Biology subjects

West, J.

Publications and source records attributed to West, J..

At least 19 recordsLinked to original sources

bioRxiv2026

The filopodial scaffold polyphosphate dictates cell adhesion-versus-invasion decisions

Inorganic polyphosphate (polyP) is an ancient polymer conserved across all life, serving cell type and location specific functions in every major compartment. Yet its role at the plasma membrane, where it accumulates to peak levels in many primary cells, is largely unknown. Here we identify polyP as a stabilizing component of filopodia, actin based membrane protrusions that govern cell adhesion, contact inhibition, and chemotaxis. Elevating cellular polyP increases filopodial stability and enhances cell adhesion, whereas reducing polyP accelerates filopodial disassembly and promotes cell migration. Mechanistically, we find that polyP acts as a structural filopodial scaffold, recruiting and organizing IRSp53, a membrane curvature inducing protein. We show that metastatic fibroblasts and breast cancer organoids carry markedly reduced and intracellularly reorganized polyP levels relative to their non transformed counterparts. Restoring endogenous polyP via lipid nanoparticle delivery suppresses their invasive phenotypes and reverses prometastatic gene expression signatures, implicating polyP as a primordial tumor suppressor.

cell biology↗

bioRxiv2026

A generalized resource-allocation growth law reveals mechanisms of differential responses to intermittent androgen deprivation therapy in prostate cancer

Resource-limited growth frameworks often developed independently. Here, we derived a growth law by assuming a cell balancing internal competing resource demands and generalizing the growth signal through a shape parameter h, the trade-off exponent. In Liebig's single-limiting-resource regime, it recovers Droop's cell quota at h=1 and approaches Prater's growth efficiency as h grows large. h determines how sharply growth declines when allocation departs from optimal, thereby shaping populations evolution. Cyclic environmental stress tests such growth laws. Hence, we built a model from this growth law and applied it to prostate cancer growth in patients undergoing cyclic intermittent androgen deprivation therapy. We showed the model recapitulated longitudinal prostate specific antigen (PSA) and serum androgen measurements from 71 prostate cancer patients using a nonlinear mixed-effects framework (pooled and median individual R^2 {approx} 0.9 for PSA and {approx} 0.8 for serum androgen). h is well-constrained by the data and separates treatment outcomes (success vs. failure, p = 0.003). The results predict that failing cases have cancer that can adapt to a wide range of growth conditions with minimal cost. A simplified model recapitulated PSA dynamics from 32 prostate cancer patients on cyclic adaptive therapy (R^2 {approx} 0.8). Estimates of h for castration resistant cancer in adaptive cohort were similar to failure cases in the intermittent cohort. We found no statistical differences in estimated parameters between the adaptive vs. standard of care arms, suggesting that adaptive schedule may drive the differential outcome. The results support this growth law, providing a foundation for resource-limited growth across biological systems.

ecology↗

bioRxiv2026

A shark variable new antigen receptor recognizes an occluded epitope of fibroblast activation protein

Variable new antigen receptors (VNARs) are the smallest naturally occurring antibody binding domains. Their size allows VNARs to access sterically restricted epitopes that are inaccessible to conventional antibodies. We recently identified a suite of VNARs that target fibroblast activation protein (FAP), a stromal serine protease indicative of extracellular matrix remodeling. The presence of FAP on the surface of cancer-associated fibroblasts (CAFs) that promote immunosuppression has made FAP a compelling therapeutic target for cancer therapy. Although antibodies targeting FAP have been developed, there is a paucity of information on how biologics engage FAP. Here, we used single-particle cryogenic electron microscopy (cryo-EM) to compare FAP recognition of three antibody architectures: a shark-derived VNAR, variable heavy (VH) and light domains (VL) of a humanized Immunoglobulin G (IgG), and a camelid-derived VHH. The humanized VH-VL domains and camelid VHH both target a solvent-exposed {beta}-propeller domain, whereas the VNAR binds a highly conserved, topologically recessed epitope at the FAP dimer interface. Radical-footprinting mass spectrometry (MS) further mapped two additional immune-derived VNARs to distinct FAP surfaces outside the shared {beta}-propeller epitope. These findings demonstrate how unique VNAR architecture can expand access to underexplored FAP surfaces and establish a structural framework for rational multiepitope targeting strategies.

biochemistry↗

bioRxiv2026

Droplet microfluidics reports digital and tuneable single-platelet ADP secretion describing primed, active and hyper-active states

New platelet function assays that provide an accurate assessment of platelet reactivity as a surrogate for thrombosis risk could change the paradigm for acute myocardial infarction and stroke prevention. Considering ADP secretion as a hallmark of platelet activation, we developed a method for encapsulating single platelets with a fluorescent reporter for extracellular ADP in picolitre droplets. The method, termed the Droplet ADP Secretion Assay (DASA), robustly detected dose-dependent ADP secretion responses to agonists. Digital ADP secretion heterogeneity was observed with the major fraction of platelets responding and the remaining fraction being non-responders. Primed platelets had elevated responses to agonists, with increased ADP secretion and an increased fraction of secreting platelets, demonstrating that priming can convert otherwise inactive platelets to a reactive state. Uniquely, the method detected ADP secretion from primed platelets in the absence of agonists. In contrast, primed platelets were not detected by flow cytometry involving CD63 and CD62P endpoints. In a preliminary clinical study, some patients had platelets with a priming-like ADP secretion signature, suggesting treatment with P2Y12 inhibitors may be warranted. In vitro aspirin and ticagrelor treatments reduced ADP secretion responses to agonists. In summary, DASA offers a novel approach to assess platelet reactivity and holds promise for assessing thrombotic tendency and personalised therapeutics.

pathology↗

bioRxiv2026

Ecological axes of skull diversification in a massive 1 vertebrate radiation

Eupercarian spiny-rayed fishes are one of the largest vertebrate radiations, rivaling mammals and occupying nearly every aquatic habitat. We present a densely sampled, time-calibrated phylogenomic framework for Eupercaria, supporting a revised classification, combined with the largest cranial phenomics dataset for fishes. Habitat and trophic ecology make independent, complementary contributions to skull shape. Most species cluster around a conserved generalized architecture, the Percomorph Pile, from which one clade of pufferfishes, anglerfishes, butterflyfishes, and surgeonfishes repeatedly invaded novel morphospace; exceptionally high rates on its deep branches indicate that rapid skull evolution arose early in this clade. Freshwater lineages converge on the ancestral condition, reflecting late arrival into systems occupied by older otophysans, whereas durophages show the greatest disparity and converge on derived forms. Cranial diversity was partitioned among subclades during the Cretaceous and later within them across the Cenozoic, showing that clade-level differences in evolutionary rates and ecological opportunity jointly shaped skull diversification.

evolutionary biology↗

bioRxiv2026

Mechanistic learning to predict and understand minimal residual disease

Mechanistic modeling has long been used as a tool to describe the dynamics of biological systems, especially cancer in response to treatment. Their key advantage lies in interpretability of relationships between input parameters and outcomes of interest. Mechanistic models may also be calibrated to a cohort of patients and scaled up to generate a simulated set of virtual patients whose aggregate behavior reproduces key characteristics of the real patient population. In contrast, machine learning techniques offer strong prediction performance, especially for high dimensional datasets that are common in oncology. Here, we employ a Mechanstic Learning framework that combines the advantages of both approaches by training machine learning models on mechanistic parameters inferred from clinical patient data. We assess the ability of virtual clinical cohorts for the purpose of 1) scaling up small cohort sizes and 2) balancing unbalanced patient subgroups in the setting of BCR::ABL1 positive lymphoblastic leukemia. Our mechanistic model (a Markov chain model) contains sixteen parameters that describe the rate of cell fate transitions that occur in patients with B-cell precursor acute lymphoblastic leukemia. The machine learning (a ridge logistic regression model) is trained on these parameters to predict two clinically-relevant features: BCR::ABL1 fusion gene status (positive or negative) and minimal residual disease status (positive or negative) post-induction chemotherapy. Model training is done in an iterative fashion to assess which (and how many) parameters are critical to maintain high predictive performance. Using machine learning models trained on the clinical flow-cytometry data, we find that the stem-like cell state alone is the most predictive feature for both BCR::ABL1-positive and MRD-positive disease, with composite scores (defined as the average of accuracy, balanced accuracy, and area under the curve) of 0.80 and 0.67, respectively. By comparison, mechanistic learning achieves comparable or improved composite scores for BCR::ABL1-positive and MRD-positive disease, with scores of 0.81 and 0.71, respectively, using only de-differentiation for BCR::ABL1 and stem-state persistence together with differentiation-directed exit for MRD. Virtual Patient (VP) expansion is informative for robustness analysis and class balancing, but full cohort expansion introduced additional heterogeneity, reduced predictive performance, and required larger models, whereas VP-based balancing yielded only a modest gain over class weighting at substantially greater computational cost. In summary, a mechanistic-learning approach not only preserves predictive performance, but also provides a biological hypothesis for why stemness is predictive of these clinically relevant outcomes.

cancer biology↗

bioRxiv2026

A MET-Targeted Variable New Antigen Receptor Theranostic for Non-Small Cell Lung Cancer

The MET receptor tyrosine kinase is mutated or amplified in [~]6% of non-small cell lung cancer (NSCLC) and overexpressed in [~]80% of all NSCLC cases. A theranostic agent that can both see and treat MET-altered NSCLC has never been described before in the literature. Here, we report a shark-derived single-domain variable new antigen receptor (VNAR) for MET with theranostic applications. Following the immunization of a juvenile nurse shark (Ginglymostoma cirratum) with the extracellular domain of human MET, we identified a VNAR clone that specifically engaged MET with high affinity. Engineering the lead VNAR into a bivalent human Fc, vMET1-Fc, yielded a construct that selectively targeted and was internalized by MET-positive cells without affecting cell viability or downstream MET signaling. When radiolabeled with the positron emitting isotope Zr-89, [89Zr]Zr-vMET1-Fc enabled longitudinal PET/CT imaging. High tumor uptake with low background was observed in MET-positive NSCLC xenografts administered [89Zr]Zr-vMET1-Fc. As a targeted beta-particle radiotherapy, [{superscript 1}Lu]Lu-vMET1-Fc resulted in marked tumor-growth delay and exhibited a favorable toxicity profile, collectively improving progression-free survival in NSCLC mouse models. Non-human primate PET/CT imaging studies with ([Zr]Zr-vMET1-Fc in healthy rhesus macaques confirmed favorable biodistribution and dosimetry, predictable clearance, and minimal off-target uptake. Additional blood chemistry analysis found no significant immune response or cytotoxicity. Together, these findings establish vMET1-Fc as a theranostic agent for imaging and treating MET-altered NSCLC. Statement of SignificanceA shark-derived antibody selectively targeting MET shows preclinical efficacy as a theranostic agent for MET-altered cancer.

cancer biology↗

bioRxiv2026

75 Years of Mathematical Oncology

Constructing a comprehensive overview of any scientific field requires accurate literature selection, yet conventional keyword-based searches are susceptible to false positives. This problem is magnified in growing or interdisciplinary fields such as mathematical modeling in oncology that contain a rich but heterogeneous body of literature. Here, a generalizable, context-enriched artificial intelligence pipeline based on large language models (LLMs) curates large scientific corpora according to a user-defined field: mathematical modeling in oncology (>35k publications). Benchmarking against expert evaluation demonstrates high accuracy (ROC AUC[~]0.95) and agreement with human judgement (correlation[~]0.68), outperforming zero-shot LLM curation Analysis of the curated corpus ([~]14k) suggests that Mathematical Oncology s distinct from either Systems Biology and Pharmacokinetics/Pharmacodynamics despite employing overlapping methods. Co-occurring citation network analysis defines nine research clusters focused on a range of applications including drug delivery, optimal control, stochastic modeling, tumor microenvironment, radiation, cancer evolution, and spatial multiscale modeling. Significance StatementA generalizable, context-enriched artificial intelligence pipeline accurately curates large scientific corpora Analysis of the curated dataset applied to the se of mathematics n oncology provides comprehensive view of mathematical modeling in oncology across 140 years, revealing its shift from fundamental cancer biology towards therapeutic modelling.

cancer biology↗

bioRxiv2025

Collagen remodeling promotes a GPCR-mediated mechanosensory immune checkpoint in ADGRG1+ CD8+ T cells and serves as a spatial biomarker of response to immunotherapy

Accessibility of immune cells to the tumor microenvironment (TME) in many solid tumors can be influenced by extracellular matrix (ECM) deposition, organization, and remodeling within tumor stroma. Specifically, lysyl hydroxylase-2 (LH2)-catalyzed lysine hydroxylation in type-I collagen telopeptides leads to formation of intermolecular collagen cross-links creating a stiffened and proteolytically resistant, stable ECM. Advanced head and neck squamous cell carcinomas (HNSCC) frequently exhibit desmoplasia with elevated LH2 expression, and Immune-checkpoint (ICI) therapy is effective in only <20% patients, suggesting that ECM remodeling mechanistically governs the composition and function of TME infiltrates. We show that elevated LH2 and collagen alignment promotes stromal accumulation of CD8 T-cells, and poor response to ICI in HPV-HNSCCs. Integration of clinical biopsies, transcriptomic datasets, and an immunocompetent syngeneic mouse model revealed that aligned collagen spatially restricts adhesion G protein-coupled receptor positive (ADGRG1) CD8 T-cells to activate a non-canonical GPCR-mediated mechanosensory program that drives dysfunction and exhaustion. Statement of significanceDesmoplasia is common in solid tumors, and immune checkpoint inhibitors benefit only some patients. Current biomarkers like PD-L1 and TMB have limited value. Our findings reveal a previously unrecognized collagen-ADGRG1 mechanosensory immune checkpoint, offering a clinically tractable, spatially resolved biomarker to better stratify patients for immunotherapy.

cancer biology↗

bioRxiv2025

Wnt5a-mediated Adipo-Cardiac Interorgan Communication in HFpEF

BackgroundObesity is an important risk factor in heart failure with preserved ejection fraction (HFpEF), but the precise mechanisms that drive obesity-associated cardiac remodeling are not well understood. Our previous work has shown that increased expression of the natriuretic peptide clearance receptor (Nprc) may drive cardiac remodeling in response to high fat diet. In this study, we hypothesized that Nprc plays a central role in preventing and reversing experimental HFpEF. MethodsNprc knockout mice were generated to induce global, cardiomyocyte-specific, or adipocyte-specific disruption of the Nprc (Npr3) gene. HFpEF was induced by the 2-hit stress of L-NAME and high fat diet. Outcomes measured included echocardiography, exercise endurance, invasive catheterization, and histologic assessment. Differential gene expression in adipocyte Nprc knockout visceral adipose tissue was investigated via bulk RNA sequencing and validated by RT-qPCR and culture of H9C2 cells with or without Wnt5a treatment. Adipocyte-mediated Wnt ligand release was interrupted in vivo via LGK974 injection in mice subjected to HFpEF conditions. ResultsGlobal inducible Nprc knockout prevented and reversed structural, hemodynamic, echocardiographic, and exercise tolerance features of HFpEF. This effect was found to be driven by adipocyte-specific, not cardiomyocyte-specific Nprc expression. Bulk RNA sequencing of adipocyte-specific Nprc knockout in peri-gonadal visceral adipose tissue identified downregulation of several secretory pathways, including Wnt pathways. Wnt5a was identified as one of the most downregulated genes by RNA sequencing and specifically validated by qPCR. Wnt5a exposure increased cardiomyocyte hypertrophy in vitro, and LGK974 (PORCN inhibitor) treatment in vivo decreased circulating Wnt5a levels and improved cardiac remodeling in HFpEF. ConclusionsOur study identifies a novel crosstalk mechanism between cardiomyocytes and adipocytes in obesity-associated HFpEF driven by natriuretic peptide-mediated inhibition of release of Wnt5a from adipocytes.

molecular biology↗

bioRxiv2025

Reducing Reactive Lipids Improves Cardiac Metabolic and Diastolic Function in Pulmonary Hypertension Models

BackgroundReactive oxygen species are increased across most pulmonary hypertension (PH) etiologies, resulting in increased reactive lipid dicarbonyls, which form protein adducts and impair mitochondrial function. We hypothesized that reducing reactive lipids would reduce right ventricular systolic pressure (RVSP) and improve cardiac function by eliminating protein-lipid damage feedback loops. MethodsWe used 2-hydroxybenzylamine (2-HOBA) to scavenge reactive lipids in three complimentary mouse models of PH: AKR-high fat diet (HFD, metabolic stress), LNAME-HFD (cardiometabolic syndrome), and pulmonary artery banding (PAB, load stress). Cardiac function was measured by echocardiography and catheterization. RV energy metabolism was determined by oxygraphy. Mass spectrometry analyzed lipids and ceramides; O-link and RNA-Seq evaluated proteomic and gene expression in lungs, RV, and LV. ResultsReducing reactive lipids with 2-HOBA resulted in a [~]10% reduction in RVSP, reduced diastolic dysfunction, reduced plasma lipids and ceramides, and normalized RV fatty acid oxidation that was severely impaired in the AKR-HFD and PAB models. Proteomic and RNA changes in the lungs, RV, and LV suggested reduced oxidative damage and inflammatory signaling and altered developmental and actin organization signaling; these changes are plausibly associated with the improved adaptation. Some changes were sex specific, including a 4x higher cardiac fatty acid content in males than females. ConclusionsReactive lipid scavenging improves cardiac metabolic and diastolic function and pulmonary vascular resistance through restoration of mitochondrial function and reduced oxidative protein damage. The magnitude of hemodynamic improvement combined with substantial diastolic function improvement suggests clinical potential, particularly for PH patients with metabolic comorbidities.

molecular biology↗

bioRxiv2025

Evolutionary antifragile therapy

A population of cells within a tumor can be described as antifragile (the opposite of fragile) if they derive a benefit from fluctuations or perturbations in environmental conditions induced by treatment. We hypothesized that treatment fluctuations may either promote (antifragile tumor) or inhibit (fragile tumor) the evolution of treatment resistance to targeted therapies. Analysis of the convexity of dose response curves provides a direct prediction of response to prescribed fluctuations in treatment. Theory predicts that continuous treatment protocols (i.e. zero prescribed fluctuations in treatment) will outperform uneven protocols when dose response is convex. We apply this theory to predict in vivo response to targeted therapy and validate these predictions by experimentally testing high/low intermittent dosing (uneven dosing) and continuous dosing (even dosing) schedules. Convexity (and its inverse, concavity) explains two phenomena: dose response is a convex (fragile) function but resistance onset rate is a concave (antifragile) function. Thus, we design, propose, and validate alternative treatment schedules which maximize response while maintaining prolonged sensitivity to treatment. These analyses provide supporting evidence that fluctuations alter the evolutionary trajectory of tumors in response to targeted therapy, even without altering the cumulative dose. This insight is used to design alternative, switching treatment protocols to limit the evolution of resistance, a process which we call evolutionary antifragile therapy.

cancer biology↗

bioRxiv2025

Light-Activated Nucleic Acid Amplification Systems Using Photo-caged DNA Polymerase or Primers

Precise control over nucleic acid amplification is essential for achieving reliable, quantitative, high-throughput, and multiplexed molecular diagnostics, particularly in point-of-care and field settings. However, conventional isothermal amplification methods, especially rapid assays at ambient temperature such as recombinase-aided amplification (RAA), suffer from spontaneous initiation and lack of synchronization across parallel reactions. Here, we report light-activatable RAA systems employing two distinct photocaging strategies to achieve spatiotemporal control. In the first, a photocaged DNA polymerase was engineered via site-specific incorporation of p-azido-L-phenylalanine and conjugation with a 2-nitrobenzyl-modified ssDNA blocker through click chemistry. This approach offers high stability, making it advantageous for long-term storage and lyophilized formats. In the second, 5'-nitrobenzyl-modified primers were synthesized to block hybridization or extension until UV activation, offering operational simplicity and rapid integration into existing workflows. Both strategies independently suppressed background activity in the dark and restored full amplification efficiency upon 365 nm UV exposure. The systems exhibited high sensitivity, low background, and compatibility with portable diagnostics. A custom-built device integrating UV activation and real-time fluorescence detection enabled seamless, on-demand operation. This modular platform provides flexible light-gated amplification solutions, allowing the selection of polymerase- or primer-based caging according to storage stability or workflow requirements, thereby advancing precise and field-ready molecular diagnostics.

molecular biology↗

bioRxiv2025

CD33 and Clusterin Interact Biophysically and Genetically to Modulate Alzheimer Risk

We report the results of structural, functional and genetic studies on the CD33 sialic acid- binding receptor that reveal how non-coding variants in CD33 alter risk for Alzheimers disease (AD). The full-length CD33M isoform, whose expression is upregulated by non-coding AD-risk alleles, preferentially forms dimers at the cell surface, where they interact with AD-related proteins (clusterin and A{beta}). This interaction induces CD33M inhibitory signalling and downregulates protective microglial functions including phagocytic removal of amyloid plaques. Human brain expression quantitative trait loci (eQTL) and causal mediation analyses confirm that quantitative interactions between CLU and CD33 genotypes modulate AD phenotypes and suggest that genotypes at these loci might be used to personalise future therapeutic approaches. Our work also highlights several other unexpected aspects of CD33 biology, including a soluble shed extracellular fragment of CD33M and a similar soluble secreted product arising from a truncating mutation in the CD33 extracellular domain (CD33M{Delta}4bp).

neuroscience↗

bioRxiv2025

Spatial profiling reveals TREM2+ macrophages as central to Mycobacterium tuberculosis pathogenesis in human pulmonary tuberculosis

Pulmonary tuberculosis (TB) exhibits marked spatial heterogeneity, with alveolar pneumonia and organized granulomas frequently coexisting within the same lung. While granulomas have long dominated conceptual models of TB pathogenesis, the immune programs operating within alveolar TB pneumonia in humans remain incompletely defined. Here, we integrate spatial transcriptomics, single-cell RNA sequencing, high-resolution imaging, and functional assays of human lung biopsies to directly compare alveolar pneumonia with adjacent granulomas from the same individuals. We demonstrate that alveolar TB pneumonia is enriched for TREM2 lipid-laden macrophages characterized by lipid metabolic reprogramming, sparse T-cell infiltration, attenuated antimicrobial gene expression, and abundant Mycobacterium tuberculosis (Mtb) transcripts and antigens. In contrast, neighboring granulomas exhibit organized lymphoid architecture and robust antimicrobial programs. Mechanistically, the mycobacterial virulence lipid phthiocerol dimycocerosate (PDIM) and free mycolic acids induce TREM2 expression and activate TREM2-DAP12 signaling, promoting lipid droplet accumulation, suppressing autophagy, and enhancing intracellular Mtb survival in human macrophages. This immunometabolic state is pharmacologically reversible: 1,25-dihydroxyvitamin D downregulates TREM2, restores autophagy, reduces lipid droplets, and limits bacterial viability. Together, these findings define a spatially localized TREM2 foamy macrophage program within alveolar pneumonia that contrasts sharply with adjacent granulomatous immunity, establishing an niche permissive for bacillary persistence and potentially transmission, as well as identifying a tractable host pathway in human TB pathogenesis.

immunology↗

bioRxiv2025

CES1 DEFICIENCY IS ASSOCIATED WITH METABOLIC REPROGRAMING AND ENDOTHELIAL DYSFUNCTION IN PULMONARY ARTERIAL HYPERTENSION

BackgroundPulmonary arterial hypertension (PAH) is a progressive disease characterized by pulmonary microvascular loss and obliterative remodeling, driven by metabolic reprogramming, oxidative stress, and endothelial dysfunction. While BMPR2 mutations contribute to metabolic shifts in pulmonary microvascular endothelial cells (PMVECs), their low penetrance suggests additional genetic modifiers play a role. A genetic screen of PAH PMVECs identified carboxylesterase 1 (CES1)--an endoplasmic reticulum (ER) enzyme involved in lipid metabolism and detoxification--as a candidate regulator of endothelial metabolism and angiogenesis. We hypothesize that CES1 loss promotes endothelial dysfunction via metabolic reprogramming, lipotoxicity, and oxidative stress. MethodsPAH and healthy PMVECs and lung tissues were obtained from transplant donors and commercial sources. CES1 expression was modulated in PMVECs using siRNA knockdown and plasmid overexpression. Mitochondrial and ER function were assessed via confocal microscopy and proteomics. CES1 heterozygous knockout (HET KO) and endothelial-specific knockout (ECKO) mice were exposed to normoxia or hypoxia, with lung tissues analyzed by single-cell RNA sequencing (scRNA-seq) and histopathology. ResultsCES1 expression was significantly reduced in PAH PMVECs and vascular lesions. CES1-deficient PMVECs exhibited increased apoptosis, reactive oxygen species (ROS) production, mitochondrial fragmentation, ER stress, and impaired angiogenesis. Confocal imaging and metabolic studies revealed lipid droplet accumulation, reduced fatty acid oxidation, and a glycolytic shift-- phenotypes reversed by CES1 restoration. Mechanistically, CES1 transcription was induced by BMPR2 via NRF2 activation, a key regulator of redox and metabolic homeostasis. In vivo, CES1-deficient mice developed severe pulmonary hypertension (PH) under hypoxia, with extensive vascular remodeling, right ventricular dysfunction, and dysregulated angiogenesis and lipid metabolism pathways, as confirmed by lung scRNA-seq. ConclusionsCES1 is essential for pulmonary endothelial homeostasis and serves as a critical modifier of BMPR2 signaling. Given the limited efficacy of current PAH therapies in reversing endothelial dysfunction and small-vessel loss, restoring CES1 expression represents a promising therapeutic strategy.

biochemistry↗

bioRxiv2025

Cell state transitions drive the evolution of disease progression in B-lymphoblastic leukemia

Cancer stem cells (CSCs) are hypothesized to promote tumor progression through innate chemoresistance and self-renewal. CSCs reside in the CD34+/CD38- immunophenotypic subpopulation of acute myeloid leukemia (AML); correspondingly, the size of this subpopulation has a strong negative impact on overall survival. Isolation of CSCs from B-lymphoblastic leukemia (B-ALL) has proven difficult, and the cells of interest apparently are not isolated to the CD34+/CD38- compartment. This may be explained, in part, by temporal variations of CD34 and CD38 expression which result in stochastic cell state transitions (e.g., from CD34+/CD38+ to CD34+/CD38-). We present a mathematical model of these transitions and correlate salient findings with BCR::ABL1 status, minimal residual disease (MRD), and relapse in adult B-ALL. As the CSC hypothesis is well supported in AML, we focus on transitions to and from the hematopoietic stem cell compartment (CD34+/CD38-), which our findings suggest can be estimated from peripheral blood or bone marrow samples. Additionally, we find that BCR::ABL1 positive patient samples are associated with high transition rates into the CD34+/CD38- compartment, including self-renewal. In contrast, BCR::ABL1 negative patient samples have low CD34+/CD38- self-renewal rates and either high CD34+/CD38+ or CD34-/CD38+ incoming rates. High CD34+/CD38- self renewal is also associated with MRD post-induction chemotherapy. We find a lack of observable changes in cell state transitions between diagnosis and relapse specimens. Our analysis provide evidence of de-differentiation transitions to a CD34+/CD38-stem cell-like immunophenotype in leukemia samples collected from B-ALL patients, and the tendency for these transitions is especially strong for B-ALL with BCR::ABL1. The modeling framework used here is a novel, useful tool to infer both prognosis and genotype from routine flow cytometry data. Significance StatementFlow cytometry characterization of B-lymphoblastic leukemia samples (diagnosis, remission, relapse) is used to parameterize a mathematical model of cell state transition rates and stratify patients at risk for post-induction chemotherapy minimal residual disease.

cancer biology↗

bioRxiv2025

Combined inhibition of NAD synthesis and C-terminal binding protein cooperatively induce cell death and inhibit growth of High Grade Serous Ovarian Carcinoma

The transcriptional scaffolds C-terminal Binding Proteins (CtBP) 1 and 2 are overexpressed and act as oncogenic dependencies in multiple cancers but importantly encode a chemically targetable dehydrogenase domain. CtBP promotes survival of high grade serous ovarian carcinoma (HGSOC) cells by repressing expression of Death Receptors (DR) 4 and 5, which activate caspase 8-dependent apoptosis. We have previously developed a series of substrate competitive CtBP dehydrogenase inhibitors active in multiple cell and preclinical solid tumor models. In the current study, we validated CtBP 1 and 2 overexpression in a longitudinal series of primary and metastatic/recurrent HGSOC cases. Furthermore, our lead CtBP dehydrogenase inhibitor, JW-98 induced apoptosis and exhibited variable single agent IC50 values in HGSOC cell lines, but depletion of nicotinamide adenine dinucleotide (NAD) using the NAD synthesis inhibitor GMX1778 strikingly sensitized tumor cells to JW-98 treatment. Mechanistically, the JW-98/GMX-1778 combination effectively disrupted CtBP dimerization that requires stoichiometric levels of intracellular NAD and is required for oncogenic transcriptional activities. Highlighting the translational potential of this combination, combined JW-98/GMX1778 treatment of OVCAR3 HGSOC xenografts in immunodeficient mice abrogated tumor growth without observable toxicity. CtBP/NAD combined inhibition represents a novel therapeutic strategy that could improve outcomes in chemoresistant HGSOC.

cancer biology↗