Biology subjects

Zhu, G.

Publications and source records attributed to Zhu, G..

At least 19 recordsLinked to original sources

bioRxiv2026

Venetoclax Resistance Creates Canonical Pyroptosis Vulnerability in AML

Venetoclax has transformed acute myeloid leukemia (AML) therapy, yet resistance is almost inevitable. Its diverse, often difficult-to-target drivers frequently converge on monocytic differentiation, a state that survives on MCL1 rather than BCL2. Here, we show that the very cells that escape BCL2 inhibition retain the canonical pyroptosis machinery of normal monocytes. Across 15 bulk and 4 single-cell cohorts, the canonical pyroptosis program was enriched in monocytic AML and monocytic leukemia stem cells, correlated with venetoclax resistance, and associated with inferior survival specifically after venetoclax-based therapy. In 24 cell lines and 142 patient specimens, both DPP8/9 inhibition by Val-boroPro and NLRP3 activation by lipopolysaccharide (LPS) plus nigericin preferentially killed monocytic AML cells through GSDMD-mediated pyroptosis, largely sparing non-monocytic AML and lymphoid leukemias. Venetoclax preferentially depleted primitive AML blasts but enriched a monocytic residuum vulnerable to canonical pyroptosis; combining venetoclax with Val-boroPro achieved deeper ex vivo clearance than either agent alone. In venetoclax-resistant xenografts, Val-boroPro suppressed leukemia progression, and adding venetoclax further reduced leukemia burden and prolonged survival beyond either monotherapy. Thus, venetoclax resistance itself exposes an alternative, druggable cell-death program that can be therapeutically exploited to overcome this resistance.

cancer biology↗

bioRxiv2026

Neutrophils orchestrate pre-metastatic immunosuppressive bone marrow remodeling during prostate cancer metastasis

The dynamic reprogramming of the bone marrow (BM) microenvironment during metastatic progression is poorly defined. Through single-cell profiling of BM samples spanning benign conditions, high-risk bone metastatic potential localized prostate cancer (HMP) and established bone metastatic prostate cancer (PCa), we uncovered a primary tumor-to-BM signaling axis that orchestrates niche formation through neutrophil-mediated remodeling. Tumor-associated neutrophils (TANs) emerge during the HMP stage, persist throughout metastatic progression, correlate with poor patient prognosis, and exhibit direct immunosuppressive activity that contributes to a BM environment permissive to metastatic colonization. Functional and genetic studies showed that tumor-associated systemic IGF1 reprogrammed BM neutrophils through IGF1R-MAPK/ERK-KLF4 signaling, with IL-1{beta}, reactive oxygen species and nitric oxide contributing to TAN-mediated T cell suppression. Tumor-cell Igf1 perturbation, IGF1R blockade and neutrophil-specific Igf1r deletion attenuated TAN-associated BM remodeling, and reduced subsequent bone metastatic progression. In bone-metastasis models, combined IGF1R and PD-1 blockade suppressed bone-metastatic progression. Translationally, our investigator-initiated clinical trial (NCT06866548) of teprotumumab plus tislelizumab in patients with established metastatic castration-resistant prostate cancer (mCRPC) provided initial safety data and exploratory clinical observations. Together, these findings identify IGF1R-dependent neutrophil reprogramming as a functionally important component of the evolving PCa bone metastatic microenvironment and provide a rationale for therapeutic targeting of IGF1R signaling together with immune checkpoint blockade.

cancer biology↗

bioRxiv2026

TRACER navigates rearrangement-driven sesterterpene chemical space via multimodal enzyme-product representation learning

Skeletal rearrangement drives the immense structural complexity of terpene, yet predicting it remains a formidable challenge due to sequence-function decoupling in terpene synthases. Here, we established TRACER (terpene rearrangement annotation via co-attentive enzyme-product representation), a multimodal framework mapping the latent associations between sequence-derived enzyme representations and product chemotypes. Retrospective validation proved TRACERs exceptional precision in predicting compound classes and discriminating skeletal rearrangement (SR) from non-skeletal rearrangement (NSR) pathways. TRACER-guided genome mining characterized two bifunctional synthases, FsPS and AcPS, uncovering four unprecedented carbon skeletons. Density functional theory calculations deciphered these cyclization cascades, pinpointing a critical 5/6/11 tricyclic intermediate as the key branching node for scaffold diversification. Mutagenesis and molecular dynamics simulations suggested that E305 in FsPS enables rearrangement by maintaining active-site water exclusion, whereas its alanine mutation causes premature carbocation quenching. Collectively, this work establishes a predictive paradigm for the rational discovery and mechanistic elucidation of complex terpene architectures.

synthetic biology↗

bioRxiv2026

Proteoform Barcode: An Intuitive Visualization Framework for Top-Down Proteomics

Top-down proteomics (TDP) advances biomedical research by providing a birds-eye view of proteoforms in cells, tissues, and biofluids. Thousands of proteoforms can be characterized using well-established TDP technologies, and potential proteoform biomarkers of diseases have been discovered. However, there is a lack of an easy and biologically informative approach to present the quantitative global TDP data. Here, we present proteoform barcode as a straightforward visualization approach that simultaneously displays proteoform abundance and their associated Gene Ontology (GO) biological processes, converting a list of proteoforms to a biologically informative image. The proteoform barcode allows 1) a global view of proteoforms (i.e., relative abundance and functional information) in complex biological systems (i.e., bacteria, yeast, human cells, and human plasma) and 2) the accurate distinction of samples in diverse biological conditions (i.e., control and disease) assisted by machine learning approaches. The proteoform barcode, assisted by the random forest model, accurately separated the human plasma samples of healthy controls and early-stage breast cancer. The data demonstrates the high potential of the proteoform barcode-based approach for early diagnosis of diseases in an easy and biologically informative manner.

systems biology↗

bioRxiv2026

A rapid sporozoite viability assay identifies anti-Cryptosporidium parvum leads and targetable enzymatic activities in the invasive stage

Current phenotypic screens for anti-Cryptosporidium compounds typically quantify intracellular parasite growth in host cell cultures after two days of infection. Here, we developed a rapid, host cell-free phenotypic assay that directly measures compound-induced loss of viability in excysted Cryptosporidium parvum sporozoites, the invasive stage that initiates infection. We first compared qRT-PCR, luminescence ATP, and resazurin fluorescence readouts for detecting viable sporozoites. The luminescence ATP assay provided the best balance of linear dynamic range, assay time, parasite input, and cost, and was therefore adapted for high-throughput screening. Screening 5,000 bioactive compounds at 40 M identified 28 primary hits with [≥]50% inhibition of sporozoite viability, including 14 with >60% inhibition. Secondary screening of these 14 compounds at 4 M identified five hits retaining >50% inhibition: ZL0420, sulbactam, abexinostat, kojic acid, and SIB-1757. All five showed submicromolar activity against free sporozoites, with EC50 values of 0.073-0.311 M. Four compounds, abexinostat, ZL0420, SIB-1757, and sulbactam, also inhibited intracellular parasite growth in vitro, with EC50 values of 0.316-11.87 M and selectivity indices from >17 to >107. In an IFN-{gamma}-knockout mouse model, these four compounds reduced oocyst shedding over the 35-day experiment by 53.7-79.0% based on area-under-the-curve analysis and improved body-weight trajectories and ileal histopathology. Biochemical assays further showed that abexinostat inhibited native parasite HDAC activity at low nanomolar concentrations, while sulbactam inhibited a {beta}-lactamase-like activity in sporozoite lysates. These findings establish sporozoite viability as a rapid screening endpoint and identify anti-Cryptosporidium leads associated with targetable enzymatic activities in the invasive stage. Author summaryCryptosporidium parvum is a major cause of diarrheal disease in humans and young animals, but treatment options remain limited. Most laboratory screens for new drugs against this parasite require infection of host cells and measurement of parasite growth after one or more days. We developed a faster approach that tests whether compounds can directly damage freshly excysted sporozoites -- the parasite stage that first invades intestinal cells -- or reduce their viability. This assay can be completed within a few hours and does not require host cells. Using this approach, we screened 5,000 bioactive compounds and identified several molecules that rapidly reduced sporozoite viability. Four of these compounds also inhibited parasite growth in cell culture and reduced infection severity in a mouse model, as measured by parasite shedding, body-weight changes, and intestinal pathology. We further showed that one compound inhibits parasite histone deacetylase activity, while another inhibits a {beta}-lactamase-like activity present in sporozoites. Our study provides a rapid screening strategy and highlights vulnerable biological activities in the invasive stage of C. parvum.

microbiology↗

bioRxiv2026

Assessing Microcirculation Impairment in Ischemic Stroke Mice Using Arteriovenous Co-fluctuation Analysis

Accurate assessment of cerebral hemodynamics impairment traditionally relies on arterial metrics, yet often overlooks venous drainage and arteriovenous dynamics, thereby limiting the evaluation of ischemia-induced microvascular dysfunction. To address this limitation, we implemented a signal-averaging framework, combined with co-fluctuation analysis, to extract predominantly arterial and venous hemodynamic signals and construct a dynamic arteriovenous co-fluctuation index that quantifies frame-by-frame coordination between arterial inflow and venous outflow activity. This time-resolved index enables spatial characterization of large-scale cortical arteriovenous coordination beyond conventional static correlation-based analyses. Comparative analyses between healthy controls and acute ischemic stroke mice demonstrated that the arteriovenous co-fluctuation index sensitively detects disruption of vascular coordination, revealing a slower state transition that occurs alongside distinct temporal abnormalities and regional heterogeneity between ischemic core and penumbral regions. These findings underscore the utility of arteriovenous coordination as a sensitive indicator of microcirculatory dysfunction, offering a practical analytical tool for assessing stroke-induced microvascular impairment.

neuroscience↗

bioRxiv2026

BCMA/CD19 dual-targeting with FasTCAR: AZD0120 demonstrates potent preclinical efficacy in multiple myeloma

Chimeric antigen receptor (CAR)-T cell therapy has improved outcomes for patients with multiple myeloma (MM), but its broader use is restricted by manufacturing complexities and treatment-related toxicities. AZD0120 is a dual-targeting B-cell maturation antigen (BCMA)/CD19 CAR-T cell therapy manufactured via the rapid FasTCAR process. We developed a dual-targeting "loop" CAR that incorporates a novel humanized anti-BCMA single-chain variable fragment (scFv), clone SG, and an FMC63-derived anti-CD19 scFv. This AZD0120 CAR preserved functional binding to both antigens and conferred robust in vitro and in vivo cytotoxicity while maintaining single-antigen reactivity. Conventional manufacture of CAR-T cells with the AZD0120 CAR (AZD0120C) yielded cells with minimal tonic signaling, limited responsiveness to soluble BCMA, and preservation of naive/stem cell memory-enriched phenotypes, yet robust cytokine production upon BCMA+ target engagement. AZD0120C demonstrated cytotoxicity comparable to benchmark BCMA CAR-Ts across MM lines in vitro and showed strong in vivo expansion and tumor control in xenograft models. FasTCAR manufacturing - designed to shorten vein-to-vein timelines and enrich less-differentiated phenotypes - further enhanced in vivo performance: AZD0120 consistently achieved superior tumor control and greater CAR-T expansion vs AZD0120C across disseminated MM.1S, NALM-6, and JeKo-1 models, with superior efficacy observed at lower cell doses. Collectively, these data support clinical evaluation of AZD0120 as a differentiated BCMA/CD19 CAR-T cell therapy with the potential to improve disease control and patient access in MM. Key PointsO_LIAZD0120 is a dual-targeting CAR-T that displays a favorable anti-myeloma functional profile and co-targets a source of potential relapse C_LIO_LIThe FasTCAR process yields TN/SCM-rich CAR-T populations, promotes in vivo expansion and achieves potent tumor control in xenograft models C_LI

cancer biology↗

bioRxiv2026

Wheat MYB transcription factor TaMYB83-7B regulates seed dormancy by influencing the balance between abscisic acid and gibberellin

In wheat, weak seed dormancy (SD) is related to an increased tendency for pre-harvest sprouting (PHS), which reduces yield and quality. However, the molecular mechanism underlying SD remains elusive. Here, we identified a wheat R2R3-MYB transcription factor (TaMYB83-7B) related to SD. Expression analysis showed that TaMYB83-7B was highly expressed in wheat seeds, and was more highly expressed in strong-dormancy varieties than in weak-dormancy varieties. Sequence and association analysis indicated that T/C mutations at -907 bp and -1133 bp in the TaMYB83-7B promoter were significantly associated with wheat SD, with C at both sites related to strong dormancy. Dual-luciferase reporter assays demonstrated that the transcriptional activity of the TaMYB83-7B promoter was significantly higher in strong-dormancy varieties than in weak-dormancy varieties. Further analyses indicated that TaMYB83-7B functions as a transcriptional inhibitor. Germination experiments revealed that overexpression of TaMYB83-7B significantly enhanced SD, while its loss-of-function reduced SD. Finally, TaMYB83-7B was found to regulate SD by influencing the balance between abscisic acid (ABA) and gibberellin (GA) in wheat seeds. Overall, the results of this study enhance our understanding of the complex regulatory mechanism underlying SD, and provide gene targets and molecular markers for the genetic improvement of PHS resistance in wheat.

molecular biology↗

bioRxiv2026

Mapping Tumor-Microenvironment dependencies with TMEformer: A spatial foundation framework enabling in silico perturbation

Despite the fundamental role of spatial context in driving tumor progression, most current computational models for virtual perturbation have largely overlooked its importance. Here, we introduce TMEformer, a tumor microenvironment-aware deep learning framework that leverages high-resolution spatial transcriptomics to jointly model intrinsic tumor cell programs and local microenvironmental signals by explicitly incorporating spatial architecture. Validated across diverse tumor spatial transcriptomic cohorts, TMEformer enables virtual perturbations that capture functional dependencies within local cellular ecosystems. Despite being trained on cancer-specific spatial datasets, TMEformer outperforms baseline models pretrained on large-scale corpora in capturing key tumor transitions, including lineage plasticity and the emergence of therapy resistance. Systematic perturbation analyses prioritize tumor-intrinsic transcription factors and TME-derived ligands that drive disease progression, recovering established regulators and revealing novel candidates. Furthermore, TME- derived embeddings improve the spatial stratification of tumor cells and align more closely with pathological architecture. Together, TMEformer establishes a general framework for modeling tumors as spatially coupled, perturbable ecosystems. An online TMEformer web platform for perturbation prediction, analysis, and visualization is available at http://www.pradcellatlas.com.

bioinformatics↗

bioRxiv2026

A suture-specific oocyst wall protein COWP4 is essential for excystation and infectivity, while COWP6 links wall architecture to host interaction in Cryptosporidium parvum

The oocyst of Cryptosporidium is a highly resilient transmission stage that protects sporozoites in the environment and mediates infection through a specialized opening known as the suture. While recent studies have identified Cryptosporidium oocyst wall proteins (COWPs) as structural components of the oocyst wall, the functional roles of individual COWPs and the molecular basis of suture biology remain poorly understood. Here, we performed a detailed characterization of two COWP family members, COWP4 and COWP6, combining immunolocalization, ultrastructural analysis, protein interaction assays, and genetic manipulation. We show that COWP4 is strictly localized to the oocyst suture, whereas COWP6 is distributed throughout the oocyst wall inner layer and enriched at the suture. COWP6 is additionally present in sporozoites and is secreted during parasite motility and host cell invasion, where it exhibits high-affinity binding to host cells. Structural analyses indicate that both proteins are cysteine-rich and likely form disulfide-stabilized architectures consistent with roles in wall assembly. Functional analyses reveal that COWP4 is essential for proper suture formation, excystation, and parasite infectivity, establishing the suture as a genetically defined gatekeeper for parasite transmission. In contrast, COWP6 functions as a multifunctional protein linking oocyst wall architecture to host interaction. We further demonstrate that COWP4 and COWP6 interact, suggesting coordinated assembly within the oocyst wall. Together, these findings provide a functional dissection of the Cryptosporidium oocyst suture and reveal distinct, non-redundant roles for individual COWPs. This work advances our understanding of oocyst wall biology and identifies COWP4 as an essential determinant of parasite transmission that may be targeted to disrupt the infectious cycle. Author summaryCryptosporidium is a major cause of diarrheal disease worldwide and is transmitted through environmentally resistant oocysts that protect infectious stages of the parasite. A defining feature of the oocyst is a specialized seam-like structure, called the suture, through which parasites exit to initiate infection. Although oocyst wall proteins (COWPs) have been identified, how individual proteins contribute to the structure and function of the oocyst wall, particularly the suture, has remained unclear. In this study, we investigated two oocyst wall proteins, COWP4 and COWP6, and uncovered distinct roles for each. We found that COWP4 is specifically localized to the suture and is essential for its proper formation, enabling parasites to exit the oocyst and establish infection. In contrast, COWP6 is distributed more broadly in the oocyst wall and also functions beyond it, being secreted during parasite movement and interacting with host cells. These findings reveal that the oocyst wall is composed of specialized proteins with non-redundant functions and identify the suture as a critical control point for parasite transmission. Understanding these mechanisms may help guide the development of new strategies to block infection by disrupting oocyst integrity or parasite release. HighlightsO_LICOWP4 is a suture-specific protein essential for oocyst excystation and infectivity C_LIO_LIGenetic disruption of COWP4 produces non-infectious oocysts with impaired viability C_LIO_LIThe oocyst suture is a genetically defined gatekeeper for parasite transmission C_LIO_LICOWP6 localizes to the wall inner layer and is enriched at the suture C_LIO_LICOWP6 is secreted by sporozoites and binds host cells with nanomolar affinity C_LIO_LI{middle dot} COWP4 and COWP6 directly interact, linking wall architecture to host interaction C_LI

microbiology↗

bioRxiv2026

Sleeve gastrectomy improves metabolic health, cognition, and Alzheimer's Disease pathology in 3xTG mice

Obesity and diabetes are well-established risk factors for Alzheimers disease (AD), implicating metabolic dysfunction in AD pathogenesis. Sleeve gastrectomy (SG) is among the most effective metabolic interventions available, yet its impact on AD progression remains poorly understood. We hypothesized that SG performed early in life would improve metabolic health, attenuate AD pathology, and preserve cognition in a transgenic AD mouse model. Five-week-old female 3xTg-AD mice were preconditioned on a Western diet (WD) to induce obesity and glucose intolerance, then randomized to SG or sham surgery and maintained on either standard chow or continued WD for 12 months. Metabolic phenotyping, body composition, and cognitive assessments (Novel Object Recognition, Barnes Maze, Fear Conditioning) were performed longitudinally, with histological and molecular analysis of brain tissue at endpoint. Under chow-fed conditions, SG reduced adiposity, improved insulin sensitivity, and decreased cortical A{beta} plaque burden, accompanied by attenuated gliosis (GFAP, IBA1) and region-specific, insulin pathway-dependent modulation of autophagy. Under persistent WD, SG improved metabolic health, frailty, spatial cognition, and A{beta} pathology, again with corresponding perturbations in autophagy pathway activity. Across all groups, food intake did not differ significantly, indicating that these effects were not secondary to caloric restriction. Collectively, these data suggest that SG engages neuroprotective brain insulin signaling pathways, supporting metabolic surgery as a promising disease-modifying intervention for AD prevention in individuals with obesity.

neuroscience↗

bioRxiv2026

Ultra-low-illumination, high-fidelity longitudinal monitoring of cerebral perfusion via deep learning-enhanced laser speckle contrast imaging

Laser Speckle Contrast Imaging (LSCI) is a non-contact, label-free optical technique widely used in biomedical research and clinical applications. It enables real-time visualization and quantification of microvascular blood flow by analyzing the temporal fluctuations of laser speckles induced by moving red blood cells. However, conventional LSCI uses visible or near-infrared illumination, which--during prolonged exposure (e.g., >1{square}hr)--can induce sublethal neural stress and cause signal drift, compromising physiological relevance and raising ethical concerns. To mitigate these limitations, we introduce TunLSCI--a TransUNet-based recovery network designed to reconstruct high-fidelity mouse cerebral blood flow (CBF) indices from ultra-low-illumination LSCI. We train our network on paired ultra-low-illumination (1.27 {micro}W/mm2) and conventional LSCI data ([~]200 {micro}W/mm2 illumination, the latter as reference), and demonstrate that it outperforms the conventional standard analytical LSCI processing pipeline based on stLASCA, particularly in reconstructing fine vasculature from few frames, suppressing speckle noise, and maintaining robustness against exposure variations. We validate that the proposed TunLSCI reduces illumination power density by [~]157-fold compared with conventional stLASCA, well below the safety threshold for cortical exposure in mice and markedly improves stability during a 2-hour continuous mouse CBF monitoring. Our method significantly minimizes the phototoxic burden of LSCI while preserving spatiotemporal fidelity and quantitative accuracy, thus enabling longitudinal, high-biosafety cerebral perfusion tracking in vivo over multi-hours.

bioengineering↗

bioRxiv2026

Ultra-flexible PINE arrays for month-long, continuous intracellular ion flux monitoring in plants with nanomolar accuracy

High-precision in vivo monitoring of ion fluxes is essential yet challenging studying plant electrophysiology such as growth regulation, signal transduction and stress responses. Existing methods for probing ion dynamics are limited by low sensitivity, high invasiveness that interferes physiological processes, and the inability to accurately resolve ion homeostasis with required spatial and temporal resolution. Here, we introduce ultraflexible, plant implantable nanoelectrode (PINE) arrays manufactured on 1.2-m-thick polymer substrates, which enable ultrasensitive and selective measurement of ionic current for month-long via scalable nanofabrication techniques. The fabricated PINE arrays have a smaller dimension than typical plant cells as well as less stiffness, facilitating minimally invasive integration with living plant cells. This subcellular-scale plant-electronic interface allows for reliable, selective detection of K+ flux with a detection limit of [~]10- M, and thus allows continuous, stable monitoring of tomato stem cells over six weeks, capturing dynamic potassium fluctuations during all key growth stages. More importantly, the method permits long-term, real-time tracking of ion-specific dynamics without disrupting plant cellular structure or altering endogenous ion concentrations. Therefore, PINE provides unprecedented access to ion homeostasis and signaling networks, making it an excellent platform for precision agriculture and a foundational tool for future digital plant engineering.

plant biology↗

bioRxiv2026

Decades of dreams coming true: capillary zone electrophoresis-mass spectrometry for reproducible multi-level proteomics

Capillary zone electrophoresis (CZE)-mass spectrometry (MS) has been proposed as a powerful analytical tool for bottom-up, top-down, and native proteomics (multi-level proteomics) decades ago to analyze complex biological samples at the levels of peptides (bottom-up), proteoforms (top-down), and complexoforms (native). However, its broad adoption has been impeded by the limited robustness and reproducibility. Here, we present multi-level proteomics data from nearly 170 CZE-MS runs ([~]170 hours of instrument time), demonstrating qualitatively (i.e., the number of identified peptides and proteoforms, the number of detected complexoforms, and their migration time) and quantitatively (i.e., peptide, proteoform, and complexoform intensity) reproducible measurement of complex samples with varying levels of complexity, i.e., Escherichia coli cells, HeLa cells, and human plasma. CZE-MS-based native proteomics enabled the detection of hundreds of complexoforms up to 800 kDa from the complex systems via consuming only nanograms of protein material. The results indicate that CZE-MS is sensitive and reproducible enough for broad adoption for multi-level proteomics-based biomedical research.

systems biology↗

bioRxiv2026

A Sensitized ENU Mutagenesis Screen for Thrombosis Modifiers Identifies Suppressor Variants in Non-mutagenized Parental Generations Due to Antithrombotic Selective Pressures

Thrombosis is a leading cause of morbidity and mortality. We used a mouse forward genetic ENU screen to identify genomic variants that suppress F5L/L Tfpi+/- lethal thrombosis. Surviving F5L/L Tfpi+/- mice from our Modifier of Factor 5 Leiden 16 (MF5L16) ENU line were subjected to whole-genome sequencing analysis. This revealed that instead of an ENU-induced mutation, four mutations introduced from our F5L/L breeding stock were responsible for survival, which we named sMF5L1-4 for spontaneous Modifier of Factor 5 Leiden. In our colony, F5L/L female breeders carrying all four sMF5L mutations produced more litters and offspring than breeders with three or fewer mutations (p<0.006). Genotyping of 13 additional MF5L lines demonstrated that the four sMF5L mutations were present in all lines and were consistently associated with survival. Of these four mutations, a single G to A intergenic variant on Chromosome 18 (Chr18A, sMF5L4), was most significantly associated with survival (p=0.003), with [~]15% penetrance for conferring the survival phenotype. Furthermore, platelet aggregation was significantly reduced in Chr18A mice, suggesting an additional mechanism by which Chr18A could suppress lethal thrombosis. Comparative transcriptomics analysis of livers from Chr18A mice versus wildtype littermate controls revealed a small number of differentially expressed genes both known and unknown to affect thrombosis. In summary, we have identified four variants exerting a significant selective breeding advantage along with antithrombotic effects. Superimposing our mutagenesis screen on a selective background illustrates the interplay of natural strain background variants and de novo ENU mutations in suppressing F5L/L Tfpi+/- lethal thrombosis.

genetics↗

bioRxiv2026

A comprehensive proteome and the first phosphoproteome reveal extensive phosphorylation of carbohydrate metabolism in Cryptosporidium parvum sporozoites

Cryptosporidium parvum is an obligate intracellular apicomplexan parasite and a major cause of diarrheal disease in humans and animals worldwide. Despite its public health importance, the molecular regulation of parasite metabolism, particularly at the post-translational level, remains poorly understood. Here, we present a comprehensive proteomic analysis and the first phosphoproteomic profile of excysted C. parvum sporozoites, the invasive stage responsible for host cell entry. Using data-independent acquisition-based mass spectrometry, we identified 2,272 proteins, representing approximately 58% of the predicted parasite proteome, and 8,994 phosphorylation sites across 833 phosphoproteins. Comparative analyses revealed weak correlations between transcript and protein abundance, underscoring extensive post- transcriptional regulation in sporozoites. Functional enrichment analyses showed that proteins involved in carbohydrate metabolism, particularly glycolysis, are highly abundant in the sporozoite proteome. In contrast, phosphoproteomic data revealed that many core glycolytic enzymes exhibit relatively low phosphorylation propensity, suggesting limited reliance on phosphorylation-based regulation for basal energy metabolism at this stage. To integrate proteomic and phosphoproteomic measurements acquired independently, we developed a relative phosphorylation index (RPI) that enables comparative assessment of phosphorylation propensity across proteins. Application of this metric highlighted selective phosphorylation of proteins associated with signaling, cytoskeletal organization, and host-parasite interaction, while key metabolic entry-point enzymes, such as hexokinase, showed high abundance but minimal detectable phosphorylation, in contrast to their mammalian counterparts. Together, these findings provide the most comprehensive molecular resource to date for C. parvum sporozoites and reveal a phosphorylation landscape that emphasizes regulatory and structural processes over core metabolic flux. This work establishes a foundation for understanding parasite-specific regulatory strategies and may inform the identification of novel therapeutic targets against cryptosporidiosis. Author SummaryCryptosporidium parvum is a microscopic parasite that causes diarrheal disease in humans and animals worldwide, yet we still know surprisingly little about how it regulates its biology at the molecular level. In this study, we set out to better understand how the parasite prepares for infection by examining the proteins present in sporozoites, the life stage that actively invades host cells. We generated the most comprehensive protein catalog to date for C. parvum sporozoites and, for the first time, mapped thousands of chemical modifications known as protein phosphorylation. These modifications often act as molecular switches that control how proteins behave. We found that proteins involved in basic energy production are extremely abundant but show relatively little phosphorylation, while proteins linked to cell structure, movement, and interaction with the host are more frequently modified. This suggests that the parasite prioritizes regulation of invasion-related processes over fine-tuning its core metabolism at this stage. By providing a detailed molecular resource and a new way to compare protein phosphorylation patterns, our work lays the groundwork for future studies of parasite biology and may help guide the search for new strategies to combat cryptosporidiosis.

microbiology↗

bioRxiv2025

ATRX Deficiency Drives Aberrant Type I Interferon Signalling Through cGAS-Dependent Transcriptional Dysregulation

The X-linked -thalassaemia intellectual disability syndrome (ATRX) protein is a chromatin remodeller involved in transcriptional regulation and genome stability. While the importance of ATRX in development and malignancy is well recognised, its role in innate immunity is less well defined. In two unrelated patients demonstrating cerebral white matter disease, learning difficulties and a persistent upregulation of interferon stimulated gene expression in whole blood, we identified the same Y1758C missense substitution in ATRX. Using patient-derived cells, engineered fibroblasts and neuronal models, we show that this substitution, and other loss of function mutations in ATRX, result in enhanced type I interferon signalling through a cGAS-dependent mechanism uncoupled from the DNA sensing activity of cGAS. Loss of ATRX function leads to alterations in the chromatin distribution of DAXX and H3.3, with cGAS essential for the changes in nucleosome composition and gene expression mediated by ATRX deficiency. Thus, our study highlights a previously unrecognized link between ATRX dysfunction and inflammation involving a non-canonical role of cGAS.

immunology↗

bioRxiv2025

Defective Microhomology-Mediated End-joining in SMARCB1-Deficient Tumors

Rhabdoid tumors (RTs) are highly aggressive cancers driven by biallelic mutation of SMARCB1, a core subunit of the BAF (SWI/SNF) complex. We found that SMARCB1-deficient tumors have a defect in the microhomology-mediated end-joining (MMEJ) pathway, and SMARCB1 is essential for maintaining the protein level of the core MMEJ protein Polymerase Q (POLQ). Mechanistically, SMARCB1 facilitates the nuclear export of the POLQ mRNA through its interaction with the nuclear pore complex. Interestingly, loss of MMEJ in RT cells leads to a compensatory activation of, and a hyper-dependence on, the Fanconi Anemia (FA)/BRCA pathway. Knockout or inhibition of this pathway selectively kills RT cells. Notably, RBM39 degraders, novel splicing modulators, effectively inhibit the FA/BRCA pathway and kill RT cells. SMARCB1 and other cBAF/pBAF components are important for maintenance of MMEJ activity and POLQ protein level, suggesting that BAF-deficient cancers more broadly may be treated by targeted inhibition of the FA/BRCA pathway. TeaserSMARCB1-deficient tumors lose POLQ protein and MMEJ repair, forcing a hyper-dependence on the FA/BRCA pathway.

cancer biology↗