bioRxiv Science⌕ Search

Biology subjects

Li, R.

Publications and source records attributed to Li, R..

At least 91 records · Page 5Linked to original sources

A structure-informed deep learning framework for modeling TCR-peptide-HLA interactions

The interaction between T cell receptors (TCRs), peptides, and human leukocyte antigens (HLAs) underlies antigen-specific T cell immunity. Despite substantial advances in peptide- HLA presentation prediction, accurate modeling of coupled TCR-peptide-HLA recognition remains underdeveloped, limiting applications such as TCR and neoepitope prioritization in cancer and antigen identification in autoimmunity. Here we present StriMap, a unified framework for predicting TCR-peptide-HLA interactions by integrating physicochemical, sequence-context, and structural features at recognition interfaces. StriMap achieves state-of-the-art performance with improved generalizability and enables applications in both cancer and autoimmunity. As a case study in ankylosing spondylitis (AS), we screened 13 million peptides derived from 43,241 bacterial proteins and identified candidate molecular mimics that were experimentally validated to activate T cells expressing an AS-associated TCR. Notably, a top validated peptide was enriched in patients with inflammatory bowel disease (IBD), suggesting potential shared microbial triggers between AS and IBD. Overall, StriMap provides a generalizable framework for rational immunotherapy design and for dissecting antigenic drivers of autoimmunity.

bioinformatics↗

Ovarian extracellular matrix mechanics regulate oocyte-follicle interactions during female reproductive aging

Female reproductive aging is associated with ovarian functional decline, leading to infertility. During aging, biochemical and biophysical changes in the ovarian extracellular matrix (ECM) occur, yet how these properties affect follicle growth and oocyte quality remains poorly understood. Here we describe spatiotemporal changes in the ovarian ECM with age using mass spectrometry, immunohistochemistry, and nanoindentation. While follicle stiffness remains unchanged, stromal matrix remodeling is associated with a [~]2.5-fold increase in stiffness. To understand how this increase in stromal stiffness affects age-related follicular dysfunction, isolated young follicles were cultured in soft and stiff hydrogels mimicking young and aged ovarian stromal stiffness, respectively. Higher stiffness leads to a decrease in granulosa cell (GC) proliferation, oocyte quality, and GC-oocyte interactions mediated via transzonal projections (TZPs). RNA-seq revealed TGF-{beta} signaling as a major pathway affected by stiffness, and activation of TGF-{beta} signaling through Mongersen treatment rescued TZP formation and oocyte quality in stiff matrix. These findings provide mechanistic insight into how changes in ECM mechanics contribute to ovarian aging functional decline and reveal potential therapeutic targets to counter fertility loss associated with tissue aging and fibrosis.

cell biology↗

Single-Cell Profiling Reveals Developmental Trajectories and identifies SYK and TIM3 as Targets in some T Cell Lymphomas

T cell lymphomas (TCL) are a heterogeneous collection of malignancies whose origins and pathogenesis are poorly understood and for which few efficacious therapeutic options exist. Here, we conduct single-cell transcriptomic profiling spanning eight TCL entities and describe entity-associated programmes. We predict the cell of origin for these tumours through an integrative analysis of transcriptome and T cell receptor (TCR) maturation states. By identifying tumours with TCR states ranging from the pre-TCR through non-productive and productive TCR alpha and beta chain rearrangements we shed new light on their developmental origins. Furthermore, we apply our drug2cell computational drug target predictions with drug screens using patient-derived cell models, systematically benchmarking the performance of drug2cell and validating compounds and targets. This process identifies SYK inhibitors as a therapeutic opportunity and prioritises TIM3 for immunotherapy based on combined spatial transcriptomics analysis. Overall, our data provide a resource for diagnostics and therapies for tumours of critical unmet need.

cancer biology↗

System identification and surrogate data analyses imply approximate Gaussianity and non-stationarity of resting-brain dynamics

Compared with model-based and phenomenological descriptions of the spatiotemporal dynamics of resting-brain activity, statistical characterizations of resting-state fMRI (rs-fMRI) data remain relatively underexplored. Some sophisticated analysis techniques, such as Mapper-based topological data analysis (TDA) and innovation-driven coactivation pattern analysis (iCAP), can distinguish real data from phase-randomized (PR) surrogates, suggesting that rs-fMRI data are not as simple as stationary Gaussian processes. However, the exact statistical properties that distinguish real rs-fMRI data from PR surrogates have not yet been determined. In this study, we conducted system identification analysis and surrogate data analysis to specify key statistical properties that allow TDA and iCAP to discriminate real rs-fMRI data from PR surrogates. We first analyzed rs-fMRI data concatenated across scans using autoregressive (AR) modeling and found that the scan-concatenated rs-fMRI data were weakly non-Gaussian. However, non-Gaussianity alone was insufficient to reproduce realistic TDA and iCAP results because of non-stationarity across scans. AR modeling of single-scan data revealed that rs-fMRI data were statistically indistinguishable from a Gaussian distribution within a single scan, although TDA and iCAP results still differed between the real data and PR surrogates. A new surrogate dataset designed to preserve non-stationarity successfully reproduced realistic TDA and iCAP results, suggesting that TDA and iCAP likely capture the non-stationarity of rs-fMRI data to distinguish it from PR surrogates. Together, these results indicate approximate Gaussianity and non-stationarity in rs-fMRI data, providing a data-driven and statistical characterization of resting-state brain activity that can serve as a quantitative reference for whole brain simulations and generative models.

neuroscience↗

Functional connectome harmonics capture early brain organization and maturity in neonates

The functional organization of the human brain is established early, yet the ontogeny of its large-scale functional gradients remains unclear. Using resting-state fMRI data from 714 neonates in the Developing Human Connectome Project, we mapped neonatal brain gradients via functional connectome harmonics (FCH). We identified adult-like sensory-to-multimodal and cognitive gradient patterns present at birth. Applying three FCH-derived metrics--entropy, power, and energy--we found that power and energy were higher in term-born compared to preterm neonates, while entropy was elevated in preterms. These metrics predicted up to ~30% of postmenstrual age, indicating their biological relevance. Our findings reveal that the neonatal brain possesses a robust gradient architecture underpinning early functional organization, offering novel biomarkers for assessing brain maturity and the impact of prematurity on neurodevelopment.

neuroscience↗

Dynamic optimization of extrachromosomal DNA copy number drives tumour evolution

Extrachromosomal DNA (ecDNA) is common in human cancers and is associated with poor clinical outcomes, yet how ecDNA-driven genetic heterogeneity is translated into functional heterogeneity remains unclear. Using single-cell multiomics sequencing and multiplexed IF-FISH, we show that asymmetric inheritance of ecDNA generates copy number heterogeneity that propagates to gene expression programs, including oncogenic signaling and cellular stress responses. Transgenerational live-cell lineage tracking directly shows that ecDNA heterogeneity arises within only a few cell divisions and modulates daughter cell division timing in a copy number-dependent manner, a property not observed for evenly inherited chromosomal amplicons. We identify an optimal middle ecDNA copy number range that maximizes proliferative fitness at baseline, while drug selection pressure induced by low-dose CHK1 inhibition selects for cells with a new optimal range at low ecDNA copy numbers. These low ecDNA copy number cells pre-exist in the population and can be generated de novo, driving copy number shifts promoting drug resistance. In vivo experiments further demonstrate that shifts toward ecDNA copy numbers that are optimal under the tumour microenvironment enhance tumourigenicity. Together, these findings establish ecDNA copy number plasticity as a central driver of tumour evolution.

cancer biology↗

Metabolic compensation via gluconeogenesis explains the non-essentiality of glycogen phosphorylase as an insecticidal target in Plutella xylostella

Glycogen phosphorylase (GP) catalyzes the rate-limiting step of glycogenolysis and occupies a central position in insect carbohydrate metabolism, supplying precursors for chitin biosynthesis. Acyl urea compounds structurally related to benzoylphenylurea (BPU) insecticides are potent inhibitors of mammalian GP, raising the question of whether insect GP could serve as an independent insecticidal target. Here, we systematically evaluate this possibility in the diamondback moth Plutella xylostella. We show that a mammalian GP inhibitor (GPI) potently inhibits recombinant PxGP (IC50 = 2.96 nM), while the BPU insecticide diflubenzuron (DFB) does not. Molecular docking and MM/GBSA analysis predict that this selectivity reflects differential side-chain engagement: GPI is predicted to occupy the allosteric site at the dimer interface via contacts with seven residues spanning both subunits ({Delta}G = -34.63 kcal/mol), whereas DFB's difluorobenzoyl moiety is predicted to remain solvent exposed without productive protein contacts ({Delta}G = -29.29 kcal/mol). Despite potent in vitro inhibition, GPI exhibits no insecticidal activity, and RNAi-mediated knockdown of PxGP (confirmed by enzyme activity measurements showing ~29% reduction in per-larva GP-a activity) does not impair development or survival. We provide evidence that insects compensate through a multi-layered metabolic response: upregulation of gluconeogenic enzymes (PEPCK, G-6-Pase), selective upregulation of glycogen branching enzyme (GBE) but not -amylase, and changes in protein content suggestive of catabolic substrate mobilization. Fitness assessment reveals transient larval weight loss (24-48 h) with complete recovery of pupal weight, adult wing morphology, and female fecundity, indicating that the metabolic compensation response is ultimately effective in sustaining development. These findings suggest that GP is functionally non-essential under these conditions, likely through a combination of gluconeogenic compensation and the availability of alternative carbon sources, and highlight the importance of considering metabolic network redundancy in target-based insecticide design.

biochemistry↗

STRESS HISTORY ESTABLISHES A TRANSIENT TOLERANT STATE THAT SHAPES ANTIBIOTIC SURVIVAL UPON RESUSCITATION

Antibiotic treatment failure, often driven by non-genetic mechanisms such as tolerance and persistence, remains a major global health challenge. {beta}-lactams, the most widely prescribed antibiotic class, are particularly compromised by tolerance in dormant, non-growing cells; yet, how these drugs act on cells resuscitating from dormancy remains poorly understood. Here, we investigate the resuscitation phase at an unprecedented scale using Hi-DFA (High-throughput Dynamic Fate Analyser), a single-cell microfluidic platform integrating time-lapse imaging with machine-learning-based image analysis for dynamic cell-fate tracking. We identify a distinct survival strategy: a significant fraction of resuscitating cells transiently slow their growth, facilitating survival upon {beta}-lactam exposure. This transiently tolerant phenotype is considerably less frequent in unstressed, exponentially growing cells, indicating that prior starvation history predisposes cells to this state. Using simulated in vitro pharmacokinetic treatment profiles, we show that suboptimal dosing selectively enriches for this transient tolerance state. A population dynamics model built from this single-cell antibiotic-response data suggests that these transient-tolerant cells, not typical starvation-triggered persisters, may be the primary drivers of rapid population regrowth post-treatment under clinically relevant conditions. Together, our findings define a distinct class of antibiotic survival shaped by stress history and treatment profile, offering a quantitative framework for optimising antibiotic dosing strategy.

systems biology↗

Functional connectome harmonics and dynamic connectivity maps of the preadolescent brain

The maturation of large-scale functional brain networks during preadolescence underpins critical cognitive and behavioral development. However, the spatial and temporal organization of these networks in this age group remains incompletely characterized. Here we applied Functional Connectome Harmonics (FCH) and Leading Eigenvector Dynamics Analysis (LEiDA) to resting-state fMRI data from over 11,000 children aged 9-10 years in the ABCD Study. FCH revealed hierarchical spatial gradients spanning cortical and subcortical regions, while LEiDA identified recurrent dynamic brain states aligned with canonical intrinsic connectivity networks. Linking these spatial and temporal components, we established a low-dimensional harmonic scaffold constraining brain dynamics during this developmental window. These findings provide a large-scale spatiotemporal reference framework of preadolescent functional brain organization, offering a foundation for characterizing neurodevelopmental benchmarks and early neural markers relevant to adolescent mental health.

neuroscience↗

Tmn blocks phage spread via plasmolysis and triggers synergistic defence responses

Membrane-associated phage defences remain poorly understood. Here we characterise Tmn, a YobI-family transmembrane P-loop NTPase that protects bacteria from phage infection by establishing a plasmolysis-associated antiviral state. Upon recognising phage T2 RIIB protein, Tmn enhances ATP turnover and selectively exports Mg2+, causing rapid cytoplasmic collapse that arrests phage replication without detectable membrane depolarisation or gross leakage of the cell content. Cryo-electron microscopy shows that Tmn assembles into a decameric membrane complex with extended cytosolic arms, an uncommon architecture among P-loop NTPases. The cytosolic arms, including a solenoid-like repeat domain, mediate trigger interaction and determine specificity. In addition to its primary defence function, Tmn-driven ATP collapse activates otherwise silent ATP-depletion-sensing defences, including Gabija and Septu type I, providing a mechanistic basis for synergy among defence systems and limiting secondary phage spread. These findings demonstrate that Tmn is a membrane-integrated sensor-effector that couples phage recognition to metabolic collapse and coordinated multi-layered immunity.

microbiology↗

Proteomic Screening Identifies HNRNPA2B1 as an Epigenetic Repressor of Epstein-Barr Virus Reactivation

Epstein-Barr virus (EBV) establishes lifelong persistent infection in over 90% of the worlds population. The virus persists as an episome in the host cells during latency and periodically reactivates through transcriptional activation of the immediate-early (IE) genes. While epigenetic regulation is central to maintaining viral latency, the host factors that enforce repression at these promoters remain incompletely defined. Here, we employed a novel Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/dCas9-based engineered DNA-binding molecule-mediated chromatin immunoprecipitation coupled with mass spectrometry (enChIP-MS) approach to identify proteins associated with the promoter of EBV IE gene ZTA. This approach revealed an enrichment of multiple heterogeneous nuclear ribonucleoproteins and identified HNRNPA2B1 as a potential regulator of EBV ZTA gene expression. Functional analyses across multiple EBV+ cancer cell models demonstrated that HNRNPA2B1 acts as a restriction factor for EBV lytic reactivation. Depletion of HNRNPA2B1 led to increased expression of IE and downstream lytic genes, enhanced RNA polymerase II recruitment to the ZTA and RTA promoters, and elevated the proportion of cells entering the lytic cycle. Conversely, enforced expression of HNRNPA2B1 suppressed EBV lytic reactivation. Mechanistically, HNRNPA2B1 enhances repressive viral chromatin states by facilitating recruitment of the histone demethylase KDM1A to EBV IE gene promoters, thereby limiting the activating histone H3 lysine 4 trimethylation. Together, these findings identify HNRNPA2B1 as a key epigenetic regulator of EBV latency and link RNA-binding proteins to epigenetic control of viral reactivation. IMPORTANCEThis study identifies HNRNPA2B1 as a previously unrecognized host factor that promotes Epstein-Barr virus (EBV) latency through direct regulation of viral chromatin at immediate-early gene promoters. By integrating locus-specific chromatin proteomics with functional and mechanistic analyses, our work reveals how an RNA-binding protein HNRNPA2B1 recruits a histone-modifying enzyme to control EBV reactivation. These findings provide new insights into host-virus interactions that controls EBV latency and reactivation and highlight the role of RNA-binding proteins in chromatin regulation that may be broadly relevant to other latent DNA viruses.

microbiology↗

Macrophage Iron Metabolism in Allografts and Tumors

Macrophages are present at high frequencies in transplanted organs and solid tumors. These infiltrating macrophages are highly tuned by tissue niche signals. However, the underlying mechanisms that orchestrate the activation of distinct macrophage populations remain unclear. Here, using heart transplantation and tumor implantation models, we found that macrophages in cardiac allografts exhibited higher intracellular iron (Fe2+) level and higher expression of the iron transporter SLC11A1 than those in the solid tumors. In mice, the myeloid-specific deletion of Slc11a1 alleviated the proinflammatory state of macrophages and cardiac allografts rejection. Together, our findings identify SLC11A1 as a new player in immune response regulation, implicating SLC11A1 as a therapeutic target for both allograft and tumor rejection. This preprint reports initial findings; additional experiments are ongoing and will be included in a future full manuscript.

immunology↗

Interoceptive autonomic regulation in typical development and autism spectrum disorder: A computational model integrating multiple physiological systems

BackgroundInteroceptive cardiovascular signals, including heart rate (HR) and blood pressure (BP), arise from coordinated sympathetic (SNS) and parasympathetic (PSNS) regulation and contribute to affective and cognitive processes. Although atypical autonomic nervous system (ANS) modulation has been reported in autism spectrum disorder (ASD), the dynamical structure underlying branch-specific coordination remains insufficiently characterized. ObjectiveTo estimate latent ANS regulatory structure in typically developing (TD) and ASD individuals using a computational modeling framework. MethodsA closed-loop computational model integrating cardiovascular, respiratory, and autonomic dynamics was developed. ANS regulation was formalized using three autonomic control modes (coupled reciprocal, coupled nonreciprocal, and uncoupled) and parameterized by the relative activity of SNS and PSNS branches. HR and BP responses to the head-up tilt (HUT) test were simulated, and regulatory surfaces were compared with empirical HR and BP data from TD and ASD groups. Additional simulations under normal respiration, deep respiration, and absence of respiration evaluated mean arterial pressure (MAP) regulation across varying SNS-PSNS activity combinations. ResultsTD individuals exhibited differentiated SNS-PSNS coordination patterns across control modes, whereas ASD individuals showed convergence of relative SNS-PSNS activity. In TD, HR and BP distributions under coupled reciprocal mode were most consistent with expected physiological responses, characterized by high SNS and low PSNS activity during postural challenge. In ASD, empirical data extended toward regions of relatively higher PSNS weighting. Incorporation of deep respiration enhanced MAP reduction during BP recovery, particularly under over-elevated SNS activity. ConclusionThis study provides a mechanistic, state-space characterization of autonomic coordination in TD and ASD populations, enabling inference of latent autonomic regulation from measurable interoceptive phenotypes and identifying respiration as a model-based regulatory lever that augments cardiovascular stabilization.

neuroscience↗

Unwinding of RNA G-quadruplexes induces mouse and human totipotency

Totipotent stem cells (TotiSCs) have significant application prospects in regenerative medicine and assisted reproductive technologies. The mRNAs of totipotency-related genes are rich in G-quadruplex (G4) structures, while the G4 density of pluripotency-related genes mRNAs is relatively low, suggesting a potential functional link between RNA G4s and the totipotent state. Nevertheless, how G4s are involved in the establishment or maintenance of mouse and human totipotency remains poorly understood. Here, we demonstrate that FC3, a small-molecule RNA G4 unwinder, enables efficient induction and maintenance of mouse and human TotiSCs (mG4TotiSCs and hG4TotiSCs). These FC3-induced TotiSCs closely recapitulate the molecular features of 2-cell-stage blastomeres via transcriptomic and epigenomic profiling. Functionally, both mG4TotiSCs and hG4TotiSCs exhibit totipotent capacity: they differentiate into embryonic and extraembryonic lineages in vitro and in chimeric embryos; moreover, they autonomously self-organize into blastocyst-like structures without exogenous signalling. Mechanistically, we identify that Gata2 mRNA, a G4-containing transcript, is essential for FC3-mediated reprogramming. Genetic disruption of Gata2 would abolish totipotency induction. Collectively, RNA G4 unwinding is a new regulatory axis governing totipotency acquisition and maintenance, providing insight into the functional interplay between nucleic acid secondary structures and cell fate plasticity.

cell biology↗

Non-enzymatic ABHD6 interacts with Akt-FoxO1 axis to regulate selective hepatic insulin resistance

The enzymatic function of ABHD6 on insulin secretion and insulin resistance is well documented. However, its non-enzymatic function, especially its effects on selective hepatic insulin resistance and metabolic dysfunction-associated steatotic liver disease (MASLD) is completely unexplored. ABHD6 is elevated under conditions of diet-induced obesity and aging. To define the role of ABHD6 in liver physiology, we generated liver-specific ABHD6 knockout mice, as well as liver specific overexpression of native and enzymatic inactive mutant ABHD6 mouse models. We demonstrated that ABHD6 is an unidentified regulator of selective hepatic insulin resistance and contributes to MASLD and liver fibrosis. Furthermore, we found that non-enzymatic ABHD6, rather than its enzymatic form, contributes to this regulation. Mechanistically, we found that ABHD6 translocated into the nucleus and interacted with Akt/FoxO1 axis to regulate its function. In addition, knockdown of FoxO1 in primary hepatocytes or overexpression of constitutively active mutant FoxO1 by AAV approach could completely abolish the effects of ABHD6 on glucose tolerance and gluconeogenesis. Our study reveals an entirely different mechanism underlying selective hepatic insulin resistance that involves a previously unknown non-enzymatic function of ABHD6. This study opens an avenue for the development of a novel class of ABHD6 inhibitors to treat MASLD and liver fibrosis. HighlightsO_LIABHD6 expression in the liver is increased with obesity and aging. C_LIO_LIABHD6 manipulation affects selective hepatic insulin resistance, MASLD and liver fibrosis. C_LIO_LINon-enzymatic ABHD6 interacts with Akt/FoxO1 axis to regulate FoxO1 transcriptional activity. C_LIO_LIThe effects of ABHD6 on glucose tolerance and hepatic gluconeogenesis are completely dependent on FoxO1 activity. C_LI

physiology↗

Recruitment of SERK co-receptors determines signaling specificity within the systemin peptide family

The phytocytokine systemin (SYS1) regulates defense responses of tomato plants against herbivores and necrotrophic pathogens. For more than three decades, systemin signaling was thought to rely solely on SYS1, although the tomato genome encodes the precursors of at least three additional systemin-like peptides (SYS2, SYS3 and SYS4). We show that these recently discovered peptides are processed in a wound-inducible manner and act as genuine wound signals that activate early defense signaling via the receptor SYR1. Although all systemins depend on SYR1 for perception, the new peptides elicit downstream responses distinct from those triggered by SYS1, including sustained ethylene production and extensive transcriptional reprogramming. Signaling specificity is governed by a single C-terminal residue that determines the ability of SYS peptides to recruit SERK co-receptors into the receptor complex. The resulting increase in complex stability underlies the amplified and prolonged signaling responses observed for the new SYS peptides compared to SYS1. Our findings reveal how subtle sequence changes within the systemin peptide family can remodel receptor-co-receptor interactions to generate ligand-specific signaling outputs. This mechanism allows a single receptor to decode related ligands into distinct physiological responses and may represent a broader principle allowing for the diversification of peptide-mediated signaling in plants.

plant biology↗

Dynamic Consistency Reveals Predictable Genes in Cross-Cell Type Temporal scRNA-Seq Data

Understanding how gene expression evolves over time after trauma is central to modeling immune responses, yet single-cell temporal data remain sparse and heterogeneous across cell types. Using a temporal trauma scRNA-seq dataset, we formulate the task of predicting next-time gene expression from earlier observations under a cross-cell-type generalization setting. We introduce the Dynamic Consistency Index (DCI), which quantifies how consistently a genes temporal trajectory aligns across cell types, serving as a measure of biological regularity and predictability. High-DCI genes exhibit reproducible temporal dynamics and are markedly easier to model. By integrating DCI-based gene selection with a recurrent neural architecture trained under a Gaussian negative log-likelihood objective, we achieve superior accuracy and well-calibrated uncertainty compared to deterministic baselines. Overall, DCI reliably identifies dynamically consistent genes, and uncertainty-aware recurrent modeling provides a robust framework for capturing cross-cell-type gene-expression evolution.

bioinformatics↗

A new lineage of Ranavirus micropterus1 infects ornamental wrasses from the Great Barrier Reef and causes severe disease in captivity

The Great Barrier Reef (GBR) supports remarkable vertebrate diversity but is among the most fragile ecosystems globally, and diseases affecting reef fishes remain poorly understood. We employed traditional veterinary diagnostic techniques and metatranscriptomics to investigate a disease outbreak with 100% mortality in captive wrasses (Macropharyngodon choati) from the GBR. Histopathology revealed multifocal necrosis of renal tubules, and cytopathic effect was observed in bluegill fry cell lines. A novel ranavirus isolate, Macropharyngodon choati ranavirus (McRV), was identified at exceptionally high transcript abundance across different host tissues, alongside strong expression of host genes linked to cellular stress and immune function. Phylogenetic analysis placed McRV in a distinct clade of wrasse ranaviruses, clustering with a virus previously identified on the GBR, suggesting that wild wrasses serve as natural hosts. These data emphasise the need for enhanced pathogen monitoring in marine wildlife increasingly threatened by anthropogenic change.

microbiology↗