved, coordinated DNA-histone methylation axis governing KMT2A amplifications and rearrangement susceptibility, revealing biomarkers and therapeutic targets to predict and intercept these events in cancer.

cancer biology↗

bioRxiv2026

NLRX1 is an essential, druggable regulator of mitochondrial permeability transition

The molecular composition of the mitochondrial permeability transition pore (mPTP) remains contested, and several efficacious mPTP inhibitors act through undefined, cyclophilin D (CypD)-independent targets. Using two structurally distinct chemotypes of optimised, brain-penetrant mPTP inhibitors as chemical probes, we applied affinity-based chemoproteomics to identify the mitochondrial NOD-like receptor NLRX1 as their shared target. Both chemotypes bind NLRX1, and binding potency across a compound series tracks mPTP-inhibitory activity. Using CRISPR-Cas9-edited human cells and Nlrx1-/- mouse tissues, we show that NLRX1 is required for normal calcium-induced mPTP opening: its loss raises the calcium threshold for pore opening and its overexpression lowers it, independently of CypD. NLRX1 associates with postulated mPTP components, including ATP synthase and the adenine nucleotide translocase, in a compound-sensitive manner, and sustains mitochondrial protein homeostasis over longer timescales. The lead compound, GSK900, is orally bioavailable, brain-penetrant, and active in an mPTP-sensitive neurological injury model. These findings, converging with recent genetic studies, establish NLRX1 as an essential, CypD-independent regulator of mitochondrial permeability transition and provide brain-penetrant chemical tools to interrogate this biology.

cell biology↗

bioRxiv2026

Exercise engages a mechanically activated astrocyte state linking muscle activity to hippocampal plasticity

Physical exercise promotes brain health in part through muscle-derived factors that enter the brain, but how peripheral signals are translated into neural responses remain unclear. Here, we identify astrocyte contraction as a previously unrecognized physiological response to exercise signals that may contribute to adult hippocampal neurogenesis. In vivo, voluntary running rapidly induced nuclear localization of the mechanically sensitive transcriptional regulator Yes-associated protein (YAP), and increased non-muscle myosin II phosphorylation in hilar astrocytes in mice, consistent with acute contraction. Using an in vitro platform with ultrasensitive force sensors, we found that factors released by contracting skeletal muscles activated astrocytes which in turn increased contraction that was necessary and sufficient for their proliferation and expansion. Activated astrocytes subsequently released soluble factors that modulated neuronal network tension and promoted immature neuron abundance. These findings identify astrocyte contractility as a physiological transducer of exercise-derived muscle signals and establish cellular force generation as a potential mechanism regulating neuroplasticity.

neuroscience↗

bioRxiv2026

Gateway: patient olfactory neurons for large-scale discovery in neurodegenerative disease

An estimated 42% of Americans over age 55 will develop dementia, but the molecular understanding of dementia and neurodegenerative disease is constrained because the living human brain cannot be routinely sampled during disease progression. Olfactory sensory neurons provide a clinically accessible neuronal tissue source with developmental, transcriptional, and disease-relevant links to the central nervous system. Here we describe Gateway, a platform that combines device guided olfactory epithelium biopsy, onsite fixation, and 10x Genomics FLEX RNA profiling to generate single-cell transcriptomic data from living patient neurons. We present a 4-million-cell atlas representing 202 human donors, including healthy controls and individuals with neurodegenerative diseases, and release it as an open resource through CELLxGENE. We define the cellular composition of the human olfactory epithelium and show that Gateway captures neuronal functional and compartmental programs and detects more brain-enriched genes than other clinically accessible transcriptomic sample types. In exploratory analyses of Alzheimers Disease and Parkinsons Disease, we identify dys-regulation of pathways and GWAS-implicated genes related to key neurodegenerative mechanisms such as neuroinflammation, endolysosomal biology, proteostasis, and synaptic maintenance. Together, this atlas and clinical workflow establish living patient olfactory neurons as a scalable complementary modality for neuroscience research, target discovery, and biomarker development in neurodegenerative disease.

neuroscience↗

bioRxiv2026

Intestinal fructose metabolism drives unsaturated fat absorption and synergizes with GLP-1 receptor agonism to promote weight loss

High-fat, high-sucrose (HFHS) diets are established risk factors for obesity. In the intestine, sucrose is hydrolyzed into glucose and fructose, with fructose being taken up by epithelial cells and phosphorylated by ketohexokinase (KHK). We hypothesized that KHK is required for the obesogenic effects of HFHS diets and performed genetic and pharmacologic experiments in mice using diet-induced obesity (DIO) models. We show that genetic loss of KHK prevents HFHS-induced weight gain and intestinal villus elongation. Moreover, pharmacologic inhibition of KHK (KHKi) promotes weight and fat loss during continued HFHS feeding in DIO mice and enhances weight loss and weight maintenance during and after incretin-mimetic therapy. The anti-obesogenic effects of KHKi were associated with delayed intestinal lipid absorption, reprogramming of lipid metabolism in the distal intestinal epithelium, and reduced absorption of unsaturated dietary fats. Together, these findings identify fructose metabolism as a key regulator of intestinal lipid handling and suggest that fructose promotes obesity, in part, by enhancing intestinal lipid absorption and metabolism.

cell biology↗

bioRxiv2026

Bronchus associated lymphoid tissue induced by an attenuated Mycobacterium tuberculosis vaccine prevents tuberculosis from heterologous TB challenge

Tuberculosis (TB) remains a leading cause of death from infectious disease worldwide, underscoring the urgent need for vaccines with greater and more consistent efficacy than Bacille Calmette-Guerin (BCG). We previously showed that mucosal vaccination with an isogenic Mycobacterium tuberculosis (Mtb) mutant lacking the stress-response transcription factor SigH ({Delta}sigH) prevents pulmonary TB in two macaque species. In the absence of SigH, Mtb is unable to effectively counter host oxidative stress. Vaccinated macaques were notably protected from disease, exhibiting an absence of granulomatous pathology together with the formation of lymphoid follicles and robust antigen-specific CD4+ and CD8+ T cell responses, identifying{Delta} sigH as a promising live-attenuated TB vaccine candidate. The{Delta} sigH mutant used in prior studies was generated in the Mtb CDC1551 background, a commonly used laboratory strain for challenge studies. Here, we evaluated whether{Delta} sigH-mediated protection extends to heterologous challenge with the more virulent Mtb Erdman strain. Mucosal{Delta} sigH vaccination conferred significant protection against heterologous challenge, markedly reducing pulmonary bacterial burden and TB-associated pathology. Longitudinal high-resolution PET/CT imaging demonstrated that aerosol{Delta} sigH vaccination induced robust inducible bronchus-associated lymphoid tissue (iBALT) responses in the lung. Unlike granulomas, these iBALT structures resolved over time while remaining associated with protection against subsequent Mtb challenge. Protection of highly susceptible rhesus macaques against virulent heterologous Mtb challenge following aerosol{Delta} sigH vaccination supports the further preclinical development of{Delta} sigH-based live-attenuated TB vaccines and highlights iBALT induction as a potential correlate and mechanistic driver of protective immunity against TB.

immunology↗

bioRxiv2026

Mass spectrometric analysis of free methionine oxidation levels in E. coli

Oxidation of free methionine plays important roles in cellular redox homeostasis, yet its accurate quantification has been hindered by methodological challenges. Here, we introduce free Methionine Oxidation by Blocking (fMObB), a mass spectrometry-based method that enables accurate measurement of the fractional oxidation of free methionines. Applying fMObB to Escherichia coli, we quantify free methionine oxidation under basal and oxidative stress conditions, and in strains lacking methionine sulfoxide reductases. We find that during oxidative stress, free methionines exhibit higher oxidation levels than protein-bound methionines and that methionine sulfoxide reductases play a central role in maintaining reduced free methionine pools. Together, this work establishes fMObB as a generalizable strategy for probing free methionine redox states in cellular systems.

biochemistry↗

bioRxiv2026

Modeling and optimization of a central diamond shape threefold hexagon metamaterial sensor for glioblastoma cell detection

The present study introduces a novel design and analysis of a sensor based on a terahertz metamaterial absorber (MMA) to identify Glioblastoma cell by employing microwave imaging techniques. Terahertz (THz) frequencies offer unique advantages for biomedical applications. Computer Simulation Technology (CST) employs a finite integration (FIT) approach to simulate the suggested structure in the resonant frequency (RF) range of 4.5 THz to 6 THz. The crystal structure displays three distinct absorption peaks at resonance frequencies. The MTA can absorb energy in three specific spectral bands: 4.782 THz, 5.30 THz, and 5.7319 THz. At these frequencies, the MTM achieves exceptionally high absorption, reaching 99.99%, 99.98%, and 99.68% peak absorption, respectively. The electric field (E), magnetic field (H), and surface current of the MTM are also examined. Finally, detecting Glioblastoma cells is also being investigated by analyzing the E-field H-field using microwave imaging. The suggested biosensor features a high-quality factor of 143.63, a frequency shifts per refractive index of 1.45 THz/RIU. In this study, the PCR value is measured at 0.95 at a frequency of 4.782 THz, indicating a high efficiency in polarization conversion. Polarization Conversion Ratio (PCR) quantifies the efficiency of a metamaterial in converting the polarization of an incident electromagnetic wave. Extensive simulation studies confirm the sensors capability to distinguish between healthy and cancerous cervical tissue. The suggested MMA-based sensor has numerous advantages and can be utilized for Glioblastoma cell detection.

bioengineering↗

bioRxiv2026

Impacts of Morphology and Elasticity on Cancer Cell Deformation in Shear-flows

PurposeThis work investigates the role of the cancer cell morphology and elasticity on the deformation patterns under shear-flow in a micro-channel. MethodsA novel hybrid continuum-particle framework is developed to simulate cancer-cell dynamics. Cell membrane and nucleus geometries are reconstructed from microscopic images and modeled using Dissipative Particle Dynamics, while the surrounding blood plasma is treated as an incompressible Newtonian fluid. Cell-flow interactions are captured via an immersed boundary method. ResultsAll cancer-cell models exhibited a rapid deformation response within the first 1-2 ms, followed by morphology- and stiffness-dependent shape evolution. The compact morphologies showed strong recovery, whereas the other models evolved toward folded/lobed states with only intermittent partial recovery during shape transitions. Membrane stiffening dominated elongation and compactness loss, while nuclear stiffening modulated deformation excursions and partial recovery. These shape transitions were accompanied by near-field vortex reorganization and traction localization. Similar to deformation response the net membrane force exhibited a common start-up rise within 0-0.5 ms followed by relaxation. Compact morphologies produce lower and steadier forces. They show minimal stiffness dependence. Deformation-prone morphologies show stronger unsteadiness and clearer stiffness modulation. Cross-sectional velocity and vorticity fields showed a dominant x-directed hydrodynamic imbalance and lateral migration. ConclusionOur results demonstrate that morphology sets the stiffness modulated deformation patterns which effects the extracellular flow dynamics and traction. In turn, the resulting flow field and traction distribution feed back to influence subsequent deformation and migration. This mechanistic link provides a framework for interpreting circulating tumor cell transport in shear-dominated metastatic environments.

bioengineering↗

bioRxiv2026

Benchmarking the quantitative performance of metabarcoding and shotgun sequencing using mock communities of marine nematodes

High-throughput sequencing has transformed biodiversity assessment and ecological monitoring, yet its quantitative reliability remains unclear. Here, we assembled two experiments of nematode mock communities: one based on extracted DNA and one on individual specimens. Although DNA extraction was required in both experiments to assess the quantitative performance of the sequencing approaches, we essentially evaluated whether this performance was influenced by differences in the start material used to constructed the mock communities. Each community was analyzed using 18S and 28S metabarcoding and shotgun sequencing to evaluate their ability to resolve quantitative information. Across datasets, the number of observed taxa increased with sequencing depth despite controlled input, indicating that higher read numbers primarily revealed intragenomic variation in nematodes than true diversity. Community composition was more accurately recovered by 18S metabarcoding and shotgun sequencing than by 28S. Both sequencing approaches reflected DNA input reasonably well; however, shotgun sequencing provided more consistent abundance estimates relative to individual counts, particularly for nematodes with relatively large-bodied size. In contrast, all methods showed limited ability to accurately quantify taxa with low DNA input or small body size. Comparisons between mock community types showed strong correspondence between read abundance and DNA input, but weaker relationships with individual counts. Overall, both metabarcoding and shotgun sequencing effectively detected community-level patterns and within-taxon abundance, but shotgun sequencing was more reliable for cross-taxon quantitative comparisons. Our findings demonstrate how input material, primer choice, and sequencing approach influence the accuracy of nematode abundance estimates, and provide guidance for improving quantitative applications in nematode-based bioindication and, more broadly environmental DNA biomonitoring.

ecology↗

bioRxiv2026

Acute Sublethal Heat Stress Impairs Blood Feeding and Trypanosome Infection in the Kissing Bug, Rhodnius prolixus

Kissing bugs are the primary vectors of Trypanosoma cruzi, the causative agent of Chagas disease. Kissing bugs are exposed to thermal variability, including short periods of heat stress, which can induce mortality or exert sublethal effects. This study investigated Rhodnius prolixus following brief periods of high thermal stress with respect to survival, blood feeding, developmental processes, and T. cruzi infection, with a focus on sublethal effects. Our results demonstrated a significant decrease in survival for R. prolixus at 42 {degrees}C for 8 hours. When exposed to sub-lethal thermal stress (40{degrees}C for 8 hours), blood ingestion (amount and proportion) was reduced after 24 hours of recovery from thermal stress. Among the bugs that fed after 24 hours, molting was not impacted by temperature exposure. The infection rate decreased after heat exposure, likely due to reduced blood volume ingested when feeding 24 hours after heat stress. A week of recovery after exposure to higher temperatures improved feeding and increased infection rates to levels comparable to those of kissing bugs not exposed to thermal stress. Our findings offer insights into how extreme temperature events may influence Chagas disease. Specifically, these studies highlight the need to clarify how temperature, particularly at sublethal levels, interacts with vector biology to alter parasite transmission.

physiology↗

bioRxiv2026

Molecular and spatial profiling identifies immune endotypes for the stratification of OA patients

Osteoarthritis (OA) is a prevalent and heterogeneous joint disease in which synovial inflammation drives structural progression and pain. Despite the recognized heterogeneity of OA, the cellular and molecular organization of synovial tissue remains poorly characterized and defining distinct histological and immune endotypes could guide precision medicine and therapeutic targeting. We show that histologically defined synovial pathotypes are conserved across independent cohorts and correspond to distinct molecular immune endotypes. Integration of bulk and spatial transcriptomics with proteomics revealed niche-specific gene and protein signatures, reflecting the anatomical and functional diversity of OA synovium. The lympho-myeloid pathotype was characterized by mature ectopic lymphoid structures containing CD21+CD23+ follicular dendritic cells, spatially organized T and B cell zones, and clonally expanded T and B cells with shared immune cell receptor motifs, consistent with local adaptive immune activity correlating with radiological joint damage. These findings highlight how immune organization and cellular composition shape OA pathogenesis and provide a framework for endotype-guided stratification and therapeutic targeting.

immunology↗

bioRxiv2025

Cyclic AMP compartmentalization drives signal specificity to control vector colonization and mammalian host infection by American trypanosomes

Cyclic AMP (cAMP) signaling is crucial for environmental sensing and response to stress conditions in trypanosomatids. However, the mechanisms driving the specificity of cAMP signals remain poorly understood in these protozoan parasites. We recently identified two putative cAMP microdomains in Trypanosoma cruzi, the causative agent of Chagas disease. Here, considering the localization of three phosphodiesterases, PDEC at the contractile vacuole complex (CVC), and PDEB1 and PDEB2 along the flagellum, we modulated their expression to functionally characterize the flagellar tip (FT) and the CVC as individual cAMP microdomains, named FT-cAMP and CVC-cAMP, respectively. We generated PDE knockout and overexpression cell lines to selectively alter cAMP signals generated in each compartment. Our results indicate that FT-cAMP mediates cell adhesion, metacyclogenesis, host cell invasion, and intracellular replication, while CVC-cAMP is required for osmoregulation and epimastigote proliferation. In addition, ablation of flagellar PDEB1 and PDEB2 enhanced the parasites ability to colonize the hindgut of the triatomine vector, whereas PDEC-KO parasites were impaired in their establishment in the insects hindgut. The observed phenotypes were compartment-specific, demonstrating functional segregation between the two cAMP microdomains. Our data provide robust evidence on the presence of compartmentalized cAMP signals in T. cruzi, linking the role of locally synthesized cAMP pools to specific cellular responses during the parasites life cycle. Author summaryChagas disease is a life-threatening infectious disease caused by the protozoan parasite Trypanosoma cruzi, which is spread through the feces of infected kissing bugs. The parasite survives in challenging environments as it transitions between the insect vector and the mammalian host by differentiating into distinct developmental forms. cAMP is a universal second messenger that mediates specific cellular processes in the life cycle of T. cruzi. However, the spatial-temporal dynamics of cAMP signal remain largely unexplored in trypanosomes. We previously reported several cAMP signaling proteins in two compartments of T. cruzi: the contractile vacuole complex (CVC) and the flagellar tip (FT). In this study, we characterized the individual functions of these microdomains. We specifically disturbed cAMP signaling in these compartments by modulating the expression of their resident phosphodiesterases. We observed that the FT microdomain is specifically involved in parasite differentiation, host cell invasion, intracellular replication, and vector colonization, while the CVC microdomain is important for osmoregulation and parasite survival within the kissing bug. Our results unequivocally demonstrate that T. cruzi utilizes specific cAMP pools to address different environmental challenges. These findings highlight cAMP signaling as an essential pathway that could be further explored for the development of novel antiparasitic interventions.

cell biology↗

bioRxiv2025

Loss of ADAMTS9 results in Nephronophthisis like polycystic kidneys by disrupting ciliogenesis and ECM dynamics

ADAMTS9 mutations cause the ciliopathies nephronophthisis and Joubert syndrome. Here we show that deletion of ADAMTS9 in the proximal nephron leads to polycystic kidney development in mice. In males, Adamts9 deletion cause kidneys to become highly cystic but remain small without undergoing enlargement, causing early postnatal lethality. Female mice on the other hand, develop cystic kidneys but progress slowly. ADAMTS9 deletion disrupted ciliogenesis by the loss of ciliary transition zone (TZ) protein TMEM67 cleavage, leading to loss of the MKS/B9 module - a key component of the ciliary gate. Functional analysis of all eight ciliopathy patient variants of ADAMTS9 identified to date, showed TMEM67 C-terminus failed to localize to the transition zone, thus disrupting a key regulatory mechanism in patient renal ciliogenesis. Modeling ADAMTS9-mediated TMEM67 cleavage utilizing our novel TMEM67-cleavage deficient mice revealed loss of TZ formation but not elevated canonical Wnt signaling as the underlying mechanism driving cystogenesis. We show that Adamts9 deletion leads to comparatively intense interstitial collagen deposition, which likely restricts kidney enlargement resulting in the characteristically small kidney phenotype in nephronophthisis and increased immune response. By comparative analysis of four interconnected polycystic kidney models in addition to Pkd1 and Pkd2 deleted kidneys, we identify differential collagen homeostasis is the principle determining factor deciphering cystic kidney size and type.

cell biology↗

bioRxiv2025

The impacts of shape in lateral migration of cancer cells in a microchannel

This work presents the development of a novel approach to model the dynamics of cancer cells in microcirculation. We investigate the role the membrane elasticity, and cancer cell shape on deformation dynamics under the shear and pressure forces in a micro-channel. The proposed numerical model is based on a hybrid continuum-particle approach. The cancer cell model includes the cell membrane, nucleus, cytoplasm and the cytoskeleton. The Dissipative Particle Dynamics method was employed to simulate the mechanical components. The blood plasma is modeled as a Newtonian incompressible fluid. A Fluid-Structure Interaction coupling, leveraging the Immersed Boundary Method is developed to simulate the cells response to flow dynamics. We quantify how subtle variations in these biophysical properties alter deformation indices such as sphericity and aspect ratio, and stress distributions on the membrane of the cancer cell. Our findings align well with existing computational and experimental studies. Results reveal that increased membrane stiffness reduces overall deformation as well as the total distance traveled. Similarly, cell geometry strongly influences flow-structure interactions: near-spherical morphologies exhibit stable deformation with minimal sensitivity to shear variations, whereas elongated geometries show pronounced orientation and stretching effects. Collectively, these findings highlight the critical importance of cell-specific heterogeneity in governing cell dynamics in microvascular flows. Furthermore, the intracellular and extracellular dynamics response of the cancer cell are intrinsically linked to their shape, in which certain morphologies displayed strong resistance to the fluid-induced forces and the ability to migrate in various directions. The insights obtained provide a mechanistic framework for understanding circulating tumor cell transport in shear-dominated environments during metastasis. Our work may inform the design of biomimetic microfluidic systems and therapeutic strategies targeting cancer cell detection and cancer prognosis.

biophysics↗

bioRxiv2025

Menin inhibition impairs metastatic colonization of Ewing sarcoma

Menin is a scaffolding protein that interacts with context-specific partners to regulate gene expression. In MLL-rearranged leukemias, Menin:MLL interactions drive leukemogenesis and Menin inhibitors have been FDA approved for these cancers. We previously reported that Menin promotes oncogenic phenotypes in Ewing sarcoma (EwS). Here, we sought to define EwS-specific functions of Menin and determine if Menin inhibitors could be therapeutically leveraged for these tumors. Genetic knockout of Menin had no impact on EwS cell proliferation in vitro but metastatic potential of Menin-depleted cells in vivo was impaired. Transcriptional profiling of Menin knockout cells in vitro showed reproducible downregulation of MYC signature genes and upregulation of developmental programs. Conversely, transcriptional rewiring of developmental genes and restoration of MYC target gene expression were evident in tumors that arose from Menin knockout cells. Exposing EwS cells to the Menin inhibitor VTP50469 (revumenib) inhibited expression of MYC targets and co-immunoprecipitation studies detected Menin:MYC interactions that were partially disrupted by the drug. Metastatic colonization of disseminated EwS cells in vivo was significantly inhibited in mice fed VTP50469 chow. Together these findings implicate Menin as a mediator of EwS metastasis and suggest that Menin inhibitors warrant investigation as novel therapeutics for patients with high-risk disease.

cancer biology↗