Biology subjects

Zeng, C.

Publications and source records attributed to Zeng, C..

At least 19 recordsLinked to original sources

bioRxiv2026

An information-borrowing Bayesian method for inferring high-dimensional population-level brain connectivity from small samples

Estimating population-level dependence between brain regions is challenging when the number of regions greatly exceeds the number of individuals. We introduce an information-borrowing generalized Bayesian method for high-dimensional covariance estimation from region-level brain measurements. A divide-and-conquer parameterization separates marginal variances from correlation calibrations: an empirical \emph{pilot} correlation matrix--by default, obtained by standardizing a sample covariance matrix (SCM)--provides a reference structure that is adaptively calibrated through region-specific parameters shared across pairwise correlations, reducing the number of free parameters from $\mathcal{O}(d^2)$ to $\mathcal{O}(d)$ ($d$ is the number of regions) while guaranteeing a positive-definite covariance through the inclusion of a ridge term. Horseshoe priors on the calibration parameters enable selective borrowing and shrinkage of pilot information. Under suitable conditions on pilot accuracy, we establish theoretical guarantees for covariance estimation while retaining scalability in ultra-high-dimensional settings via a low-rank likelihood representation and a Woodbury-accelerated Hamiltonian Monte Carlo algorithm. Simulations showed lower estimation error than the SCM, bagging and iteratively refined principal orthogonal complement thresholding (POETRY). Applications to a semi-synthetic cortical-thickness and ADHD resting-state fMRI data revealed significant group differences in the default-mode--visual network and somatomotor network--limbic network blocks after Benjamini--Hochberg correction.

neuroscience↗

bioRxiv2026

Cysteine reduction rather than methionine restriction promotes immunometabolic fitness to confer survival benefit in aging

Elevated sulfur-containing amino acids (SAA; methionine and cystine) are linked to human mortality. While methionine restriction (MR) extends lifespan in animals, it is often ignored that traditional longevity-promoting MR diets also lack cystine. When dietary cystine is eliminated, host redirects substrates from methionine cycle and generates cysteine via cystathionine {gamma}-lyase (CTH) in transsulfuration pathway, leaving it unclear which SAA controls aging. Here, we show that selective cysteine restriction in Caenorhabditis elegans enhanced lifespan and stress survival independently of methionine. Notably, cysteine-free diets (methionine-replete or restricted) in Cth-deficient mice induced pro-metabolic effects, whereas MR with normal cysteine was ineffective. Sustained 70% cysteine reduction in aged Cth-/- mice reprogrammed the immunometabolic axis, conferring healthspan benefits. Thus, lowering cysteine while keeping the methionine pool intact enhances healthy lifespan.

physiology↗

bioRxiv2026

An Integrated Framework for Transcriptomic Characterization and Lorentzian Hyperbolic Visualization of a High-Risk Topological Branch in Alzheimer's Disease

AO_SCPLOWBSTRACTC_SCPLOWAlzheimers disease (AD) is a highly heterogeneous brain disorder in which molecular alterations vary across brain regions, disease stages, and patient subgroups. This study introduces an integrated analytical framework for characterizing transcriptomic variation associated with a high-risk topological branch, which was identified based on Lorentz distance in postmortem Brodmann area 36 samples from the Mount Sinai Brain Bank cohort, where over 70% of samples were in Braak stages V--VI. The framework integrates weighted gene co-expression network analysis, repeated stability-based differential expression analysis, network-level gene filtering, Gene Ontology enrichment, and nested stratified cross-validation to evaluate whether topological branch-associated genes capture biologically meaningful signals and carry predictive information for high-Braak group status. The identified gene sets were functionally enriched for neuronal development, neuron projection organization, synaptic signaling, vesicle fusion, and regulated synaptic release, suggesting that the high-risk topological branch reflects biologically relevant transcriptomic programs linked to neurodegenerative progression. Nested cross-validation further showed that the selected genes achieved measurable internal predictive performance for distinguishing high-Braak samples. As a second methodological contribution, we introduced a Lorentzian hyperbolic variant of t-distributed stochastic neighbor embedding (Lorentz t-SNE) to explore latent non-Euclidean structure in transcriptomic data. This method embeds samples in hyperbolic space, providing an alternative to Euclidean embeddings for representing hierarchical or nonlinear structures. Compared with conventional Euclidean embeddings, the proposed Lorentz t-SNE revealed a more localized organization of high-Braak samples. Together, these results demonstrate the utility of the proposed analytical framework and Lorentz t-SNE for investigating heterogeneous, potentially non-Euclidean organization in AD transcriptomes.

bioinformatics↗

bioRxiv2026

Aberrant neuron-OPC synaptic transmission and deficient myelination define sex bias in major depressive disorder

Sex bias is a notable feature of major depressive disorder (MDD), yet its cellular and molecular origins remain unclear. We integrated computational analyses of human patient data with histological and biochemical validation in animal models to uncover female-specific MDD pathways. We identified female-specific mechanisms involving oligodendroglial lineage cells, especially oligodendrocyte precursor cells (OPCs), as key signal receivers with unidirectional preference in interactome networks. The neurexin (NRXN) pathway emerged as the most perturbed in MDD, with greater disruption in females. Subclustering further identified committed OPCs (cOPCs) as a disease-associated oligodendroglial subpopulation characterized by high expression of synaptic genes; cOPCs were also enriched of MDD-related transcriptional signatures revealed by trajectory analysis. High-dimensional weighted gene co-expression network analysis identified GABRG3 as an MDD-specific hub gene in cOPCs. The GABRG3 was also involved in the NRXN synaptic assembly cascade. Using Gabrg3 conditional knockout mice, we validated findings in patients and demonstrated that conditional deletion of Gabrg3 in cOPCs recapitulates MDD-like phenotypes, highlighting impaired neuron-cOPC synaptic communication, abnormal myelination, and depression-like behaviors. Together, our work defines a sex-specific cellular and molecular pathobiology of MDD, bridges clinical discovery with preclinical context, and provides a translatable framework for precision medicine targeting fundamental sex differences.

neuroscience↗

bioRxiv2026

Workload-induced changes to cell state contribute to β-cell failure in diabetes

Insufficient insulin secretion relative to insulin demand is a key feature of type 2 diabetes (T2D). While the defects of insulin-producing {beta}-cells in T2D are well defined, little is known about how {beta}-cells progress from the functionally normal state to the decompensated state during the natural history of this disease. Here, we provide evidence that workload-induced {beta}-cell overstimulation precipitates {beta}-cell failure in T2D. We employ scRNA-seq to define workload-induced changes to {beta}-cell transcriptional states, identifying a novel compensating state that is distinct from the stressed state of decompensated {beta}-cells. We demonstrate a key role for the chromatin-modifying enzyme Lysine-specific demethylase 1 (Lsd1) in restraining workload-induced {beta}-cell state transitions, indicating epigenomic control of {beta}-cell state. Experimental manipulations that promote the compensating state accelerate {beta}-cell failure in mouse models of diabetes. Altogether, these findings show that the compensatory response of the {beta}-cell to increased workload becomes maladaptive over time and contributes to the pathogenesis of T2D.

physiology↗

bioRxiv2026

MetaReact: A Reaction-Aware Transformer for End-to-End Prediction of Drug Metabolism

Accurate prediction of drug metabolites and enzyme selectivity is essential for rational drug design and safety assessment. However, existing computational approaches are often limited to specific enzyme families or reaction types, lacking the capacity to model enzyme-subtype specificity and prioritize major metabolites. Here, we present MetaReact, an end-to-end generalizable Transformer-based model that unifies the prediction of metabolic enzymes, metabolites, and sites of metabolism (SOM). By integrating structure-aware encoding ReactSeq, a chemistry reaction-based pretraining, MetaReact consistently outperforms state-of-the-art methods across multiple benchmarks under three settings: enzyme-agnostic, enzyme-completion, enzyme-conditioned. Notably, it achieves 60% Top-3 accuracy in identifying major metabolites and superior CYP450 enzyme-subtype prediction/SOM recognition. Case studies validate its applicability to complex natural products, synthetic cannabinoids, and clinical candidates, facilitating toxicity assessment and molecular optimization. This scalable, rule-free solution advances human metabolism modeling, with potential for computational pharmacokinetics and early drug discovery.

biochemistry↗

bioRxiv2026

CD8+ T cells are primed by cDC1 and exacerbate tau-mediated neurodegeneration

There are changes in adaptive immunity in Alzheimers disease (AD) and increases in activated CD8+ T cells in brain correlate with tau pathology1-3. However, which cells mediate T cell priming in tau-mediated neurodegeneration remains unclear. In different conditions such as cancer, viral infections, and autoimmune diseases outside the CNS, conventional type-1 dendritic cells (cDC1) perform antigen cross-presentation to prime CD8+ T cells4,5. We demonstrate that tauopathy mice deficient in cDC1 are markedly protected against tau-mediated neurodegeneration and display a selective decrease in brain CD8+ T cell infiltration and glial reactivity. The remaining CD8+ T cells showed an antigen inexperienced status with less clonal expansion, indicating suboptimal T cell priming. We confirm that brain derived antigens are presented in secondary lymphoid tissues to prime CD8+ T cells. Our study identifies cDC1 cells as critical for CD8+ T cell priming outside the CNS. This priming is required for a large increase of activated CD8+ T cells in the brain which promotes tau-mediated neurodegeneration.

neuroscience↗

bioRxiv2026

Stemona genomes illuminate fatty acid partitioning between seeds and elaiosomes mediating wasp dispersal

O_LISeed dispersal by wasps (vespicochory) is documented in five angiosperm families, with phylogenies suggesting that most vespicochorous lineages evolved from ant-dispersed (myrmecochorous) ancestors. While recent work has identified cues attracting wasp dispersers, the molecular basis remains unclear. C_LIO_LITo shed light on the molecular basis of vespicochory, we generated chromosome-level genomes for the wasp-dispersed Stemona tuberosa, and its close ant-dispersed relative S. mairei. Combining comparative genomic, transcriptomic, lipidomic, and functional analyses, we ask (i) how chemical elaiosome differentiation occurs during seed development, and (ii) how key mutualism-associated genes evolved in Stemona. C_LIO_LIWe show that elaiosomes up-regulate stearoyl-ACP {Delta}9 desaturases (SAD) and accumulate oleic acid and 1,2-diolein, which serve both as food rewards and as precursors for CER1/3-mediated biosynthesis of (Z)-9-tricosene, the key wasp attractant. By contrast, high expression of FatB and DGAT1 in seeds is associated with medium-chain fatty acids (MCFAs) production. Comparative genomics indicates conservation of these genes across Stemona, with S. tuberosa-specific FatB expansion and SAD/CER1/3 repertoire divergence. C_LIO_LIOur work supports a model for elaiosome-seed fatty-acid differentiation linking recruitment and nourishment in vespicochory. Given that oleic acid and 1,2-diolein are also key cues in myrmecochory, this shared biochemical basis may help explain how vespicochory evolves from ant-dispersed ancestors. C_LI

evolutionary biology↗

bioRxiv2026

Inhibition of Endocannabinoid Degradation in Astrocytes Reprograms Glial Reactivity and Prevents Seizure Sequelae

BackgroundTemporal lobe epilepsy (TLE) is the most common form of focal epilepsy and is characterized by a pathological cascade of excitotoxicity that leads to neuroinflammation, progressive neuronal loss, and subsequent cognitive decline. Despite its prevalence, effective disease-modifying therapies remain lacking. Previous studies have demonstrated that the endocannabinoid system contributes to epileptic activity. In particular, inactivation of monoacylglycerol lipase (MAGL), the key rate-limiting enzyme responsible for the degradation of the endocannabinoid 2-arachidonoylglycerol (2-AG), an endogenous lipid mediator with anti-inflammatory and neuroprotective properties, suppresses seizures and reduces neuroinflammation. However, the cellular and molecular mechanisms underlying these protective effects remain unclear. MethodsTo dissect the cellular mechanisms underlying MAGL-mediated neuroprotection, we employed a kainic acid (KA)-induced status epilepticus model in mice with global, astrocyte-specific (aKO), and neuron-specific (nKO) deletion of mgll. We combined single-nucleus RNA sequencing (snRNA-seq) to map the transcriptomic landscape of glial responses with pharmacological interventions to validate key signaling pathways, as well as behavioral assays to assess functional recovery. ResultsWe demonstrated that astrocyte-specific, but not neuron-specific, mgll deletion was sufficient to attenuate seizure susceptibility and hippocampal neurodegeneration, thereby recapitulating the protective phenotype observed in global knockouts. Transcriptomic profiling revealed that astrocytic MAGL deficiency fundamentally reshaped the glial response to injury by preventing the transition to pro-inflammatory reactive astrocyte states and suppressing the activation of disease-associated microglia (DAM). Mechanistically, we identified a signaling pathway in which the neuroprotective effects of MAGL inhibition depend on cannabinoid receptor 1 (CB1) activation and are mediated by downstream peroxisome proliferator-activated receptor {gamma} (PPAR-{gamma}) signaling. Either genetic deletion of CB1 or pharmacological blockade of PPAR-{gamma} abolished the protective effects. Furthermore, aKO mice exhibited reduced neuronal loss, preserved synaptic structural integrity and protection against post-seizure cognitive deficits. ConclusionThese findings reveal astrocytic MAGL as a crucial regulatory node in the epileptic brain and demonstrated that enhancing 2-AG signaling in astrocytes orchestrates neuroprotection via CB1-PPAR-{gamma} signaling pathways, thereby attenuating neuroinflammation, preserving synaptic function, and preventing the cognitive comorbidities associated with epilepsy.

neuroscience↗

bioRxiv2026

Macrophage Antigen Presentation Is Unleashed by Pan-RAS Inhibition to Promote Antitumor Immunity

Pan-RAS inhibitors have emerged as potent targeted therapies designed to suppress oncogenic signaling in RAS-mutant tumors. However, whether these inhibitors possess therapeutic utility beyond tumors with intrinsic RAS dependency remains unclear. Here we show that the clinical-stage pan-RAS(ON) inhibitor RMC-6236 (Daraxonrasib) induces robust regression of NRAS-wild-type B16 tumors in immunocompetent mice, a response mediated by a mechanism independent of direct tumor-cell targeting. Instead, RMC-6236 acts by remodeling the tumor microenvironment, specifically enhancing the antigen-presenting capacity of tumor-associated macrophages through upregulated MHC-I expression. This anti-tumor efficacy is abrogated in T cell-deficient hosts, identifying a macrophage-dependent, T cell-mediated mechanism of control. Mechanistically, RMC-6236 does not directly block canonical RAS signaling in macrophages. Rather, it suppresses a Myc-Hdac2 epigenetic program, leading to enhanced histone H4 acetylation at the Nlrc5 locus and subsequent activation of the MHC-I master regulator NLRC5. Together, our findings reveal a macrophage-centered, epigenetically wired immune mechanism for pan-RAS inhibition that broadens the therapeutic scope of targeting the "undruggable" RAS pathway beyond tumor genotype towards systemic immune modulation.

immunology↗

bioRxiv2025

Efficient Generation of Humanized Cloned Cattle via Embryonic Stem Cell-Mediated Dual-Round Site-Specific Editing

Transgenic cloning allows genetic modification in cattle, yet its translational potential is constrained by low cloning efficiency and limited gene-editing capacity, due largely to the restricted proliferative ability of somatic donor cells. Pluripotent stem cells (PSCs), with their unlimited self-renewal ability, represent a promising alternative to overcome these bottlenecks. Here, we first established stable bovine epiblast stem cell lines (bEpiSCs) and achieved site-specific integration of the HCSN2-HLF-GFP cassette into the {beta}-casein locus, with high transfection (72.07%) and correct integration efficiency (80.48%). Following Cre LoxP mediated excision of the selectable marker, we obtained marker free HCSN2-HLF bEpiSCs that retained pluripotency markers, tri lineage differentiation potential, and supported target protein expression in immortalized bovine mammary epithelial cells. When used as nuclear donors, these cells produced blastocysts with quality comparable to in vitro fertilization (IVF) embryos. Notably, cloning with HCSN2-HLF bEpiSCs resulted in the birth of twelve calves, with significantly higher birth and survival rates (30.71% and 16.74%, respectively) than those obtained using fibroblasts. Both PCR-based genotyping of the edited loci and microsatellite kinship analysis confirmed that all cloned calves were genetically derived from the HCSN2-HLF bEpiSCs. Collectively, this study establishes an efficient embryonic stem cell based platform for targeted gene editing and rapid production of multigene edited cloned cattle, offering a scalable strategy with strong potential for industrial translation.

bioengineering↗

bioRxiv2025

Genetic and Functional Characterization of AMH Signaling in Zebrafish - Evidence for Roles of Amh-Bmpr2a-Bmpr1bb Pathway in Controlling Gonadal Homeostasis

Anti-Mullerian hormone (AMH), a member of the TGF-{beta} superfamily, plays a crucial role in Mullerian duct regression in mammals. AMH signals through a specific type II receptor (AMHRII) and a type I receptor to activate the downstream Smad1/5/9 signaling pathway. Interestingly, non-mammalian vertebrates, including teleosts, also express AMH despite lacking Mullerian ducts. Accumulating evidence indicates that AMH influences gonadal development and function across vertebrates. Intriguingly, zebrafish, a popular model organism, possesses AMH (Amh/amh) but lacks specific type II receptor (Amhr2). Based on our previous studies and data from others, we propose that Amh may signal through a novel pathway in zebrafish involving the BMP type II receptor Bmpr2a and type I receptor Bmpr1bb. In this study, we provide genetic and functional evidence for the existence of the Amh-Bmpr2a-Bmpr1bb signaling pathway in zebrafish and its role in controlling gonadal homeostasis. Our experimental data excluded the participation of Bmpr2b and Bmpr1ba, paralogues of Bmpr2a and Bmpr1bb respectively, in Amh signaling. Additionally, we also provide genetic evidence that the phenotypes exhibited by amh, bmpr2a, and bmpr1bb mutants, i.e., gonadal hypertrophy, were all dependent on gonadotropin signaling, and that the two gonadotropins (FSH and LH) showed similar potency in driving the development of hypertrophic gonadal growth resulting from dysfunction in the Amh-Bmpr2a-Bmpr1bb signaling pathway. In summary, the present study provides comprehensive evidence for Amh signaling through Bmpr2a-Bmpr1bb pathway and its interplay with gonadotropins in controlling germ cell proliferation and differentiation.

genetics↗

bioRxiv2025

Myofibroblastic CAFs arising from bone-resident osteoblast precursors retain an osteolineage signature and support breast cancer progression via Osterix-mediated signaling.

Cancer-associated fibroblasts (CAFs) are a major component of the breast cancer (BC) microenvironment, involved in tumor progression and resistance to therapy. Despite the recent identification of multiple CAF subtypes with unique functions, it remains unclear whether each subtype arises from a distinct precursor or a shared common progenitor. Here, we identified a unique subpopulation of myofibroblast CAFs (myCAFs) arising from committed Osterix (Osx)+ osteoblast progenitors in the bone, recruited to primary tumors in both murine BC models and BC patients. Osx+myCAFs exhibit strong protumorigenic features and retain osteoblastic gene expression, which distinguishes them from OsxnegCAF subsets. Osx drives the expression of extracellular matrix remodeling genes and promotes tumor growth via the secretion of MMP13, a key Osx target gene. Finally, we find that increased Osx+myCAFs and a stromal osteolineage gene signature correlate with poor therapeutic response and reduced BC patient survival.

cancer biology↗

bioRxiv2025

Structural insights and engineering of deep-sea halophilic PET hydrolytic enzymes

Pervasive use of polyethylene terephthalate (PET) poses tremendous challenges for global waste management and environmental sustainability, fueling growing interests in enzymatic degradation as an eco-friendly solution. While PET hydrolases hold significant promise, their industrial deployment is hindered by insufficient performance, particularly under high-salinity conditions raised from high substrate loads. Building on our previous discovery of three deep-sea PET hydrolases (dsPETase01, dsPETase05 and dsPETase06) with exceptional halophilicity and PET-degrading activity, we here present their three-dimensional structures and mechanistic characterization. Structural comparison, site-directed mutagenesis, and domain swapping reveal key structural features and the essential role of C-terminal acidic residues in salt tolerance. Integrating semi-rational protein design, Transformer-based modeling, and disulfide bond engineering, we synergistically enhance the thermostability and catalytic efficiency of dsPETase05. These findings elucidate the unique structural features and salt adaptation mechanisms of deep-sea halophilic PET hydrolases, and inform the future engineering of biocatalysts for application in harsh industrial environments.

molecular biology↗

bioRxiv2025

The Human LRRK2-R1441G Mutation Drives Age-Dependent Oxidative Stress and Mitochondrial Dysfunction in Dopaminergic Neurons

Mitochondrial dysfunction and oxidative stress are central to Parkinsons disease (PD) pathogenesis, particularly affecting substantia nigra pars compacta (SNc) dopamine (DA) neurons. Here, we investigate how the R1441G mutation in leucine-rich repeat kinase 2 (LRRK2), a key genetic contributor to familial and sporadic PD, impacts mitochondrial function in midbrain DA neurons. Using a BAC transgenic mouse model overexpressing human LRRK2-R1441G, we crossed these mice with TH-mito-roGFP mice, enabling mitochondria-targeted redox imaging in DA neurons. The two-photon imaging of acute brain slices from 3-, 6-, and 10-month-old mice revealed a progressive elevated oxidative stress in SNc DA neurons and their striatal projections, accompanied with reduced respiratory complex activity and decline in mitochondrial health. Spatial transcriptomics via GeoMx Digital Spatial Profiler identified molecular changes linked to dysregulated mitochondrial uncoupling protein function and calcium homeostasis. These findings demonstrate age-dependent mitochondrial dysfunction in LRRK2-mutant SNc DA neurons, highlighting calcium channels and uncoupling proteins as potential therapeutic targets to slow PD progression.

neuroscience↗

bioRxiv2025

Mitotic phosphorylation of ADAR1 regulates its centromeric localization and is required for faithful mitotic progression

Adenosine Deaminase Acting on RNA 1 p110 (ADAR1p110), the constitutively expressed nuclear isoform of the RNA-editing enzyme ADAR1, plays well-established roles in adenosine-to-inosine RNA editing, but its functions during mitosis remain poorly defined. Here, we identify ADAR1p110 as a chromatin-associated factor essential for mitotic chromosome segregation and cell viability. Depletion of ADAR1 caused metaphase arrest, DNA damage accumulation, and apoptosis. Co-immunoprecipitation experiments revealed that ADAR1p110 physically interacts with Structural Maintenance of Chromosome 3 (SMC3), a core component of the cohesin complex. Genome-wide DNA immunoprecipitation sequencing (DIP-seq) showed that ADAR1p110 selectively binds centromeric -satellite DNA during mitosis, a finding validated by DNA immunoprecipitation quantitative polymerase chain reaction (DIP-qPCR). Complementary DNA-RNA immunoprecipitation sequencing (DRIP-seq) revealed that RNA:DNA hybrids (R-loops) are enriched in centromeric regions during mitosis and are further augmented by ADAR1 overexpression. We identified serine 614 (S614) as a key mitosis-specific phosphorylation site on ADAR1p110, and demonstrated that this post-translational modification is essential for its chromatin recruitment, stability, and mitotic function. Rescue experiments using phospho-mimetic mutants (S614D and 3xD) successfully restored mitotic progression in ADAR1-deficient cells, whereas non-phosphorylatable variants failed to do so. These results reveal that ADAR1p110 is phosphorylated in a cell cycle-dependent manner and functions at the intersection of post-transcriptional and post-translational regulation. By coordinating R-loop recognition at centromeres with chromosome cohesion, ADAR1p110 safeguards genome integrity during mitosis. Our findings uncover a previously uncharacterized mechanism through which a canonical RNA-editing enzyme contributes to chromosomal dynamics independent of its deaminase activity.

molecular biology↗

bioRxiv2025

H3K79 methylation and H3K36 tri-methylation synergistically regulate gene expression in pluripotent stem cells

In metazoans, nucleosomes harboring H3K79 methylation (H3K79me) deposited by the histone methyltransferase DOT1L decorate actively transcribed genes. Although DOT1L is implicated in transcription regulation and pathogenesis of human diseases such as leukemia and neurological disorders, the role of H3K79me in these biological processes remains elusive. Here, we reveal a novel functional synergism between H3K79me and H3K36 tri-methylation (H3K36me3), another histone modification enriched at active genes, in regulating gene expression and neural cell fate transition. Simultaneous catalytic inactivation of DOT1L and the H3K36 methyltransferase SETD2 via gene editing leads to the global loss of H3K79me and H3K36me3, hyperactive transcription, and failures in neural differentiation. Interestingly, the loss of H3K79me and H3K36me3 causes increased transcription elongation, gained chromatin accessibility at a group of enhancers, and increased binding of TEAD4 transcription factor and its co-activator YAP1 at these enhancers. Furthermore, YAP-TEAD inhibition partially restores the expression levels of hyperactivated genes upon H3K79me/H3K36me3 loss. Taken together, our study demonstrates a synergistic role of H3K79me and H3K36me3 in regulating transcription and cell fate transition, unveils novel mechanisms underlying such synergism, and provides insight into designing therapies that target diseases driven by misregulation or mutations of DOT1L and/or SETD2.

genetics↗

bioRxiv2025

Bridging 3D Molecular Structures and Artificial Intelligence by a Conformation Description Language

Artificial intelligence, particularly language models (LMs), is reshaping research paradigms across scientific domains. In the fields of chemistry and pharmacy, chemical language models (CLMs) have achieved remarkable success in two-dimensional (2D) molecular modeling tasks by leveraging one-dimensional (1D) representations of molecules, such as SMILES and SELFIES. However, extending these successes to three-dimensional (3D) molecular modeling remains a significant challenge, largely due to the absence of effective 1D representations for capturing 3D molecular structures. To address this gap, we introduce ConfSeq, a novel molecular conformation description language that integrates SMILES with internal coordinates including dihedral angles, bond angles, and pseudo-chirality. This design naturally ensures SE(3) invariance, while preserving the human readability and conciseness characteristic of SMILES. ConfSeq enables the reformulation of a range of 3D molecular modeling tasks, such as molecular conformation prediction, 3D molecular generation, and 3D molecular representation, into sequence modeling problems. Then, by simply employing a standard Transformer architecture, we achieve state-of-the-art performance on various benchmark sets. Furthermore, compared to widely used diffusion-based approaches in 3D molecular modeling, the ConfSeq-based method offers unique advantages in inference efficiency, generation controllability, and enables scoring of generated molecules. We believe that ConfSeq can serve as a foundational tool, advancing the development of sequence-based 3D molecular modeling methods.

bioinformatics↗