Biology subjects

Zhao, L.

Publications and source records attributed to Zhao, L..

At least 91 records · Page 5Linked to original sources

bioRxiv2025

BIN1 deficiency leads to DNA damage and neuronal insulin resistance through ATM dysregulation

The major neuronal isoform of the AD risk gene BIN1 is specifically reduced in patients. In the present work, we demonstrate that BIN1 is necessary for intact insulin signaling and its loss leads to cellular-level insulin resistance. Persistently activated mTORC1 feedback inhibits the insulin signaling; meanwhile, ATM-dependent DNA Damage Response decreases the expression of multiple insulin signaling pathway members. Unexpectedly, nuclear ATM activation is accompanied by autophagic degradation of the cytoplasmic ATM, rendering neurons susceptible to oxidative stress, which predisposes oxidative DNA damage, DNA strand breaks, and ATM-dependent DNA Damage Response. Treating BIN1-deficient mice with rapamycin or liraglutide to improve the insulin response, or with the natural antioxidant alpha-lipoic acid to attenuate oxidative stress, both effectively preserved the spatial cognitive ability. Lastly, we reanalyzed a single-cell transcriptomic dataset from human neurons and identified positive correlations between levels of BIN1 and the insulin signaling, as well as neuronal activity. Together, this work revealed an ATM-centered mechanism that globally damages neuronal health in BIN1-deficient pyramidal neurons, which could be a driving force in the AD disease course.

cell biology↗

bioRxiv2025

A predicted structural interactome reveals binding interference from intrinsically disordered regions

Proteins function through dynamic interactions with other proteins in cells, forming complex networks fundamental to cellular processes. While high-resolution and high-throughput methods have significantly advanced our understanding of how proteins interact with each other, the molecular details of many important protein-protein interactions are still poorly characterized, especially in non-mammalian species, including Drosophila. Recent advancements in deep learning techniques have enabled the prediction of molecular details in various cellular pathways at the network level. In this study, we used AlphaFold2 multimer to examine and predict protein-protein interactions from both physical and functional datasets in Drosophila. We found that functional associations contribute significantly to high-confidence predictions. Through detailed structural analysis, we also found the importance of intrinsically disordered regions in the predicted high-confidence interactions. Our study highlights the importance of disordered regions in protein-protein interactions and demonstrates the importance of incorporating functional interactions in predicting physical interactions between proteins. We further compiled an interactive web interface to present the predictions, facilitating functional exploration, comparative analysis, and the generation of mechanistic hypotheses for future studies. Author SummaryUnderstanding which proteins interact with each other and how they interact is essential for uncovering fundamental biology and for identifying new pathways involved in health and disease. However, identifying protein-protein interactions experimentally is often challenging and error-prone, and many organisms still lack comprehensive interaction maps. In this study, we use AlphaFold2-multimer, a powerful artificial intelligence tool, to generate high-confidence predictions of PPIs in Drosophila melanogaster, a widely used model organism. We highlight the importance of incorporating often neglected functional associations when predicting protein-protein interactions at a genomic scale. The predictions enable us to examine how intrinsically disordered regions can mediate binding across large interaction networks, revealing widespread, structurally plausible interactions in vivo. Overall, our work demonstrates how AlphaFold predictions can greatly expand our understanding of the structural forces that shape protein interaction networks and help reveal hidden layers of cellular complexes and pathways.

genomics↗

bioRxiv2025

A chimeric Ad5-Envp-VLP vaccine platform confers broad-spectrum immunity against emerging and re-emerging pathogens

Integrating complementary vaccine modalities is essential for combating emerging infectious threats. Here, we developed Ad5-Envp-VLP, a chimeric adenoviral platform synergizing adenoviral delivery efficiency with virus-like particle (VLP) structural mimicry. This system stably produces self-assembling VLPs in suspension HEK293 cultures, exhibiting enhanced immunogenicity over soluble antigens. Following intramuscular immunization, the platform induces early B cell expansion and sustains germinal center reactions, driven by the upregulation of B cell cycle-related genes (Cdc6, Cdc45, Cdc20, Cdc25C, Aurka, Aurkb, and Ccnb1/2) and robust T follicular helper (Tfh) cell differentiation, generating durable neutralizing antibodies against both influenza virus and rabies virus. These effects are conserved across mouse, canine, and feline models. Crucially, integrated flow cytometry and scRNA-seq demonstrate that intranasal delivery recruits and functionally reprograms lung innate immune cells (notably alveolar macrophages and dendritic cells), driving mucosal sIgA secretion and CTL responses. A single nasal dose confers lasting protection against homologous and heterologous influenza A strains. The platform also elicits cross-neutralizing antibodies against SARS-CoV-2 variants. Together, Ad5-Envp-VLP thus establishes a modular vaccine platform for antigenically plastic pathogens by combining in vivo self-assembly with dual pulmonary-muscular delivery. One Sentence SummaryNovel mucosal and systemic vaccine delivers self-assembling particles, triggering strong lung immunity and broad virus protection across species.

immunology↗

bioRxiv2025

Labile iron pool dynamics do not drive ferroptosis potentiation in colorectal cancer cells

Colorectal cancer (CRC) is the second leading cause of cancer-related mortality in the United States. CRC tumors exhibit aberrant iron accumulation, which supports tumor cell proliferation through multiple metabolic pathways. However, the oncogenic benefits of elevated iron must be counterbalanced by its potential to catalyze oxidative damage via reactive oxygen species generated from labile, redox-active iron. Ferroptosis is a regulated, non-apoptotic form of cell death characterized by iron-dependent lipid peroxidation. This process is tightly controlled by the selenoenzyme glutathione peroxidase 4 (GPX4), which reduces lipid peroxides and can be pharmacologically inhibited by agents such as RSL3 and JKE1674. A key source of redox-active iron is the labile iron pool (LIP), yet its role in regulating ferroptosis remains incompletely defined. To examine this, we supplemented CRC cells with exogenous iron following pharmacologic induction of ferroptosis. Iron supplementation significantly reduced cell viability, suggesting that expansion of the LIP potentiates ferroptotic cell death. However, whether ferroptosis is accompanied by dynamic changes in the LIP, and if such changes are mechanistically required for its potentiation, were unknown. To further characterize this response, we profiled the expression of iron regulatory genes under ferroptotic conditions and observed no change in transcriptional response in iron homeostasis genes. Using a reactivity-based probe of labile iron, we found that the LIP did not measurably increase during ferroptosis induction with GPX4 inhibition or inhibition of the SLC7A11 cysteine/glutamate antiporter. These findings suggest that the LIP does not expand upon pharmacological initiated ferroptosis, despite the potentiating effect of exogenous iron supplementation.

cancer biology↗

bioRxiv2025

Persistent Activation of Endothelial Cells is Linked to Thrombosis and Inflammation in Cerebral Cavernous Malformation Disease

AbstractO_ST_ABSBACKGROUNDC_ST_ABSCerebral cavernous malformations (CCM) are neurovascular lesions that affect both children and adults, and morbidity often results from thrombosis, bleeding, and neurological dysfunction. Studies indicate that inflammation-related activation of endothelial cells contributes significantly to the worsening of CCM disease. This suggests that ongoing vascular inflammation and endothelial dysfunction are key factors associated with thrombosis and bleeding in CCM disease. However, the inflammatory mechanisms leading to altered brain endothelial cell function with a high propensity for thrombosis, inflammation, and dysfunction are not fully understood. METHODSMulti-omic analyses was conducted by performing simultaneous high-throughput single-nucleus RNA sequencing (snRNA-seq) and single-nucleus transposase-accessible chromatin sequencing (snATAC-seq) with the 10x Genomics multiome platform in combination with immunofluorescence to study CCM pathogenesis in both female and male mice with CCM (Slco1c1-CreERT2; Pdcd10fl/fl) disease. The analysis was complemented with bulk RNA-seq, bulk ATAC-seq, and ChIP-seq (Chromatin immunoprecipitation sequencing) using an in vitro human CCM model. An AAV-BR1 viral system selectively upregulates the activator protein-1 (AP-1) transcription factor JUNB in brain endothelial cells was used to evaluate its effectiveness in maintaining a persistent activated cell state during the pathogenesis of CCM. RESULTSWe found that epigenetics significantly influences the subtype identity and function of brain endothelial cells within the arteriovenous axis. Through multi-omic analyses, specific regulatory elements and enhancers (cis-Regulatory Elements, cCREs) in mouse brain endothelial cells were identified that influence subtype-specific transcriptional programs and the transcription factors responsible for establishing the various subtypes of brain endothelial cells. Additionally, large-scale epigenomic reprogramming of brain endothelial cell subtypes was observed during the pathogenesis of CCM disease. Among the most significant changes were alterations in the chromatin state of endothelial cells, along with transcriptional processes associated with a persistently activated endothelial cell state, which renders them susceptible to inflammation and thrombosis. The activator AP-1 transcription factor JUNB was identified as a key regulator of the persistently activated endothelial state during chronic neuroinflammation. Moreover, both trans- and cis-regulatory factors conserved between mice and humans were discovered and contribute to the progression of chronic CCM disease. CONCLUSIONSEpigenetics plays a crucial role in determining the transcription patterns and functions of brain arteriovenous endothelial cells. The activator JUNB is identified as a driver of chronic brain vascular inflammation by inducing a persistent activated endothelial cell state from epigenome reprogramming. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=111 SRC="FIGDIR/small/662238v1_ufig1.gif" ALT="Figure 1"> View larger version (30K): org.highwire.dtl.DTLVardef@1297edforg.highwire.dtl.DTLVardef@1488e27org.highwire.dtl.DTLVardef@6cae62org.highwire.dtl.DTLVardef@12cb282_HPS_FORMAT_FIGEXP M_FIG C_FIG

genomics↗

bioRxiv2025

5-azacytosine induces cytotoxicity via 5-methylcytosine depletion on chromatin-associated RNA in leukemia

5-azacytidine (5-azaC) is a DNA hypomethylating agent clinically used to improve outcomes in myeloid malignancies. However, 5-azaC treatment causes gene dysregulation inconsistent with DNA hypomethylation changes, suggesting alternative mechanisms of action by 5-azaC. As a ribonucleoside analogue, 5-azaC is more readily incorporated into nascent RNA. Here, we demonstrate that RNA 5-methylcytosine (m5C) depletion by 5-azaC treatment, particularly at early time points, is sufficient to induce leukemia cell death. In contrast to its DNA demethylation function, the RNA-dependent effect of 5-azaC causes transcriptional repression, disrupting genes involved in cell cycle regulation and DNA repair. Mechanistically, 5-azaC impairs two specific m5C-mediated transcriptional regulatory pathways. First, depletion of m5C in chromatin-associated RNA (caRNA) disrupts the MBD6-mediated H2AK119ub deubiquitination. In parallel, this also impairs SRSF2 recruitment and the downstream H3K27ac deposition by p300. Indeed, loss of the caRNA methyltransferase NSUN2 caused prolonged cell cycle, defective DNA repair, and shifted hematopoietic lineage commitment toward erythropoiesis, mirroring the effects of 5-azaC treatment. Furthermore, we performed a leukemia cell line screen and identified that TET2 and IKZF1 depletion can sensitize 5-azaC treatment, consistent with the observed RNA-dependent cytotoxicity of 5-azaC in leukemic cells. In summary, our findings highlight the transcription repression by 5-azaC through depleting caRNA m5C, providing additional insights into the mechanism of action for 5-azaC, the prediction of its efficacy, and future directions for therapy developments based on 5-azaC. HIGHLIGHTO_LIRNA-dependent effects of 5-azaC are sufficient to drive leukemia cell cytotoxicity through transcriptional repression. C_LIO_LI5-azaC-induced caRNA m5C depletion impairs MBD6 binding and H2AK119ub deubiquitination. C_LIO_LI5-azaC-induced caRNA m5C depletion disrupts SRSF2 chromatin-binding, impeding p300 recruitment and H3K27ac deposition. C_LIO_LITET2 or IKZF1 depletion synergizes leukemia sensitivity to 5-azaC C_LI

molecular biology↗

bioRxiv2025

Population-specific brain charts reveal Chinese-Western differences in neurodevelopmental trajectories

Human brain charts provide unprecedented opportunities for decoding neurodevelopmental milestones and establishing clinical benchmarks for precision brain medicine 1-7. However, current lifespan brain charts are primarily derived from European and North American cohorts, with Asian populations severely underrepresented. Here, we present the first population-specific brain charts for China, developed through the Chinese Lifespan Brain Mapping Consortium (Phase I) using neuroimaging data from 43,037 participants (aged 0-100 years) across 384 sites nationwide. We establish the lifespan normative trajectories for 296 structural brain phenotypes, encompassing global, subcortical, and cortical measures. Cross-population comparisons with Western brain charts (based on data from 56,339 participants aged 0-100 years) reveal distinct neurodevelopmental patterns in the Chinese population, including prolonged cortical and subcortical maturation, accelerated cerebellar growth, and earlier development of sensorimotor regions relative to paralimbic regions. Crucially, these Chinese-specific charts outperform Western-derived models in predicting healthy brain phenotypes and detecting pathological deviations in Chinese clinical cohorts. These findings highlight the urgent need for diverse, population-representative brain charts to advance equitable precision neuroscience and improve clinical validity across populations.

neuroscience↗

bioRxiv2025

Mechanisms of KCNQ1 gating modulation by KCNE1/3 for cell-specific function

KCNQ1 potassium channels are essential for physiological processes such as cardiac rhythm and intestinal chloride secretion. KCNE-family subunits (KCNE1-5) associate with KCNQ1, conferring distinct properties across various tissues. KCNQ1 activation requires membrane depolarization and phosphatidylinositol 4,5-bisphosphate (PIP2) whose cellular levels are controlled by Gq-coupled GPCR activation. While modulation of KCNQ1s voltage-dependent activation by KCNE1/3 is well-characterized, their effects on PIP2-dependent gating of KCNQ1 via GPCR signaling remain less understood. Here we resolved structures of KCNQ1-KCNE1 and reassessed reported KCNQ1-KCNE3 structures with and without PIP2. We revealed that KCNQ1-KCNE1/3 complexes feature two PIP2-binding sites, with KCNE1/3 contributing to a previously overlooked, uncharacterized site involving residues critical for voltage sensor and pore domain coupling. Via this site, KCNE1 and KCNE3 distinctly modulate the PIP2-dependent gating, in addition to the voltage sensitivity, of KCNQ1. Consequently, KCNE3 converts KCNQ1 into a voltage-insensitive PIP2-gated channel governed by GPCR signaling to maintain ion homeostasis in non-excitable cells. KCNE1, by significantly enhancing KCNQ1s PIP2 affinity and resistance to GPCR regulation, forms predominantly voltage-gated channels with KCNQ1 for conducting the slow-delayed rectifier current in excitable cardiac cells. Our study highlights how KCNE1/3 modulates KCNQ1 gating in different cellular contexts, providing insights for tissue-specifically targeting multi-functional channels.

biochemistry↗

bioRxiv2025

Competing Subclones and Fitness Diversity Shape Tumor Evolution Across Cancer Types

Intratumor heterogeneity arises from ongoing somatic evolution complicating cancer diagnosis, prognosis, and treatment. Here we present TEATIME (estimating evolutionary events through single-timepoint sequencing), a novel computational framework that models tumors as mixtures of two competing cell populations: an ancestral clone with baseline fitness and a derived subclone with elevated fitness. Using cross-sectional bulk sequencing data, TEATIME estimates mutation rates, timing of subclone emergence, relative fitness, and number of generations of growth. To quantify intratumor fitness asymmetries, we introduce a novel metric--fitness diversity--which captures the imbalance between competing cell populations and serves as a measure of functional intratumor heterogeneity. Applying TEATIME to 33 tumor types from The Cancer Genome Atlas, we revealed divergent as well as convergent evolutionary patterns. Notably, we found that immune-hot microenvironments constraint subclonal expansion and limit fitness diversity. Moreover, we detected temporal dependencies in mutation acquisition, where early driver mutations in ancestral clones epistatically shape the fitness landscape, predisposing specific subclones to selective advantages. These findings underscore the importance of intratumor competition and tumor-microenvironment interactions in shaping evolutionary trajectories, driving intratumor heterogeneity. Lastly, we demonstrate that TEATIME-derived evolutionary parameters and fitness diversity offer novel prognostic insights across multiple cancer types.

bioinformatics↗

bioRxiv2025

The XPF-like domain in SHOC1 required for homologous recombination and safeguarding autosome from meiotic silencing of unsynapsed chromatin

During meiosis, a group of evolutionarily conserved ZMM proteins plays essential roles in stabilizing the recombination intermediates and promoting crossover (CO) formation. In mice, SHOC1 forms a trimeric complex with the other two ZMM proteins, SPO16 and TEX11, to bind recombination intermediates after strand invasion. Although genetic variants of SHOC1 are clinically associated with meiotic arrest and male infertility, their precise molecular mechanisms and evolutionarily conserved functions in human gametogenesis remain enigmatic. Here, we delineated species-specific divergences between human and mouse SHOC1 complex, and identified a missense variant within the XPF-like domain in SHOC1 (c.A1769G:p.Q590R) that was associated with meiotic arrest and non-obstructive azoospermia (NOA). The disorder of the XPF-like domain in SHOC1 impaired DNA double-strand breaks repair by compromising its ability to bind branched DNA structures and the recruitment of M1AP, REDIC1, and ZMM factors to recombination intermediates, ultimately abolishing CO formation. Furthermore, the variant disrupted dynamic 3D chromatin structure in pachytene spermatocytes and induced defects in homologous chromosome synapsis. More importantly, the XPF-like domain in SHOC1 was revealed to prevent autosome intrusion into the sex body compartment, thereby safeguarding critical autosomal loci from meiotic silencing of unsynapsed chromatin (MSUC). Overall, our study demonstrated that the XPF-like domain in SHOC1 is required for homologous recombination and safeguarding autosome from MSUC in meiosis.

developmental biology↗

bioRxiv2025

Complete360: A Multi-Omics Liquid Biopsy Platform with Attomole Sensitivity and High Reproducibility

Advancements in liquid biopsy platforms can uncovered disease-associated molecular changes that may indicate disease. Despite recent progress in the detection of a number of analytes, the current liquid biopsy platforms struggle with specificity, sensitivity, and reproducibility, limiting their clinical utility and high-throughput applicability. Here, we describe an ultra-sensitive mass spectrometry-based liquid biopsy platform, Complete360, with an optimized library of detection parameters, meticulously refined assays to enable the simultaneous detection and quantification of a broad range of body-fluid proteins, metabolites, and lipids. The system addresses sample-specific and target-specific noises, as well as the micro-environments of proteomics during co-elution, achieving unprecedented levels of reproducibility, specificity, and sensitivity. This platform has facilitated the detection and quantification of numerous multi-omics signatures in human plasma samples, uncovering novel disease mechanisms never identified by previous approaches. Our study establishes a platform for rapid discovery and validation of molecular changes in disease panels, demonstrating its potential utilities in applications meeting clinical regulation guidelines.

systems biology↗

bioRxiv2025

ngsAMOVA: A Probabilistic Framework for Analysis of Molecular Variance, dXY and Neighbor-Joining Trees with Low Depth Sequencing Data

MotivationNext-generation sequencing (NGS) has transformed population genetics and evolutionary biology, but the data produced in studies of non-model organisms, ancient DNA, and environmental DNA often consist of low- or medium-depth sequencing. Analyses of these data rely on computational methods that utilize genotype likelihoods (GLs) to account for genotype uncertainty. Nevertheless, many widely-used analysis methods, such as analysis of molecular variance (AMOVA) and methods for estimating phylogenetic trees using nucleotide divergence (dXY) still lack the probabilistic frameworks necessary to accommodate GLs. ResultsWe introduce ngsAMOVA, a novel probabilistic framework for analyzing molecular variation in population hierarchies with low- and medium-depth sequencing data. It employs an Expectation Maximization algorithm to first estimate the joint genotype probabilities for pairs of individuals, accounting for genotype uncertainty using GLs. It then uses these estimates to generate a pairwise distance matrix, which can be used for AMOVA, estimation of dXY, and for estimating phylogenetic trees using Neighbor-Joining. Hypothesis testing is facilitated using genomic block-bootstrapping. Through extensive simulations, we demonstrate that ngsAMOVA provides more accurate results compared to genotype calling at low and medium read depths. Overall, ngsAMOVA represents a methodological advance in the analysis of molecular variance and divergence under sequencing uncertainty. It provides a robust framework, opening up numerous possibilities for gaining insights into the evolutionary histories through its applications. ngsAMOVA is available as a fast, efficient, and user-friendly program written in C/C++. AvailabilityngsAMOVA is freely available at https://github.com/isinaltinkaya/ngsAMOVA. Contactisin.altinkaya@sund.ku.dk Supplementary informationSupplementary data are available online.

bioinformatics↗

bioRxiv2025

Serine auxotrophy is a targetable vulnerability driven by PSAT1 suppression in AML

Serine metabolism is of growing biologic and therapeutic interest in cancer. Upregulation of the serine synthesis pathway (SSP) can fuel tumor growth, and cancers with this phenotype are often sensitive to SSP inhibitors. In parallel, dietary restriction of serine and glycine (SG) can suppress some cancers, but the determinants of sensitivity to this approach are poorly understood. This is especially true in acute myeloid leukemia (AML), where serine metabolism has been less explored. We report that a subset of human AML cell lines and primary samples are completely dependent on external serine, known as serine auxotrophy. These leukemias consistently suppressed the SSP enzyme PSAT1, failed to synthesize serine, responded to SG restriction in vivo, and were rescued by restoring PSAT1. We also found that AML with an SF3B1 K700E mutation showed additional dependence on the SSP enzyme PHGDH, that SG restriction synergized with venetoclax in serine auxotrophic AML, and that MECOM rearrangement was strongly associated with PSAT1 suppression and serine auxotrophy. These findings define a metabolically distinct AML subtype and nominate it for targeting by SG restriction.

cancer biology↗

bioRxiv2025

Instant preparative droplet reaction assisted by shaking

Instant micro- and macro-preparative droplet reaction assisted by hand shaking (shake reaction) was found and observed, where reactions were carried out inside aqueous droplets dispersed in an organic solvent. This shake reaction was successfully benchmarked with both organic reactions of protein reduction by dithiothreitol and alkylation by iodoacetamide as well as biological reaction of protein digestion by enzyme trypsin. The reaction time of shake reaction was substantially shortened from the traditional bulk solution reactions, specifically 1 min for reduction (from 20 min), 1 min for alkylation (from 30 min), 5 min for digestion (from 960 min). The high efficiency of shake reaction comes from the micro-nano droplet formation assisted by shaking. Shake reaction can arguably be extended to any liquid-phase inorganic, organic and biological reactions from micro- to macro-preparative scale, and thus undoubtedly find wide applications in both academic research and industry production. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=161 SRC="FIGDIR/small/651440v1_ufig1.gif" ALT="Figure 1"> View larger version (41K): org.highwire.dtl.DTLVardef@ad1414org.highwire.dtl.DTLVardef@1014a1dorg.highwire.dtl.DTLVardef@1a8eccdorg.highwire.dtl.DTLVardef@15297fe_HPS_FORMAT_FIGEXP M_FIG C_FIG

biochemistry↗

bioRxiv2025

Ancient DNA Reveals Hominoid Evolution: Intermediate DNA Sequences and Advances in Molecular Paleontology

AbstractFossils and ancient crude pottery vessels function as physical "DNA containers," preserving oriDNA (original, in situ DNA) and accumulating eDNA (environmental DNA) over time. Ancient DNA (aDNA) serves as molecular fossils, chronicling evolutionaryhistory. Using "nano-affinitybead technology", we extracted and sequenced DNAfrom Lycoptera fossils in the Jehol region and a "round-bellied jar (Jar)" from the Erlitou period in Guangwu Town, yielding 236,545 primate sequences from the fossils and 86,908 from the pottery. We observed that the AFF value of DNA sequences negatively corre lates with species divergence time1, offering a quantitative measure of DNA preservation and host divergence. Some fragments distinct from modern genomic sequences, termed "intermediate DNAsequences" (IDS), have been identified. Many IDS exhibit an upper age limit, preserving characteristics of the last common ancestor (LCA) of the Hominidae and offering molecular insights into "Darwins puzzle". Among IDS, the SRRA subtype (Sequence Reversal and Rearrangement), identified in mRNA-coding exonic sequences, arises from the incorporation of a complementary antisense strand upstream of the sense strand, either adjacent to it or separated bya sequence interval. This introduces a novel post-transcriptional regulatory mechanism at the mRNA level, driven by SRRA, which presets hairpin structures and Indels in the UTR or CDS of exonic sequences, modulating gene variation. We propose: "SRRAs played a critical trial-and-error role in early Hominidae evolution, facilitating adaptive genomic changes, with some SRRA sequences later excised from exons", positioning SRRAas an evolutionary "genetic switch". Additionally, seven species -specific fragments (SSFs) of non-human primates (NHPs) linked to Asian Homo erectus were identified in the fossils, and pottery DNA reveale d sequences from tropical species (e.g., zebrass, oil palms), providing evidence of climate-driven local extinction and supporting paleo-ecological and paleo-environmental reconstruction. This method of analyzing aDNA from non-skeletal materials opens new avenues in paleontology, archaeology, and geology, guiding the tracing of ancient migration patterns and fossil searches. DNAfragments preserved within "DNA containers " exhibit an "old-few, new-many" turnover pattern, with many aDNA fragments displaying non-deamination. This evidence challenges prevailing perspectives, the authenticity criteria for aDNA, and the capabilities and scope of the traditional research method, necessitating a thorough reevaluation of the relevant knowledge framework. Furthermore, this study opens new opportunities for frontier research.

paleontology↗

bioRxiv2025

Glycosylated IgG antibodies accelerated the recovery of haemorrhagic fever with renal syndrome patients

AbstractHaemorrhagic fever with renal syndrome (HFRS) is a fatal disease caused by Hantaan virus (HTNV) infection. Humoral immunity is essential for effective viral clearance, however, the glycosylation characteristics of immunoglobulin G (IgG) in HFRS patients is not well known. Peripheral blood mononuclear cells from HFRS patients were obtained for B subset analysis using scRNA-seq and flow cytometry. HTNV specific IgG antibody titers were detected by enzyme-linked immunosorbent assay, and IgG glycosylation was analyzed by ultra-performance liquid chromatography. The proportions of the antibody-secreting memory (ASM) B cells and plasmablasts (PB) were significantly expanded among acute HFRS patients. We discovered significantly increased fucosylated IgG and decreased bisecting N-acetylglucosamine during the convalescent phase of HTNV infection. Meanwhile, positive correlations were observed between ASM subsets and galactosylation/sialylation in the IgG Fc region, and between PB subsets and sialylation. Notably, the glycosylation-related genes, such as RPN1 and RPN2, were primarily expressed differentially in the ASM and PB subclusters which were enriched in the N-glycosylation modifications of proteins through asparagine. Our findings indicated that IgG N-glycosylation may play a crucial role in combating HTNV infection and contributing to clinical recovery, which provided new insights for optimizing glycoengineered therapeutic antibodies.

immunology↗

bioRxiv2025

Scaling Large Language Models for Next-Generation Single-Cell Analysis

AO_SCPLOWBSTRACTC_SCPLOWSingle-cell RNA sequencing has transformed our understanding of cellular diversity, yet current single-cell foundation models (scFMs) remain limited in their scalability, flexibility across diverse tasks, and ability to natively integrate textual information. In this work, we build upon the Cell2Sentence (C2S) framework, which represents scRNA-seq profiles as textual "cell sentences," to train Large Language Models (LLMs) on a corpus comprising over one billion tokens of transcriptomic data, biological text, and metadata. Scaling the model to 27 billion parameters yields consistent improvements in predictive and generative capabilities and supports advanced downstream tasks that require synthesis of information across multi-cellular contexts. Targeted fine-tuning with modern reinforcement learning techniques produces strong performance in perturbation response prediction, natural language interpretation, and complex biological reasoning. This predictive strength enabled a dual-context virtual screen that nominated the kinase inhibitor silmitasertib (CX-4945) as a candidate for context-selective upregulation of antigen presentation. Experimental assessment in human cell models unseen during training supported this prediction, demonstrating that C2S-Scale can effectively guide the discovery of context-conditioned biology. C2S-Scale unifies transcriptomic and textual data at unprecedented scales, surpassing both specialized single-cell models and general-purpose LLMs to provide a platform for next-generation single-cell analysis and the development of "virtual cells."

bioinformatics↗

bioRxiv2025

Compression of functional gradients from rest to naturalistic processing: Moderation effect of age

The functional cortical hierarchy of the human brain, a fundamental principle of brain organization, has been extensively characterized during resting state for healthy younger adults. However, functional re-organization during naturalistic settings, such as movie-watching, and its alterations across the adult lifespan remains poorly understood. Using resting-state and movie fMRI data from two large datasets, Cam-CAN (N=416) and DyNAMiC (N=156), this study conducted a comprehensive comparison of brain organization across two states. We identified a robust reorganization with compression of functional gradients from rest to movie-watching states, which is mediated by changes in functional integration and segregation of brain networks. The extent of compression from rest to movie was significantly greater in older adults and predicted worse cognitive performance among the elderly population. Our findings provide novel insights into how macroscale brain hierarchy is reorganized during naturalistic processing, and how this reorganization during aging impacts cognitive processes, offering a deeper understanding of the neural basis of aging and cognition.

neuroscience↗