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Zhang, A.

Publications and source records attributed to Zhang, A..

At least 37 records · Page 2Linked to original sources

A functional genomics screen of human B-cell differentiation reveals convergent mechanisms of inherited childhood leukemia predisposition

B-cell acute lymphoblastic leukemia (B-ALL) is the most common childhood cancer, yet the mechanisms by which inherited risk variants predispose to leukemia development remain poorly understood. A major challenge to studying these mechanisms has been the lack of model systems that faithfully capture the transient developmental states in which predisposition alleles are thought to act. Here, we establish a human B-cell differentiation platform from hematopoietic stem/progenitor cells that enables CRISPR-based engineering, recapitulates early B-cell lymphopoiesis, and enriches for rare developmental intermediates. By applying systematic perturbations with multiplexed single-cell transcriptomic profiling to mimic the effects of mutations in nine familial B-ALL predisposition genes, we decipher mechanisms by which B-cell development can be altered by such inherited variation to predispose to B-ALL. Through these studies, we identify convergent delays in B-cell differentiation at progenitor stages characterized by high-level RAG1/2 recombination activity. We propose that these delays at progenitor stages increase the likelihood that cells can undergo illegitimate RAG-mediated recombination to promote transformation, a finding consistent with similar rates of illegitimate RAG-associated genomic alterations in those with B-ALL associated with familial predisposition variants compared to sporadic cases.

cancer biology↗

Single-cell multiomic mapping of genetic predisposition to childhood B-cell acute lymphoblastic leukemia

Inherited genetic variation substantially increases the risk for developing childhood B-cell acute lymphoblastic leukemia (B-ALL), the most common cancer in children, yet the underlying mechanisms remain poorly understood. To address this limitation, we employ a single-cell multiomic framework to functionally dissect common regulatory variants associated with B-ALL risk. Coupling this multiomic analysis with assessment of allelic skews in chromatin accessibility, we reveal the impact of risk alleles and disruptions in transcription factor networks specific to B-cell progenitors, thereby providing mechanistic insights into altered regulatory programs underlying B-ALL predisposition. By constructing long-range variant-to-target gene maps, we identify 34 high-confidence B-ALL susceptibility genes. Among these, we uncover and functionally validate a risk allele that selectively upregulates expression of ELK3, a previously unrecognized regulator of B-cell development and leukemogenesis. Together, these findings establish a comprehensive variant-to-function map of cell state-specific regulatory disruptions underlying inherited predisposition to B-ALL and define new risk mechanisms, which could pave the way for future targeted prevention approaches.

cancer biology↗

IGF2BP3 amplifies antiviral innate immunity with implications for autoimmune diseases

The insulin-like growth factor 2 mRNA-binding protein 3 (IGF2BP3) is a known N6-methyladenosine (m6A) reader, but its role in antiviral innate immunity is unknown. Here, we identify IGF2BP3 as a critical positive regulator of antiviral responses. Viral infection and interferon (IFN) stimulation upregulate IGF2BP3, establishing a feedforward loop that potentiates virus-induced activation of the TBK1-IRF3 and NF-{kappa}B pathways, thereby amplifying type I interferon (IFN-I) production, and restricting viral replication in human and murine cells and in vivo. Mechanistically, IGF2BP3 directly binds and stabilizes MAVS and TBK1 mRNAs and promotes their translation by facilitating recruitment to the eIF4F/PABP-associated initiation complex. Upon infection, IGF2BP3 relocalizes to antiviral stress granules (avSGs), where it scaffolds the RIG-I-G3BP1 complex to enhance viral RNA sensing. Notably, IGF2BP3 is aberrantly upregulated in patients with systemic lupus erythematosus (SLE) and in Trex1 knockout (KO) mice, and pharmacological inhibition by curcumol suppresses IFN-I-driven pathology and improves survival. Collectively, our findings establish IGF2BP3 as a central feedforward circuit that couples viral RNA sensing to the control of RNA stability and translation of key signaling molecules, and reveals its potential as a therapeutic target in interferon-associated autoimmune diseases. Significance StatementAntiviral immunity demands rapid and coordinated gene expression, yet how RNA-binding proteins link viral recognition to downstream signaling is poorly understood. We reveal that the m6A reader IGF2BP3 acts as a central amplifier of antiviral innate immunity. Induced by both viruses and interferons, IGF2BP3 enhances viral RNA sensing, stabilizes key signaling transcripts, and boosts their translation, creating a self-reinforcing feedforward circuit that strengthens interferon responses. Beyond host defense, IGF2BP3 is aberrantly elevated in interferon-driven autoimmunity, and its pharmacological inhibition reduce disease pathology in vivo. Our findings uncover a previously unrecognized mechanism that integrates RNA metabolism, stress-granule signaling, and translational control to regulate innate immunity, offering new therapeutic perspectives for both infectious and autoimmune disease.

immunology↗

Reconstructing whole-organism cell phylogenies with resolved ancestral transcriptional states

Combining cell lineage tracing with single-cell RNA sequencing can reconstruct a phylogenetic tree to integrate single-cell transcriptomic atlas. However, the internal nodes of this tree - representing ancestral cells - remain transcriptionally silent, preventing along-lineage longitudinal tracing of cell state dynamics. Here, we overcome this by reconstructing high-resolution zygote-to-larva developmental cell phylogenies for 15 zebrafish larvae, with directly measured transcriptomes of the terminal nodes (i.e., sampled cells). Leveraging a set of lineage-committed upregulated genes (LUGs), we developed LUG-encoded ancestral projection (LEAP), a novel phylogeny-based computational framework, and successfully imputed the transcriptional states of internal nodes of the phylogenies. This enabled, for the first time in a non-nematode organism, lineage-informed longitudinal analysis of cell state dynamics throughout development. Our analysis revealed a major, previously unappreciated wave of fate specializations associated with hatching, distinct from the well-characterized events of gastrulation. Furthermore, we uncovered abundant incipient cell states that are already fate-determined but exhibit minimal transcriptional differentiation, revealing a hidden layer of developmental fate specializations. In sum, by resolving ancestral transcriptional states of a reconstructed cell phylogeny, this work paves the way for constructing lineage-resolved cell atlases in complex organisms to characterize comprehensive cell state dynamics.

developmental biology↗

Two Novel Rod-Like Circular RNAs from the Oroarctic Tundra Soil Display Candidate Ribozyme-Like Features: An In Silico Characterization

The recent discovery of obelisks, novel deltaviruses, and other viroid-like circular RNAs has greatly expanded the known diversity of autonomous RNA elements. However, cold terrestrial ecosystems remain comparatively undersampled for these molecules. Using a structure-based modification of the Tormentor pipeline, we assembled two putative non-coding rod-like circular RNAs from winter metatranscriptomes of oroarctic tundra soil collected near Kilpisjarvi, Finland. Sequence-based searches identified no meaningful homologs for either RNA. Structure-based analyses identified affinities to deltavirus-like ribozymes in Rod 1 and to hammerhead ribozymes in Rod 2, with structural compatibility confirmed by integration into an established covariation model. Rod 1 was additionally detected in independent alpine metatranscriptomic datasets, whereas Rod 2 was not identified beyond the original sample. Collectively, these results identify Rod 1 as a strong candidate viroid-like RNA bearing a putative ribozyme-like structure motif that warrants experimental validation, while Rod 1 remains a preliminary candidate requiring further confirmation.

microbiology↗

cf-Cabernet: Nick Repair Prior to End Repair Preserves Endogenous DNA Methylation Information in Cell-Free DNA Methylation Sequencing

Cell-free DNA (cfDNA) methylation profiling holds great promise for non-invasive cancer detection, yet accurate methylome analysis is compromised by DNA damage inherent to cfDNA. Standard library preparation workflows involve an end-repair step during which DNA polymerases can initiate synthesis from single-strand breaks (nicks), replacing endogenous methylated nucleotides with unmethylated nucleotides in the 3' direction and systematically erasing methylation information. This artifact is distinct from the terminal jagged-end effect and disproportionately affects cfDNA and FFPE DNA, which harbor abundant nicks. Here, we developed cf-Cabernet, which builds upon the Cabernet framework (Cao et al., 2023) -- an enzymatic methylation sequencing method featuring carrier DNA-assisted sample recovery and amplification-friendly post-conversion processing -- with the addition of a Taq DNA ligase-mediated nick repair step prior to end repair. Using matched cfDNA samples, we compared cf-Cabernet against standard EM-seq and WGBS. cf-Cabernet and EM-seq both substantially outperformed WGBS in alignment rate. Critically, while standard EM-seq exhibited globally reduced methylation levels compared to WGBS, cf-Cabernet yielded methylation levels concordant with WGBS. M-bias analysis revealed that EM-seq libraries showed persistently depressed methylation across the entire read length, whereas cf-Cabernet methylation recovered to the WGBS baseline beyond the terminal [~]40 bp jagged-end region. Nick-induced methylation erasure during end repair is a significant but previously underappreciated source of error in cfDNA methylation sequencing. cf-Cabernet effectively mitigates this artifact through pre-emptive nick ligation, enabling accurate methylome profiling from damaged DNA templates. This method is broadly applicable to cfDNA, FFPE DNA, and other clinical specimens where DNA integrity is compromised, providing a robust foundation for methylation-based liquid biopsy applications.

genetics↗

Hoxb5+ fetal liver hematopoietic stem cells establish lifelong hematopoiesis and exhibit enhanced ITGA4-dependent engraftment

Adult long-term hematopoietic stem cells (LT-HSCs) are classically defined by self-renewal, multilineage regenerative capacity, and relative quiescence, but how and when lifelong LT-HSCs are established during development remains unclear. Here, we demonstrate that Hoxb5 fetal liver HSCs exhibit bona fide LT-HSC activity, including long-term multilineage reconstitution and serial transplantation capacity, whereas Hoxb5- fetal liver HSCs display limited regenerative potential. Embryonic lineage tracing further demonstrates that E14.5 Hoxb5-expressing hematopoietic cells contribute broadly to adult hematopoiesis, including the adult HSC compartment, and give rise to functional adult LT-HSCs. Across developmental stages, single-cell transcriptional profiling revealed that fetal Hoxb5 HSCs remain highly proliferative while maintaining canonical LT-HSC transcriptional programs and superior repopulating activity relative to predominantly quiescent adult Hoxb5 HSCs. Fetal Hoxb5 HSCs also exhibited elevated ITGA4-mediated adhesion programs, and disruption of the ITGA4-VCAM1 axis impaired engraftment following transplantation. Together, these findings establish a developmental continuum linking fetal and adult LT-HSCs and identify enhanced ITGA4-mediated adhesion as a defining feature of fetal LT-HSCs.

developmental biology↗

Healing cascades and infections in wounds monitored using a wearable sensor of gaseous flux

Capabilities for quantitative monitoring of chronic wounds remain an unmet clinical need, as existing diagnostic approaches rely on semiquantitative evaluation of symptoms that lack sensitivity especially during early stages of infection. Here we present a scheme for tracking wound physiology that leverages a miniature, wireless skin-interfaced device for non-contact, transient measurements of the flux of volatile organic compounds (VOCs) and water vapor from the wound microenvironment. Unlike emerging smart bandage platforms that rely on physical contact with the fragile wound bed to interrogate liquid-phase biomarkers, this strategy uses an engineered microclimate and suspended suite of sensors to measure the diffusive transport of wound-derived gases across the wound surface but separated from it. The result enables quantitative evaluation of metabolic activity and healing progression without perturbing the healing tissues. In biofilm growth models of Staphylococcus aureus, measurements demonstrate that trends in VOC flux correlate strongly with bacterial growth kinetics and precede any visible biofilm formation. Longitudinal monitoring in infected murine wound healing models shows that concurrent measurements of water vapor and VOC flux provide complementary physiological insights, capturing both the trajectory of barrier restoration and the dynamics of bacterial burden. The findings establish this non-contact sensing scheme as a distinct and clinically translatable paradigm for wound monitoring, with broad implications for non-invasive surveillance of disease states in which tissue metabolic activity and skin barrier integrity serve as actionable physiological readouts. Significance StatementLimited capabilities in continuous, quantitative assessment of a wound make early diagnosis and effective management challenging, particularly in cases of infection that rapidly progress before symptoms appear. Non-contact approaches for wound monitoring that preserve fragile tissue can transform wound care. In this context, gaseous flux from the wound bed provides an integrative measure of microbial activity and barrier restoration. This study establishes a wearable sensing platform that quantifies these fluxes in real time, enabling early infection detection and temporal tracking of wound healing. These results highlight a path toward personalized treatment strategies and reduced reliance on episodic clinical evaluation.

bioengineering↗

Topological structure in human spatial representation revealed through drawing

Human spatial representations are often assumed to represent Euclidean properties such as length, distance, and angle. Here we test an alternative (but not mutually exclusive) possibility - that spatial memory is structured primarily around topological relations. Across four experiments, adults and children memorized simple letter-like figures and reproduced them by drawing, allowing the contents of their spatial representations to be revealed directly. Drawings showed systematic distortions of metric features, including strong biases of angles toward 90{degrees} and compression of line length towards an average value. In contrast, topologically critical features - such as T-junctions and holes - were reliably preserved, even relative to closely matched but topologically irrelevant features like L-junctions. These effects were magnified in a serial reproduction paradigm, in which participants iteratively generated new drawings from previous participant drawings: At the end of each mnemonic chain, figures converged on simplified topological structures as metric detail degraded. Similar patterns were observed in children aged five to eight years. Together, these findings suggest that basic topological relations may function as primitive building blocks of human spatial representation, with metric detail encoded secondarily.

animal behavior and cognition↗

Generalisable tissue-wide molecular reconstruction from histology

Spatial transcriptomics technologies measure gene expression within intact tissues but remain difficult to scale across large tissue sections and patient cohorts. Consequently, many studies rely on tissue microarrays (TMAs) or sparse spatial profiling designs, where molecular measurements are available for only limited tissue regions and are often generated using heterogeneous gene panels. Existing H&E to spatial gene expression prediction methods remain challenged by sparse molecular measurements, partially overlapping gene panels and tissue-wide reconstruction across heterogeneous spatial datasets. Here, we present GHIST+, a framework for tissue-wide reconstruction of single-cell molecular states from H&E histology. GHIST+ integrates cellular morphology, local tissue context and shared tissue representations to extend sparse molecular measurements into tissue-wide molecular maps across heterogeneous spatial datasets. Across multiple cancer types and GTEx breast tissues, GHIST+ reconstructs biologically meaningful tissue-wide molecular organisation from sparse TMA-derived measurements while preserving spatial tissue structure, cell-type organisation and age-associated tissue states across cancer and non-cancer settings. GHIST+ establishes a scalable framework for transforming sparse spatial profiling experiments into tissue-wide molecular maps, enabling cohort-scale molecular reconstruction from routine histology under heterogeneous spatial transcriptomic settings.

bioinformatics↗

Estrogen-Deficiency Degrades Left Ventricular Diastolic Function and Energy Metabolism in Hypertensive Female Mice

AimsHeart failure (HF) due to diastolic dysfunction (DD) but normal left ventricular (LV) ejection fraction (EF) is termed HF with preserved EF (HFpEF). Given its high prevalence in post-menopausal women, we hypothesized that 17{beta}-estradiol (E2) function is mechanistically linked to DD HF and investigated E2-deficiency in the etiology of DD in a mouse model. MethodsFemale C57BL/6J mice were divided into one group with hypertension induced by N({omega})-nitro-L-arginine methyl ester (L) and cardiac pressure overload induced by angiotensin II (A), collectively inducing DD, and one group with sham treatment. Groups were subdivided to receive an ovariectomy (OVX) to induce estrogen-deficiency and emulate menopause or sham surgery. During the next 21 days, mice were tested for cardiac function, food intake, response to E2 agonists, gene profiling, cardiomyocyte-contractility and elasticity, and cardiac mitochondrial function. ResultsOVX-associated E2-deficiency exacerbated DD in a time-dependent way without affecting EF or stroke volume, emulating a severe DD phenotype. These changes paralleled those for mitochondrial dysfunction, i.e., upregulation of genes associated with stress, energy metabolism, and fibrosis, as well as functional and structural defects in cardiomyocytes. Treatment of OVX + (L + A) with E2 or a G-protein-coupled estrogen receptor agonist normalized diastolic function, whereas estrogen receptor beta agonists did not. The OVX DD mice exhibited moderately impaired mitochondrial function, which delayed cardiomyocyte relaxation but not contraction, altered cardiac substrate utilization, reduced cardiomyocyte elasticity, increased production of reactive oxygen species, and potentiated extracellular fibrosis. ConclusionsOVX-induced E2-deficiency generates metabolic, structural, and functional changes in cardiomyocytes and the adjacent extracellular matrix, exacerbating the effects of L and A on diastolic function. This robust DD model revealed a role for E2 via ER in diastole-regulation in female mice and raised questions about similar mechanisms operative in postmenopausal women. HIGHLIGHTSO_LIOvariectomy (OVX)-induced estrogen-deficiency exacerbated diastolic dysfunction (DD) induced by hypertension and pressure overload with preserved ejection fraction in female C57BL/6J mice. C_LIO_LIIn post-OVX-treated DD mice, heart weight and fibrosis preceded other metrics of cardiac dysfunction. C_LIO_LIOVX-induced estrogen-deficiency increased the expression of genes associated with stress, energy metabolism, and especially fibrosis. C_LIO_LIMetabolic imaging of the heart by positron emission tomography revealed that DD with preserved ejection fraction was associated with mitochondrial dysfunction presenting as increased accretion of cardiac energy substrates, [18F]deoxyglucose and [11C]palmitate, effects that worsened following OVX. C_LIO_LIOVX increased cardiomyocyte stiffness and fibrosis and reduced cardiomyocyte lengthening and compliance in the context of female DD. C_LIO_LIImproved diastolic function following delivery of GPER agonists or estradiol to OVX DD female mice implicates estrogen receptor in the maintenance of normal cardiac function. C_LI

physiology↗

Donor Age and Oligosaccharide Structure Jointly Shape the Gut Microbiome Function

Non-digestible oligosaccharides are widely used as prebiotics, yet structurally related glycans can elicit distinct gut microbiome responses. Here, we combined controlled ex vivo fermentation, deep DIA metaproteomics, and targeted metabolomics to determine how oligosaccharide structure and donor age shape microbiome function. Stool microbiomes from 18 healthy donors across three age groups were cultured with seven structurally related oligosaccharides from two glycan families, fructo-oligosaccharides (FOS) and galactosyl-sucrose derivatives (GSD). We found that oligosaccharide structure organized a functional response landscape rather than simply separating substrates into broad prebiotic classes. Structurally related glycans produced more similar response profiles overall, yet closely related FOS substrates remained functionally distinguishable, indicating that subtle structural differences were resolved by the microbiome as graded functional changes. These structure-responsive functions were further associated with producer-level reorganization relative to baseline, while targeted enzyme-level analyses indicated that substrate-specific CAZyme responses could also reflect altered functional investment within shared producer backgrounds. Despite these substrate-specific entry processes, network analysis revealed convergence onto shared downstream physiological states enriched for translation, amino-acid biosynthesis, secretion/export, and chemotaxis-related pathways. Across treatments, major short-chain fatty acids increased while mucin glycan degradation-associated markers decreased, suggesting coordinated shifts toward saccharolytic metabolism and reduced host-glycan foraging. Tryptophan-associated metabolism was also consistently linked to primary fructan processing, accompanied by higher extracellular tryptophan availability. Donor age modified selected microbial functional axes and enzyme-metabolite coupling relationships rather than the overall direction of core fermentation outputs. In particular, oligosaccharides attenuated an Methanobrevibacter smithii (M. smithii) and M00567 methanogenesis-related signature in microbiomes from older adults and altered age-dependent relationships between butyrate-pathway enzymes and extracellular butyrate levels. Together, these findings show that oligosaccharide structure determines how gut microbial communities organize carbohydrate processing and downstream functional states, while donor age reshapes the taxonomic and metabolic context of these responses. This work provides a mechanistic framework for structure-aware and age-aware precision prebiotic design.

microbiology↗

Regional reconfiguration of functional brain networks during childhood and adolescence: evaluating age and sex effect

IntroductionWhile global topological properties of brain networks reach relative maturity early in development, functional reconfigurations at the regional level continue throughout adolescence to support cognitive maturation. However, regional age and sex-specific developmental patterns of functional reconfiguration remain incompletely understood. MethodsWe analyzed resting-state fMRI data from 528 participants aged 5-21 years from the Human Connectome Project in Development. Three regional graph-theory metrics (betweenness centrality, hub score, and local efficiency) were computed for each individuals functional network. Cognition was measured using NIH toolbox. Parallel factor analysis was employed to decompose an individual x region x metric array into factors representing distinct developmental properties in the full sample and separately for males and females. Brain-cognition associations were examined in developmental subgroups (<13, 13-18, >18 years). ResultsThree factors emerged, characterizing visual, multimodal integration, and higher-order factors. Across development, metrics capturing network integration (betweenness centrality and hubness) showed general stability, while metrics capturing segregation (local efficiency) presented distinct peaks, particularly in the visual factor. Females showed earlier peaks and declines in higher-order factor, while males exhibited greater variability and protracted maturation in multimodal and higher-order factors. Brain-cognition associations were modest with early childhood and crystallized cognition composites showed small negative correlations with hub score in entire sample (r=-0.212) and local efficiency in males aged <13 years (r=-0.215). ConclusionFindings highlight nonlinear, sex-specific functional reconfiguration at region-level during childhood and adolescence, underscoring the importance of sex-stratified analyses in developmental and providing a crucial foundation for future investigations of developmental disorders.

neuroscience↗

Direct RNA Sequencing reveals epitranscriptomic regulation of brain cells and Alzheimer's Disease pathology

Alternative mRNA splicing and post-transcriptional RNA modification are key mechanisms that regulate transcript function; however, their role in neuronal activity and neurodegenerative disease remains poorly defined. In this study, we evaluated two nanopore-based long-read sequencing (LR-seq) formats: cDNA-PCR sequencing (CPS) and direct RNA sequencing (DRS). We then applied DRS to profile both full-length isoforms and RNA modifications in major brain cell types derived from induced pluripotent stem cells (iPSCs) and post-mortem Alzheimers disease (AD) brains. Relative to CPS, DRS achieved higher accuracy and sensitivity for transcript quantification, de novo transcript model construction, and open reading frame (ORF) annotation across neuropathological gene sets. Focusing on iPSC-derived neurons, we built a multi-omic atlas to connect transcriptional output with translational engagement and protein abundance, by integrating DRS-based mRNA abundance, N6-methyladenosine (m6A) status and poly(A) tail length with ribosome profiling (Ribo-seq) and mass spectrometry (MS). The combination of DRS and Ribo-seq data demonstrated synergism in predicting protein abundance. This analysis also uncovered a significant inverse relationship between m6A modification and mRNA abundance, which was dependent on the engagement of the ribosomal A-site. Lastly, we applied DRS to the epitranscriptomic analysis of AD brain samples, demonstrating that m6A profiles can be used to distinguish early-versus late-stage disease.

neuroscience↗

Binding dynamics shape germinal center broadly neutralizing responses to HIV priming

Inducing broadly neutralizing antibodies (bnAbs) is central to HIV vaccine efforts, but bnAb precursors are rare, often inactive, and require extensive somatic hypermutation (SHM) to recognize diverse, glycan-shielded epitopes. Germline-targeting immunogens (GTs) aim to jump-start this process, but determinants of success remain unclear. Here we establish a bnAb precursor-trackable model that reveals a surprising driver: binding dynamics. Across a series of GTs, multivalent designs that engage B-cells transiently - not tightly - consistently outperformed others, boosting germinal center fitness and unlocking rare or more efficient SHM pathways for breadth. These effects were independent of affinity or precursor frequency. Single-cell transcriptomics uncovered gene programs that predict successful priming. Crucially, this scalable system provides general predictive power for immunogen performance, marking a major advance for not only HIV vaccine development, but also potentially establishing a broadly applicable framework for streamlining pre-clinical pipelines, including immunogenicity and safety evaluation.

immunology↗

Somatic-to-germline transmission of horizontally acquired extrachromosomal circular DNA in Brassica graft chimeras

Whether somatically acquired traits can contribute to heritable variation has remained an open question in plant biology for over a century. Here, using graft-induced periclinal chimeras between Brassica juncea and Brassica oleracea, we identified extrachromosomal circular DNA (eccDNA) as mobile genetic elements capable of crossing histological boundaries and entering the germline. We demonstrated that grafting could promote the horizontal transfer of eccDNA between somatic cell layers, enabling its stable maintenance in recipient tissues and permitting transmission through sexual reproduction across multiple generations. We found that transmitted eccDNA is non-randomly distributed across the genome, preferentially originating from gene-dense regions, and enriched for features associated with molecular persistence, such as inverted repeats, hairpin-forming sequences, and autonomously replicating sequence (ARS) consensus motifs. These genetic regions conferred replication competence, as evidenced by autonomous propagation in an ARS-less heterologous yeast system. Sexual progeny carrying graft-acquired eccDNA exhibited reproducible and lineage-dependent alterations in leaf morphology and drought tolerance, accompanied by coordinated transcriptional reprogramming. Notably, a subset of inherited eccDNA remained transcriptionally active in progeny, producing transcripts absent from self-grafted controls. Our findings establish eccDNA as heritable extrachromosomal elements that link graft-mediated somatic genetic transfer with stable germline transmission, thereby expanding the molecular scope of heritable variation in plants and providing a conceptual framework for graft-based trait transmission.

plant biology↗

The gut microbiota metabolite Urolithin A mitigates JAK signaling to suppress cytokine-mediated autoimmune diseases

Aberrant activation of type I interferon (IFN-I) is closely related to the development of autoimmune diseases. The metabolic regulation of cytokine signaling is essential for immune homeostasis. In this study, we characterized Urolithin A(UA), a natural gut-derived metabolite, as an inhibitor of Janus kinase (JAK) signaling. UA was found to broadly dampen JAK phosphorylation and the downstream signaling induced by cytokines such as type I interferons (IFN-I), type II interferons (IFN-II), and interleukin-6 (IL-6). UA can directly bind to JAK1 JH1 domain and treatment with UA attenuated autoimmune pathogenesis in Trex1-KO mice, IMQ-induced SLE and psoriasis models. Our findings unveil that UA is an anti-inflammatory metabolite that promotes immune homeostasis and could be used to treat inflammatory and autoimmune diseases.

immunology↗

Extra-lineage tissue programs define the transcription states of human pancreatic cancer

Cancers acquire alternate transcriptional states as they evolve, but the origins, timing and determinants of this plasticity are poorly understood in many tumours. We investigated the transcriptional states of pancreatic cancer by integrating [~]1000 tumour-enriched genomes and transcriptomes from 464 patients combined with scRNA-seq, multiome profiling, and spatial proteomics. Four epithelial states covering the spectrum of lineage plasticity were identified (Classical-1, Classical-2, Basal-1, Basal-2). Comparing these states to normal and pan-cancer human single cell atlases showed each state reflects distinct tissue programs found in other malignancies. Single cell analysis uncovered that the main transcription state of this disease (Classical-1) emerges before KRAS mutations. Spatial proteomics from patients and cancer-free donors showed that the Classical-1 program emerges during acinar-to-ductal metaplasia, and also unexpectedly, in normal ducts without disrupting their morphology. Overall, these findings link the extensive lineage plasticity potential of this organ to the origins of the transcriptional states.

cancer biology↗