Biology subjects

Wu, X.

Publications and source records attributed to Wu, X..

At least 127 records · Page 7Linked to original sources

bioRxiv2025

Query-driven generative AI synthesizes multi-modal spatial omics from histology

Spatial omics technologies offer unprecedented insights into the cellular organization of tissues; however, they are not yet scalable for routine clinical use. In contrast, images of histological staining remain the foundation of pathological diagnosis despite lacking molecular information. Bridging this gap requires computational methods that can accurately infer spatial molecular data from histology alone. Here, we introduce TissueCraftAI, a generative artificial intelligence framework that predicts multi-modal spatial omics maps directly from standard histology images using natural language prompts. To train and validate our model, we created PRISM-12M, a large-scale dataset comprising over twelve million spatially registered histology and spatial omics image patches across fourteen tissue types from humans and mice. TissueCraftAI significantly outperforms existing methods in generating realistic histology images and predicting spatial proteomics and transcriptomics data with high fidelity. We demonstrated its utility in various downstream applications, including improving cell type annotation and enhancing the accuracy of patient survival predictions across multiple cancer types. By enabling flexible, query-driven in silico spatial molecular analysis using routine histology images, TissueCraftAI opens up new research avenues in computational pathology.

genomics↗

bioRxiv2025

Hypernatremia Enhances Transient Outward Potassium and Late Sodium Currents in a Mouse Model of Long QT Syndrome Type 3

Cardiac voltage-gated sodium channel gain-of-function (NavGOF) is characterized by action potential duration (APD) prolongation. Hypernatremia and perinexal widening synergistically prolong cardiac APD in guinea pig. However, guinea pig lack the transient outward potassium current (Ito), which could be increased by hypernatremia and thereby shorten APD. ObjectiveDetermine whether hypernatremia and perinexal expansion synergistically prolong APD in an animal model functionally expressing Ito. MethodsWhole-cell Ito was measured in isolated genetically-modified NavGOF ({Delta}KPQ) mouse ventricular myocytes. Ventricular APD at 30 (APD30) and 90 (APD90) percent repolarization were measured from optically mapped, Langendorff-perfused wild-type (WT) and {Delta}KPQ mouse hearts at different perfusate sodium concentrations (145 or 160mM), without and with the perinexal adhesion antagonist {beta}adp1. ResultsIn isolated myocytes, hypernatremia (160mM sodium) increased Ito. In whole-heart, hypernatremia significantly decreased both APD30 and APD90 in WT but only APD30 in {Delta}KPQ preparations. Perinexal disruption with {beta}adp1 did not change APD30 or APD90 in WT hearts, however it decreased APD30 and increased APD90 in {Delta}KPQ hearts. Combination of hypernatremia and {beta}adp1 did not synergistically change APD in {Delta}KPQ hearts. Computational models predict that Ito activation can prevent synergistic APD prolongation in mouse during hypernatremia and perinexal expansion that was observed previously in a guinea pig NavGOF model lacking Ito. ConclusionsHypernatremia during NavGOF prevents early ventricular repolarization due to Ito activation (mouse) and prolongs repolarization in the absence of Ito (guinea pig). Future studies in animal models electrophysiologically similar to humans are needed to determine if hypernatremia and perinexal expansion are proarrhythmic during NavGOF.

physiology↗

bioRxiv2025

Early blood-spinal cord barrier stabilization preserves peri-lesional tissue and improves recovery after SCI

Vascular disruption is an early and critical event in spinal cord injury (SCI), but its contribution remains poorly understood. Using novel in vivo two-photon dual-dye imaging, we found simultaneous blood-spinal cord barrier (BSCB) leakage and venous dilation in both the injury epicenter and adjacent transitional segment after cervical SCI in rats. Notably, vascular permeability in the transitional zone preceded axonal and neuronal loss, revealing a therapeutic window. Systemic delivery of ferulic acid-glycol chitosan (FA-GC) nanoparticles, a membrane-sealant, rapidly stabilized the compromised vasculature, reduced neuronal loss in the transitional region, and improved forelimb muscle strength. These findings identified acute vascular leakage beyond the injury epicenter as a driver of secondary pathology and highlight early vascular stabilization as promising therapeutic strategy.

pathology↗

bioRxiv2025

Steric Gating Dictates Selective Activation of BIRC6 by UBA6 Over UBA1

The giant E2-E3 chimera BIRC6 is specifically activated by the ubiquitin-activating enzyme UBA6, but not by UBA1. This specificity allows BIRC6 to ubiquitinate downstream substrates (e.g., caspases) and thereby regulate apoptosis. However, the molecular mechanism that underlies UBA6mediated specific activation of BIRC6 remains elusive. Here, we used a UbDha (Ub residue 76 dehydroalanine) probe to achieve one-step, activity-based trapping of the transient transthioesterification intermediate, and resolved the cryo-EM structures of two key complexes: 1) the doubly loaded UBA6-BIRC6UBC-UbT-UbA complex (3.4 [A] resolution) and 2) the singly loaded UBA6-BIRC6UBC-UbT complex (3.3 [A] resolution). Structural analysis reveals that the specific BIRC6-UBA6 pairing is dictated by steric compatibility between an insertion loop (residues 4649- 4653) in BIRC6s UBC domain and UBA6s gate helix. Unlike UBA1, UBA6 avoids steric clash with this insertion loop via two key conformational changes: a ~30{degrees} clockwise rotation and a 19 [A] displacement of its gate helix. These conformational changes collectively create a compatible cavity to accommodate the insertion loop. Biochemical validation confirms two key findings: 1) truncating BIRC6s insertion loop rescues UBA1-mediated ubiquitin charging of BIRC6UBC; 2) swapping UBA6s gate helix with that of UBA1 abolishes UBA6s transthioesterification activity towards BIRC6UBC. Our study provides key structural insights into the molecular basis of E1-E2 pairing specificity and advances our mechanistic understanding of apoptotic signalling.

biochemistry↗

bioRxiv2025

3-Phenylpropionic acid, a microbiota-derived polyphenol metabolite linked to hippuric acid, ameliorates colitis as a colon-enriched PPAR-γ agonist

Polyphenols are promising therapeutics for Crohns disease (CD), yet their bioavailability is largely dependent on the gut microbiome. The bioactive metabolites, metabolic pathways, and anti-inflammatory mechanisms underlying their effects remain poorly defined. We identified hippuric acid (HIPA) as a biomarker of polyphenol-microbiome interaction. HIPA is a meta-organismal metabolite produced through a cross-organ pathway that involves synthesis from gut microbial polyphenol metabolism via 3-phenylpropionic acid (3-PPA), followed by renal clearance. We found that CD is characterised by impaired polyphenol metabolism, resulting in deficient colonic 3-PPA and reduced serum hippuric acid relative to healthy individuals. Furthermore, we demonstrate that 3-PPA is a colon-enriched, mild PPAR-{gamma} agonist that ameliorates colitis in murine model. Systemic bioinformatic profiling of metagenomic data suggested the existence of undiscovered 3-PPA producers. Through targeted microbial incubation with polyphenols, we identified the probiotic Bifidobacterium breve and a lab isolate Escherichia coli FAH as novel 3-PPA producers. Collectively, our findings establish 3-PPA as a diet-dependent, colon-produced, mild PPAR-{gamma} agonist with the potential to minimise adverse effects associated with traditional PPAR-{gamma} agonists. This work establishes a foundation for developing microbiota-targeted, polyphenol-based therapeutic strategies for CD patients.

microbiology↗

bioRxiv2025

N6-Methyladenosine Safeguards Mouse and Human Germline Competence

N6-Methyladenosine (m6A) regulation of germline entry in post-implantation-like-pluripotent states remains poorly defined. We characterized m6A depletion by Mettl3 or Mettl14 knock-down or METTL3 inhibition in in vitro models enabling primordial germ-cell-like-cell and somatic differentiation. Upon m6A depletion, mouse epiblast-like cells upregulated embryonic Ras (Eras) and PI3K-pAKT, facilitating EZH2 repression and depletion of H3K27me3. Consequently, enhancer activation promoted global gene deregulation and impaired germline entry. In mouse formative stem cells, ERAS-PI3K-pAKT upregulation resulted in unscheduled Blimp1 and Otx2 co-expression, germline entry deficiency and enhanced mesodermal differentiation. Conversely, upon m6A depletion, germline competent human pluripotent stem cells upregulated OTX2 through FGF-pERK activation, resulting in germline entry deficiency and enhanced neuroectodermal differentiation. meRIP-seq revealed preferential m6A deposition on mouse mesodermal and human neuroectodermal transcripts, suggesting a basis for differentiation bias following m6A depletion. We illustrate how decreasing m6A abundances impact signaling, chromatin epigenetics and transcript stabilities, constituting a powerful cell intrinsic barrier for germline entry.

developmental biology↗

bioRxiv2025

Multimodal AI Decodes Extreme Environment Functional Dark Matter Beyond Homology

Functional annotation of proteins from extreme environments represents a major bottleneck for bioresource discovery, as a vast reservoir of functional dark matter defies existing homology-based methods. We demonstrate that environmental pressures impart conserved physicochemical energy signatures that co-determine protein function with sequence and structure. Here we developed ACCESS, a multimodal graph neural network employing hierarchical contrastive learning with a tailored label-sample co-embedding to fuse energy, sequence, and structural information and overcome homology scarcity. ACCESS surpasses state-of-the-art methods including BLASTp and CLEAN in annotating low-identity enzymes. Applied to extreme environmental metagenomics, we constructed a function map of extremophile enzymes to expand the biocatalyst library, pinpointed functionally critical residues to guide rational design, and enabled large-scale, function-based macro-evolutionary analyses. This paradigm transcends the limitations of homology, illuminating protein dark matter and accelerating the exploration of the biospheres functional diversity for applications in biotechnology and therapeutic development.

bioinformatics↗

bioRxiv2025

Developmental control of DNA damage responses in α- and β-cells shapes the selective beta-cell susceptibility in diabetes

Accumulation of DNA damage drives {beta}-cell dysfunction, senescence, and death in Type 1 and Type 2 diabetes. While -cell dysfunction also contributes to disease pathology, they remain remarkably resistant to senescence and cell-death. The mechanisms underlying these differential responses to diabetogenic stress, particularly differences in their DNA damage vulnerability, remain unclear. We demonstrate that replication introduces a window of genomic vulnerability in both - and {beta}-cells during neonatal growth, with -cells exhibiting higher replication rates and DNA damage. We show that neonatal {beta}-cells resolve DNA damage more efficiently during mitosis and favor error-free repair, while -cells compensate for their higher DNA damage vulnerability through increased cellular turnover. Using mouse models of overnutrition and diabetes, we show that {beta}-cells exhibit greater vulnerability to terminal DNA damage and impaired repair capacity under diabetogenic stress, with compensatory replication amplifying this vulnerability. We demonstrate that developmental epigenetic programs shape the differential DNA damage vulnerability of postnatal {beta}- and -cells. Loss of de novo DNA methyltransferase Dnmt3a in pancreatic progenitors selectively increases the DNA damage vulnerability of {beta}-cells from neonatal growth through adulthood. Our findings uncover novel developmental mechanisms that shape the distinct DNA damage responses of postnatal {beta}- and -cells during growth and diabetes. Article HighlightsO_LIMechanisms underlying the differential susceptibility of pancreatic {beta}- and -cells to diabetogenic stress remain unclear. C_LIO_LIDo replication dynamics, repair fidelity, and developmental epigenetic programs determine the vulnerability of postnatal {beta}- and -cells to DNA damage, a key driver of {beta}-cell failure in diabetes? C_LIO_LIReplication introduces DNA damage vulnerability in both neonatal {beta}- and -cells, yet {beta}-cells resolve damage more efficiently. Loss of DNA methyltransferase 3a in pancreatic progenitors selectively heightens {beta}-cell DNA damage vulnerability that persists into adulthood. Moreover, diabetogenic-stress preferentially compromises {beta}-cell repair fidelity. C_LIO_LIThese findings reveal how developmental programs shape {beta}-cell resilience and may influence lifelong diabetes risk. C_LI

developmental biology↗

bioRxiv2025

A BCG toxic effector induces mitochondrial DNA compaction to refrain protective immunity

Innate immune memory typically emphasizes nuclear chromatin remodeling that determines transcriptional memory in monocytes and macrophages. Here, we show that compaction of mitochondrial DNA (mtDNA), governed by mitochondrial transcription factor A (TFAM) abundance and mtATP-dependent remodeling, defines the transcriptional and functional state of trained macrophages. While typical pathogen-associated molecular pattern (PAMPs) triggered mtDNA accessibility, Bacillus Calmette-Guerin (BCG) effector PE18 directly interacted with and activated SLC25A5 to reduce mtATP levels, thereby inhibiting TFAM degradation by AFG3L2. Accumulated TFAM restricts mtDNA accessibility, suppressing the transcription of the mtNd1 and thereby reducing mtNd1-mediated mtROS production, which diminishes the trained capacity of macrophages against secondary infections. Notably, BCG{Delta}pe18 maintains macrophages cytokine transcriptional capacity independent of classical nuclear histone modifications. Moreover, BCG{Delta}pe18 provides robust and lifelong protective immunity against Mycobacterium tuberculosis (Mtb) infection. These findings reveal mitochondrial genome as a regulatory entity in trained immunity, and suggest a potential strategy for improving vaccine performance.

immunology↗

bioRxiv2025

The Cortical Temporal Axis: MEG-Based Cross-Frequency Gradients with Biological Anchors

Neural oscillations have long been used to characterize the temporal dynamics of individual brain regions, yet a parsimonious, system-level representation that integrates multi-rhythmic activity has been lacking. Using source-localized resting-state magnetoencephalography (MEG) data, we computed regional power spectra and assessed spectral similarity, then applied diffusion map embedding to construct cross-frequency neurophysiological gradients that place whole-brain oscillations within a unified, low-dimensional coordinate system. We found the first three gradients accounted for over 40% of the variance, remained stable across individuals, and aligned with established functional, structural, and geometric cortical axes. Computational modeling showed that these gradients reflect local excitation-inhibition balance, while multimodal analyses revealed strong associations with neurotransmitter receptor distributions, cytoarchitecture, and cell-type-specific gene expression. Lifespan analyses further demonstrated systematic gradient reorganization, with distinct cognitive mappings onto functions such as language, memory, and multisensory integration. Clinically, Parkinsons disease patients displayed disrupted gradients, particularly in regions linked to language and social cognition. Finally, these gradient patterns exhibited high test-retest reliability. These findings establish MEG-derived neurophysiological gradients as robust, low-dimensional representations of cortical organization, offering a biologically grounded framework for studying brain aging and disease.

neuroscience↗

bioRxiv2025

Parkinsonian striatal acetylcholine dynamics are refractory to L-DOPA treatment

BackgroundFluctuations in striatal dopamine (DA) are interdependent with fluctuations in acetylcho- line (ACh), both of which are thought to be important for motor function and dysfunction in Parkinsons disease (PD). ObjectivesDetermine how ACh dynamics are altered by dopamine under normal and parkinsonian conditions following acute and chronic L-DOPA treatment. MethodsWe used fiber photometry to record fluorescent DA and ACh sensors in the dorsomedial striatum (DMS) of normal mice treated with vehicle or amphetamine and in the dorsolateral striatum (DLS) of mice with unilateral substantia nigra (SNc) DA neuron lesions (using 6-OHDA) subjected to an L-DOPA-induced dyskinesia (LID) protocol. ResultsUnder normal conditions, ACh exhibited transient increases followed by pauses and fluctuated at [~]1-Hz frequency in an anti-correlated manner to DA. Amphetamine treatment reduced the frequency of ACh fluctuations and amplitude of ACh transients while prolonging after-transient pauses. In 6-OHDA- lesioned mice, ACh dynamics oscillated at a higher frequency, and ACh events had reduced peaks and pauses. L-DOPA increased DA and, after repeated treatments, also reduced ACh. However, L-DOPA neither restored the anti-correlation between DA and ACh nor normalized the reduced ACh transient and pause amplitudes or the increased frequency of ACh fluctuations. In extended recordings during the tran- sition to the L-DOPA OFF state, ACh remained low as DA diminished, and ACh transient and pause amplitudes remained suppressed, and the oscillatory frequency elevated. ConclusionsDopamine depletion transforms striatal ACh dynamics and L-DOPA fails to normalize these dynamics. Because these dynamics are unresponsive to treatment, new therapies targeting them may offer symptomatic improvements for PD and LID. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=72 SRC="FIGDIR/small/686401v1_ufig1.gif" ALT="Figure 1"> View larger version (28K): org.highwire.dtl.DTLVardef@705b66org.highwire.dtl.DTLVardef@80afd2org.highwire.dtl.DTLVardef@972c41org.highwire.dtl.DTLVardef@da91f8_HPS_FORMAT_FIGEXP M_FIG C_FIG We used dual-wavelength fiber photometry to simultaneously record dopamine and acetylcholine dynam- ics in the dorsal striatum. We recorded these dynamics in control mice before and after treatment with the dopamine releaser amphetamine and in hemiparkinsonian mice before after treatment with the dopamine pre-cursor L-DOPA. We asked how these experimental manipulations alter the bulk signaling of dopa- mine and acetylcholine, their temporal relationship, and the sub-second dynamics of acetylcholine signaling.

neuroscience↗

bioRxiv2025

BMP-Smad1/9 signaling is required for PGC proliferation in zebrafish

The specification and maintenance of germ cell lineage are vital for reproductive development and heredity. The germ cell fate in some species, such as zebrafish and Xenopus, is determined by maternally supplied germ plasm, whereas in mammals it is induced by bone morphogenetic protein (BMP) signaling after implantation. It remains elusive whether BMP signaling is implicated in zebrafish germ cell development. Here, we demonstrate that, in zebrafish, BMP-Smad1/9 signaling is required for primordial germ cell (PGC) maintenance but not for PGC fate determination or migration. BMP inhibitor treatment or whole-embryo smad1/9 knockdown reduces the number of PGCs. To investigate cell-autonomous roles of BMP-Smad1/9 in PGCs, we generated PGC-specific smad1/9 knockouts using a double-transgenic approach with PGC-specific expression of Cas9 and ubiquitous expression of guide RNAs (gRNAs). Loss of Smad1/9 in PGCs leads to impaired PGC proliferation and increased apoptosis, resulting in reduced PGC numbers and adult sex bias. Moreover, transcriptome analysis of smad1-deficient PGCs revealed no significant changes in the expression of PGC-specific genes, but a marked upregulation of genes involved in cell cycle checkpoints and DNA damage repair. Notably, ectopic ATR-pChk1 activation in smad1-cKO PGCs validates cell cycle defects and DNA replication stress. ATR inhibition restores PGC numbers in mutant embryos. Collectively, these findings underscore a critical role of BMP-Smad1/9 signaling in zebrafish PGC population maintenance, while it is dispensable for PGC fate determination and migration.

developmental biology↗

bioRxiv2025

Captamer: A Novel Quantitative Protein Detecting Method Depending on Aptamer-activated Molecular Switches and RPA Signal Amplification

There are various protein assays for specific and quantitative detection and widely used for laboratory and clinic purposes, but current methods still have limitations. Immunoassays based on antibodies, like ELISA, suffer from slow response and a long antibody-screening period, while physical or electrochemical methods are generally restricted by high cost or the stringent requirement of equipment or operating skills. In this study, we developed an in vitro sensitive protein quantification method: Captamer. The Captamer system comprises a molecular switch derived from aptamer sequence and an exponential fluorescence signal amplification pathway based on recombinase polymerase amplification (RPA). We demonstrated the Captamer for SARS-CoV-2 nucleocapsid protein detection and obtained results from samples within 30 min, displaying a wide detection window from 0.2 pg/mL to 200 pg/mL with high specificity. Furthermore, we tested the Captamer for Tau441 protein (a potential Alzheimers disease biomarker) and thrombin (a classic aptamer-protein interaction model), showing the limit of detection as low as 1 ng/mL and 0.02pg/mL respectively, which suggested the capacity of Captamer to be applied to various aptamer-protein pairs. Compared with the most commonly used and recently reported protein quantification methods, Captamer stands out for its high sensitivity, short response time, low cost, and simplicity, indicating its great potential to be widely used in protein quantification. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=131 SRC="FIGDIR/small/686180v1_ufig1.gif" ALT="Figure 1"> View larger version (32K): org.highwire.dtl.DTLVardef@1e38ffaorg.highwire.dtl.DTLVardef@1019e72org.highwire.dtl.DTLVardef@1498b68org.highwire.dtl.DTLVardef@15f5ea2_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Modelling cigarette smoke-induced lung vascular dysfunction using an alveolus-on-chip

The alveolus is central to gas exchange in the lung, and alveolar damage is a characteristics of a variety of lung diseases. Understanding alveolar microvascular dynamics and epithelial-endothelial interactions is essential for accurately modeling alveolar physiology and its dysfunction in lung diseases such as Chronic Obstructive Pulmonary Disease (COPD), pulmonary fibrosis and acute respiratory distress syndrome (ARDS). In this study, we present an open-top, membrane-free alveolus-on-chip platform incorporating self-assembled, perfusable 3D vascular networks by primary human lung endothelial cells and pericytes, co-cultured with alveolar epithelial type 2 (AEC2) cells. These vascular networks were developed within 6 days under continuous flow and remained stable for at least 12 days. The inclusion of pericytes supported capillary-like vessel formation and increased gene expression of EDNRB1, a gene enriched in alveolar microvascular endothelial cells. Furthermore, CD31 gene expression was higher in 3D endothelial networks compared to 2D endothelial monolayers, suggesting increased cell-cell adhesion. Monocytes could be successfully perfused through the networks, expanding the platforms potential for studying immune interactions in lung disorders. Culturing AEC2 monolayers directly on the vascularized hydrogel enabled physiologically relevant cell-cell interactions without artificial membranes, while maintaining air-liquid interface conditions. Importantly, exposure of the AEC2 layer to whole cigarette smoke (WCS) led to complete disintegration of the underlying vascular network, an effect not observed in the absence of AEC2. This chip model provides a human-relevant system for investigating vascular-epithelial crosstalk in the alveolus, smoke-induced lung injury, and immune recruitment, offering a valuable platform for future disease modeling and drug testing applications.

bioengineering↗

bioRxiv2025

Natural variation in regulatory code revealed through Bayesian analysis of plant pan-genomes and pan-transcriptomes

Understanding the genetic code of cis-regulatory elements (CREs) is essential for engineering gene expression and modulating agronomic traits in crops. In plants, CREs underlying rapid evolution of gene expression often overlap with structural variation in promoters, making them undetectable using single-reference genomes. Here, we develop K-PROB (K-mer-based in silico PROmoter Bashing), a computational tool that learns from intraspecies promoter sequence and gene expression variation in pan-genomes and pan-transcriptomes to identify CREs controlling gene expression. K-PROB deploys a k-mer-based Bayesian variable selection framework to prioritize causal variable identification. We demonstrate the effectiveness of our approach in maize and soybean, two staple crops species. Applying K-PROB to genes with the most highly variable promoter sequences and the most diverse patterns of expression, such as nucleotide-binding leucine-rich repeat receptors, we identified k-mers enriched for bona fide transcription factor binding sequences, and overlapping with open chromatin regions and DAP-seq binding sites. Notably, multiple significant k-mers are located within presence/absence structural variants, highlighting structural variation in promoters as key drivers of transcriptional diversity of highly variable genes. We further validated the regulatory effects of identified k-mers on gene expression using luciferase reporter assays. Our results showcase a high-throughput and pangenomic approach for probing natural intraspecies cis-regulatory diversity, discovering new causative cis-elements, and facilitating future expression engineering across plant species. Significance StatementUnderstanding which DNA sequences control gene expression is essential for crop improvement. Current methods for identifying regulatory elements rely on expensive, specialized biochemical datasets typically limited to a single genotype. We developed a computational tool that links natural sequence variation and gene expression variation to identify functional regulatory sequences. Our tool employs a statistical framework that prioritizes causality over correlation, in contrast to most genome-wide association studies. Applying it to maize and soybean, two staple crops, we uncovered known and novel regulatory elements and validated them with molecular assays. Our approach is scalable, cost-effective, and efficiently utilizes natural variation from existing pangenomic datasets, opening new avenues for future crop engineering and studying gene regulation in diverse plant species.

bioinformatics↗

bioRxiv2025

Immunometabolic determinants of long-term response in leukemia patients receiving CD19 CAR T cell therapy

Although most patients with relapsed/refractory B-cell acute lymphoblastic leukemia (B-ALL) receiving CD19-targeted chimeric antigen receptor (CAR) T cell therapy achieve remission, loss of CAR T cell functionality and subsequent relapse remains an unmet therapeutic need. We applied an integrative approach to study the immunometabolism of pre- and post-infusion CD19-CAR T cells of patients with relapsed/refractory B-ALL. Pre-infusion CAR T cells of long-term responders (LTR) had increased oxidative phosphorylation, fatty acid oxidation, and pentose phosphate pathway activities, higher mitochondrial mass, tighter cristae, and lower mTOR expression compared to products of short-term responders. Post-infusion CAR T cells in bone marrow (BM) of LTR had high immunometabolic plasticity and mTOR-pS6 expression supported by the BM microenvironment. Transient inhibition of mTOR during manufacture induced metabolic reprogramming and enhanced anti-tumor activity of CAR T cells. Our findings provide insight into immunometabolic determinants of long-term response and suggest a therapeutic strategy to improve long-term remission.

immunology↗

bioRxiv2025

Normative models of individualized functional brain networks reveal language network expansion in autism

Autism spectrum disorder is a highly heterogeneous neurodevelopmental disorder, hindering mechanistic insights and the identification of biomarkers for clinical diagnosis. Recently, precision functional mapping has been developed to identify abnormalities in brain network topologies associated with various psychiatric disorders, yet its application in autism remains limited. Here, we utilized precision functional mapping and a large, multisite neuroimaging dataset (N = 1,182) to construct individualized functional networks in individuals with autism. We developed normative models using network surface area from healthy controls (n = 628) to characterize typical brain network organization across age, allowing for the quantification of individual-specific deviations in individuals with autism (n = 554). We found widespread and heterogeneous deviations from the normative model, with the language network emerging as the most significantly altered region, thereby emerging as an epicenter of functional disruption in autism. Individuals with autism were clustered into three subtypes involving distinct functional network topologies, associated with behavioral profiles marked by impairments in perception, language processing, or socio-emotional functioning. We further linked these atypical brain features to cortical gene expression patterns, revealing enriched pathways related to neurodevelopment, language, and signaling processes. Together, these findings reveal autism-specific deviations in individualized functional brain networks, offering potential clinical relevance for understanding and stratifying autism.

neuroscience↗

bioRxiv2025

Correlative 4D-STEM Ptychography and EELS for Cryogenic Single-Particle Analysis

Cryogenic electron microscopy has enabled atomic resolution structural determination of biological macromolecules. However, phase contrast imaging alone does not reveal elemental composition or other valuable chemical information. Electron energy loss spectroscopy (EELS) provides rich vibrational and chemical details, integrating it with high-resolution structural imaging for correlative analysis of biological specimens remains a major challenge, as conventional acquisition modes are often mutually exclusive. Here we propose two optical geometries that enable correlative 4D-STEM with EELS: (1) a sequential acquisition with a post-specimen beam deflector, and (2) a simultaneous acquisition with a hollow detector. We compared the two setups for biological specimens, and focused on the hollow detector geometry which allows simultaneous acquisition of diffraction patterns and EELS spectra in a single dose budget. Using an apoferritin dataset, we demonstrate sub-nanometre 3D resolution in single particle analysis, even with a hollow angle as of 55% of the convergence angle and approximately 30% of the total dose allocated to EELS. Finally, we propose a workflow that integrates ptychography with EELS for correlative, energy-resolved 3D mapping of biological macromolecules, paving the way toward unified structural, chemical, and vibrational analysis of biological specimens.

biophysics↗