Biology subjects

Wu, X.

Publications and source records attributed to Wu, X..

At least 145 records · Page 8Linked to original sources

bioRxiv2025

LabOS: The AI Co-Scientist That Sees and Works With Humans

Modern science advances fastest when thought meets action. LabOS represents the first AI co-scientist that unites computational reasoning with physical experimentation through multimodal perception, self-evolving agents, and XR-enabled, embodied human-AI collaboration. To empower agentic AI with embodied intelligence, we built LabSuperVision, the first vision-language-model (VLM) benchmark spanning biomedical and materials science laboratories, designed to evaluate scientific perception and reasoning. This endowed LabOS with visual reasoning capabilities that surpass those of general-purpose models on laboratory-specific tasks. By connecting multi-model AI agents, smart glasses, and human-AI-robot collaboration, LabOS allows AI to see what scientists see, understand experimental context, and participate in real-time execution through immersive XR interaction and robotic autonomation. Across applications-from cancer immunotherapy target discovery to cell engineering-LabOS shows that AI can move beyond computational design to participation, turning the laboratory into an intelligent, collaborative environment where human and machine discovery evolve together.

bioengineering↗

bioRxiv2025

The Arabidopsis CYSTM α 5'UTR increases protein production from transgenes in plants and bacteria.

Achieving high levels of transgene expression is often crucial for the effective production of high value pharmaceutical proteins and bioactive compounds. Here, we show a 79-nucleotide sequence of the 5 UTR of the Arabidopsis thaliana cysteine-rich transmembrane module 1 (CYSTM1) significantly increases transient and stable transgene expression at the post-transcriptional level in multicellular plants, A. thaliana and Nicotiana benthamiana, in monocotyledon wheat germ extracts, and in the unicellular bacterium Escherichia coli by up to 7-fold. We also show the 79 nt CYSTM sequence has 50 % higher transgene expression than the broadly used Tobacco Mosaic Virus omega ({Omega}) sequence in both A. thaliana and N. benthamiana. Taken together, this study provides a short transgene expression enhancer for multicellular and unicellular organisms.

plant biology↗

bioRxiv2025

Dynamic S-acylation of GSDMA regulates pyroptosis

GSDMA, the primary member of the gasdermin family found in the skin, is critical for pathogen-induced pyroptosis during infection. Recent studies revealed that another gasdermin, GSDMD, undergoes palmitoylation during pyroptosis. However, whether and how the other gasdermin members undergo lipid modification remains poorly understood. Here, we demonstrate that GSDMA is S-acylated at the conserved cysteine residues in its N-terminal domain. We show that S-acylation of GSDMA promotes pyroptosis by facilitating its membrane anchoring and protein oligomerization, a mechanism distinct from the palmitoylation of GSDMD at the N-terminal C191 residue. Additionally, we present evidence that recombinant proteins of GSDMA and GSDMD can undergo S- acylation in vitro via direct interaction with palmitoyl-CoA, suggesting they potentially possess auto-acylation capacity. Furthermore, we identify ABHD17A as one of the deacylating enzymes that regulate the dynamic fatty acylation cycle of GSDMA. Overall, our studies reveal new molecular mechanisms underlying GSDMA function through S- acylation and underscore its important role in regulating pyroptosis mediated by GSDMA. HighlightsO_LIGSDMA is S-acylated at N-terminal conserved cysteine residues. C_LIO_LIGSDMA S-acylation facilitates membrane anchoring and protein oligomerization. C_LIO_LIGSDMA and GSDMD recombinant proteins can undergo S-acylation in vitro C_LIO_LIThe ABHD17A enzyme is involved in GSDMA deacylation. C_LI

biochemistry↗

bioRxiv2025

IRG1/itaconate/NRF2/GSH axis in tumor-associated macrophages drives therapy resistance and immune evasion in BRCA1-deficient breast cancer

Tumor-associated macrophages (TAMs) are major contributors to immunosuppression and therapeutic resistance, including resistance to PARP inhibitors (PARPi) in BRCA1-deficient breast cancer. However, the mechanisms underlying TAM-mediated PARPi resistance remain unclear. Here, we demonstrate that TAM-derived glutathione (GSH) impairs the efficacy of PARPi by protecting tumor cells from DNA damage and ferroptosis while suppressing STING-mediated immune activation. Mechanistically, STAT5-driven upregulation of the IRG1/itaconate axis in TAMs rewires mitochondrial metabolism and activates NRF2-dependent GSH biosynthesis. GSH is subsequently released into the tumor microenvironment, where it is taken up by tumor cells, protecting them from PARPi-induced cytotoxicity and dampening immune responses. Pharmacological inhibition of IRG1 reverses these effects, restoring PARPi sensitivity and enhancing anti-tumor immunity in BRCA1-deficient tumor models. Collectively, these findings uncover a TAM-specific immunometabolic program that limits PARPi efficacy and highlight the IRG1/NRF2/GSH axis as a promising therapeutic target to improve treatment outcomes in BRCA1-associated breast cancer.

cancer biology↗

bioRxiv2025

Senescent Activated Naive B Cells Promote Anti-Citrullinated Antigen T Cell Responses and the Transition to Clinical Rheumatoid Arthritis

Rheumatoid arthritis (RA) is a chronic autoimmune disease marked by joint and systemic inflammation. Anti-citrullinated protein antibodies (ACPAs) define an at-risk stage that precedes clinically apparent inflammatory arthritis (clinical RA) onset, yet the molecular mechanisms driving progression remain poorly understood. Here, we applied single-cell multi-omics to profile B cells longitudinally collected from ACPA individuals who either convert to clinical RA (Converters) or do not (Nonconverters). We identified a striking expansion of CXCR5CD69 activated naive B cells (aNAVs) uniquely in Converters prior to clinical RA. These aNAVs exhibited a pro-inflammatory, senescent transcriptional program and persist through to clinical RA. In Converters, aNAVs expressed polyreactive, autoreactive IgM with distinctive V-J gene rearrangements that dominate the BCR repertoire. Furthermore, in Converters most IgM aNAVs were developmentally arrested in the peripheral blood, while a subset undergoes class switching and follows divergent somatic hypermutation trajectories. Mechanistically, aNAVs infiltrated RA synovium and served as potent antigen presenting cells to activate both anti-citrullinated antigen CD4 and CD8 T cells in an HLA-dependent manner. Chronic exposure to citrullinated antigens and CpG synergistically drove aNAV activation and senescence. These findings establish a mechanistic link between naive B cell senescence and clinical RA development in ACPA+ individuals, providing a rationale for therapeutically targeting aNAV B cells for the prevention of RA. Graphic abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=182 SRC="FIGDIR/small/682430v1_ufig1.gif" ALT="Figure 1"> View larger version (85K): org.highwire.dtl.DTLVardef@153b185org.highwire.dtl.DTLVardef@1aba6eeorg.highwire.dtl.DTLVardef@5c886eorg.highwire.dtl.DTLVardef@10109a3_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

The novel curcumin analogue AKT-100 targets mutant p53 in gynecologic cancer cells

Loss of normal p53 tumor-suppressive activity is common in advanced cancers, where TP53 mutations produce either p53-null states or highly expressed missense proteins with gain of oncogenic function. Mutant p53 proteins not only lose wild type p53 pro-apoptotic and DNA repair functions but also acquire new activities, including constitutive STAT3 activation. We hypothesize that directly targeting missense mutant p53 instead of downstream pathways is advantageous. Curcumin analogues have been reported to bind mutant p53, motivating the development of AKT-100, a novel analogue designed to restore wild type p53 functionality. AKT-100 binds mutant p53 and STAT3, as shown by fluorescence quenching, and inhibits STAT3 Tyr705 phosphorylation in KLE and COV362 cells. This agent exhibits potent cytotoxicity in gynecological cancer cells with IC50 values ranging from 4 nm to 2.51 {micro}M, and demonstrates synergy with the PARP inhibitor olaparib and with chemotherapy by suppressing alternative DNA repair mechanisms associated with therapeutic resistance. RNA sequencing and immunoblotting confirms AKT-100 reactivates wild type p53 transcriptional profiles regulating cell cycle arrest (CDKN1A/p21, GADD45A), apoptosis (PMAIP1/Noxa, DR5), and inhibits DNA replication and repair. These findings support AKT-100 as a promising therapeutic agent with the dual capabilities of directly targeting oncogenic mutant p53 and constitutively active STAT3. HighlightsO_LIAKT-100 is a novel curcumin analogue that functions as a WT p53 reactivator. C_LIO_LIAKT-100 inhibits STAT3 phosphorylation at Tyrosine 705 in endometrial and ovarian cancer cells. C_LIO_LICell proliferation is inhibited in multiple ovarian and serous endometrial cancer cell lines with AKT-100 as a single agent. C_LIO_LIAKT-100 is synergistic with PARP inhibitor olaparib and chemotherapy drugs carboplatin and paclitaxel. C_LI Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=132 SRC="FIGDIR/small/680794v3_ufig1.gif" ALT="Figure 1"> View larger version (48K): org.highwire.dtl.DTLVardef@1fdb8a8org.highwire.dtl.DTLVardef@6648acorg.highwire.dtl.DTLVardef@12d301aorg.highwire.dtl.DTLVardef@1b1370f_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

bioRxiv2025

Uterine immune dysregulation after asynchronous transfer induced embryonic apoptosis in mice

Asynchronous embryo transfer is widely used in assisted reproduction, yet its adverse effects and mechanisms remain unclear. This study investigates implantation failure in D1.5 pseudopregnant mice to elucidate mechanisms underlying asynchronous transfer. Blastocysts were transferred into uterine horns of D1.5 (Group A), D2.5 (Group B), and D3.5 (Group C) recipients. Implantation sites were counted at D7.5, and embryos were recovered within 3 hours post-transfer for analysis. Multibarcode single-cell RNA sequencing was applied to embryos and uterine tissues. Embryo recovery rate in Group A was significantly lower than in Groups B and C (p<0.01), with an abnormal embryo rate of 68.67%. Hoechst 33342/PI double staining revealed dead-cell features in abnormal embryos. Transcriptomic analysis of embryos showed downregulated DNA damage repair and structural maintenance genes in Group A. GO and KEGG analyses highlighted enrichment in transcriptional regulation and cell cycle pathways. GSEA identified activated apoptosis pathways, with intrinsic (mitochondrial) and extrinsic (death receptor TNFR-mediated) apoptosis genes significantly upregulated (p<0.05). Uterine transcriptome analysis revealed downregulated collagen family genes (ECM maintenance) but upregulated immune-related genes (IL family, CDs, C3) in Group A. Functional enrichment confirmed ECM and immune regulation pathway involvement. Gene network analysis identified Clca1, Smpdl3a, Tmprss4, Muc4, Cfb, and Nupr1 as key regulators of D1.5 uterine immunity/inflammation. D1.5 uterine immune dysregulation induces embryonic stress and inflammation. Impaired DNA damage repair activates intrinsic apoptosis, while upregulated TNFR signaling triggers extrinsic apoptosis, collectively blocking embryonic development toward implantation competence. These findings provide mechanistic insights into optimizing embryo transfer timing and improving reproductive outcomes.

immunology↗

bioRxiv2025

Phytoplankton community structure and photophysiological strategies in the oligotrophic Indian Ocean spawning ground of Southern Bluefin Tuna

The Argo Basin, a persistently oligotrophic seascape downstream of the Indonesian Throughflow (ITF), is the only known spawning ground of Southern Bluefin Tuna (Thunnus maccoyii). Its surface waters are capped by the warm, low saline, nitrate-depleted Pacific Ocean outflow, that leads to intense water-column stratification and chronic nutrient scarcity. During the BLOOFINZ campaign (R/V Roger Revelle, January-March 2022), we combined high-resolution underway surveys with Lagrangian experiments to examine hydrography, nutrient stoichiometry, and phytoplankton photophysiology across the basin. This study was motivated by the need to: 1) identify the phytoplankton communities capable of persisting in this nutrient-impoverished region, and 2) uncover the unique photophysiological traits that underpin their survival and growth, particularly under acute nitrate limitation. Nutrient fields revealed strongly negative N*, positive Si*, and elevated Si:P ratios, indicating a system of acute nitrate scarcity but with residual phosphate and latent silicate availability. Phytoplankton communities were dominated by the cyanobacteria, Prochlorococcus, whose survival strategies included small functional absorption cross section of PSII ({sigma}PSII), enhanced PSII connectivity (p), highly elastic and reversible diel photophysiology that balanced high-light stress and nitrogen scarcity. Longer turnover times especially {tau}2 ({micro}s; PSII-PSI electron transport) seen in the region around 115{degrees} and 120{degrees}E and at 15{degrees}S, and during Cycles 3 and 4 are indicative of populations that were being stressed by Fe limitation as well. Our inference of Prochlorococcus is supported by complimentary measurements of flow cytometry, phytoplankton pigment composition and microscopy all of which confirmed the dominance of Prochlorococcus in these nutrient impoverished waters. Our observations further indicate that mesoscale eddies generated by ITF-SICC (South Indian Counter Current) interactions, can episodically shoal the nutricline, triggering transient pulses of larger eukaryotes. Collectively, these results demonstrate how acute nitrate depletion, compounded by Fe stress, structures a microbial community finely tuned to oligotrophy and capable of sustaining a short food chain involving appendicularians that directly support larval tuna. The Argo Basin therefore exemplifies how circulation-nutrient coupling shapes microbial communities and ecosystem function within a globally significant spawning habitat. Highlights1) Chronic nitrate limitation, with strongly negative N* and persistent N:P imbalance defines the Argo Basin while phosphate and silicate remain in relative excess. 2) Picocyanobacteria especially Prochlorococcus dominate the ecosystem, sustaining productivity under extreme oligotrophy through photophysiological strategies of reduced {sigma}PSII, enhanced PSII connectivity, and diel recovery from light stress. 3) Mesoscale eddies at the ITF-SICC front provide episodic relief, shoaling the nutricline and fueling transient pulses of larger phytoplankton that episodically reshape phytoplankton community structure and biomass 4) This oligotrophic-frontal seascape supports a short, efficient food web, enabling transfer of picophytoplankton to Southern Bluefin Tuna larvae via mainly appendicularians.

ecology↗

bioRxiv2025

Myasthenia thymus reprograms class switched B cells into BAFF dependent survivors

Myasthenia gravis (MG) presents a clinical challenge where autoantibody titers against the neuromuscular junction fail to predict disease severity or treatment response, and thymectomy provides inconsistent benefit despite removing the source of autoreactive B cells. We hypothesized that thymic B cells acquire survival mechanisms that bypass normal tolerance checkpoints, enabling persistence independent of antigen-specific selection. Using single-cell RNA sequencing, V(D)J repertoire analysis, and spatial transcriptomics from human thymic samples, representing the largest MG atlas to date (237,661 cells), we discovered a previously unrecognized tolerance checkpoint swap in MG pathogenesis. Pathological class-switched B cells within thymic germinal centers exhibited reduced antigen presentation capacity (decreased CD74, CD1C expression) and diminished CD40 co-stimulation while upregulating TNFRSF17 to engage BAFF survival signals. This shift from T cell-dependent activation to BAFF-driven survival allowed polyclonal autoreactive B cells to persist without stringent selection and seed peripheral sites. T follicular helper cells supported this reprogramming through increased TNFSF13B and CHGB expression, the latter enabling dopamine-mediated acceleration of B cell synapses. These findings resolve longstanding clinical paradoxes in MG and identify the BAFF-BCMA axis as an actionable therapeutic target. Measuring serum BAFF and soluble BCMA could provide superior biomarkers to antibody titers, while BAFF inhibition or CD40 agonism could restore normal tolerance checkpoints, offering new therapeutic strategies for MG and potentially other autoimmune diseases. One Sentence SummaryMyasthenia gravis is characterized by a tolerance checkpoint swap where pathological B cells shift from requiring T cell help and antigen-specific selection to depending on BAFF for survival.

genomics↗

bioRxiv2025

Higher-order Residue Interactions Encode Diversified Physical Properties of Biomolecular Condensates

Biomolecular condensates often formed by proteins containing extended intrinsic disordered regions (IDPs) can coordinate versatile cellular processes. The biological functions of condensates are attributed to a variety of physical properties, including viscoelasticity, interfacial tension and saturation concentration. Comprehensive understanding of biological functions of protein condensates and the corresponding sequence encoding requires unified interpretation of the diverse physical properties by a single model. Here we report the diversified physical properties of condensate and the interactions between constituent IDPs can be interpreted on the basis of higher-order residue interactions. These findings are based on s-scale atomistic molecular dynamics simulations of three homogeneous IDP condensates (FUS PLD, ARF6 PLD, LAF-1 RGG) combined with the reported simulation trajectories of two heterogeneous condensates. In all interacting IDPs, there are residue interactions between finite motifs (3[~]5 residues) that organize in a highly cooperative way: residues form multivalent interactions and their remaking is localized. The sequence features of higher-order interactions (HOIs) are identified: tyrosine, arginine, glutamine and aspartic acid are essential, and their consecutive sequence position is also important. The interaction between corresponding motifs is highly sustained and dominates the cohesive energy of IDP. IDP condensate can be modeled as a HOI-crosslinked network. This model can successfully reproduce all reported experimental results of condensate viscoelasticity, interfacial tension and saturation concentration, and expand our insights into the molecular grammar of IDP interactions. Significance StatementThe biological functions of biomolecular condensates involve various physical properties of condensate. A unified model that describes all these physical properties is essential for the understanding of condensate functions. Our research reveals the prevalence of higher-order residue interactions in all IDP condensates we considered, which leads to extremely sustained interaction between corresponding residue motifs. Accordingly, we propose a physically crosslinked network based on higher-order residue interactions as a simplified model for condensate. This model can quantitively reproduce all reported experimental results of condensate physical properties, including viscoelasticity, interfacial tension and saturation concentration.

biophysics↗

bioRxiv2025

YAP1 drives aggressive and therapy resistant state in melanoma through reprogramming the chromatin and regulating immune evasive programs

Despite promising initial results in targeting the RAF-MEK-ERK cascade, resistance to BRAF/MEK inhibitors remains a critical challenge in nearly 50% of melanoma patients. Our study demonstrates that robust YAP1 activation in metastatic melanoma correlates with poor survival and drives transcriptional programs linked to therapeutic resistance. Mechanistically, YAP1 predominantly remodels the chromatin landscape in resistant tumors by partnering with BRD4 and TEAD, creating a permissive transcriptional state that sustains oncogenic signaling. Clinical validation in biopsies from resistant melanoma confirms elevated expression of YAP1 target genes. Furthermore, pharmacological inhibition of BRD4 or TEAD reduces YAP1-driven transcription and reactivates antitumor immunity programs. TEAD specific inhibitors (and not verteporfin which is a highly non-specific inhibitor) synergize with immune checkpoint blockade in in vivo model system by promoting increased CD8 T cell infiltration and prolonged survival in the melanoma mouse model. Collectively, these findings reveal a chromatin-centric vulnerability in BRAF/MEK inhibitor-resistant melanoma and propose TEAD specific inhibitors as a promising dual strategy to overcome resistance and reinvigorate the immune response, offering a novel therapeutic avenue for patients. Resistance to BRAF and MEK inhibitors remains a major obstacle in the treatment of melanoma. Here, we show that elevated YAP1 activity in metastatic melanoma is associated with poor patient survival and drives transcriptional programs that promote therapeutic resistance. Mechanistically, YAP1 cooperates with BRD4 and TEAD to reprogram the chromatin landscape, establishing an oncogenic transcriptional state that sustains resistance. Analysis of patient-derived melanoma biopsies confirms increased expression of YAP1 target genes in resistant tumors. Targeting this epigenetic circuitry using pharmacological inhibitors of BRD4 or TEAD effectively suppresses YAP1-driven transcriptional output and restores antitumor immune activity, as evidenced by enhanced CD8 T cell infiltration and prolonged survival in resistant melanoma models. These effects are further supported by transcriptomic and chromatin accessibility analyses, which reveal reduced expression of immune-suppressive and proliferation-associated gene networks upon TEAD inhibition. Collectively, our findings identify a chromatin-centric mechanism underlying resistance to MAPK-targeted therapy and nominate TEAD inhibition as a promising dual-action strategy to both overcome resistance and re-engage antitumor immunity. This work offers a compelling therapeutic avenue for patients with drug-resistant melanoma.

cancer biology↗

bioRxiv2025

Mitotic CDK4/6 activity sustains spindle checkpoint signalling to prevent mitotic slippage and genomic instability

The precise regulation of cell cycle entry and the maintenance of genome integrity are crucial for preventing tumorigenesis. Cyclin-dependent kinases 4 and 6 (CDK4/6) play pivotal roles in linking mitogenic signals to G1-S phase progression1-3, and their frequent deregulation in various cancers underscores their importance in driving cell proliferation and as therapeutic targets4,5. Despite this, the roles of CDK4/6 beyond the G1/S transition remain underexplored. Here, we uncover a previously unrecognised function of CDK4/6 in mitotic progression through regulation of the spindle assembly checkpoint (SAC)6. Using both cancer and non-transformed human cells, we show that acute CDK4/6 inhibition after G1/S transition leads to premature mitotic exit despite unattached kinetochores, resulting in chromosome missegregation and aneuploidy. Phosphoproteomic analyses and in vitro kinase assays reveal that CDK4 phosphorylates multiple sites on key SAC regulators, including the C-terminal tail of CENP-E, which is critical for BubR1 recruitment to kinetochores and SAC maintenance7,8. CDK4/6 inhibition reduces the phosphorylation of SAC components, attenuating checkpoint signalling and accelerating mitotic slippage. Notably, residual SAC activity persists, suggesting that CDK4/6 strengthens or stabilises SAC signalling rather than being essential for its activation. Thus, CDK4/6 functions extend beyond G1/S control to ensure mitotic fidelity, linking proliferating signals to genome stability and exposing potential vulnerabilities to anti-mitotic therapies in cancer.

cell biology↗

bioRxiv2025

Shared and distinct sequence-function signatures define different modes of human TpoR activation

The human thrombopoietin receptor (hTpoR) exists primarily as JAK2-associated monomers that become activated when converted to dimeric forms that support JAK trans-phosphorylation. This can be achieved by several different modes of stimuli, including the natural ligand Tpo, biologic agonists that bind the same site as Tpo, small-molecule drugs that bind the transmembrane (TM) domain, oncogenic mutations in and near the TM domain, and by association with constitutively active JAK V617F or a mutant form of the chaperone protein calreticulin. It is unclear how the dimeric structures induced by synthetic agonists and mutations relate to one another, and whether any of these induce the same active structure as the native ligand Tpo, yet this has important implications both for fundamental cytokine receptor biology and for development of targeted interventions for hTpoR-driven myeloproliferative diseases. Here we used deep mutational scanning (DMS) across the TM and juxtamembrane (JM) regions of hTpoR to extract feature-rich sequence-function signatures across a variety of different activating contexts. While each displayed some unique features, synthetic agonists and activating mutations all exhibited strong dependence on a common TM interface that is consistent with previous models of a left-handed, near-parallel helix dimer with H499 facing lipid. In contrast, Tpo-mediated activation was broadly insensitive to TM-JM substitutions, indicating that it does not rely on the same interface. Modeling with AlphaFold 3 (AF3) consistently yielded a right-handed, "splayed" helix dimer that is close at the extracellular face, contains H499 in the interface and diverges toward the cytosolic face, resting on an intracellular amphipathic JM helix that lies parallel to the membrane, which is also observed in a DMS/AF3 analysis of human erythropoietin receptor. This splayed Tpo-bound dimer could be stably inserted into a lipid bilayer with associated JAK2 using molecular dynamics and is supported by experiments showing that most or all of the TM domain can be replaced by poly-valine, with little effect on Tpo-driven activation but catastrophic effects on responses to synthetic ligands. Our data support at least two different structural modes of hTpoR activation that reconcile prior biochemical models, rationalize patient variants, and inform mechanism-based agonist and antagonist design.

biochemistry↗

bioRxiv2025

MondoA mediates transcriptional coordination between the MYC network and the integrated stress response in pancreatic ductal adenocarcinoma

MYC amplification contributes to poor survival and outcome in pancreatic ductal adenocarcinoma (PDAC). Here we show that in PDAC cell lines with amplified MYC, MondoA is required for viability, facilitating proliferation while suppressing apoptosis in vitro and in vivo. Transcriptional and genomic profiling demonstrates that loss of MondoA leads to altered expression of direct MondoA targets as well as MYC target genes and is accompanied by shifts in genomic occupancy of MYC, MNT, and the MondoA paralog ChREBP. This altered genomic binding by MYC network members is associated with transcriptional perturbation of multiple metabolic and stress pathways, as well as global changes in N6-methyladenosine modification (m6A) of mRNA. MondoA inhibition disrupts coordination between MYC network members and the Integrated Stress Response (ISR), resulting in decreased translation of ATF4 mRNA, discordant gene regulation of shared targets of MYC and ATF4 and, ultimately, apoptosis. Re-establishing ATF4 protein expression rescues the diminished viability due to loss of MondoA expression or activity, providing direct evidence of a link between deregulated MYC and the transcriptional machinery of the ISR. Lastly, we find that small-molecule inhibition of MondoA is lethal in a subset of PDAC cell lines, including patient-derived organoids, suggesting that the ability to target MYC via chemical inhibition of MondoA transcriptional activity may have broad efficacy. Significance StatementThis report investigates mechanisms underlying the dependence of MYC-amplified pancreatic cancer cells on the MYC network member MondoA which, as a heterodimer with MLX, is a nutrient-sensing transcription factor. We show this dependency is linked to genomic crosstalk between MYC, components of the proximal MYC network, and the master regulator of the integrated stress response, ATF4. Moreover, we find that small molecule inhibitors of MondoA-MLX transcriptional activity abrogate survival of MYC-amplified PDAC lines and patient derived organoids. The significance of this work relates to its focus on a unique vulnerability intrinsic to MYC, an oncogenic driver associated with a wide range of cancers, which is considered to be "undruggable".

cancer biology↗

bioRxiv2025

GSDME unlocks astrocyte-driven neurotoxicity in Alzheimer's Disease

Astrocytic calcium dysregulation and reactivity precede A{beta} deposition in amyloid-{beta} deposition in Alzheimers disease (AD) but the neurotoxic mechanisms remain unclear. We show that GSDME acts as a switch, linking MAM-mediated calcium release to astrocyte-driven neurotoxicity. Specifically, A{beta}-activated microglial signals activate astrocytic GSDME, releasing its N-terminal fragment, which targets MAMs and triggers ER calcium efflux. This induces biphasic CaMKII phosphorylation, initially boosting NRF2 defenses, then activating NF-{kappa}B-driven inflammation, shifting astrocytes from protective to toxic states. GSDME activation also drives astrocyte-derived exosomes (ADEs) to carry neurotoxic tau, proinflammatory miRNAs, and toxic lipids, propagating toxicity. GSDME deletion in AD mice reduces A{beta} burden, restores NF-{kappa}B/NRF2 balance, reprograms astrocytes and ADEs to protective states, and rescues cognition. Multi-omics profiling of serum ADEs from AD patients reveals a disease-specific signature with central neurotoxicity and peripheral immune regulation. These findings position GSDME as a promising dual diagnostic and therapeutic target for early AD invention.

neuroscience↗

bioRxiv2025

Visual Regularities Underlie Hierarchical Object Representations in the Human Brain and Self-supervised DNN

NeuroAI develops the interplay of neuroscience and artificial intelligence, especially on visual processing. Human visual system organizes objects based on a representational hierarchy. However, it remains unclear whether this hierarchy arises from visual or semantic information. One hypothesis posits that the visual system is structured around statistical regularities of visual information. Here, we test this hypothesis using the THINGS datasets and pure-visual deep neural networks (DNN). We constructed a low-dimensional object space based on multiple abstract object properties, reflecting statistical patterns of visual regularities. By applying voxelwise encoding models, we identified clusters in the higher visual cortex based on their property tuning, and they were found to support specific object categories. These clusters serve as the middle level to reveal a property-cluster-object hierarchical organization. Subsequently, we investigated whether this hierarchical structure could be captured by a self-supervised DNN. Through activity similarity analysis, we mapped the brain clusters onto the DNN and independently found that the DNNs clusters exhibited distinct property tuning and influenced the classification accuracy of corresponding object categories, mirroring the effects observed in the human brain. Our results demonstrate similar hierarchical structures in the human brain and self-supervised DNN, suggesting that the visual regularities shape neural architecture of visual system. This study highlights the great potential of neural computational model in neuroscience study. Index Terms Visual Processing, Abstract Property, Hierarchical Representation, Self-supervised Visual DNN

neuroscience↗

bioRxiv2025

The Darwin-Godel Drug Discovery Machine (DGDM): A Self-Improving AI Framework

Despite advances such as AlphaFold and modern generative AI models, current drug discovery pipelines lack mechanisms to refine both molecules and the pipelines themselves, limiting their ability to achieve autonomous and reliable self-improvement. To address this, we present the Darwin-Godel Drug Discovery Machine (DGDM), a self-improving artificial intelligence framework that integrates generative molecular design and evolution with adaptive meta-learning. DGDM employs a dual-loop architecture: an inner loop frames molecular optimization as a Darwinian evolutionary process guided by reinforcement learning signals, where candidate molecules generated by generative AI are evolved through search and feedback; an outer loop adaptively modifies the discovery pipeline itself. Unlike the original Godel machine, which demands formal proofs of improvement--rarely attainable in practice--DGDM uses statistical validation to bound risk and ensure reliable progress. The framework is fully compatible with modern structural biology tools, including AlphaFold, and supports evaluation through docking, binding affinity prediction, and ADMET profiling. In a proof-of-concept study, DGDM improved the median binding affinity of candidate ligands from -4.457 to -5.422 kcal/mol while maintaining 100% drug-likeness and novelty. These results suggest that bounded-risk, self-improving AI can accelerate drug discovery by continuously refining both molecular design and discovery processes, extending the Godel machine principle of self-improvement into biomedical research. All code is open-sourced at https://github.com/deep-geo/DGDM.

bioinformatics↗

bioRxiv2025

Ginkgolic acid attenuates e chinococcus granulosus infection-induced hepatic fibrosis by inhibiting Smad4 SUMOylation

BackgroundThe SUMOylation modification is closely linked to the progression of fibrotic diseases, yet its role in hepatic fibrosis associated with cystic echinococcosis (CE) remains unclear. This study aimed to investigate the function of SUMOylation in CE-related hepatic fibrosis and evaluate the anti-fibrotic effects and mechanisms of ginkgolic acid (GA) via regulation of the SUMOylation pathway. MethodologyPeri-lesional (PL) and adjacent normal (AN) liver tissues from CE patients were collected to examine histopathology and SUMO pathway proteins. A CE-infected mouse model was established and treated with GA to assess cyst burden, serum TGF-{beta}1 levels, hepatic fibrosis markers, and SUMO-related proteins. In vitro, macrophages and hepatic stellate cells (HSCs, LX-2 line) were stimulated with Echinococcus granulosus cyst fluid (EgCF) or TGF-{beta}1 to evaluate GAs effects on macrophage polarization (CD206/CD86), HSC activation (-SMA/PCNA), Smad4 SUMOylation, and nuclear translocation. Macrophage-HSC crosstalk was investigated via conditioned medium co-culture assays. ResultFibrosis was exacerbated in peri-lesional liver tissues of CE patients, accompanied by SUMO pathway activation. GA significantly alleviated hepatic fibrosis in CE mice and reversed SUMO pathway dysregulation. Mechanistically, GA inhibited EgCF-induced pro-fibrotic M2 macrophage polarization and blocked Smad4 SUMOylation and nuclear translocation by modulating SUMOylation. Furthermore, GA directly suppressed HSC activation and bidirectionally disrupted the pro-fibrotic crosstalk between macrophages and HSCs under EgCF stimulation, ultimately alleviating fibrosis. ConclusionThis study reveals the critical role of SUMOylation modification in CE-associated hepatic fibrosis and elucidates a novel anti-fibrotic mechanism whereby GA targets the SUMOylation-Smad4 axis to regulate the immune microenvironment. Author summaryThis study demonstrates aberrant activation of the SUMOylation pathway during hepatic fibrosis progression in cystic echinococcosis (CE), characterized by upregulated SUMO1/Ubc9 expression and downregulated SENP1 in peri-cystic liver tissue. Ginkgolic acid (GA) intervention significantly attenuated CE-associated liver fibrosis in mice, evidenced by reduced cyst volume, decreased TGF-{beta}1 levels, and suppressed expression of fibrotic markers (-SMA/COL1A1). GA concurrently reversed dysregulated SUMO pathway protein expression. Mechanistically, GA upregulates the deSUMOylating enzyme SENP1, thereby inhibiting Echinococcus granulosus cyst fluid (EgCF)-induced SUMOylation and nuclear translocation of Smad4. This blockade impedes macrophage polarization toward the pro-fibrotic M2 phenotype (CD206{downarrow}) and suppresses hepatic stellate cell (HSC) activation (-SMA/PCNA{downarrow}). Furthermore, GA disrupts the pro-fibrotic bidirectional crosstalk between HSCs and macrophages. Collectively, these findings indicate that GA ameliorates CE-induced hepatic fibrosis by targeting the SUMO-Smad4 axis to modulate the immune microenvironment, providing a novel therapeutic strategy.

molecular biology↗