Biology subjects

Li, Y.

Publications and source records attributed to Li, Y..

At least 433 records · Page 24Linked to original sources

bioRxiv2026

Autoregressive forecasting of future single-cell state transitions

Predicting future cell state transitions from static transcriptomic snapshots is vital for understanding and steering cellular dynamics. Although existing trajectory and RNA velocity methods can infer local transitions within observed data, they are fundamentally limited in extrapolating long-range cellular dynamics. Here, we introduce CellTempo, an autoregressive generative framework that enables long-range forecasting of cell state trajectories directly from static transcriptomic snapshots. CellTempo is pretrained on scBaseTraj, a large-scale collection of multi-step cellular transition sequences constructed by integrating diverse experimental technologies and data sources. Across diverse biological systems, CellTempo accurately predicts long-range lineage progression and reconstructs unseen cellular potential landscapes. It further distinguishes transient perturbation responses from long-term cell-fate changes, enabling prioritization of candidate compounds for cell-fate engineering. These results demonstrate that long-range cellular dynamics are inferable from static observations, establishing a foundation for predictive and controllable modeling of cell fate.

bioinformatics↗

bioRxiv2026

Characterization of the Gut Microbiota and Serum Metabolomics in Patients with Type 2 Diabetes Mellitus and Newly Diagnosed Acute Coronary Syndrome

Biomarkers for the early identification of acute coronary syndrome (ACS) risk remain inadequately investigated, particularly in patients with type 2 diabetes mellitus (T2DM), for whom timely clinical intervention may substantially enhance prognostic outcomes. The gut microbiota and serum metabolites may serve as pivotal mediators in the occurrence and progression of ACS among patients with T2DM, and whether these factors can be used for the precise discrimination of patients with T2DM complicated by ACS remains to be explored. Overall, 76 participants were enrolled (38 patients diagnosed with T2DM complicated by ACS and another 38 with T2DM without ACS). 16S rRNA sequencing combined with untargeted LC-MS metabolomics revealed a dysregulated gut-serum axis in patients with T2DM complicated by ACS: enrichment of proinflammatory microorganisms (Enterococcus spp.), reduction of butyrate producers (Butyricimonas spp.) and concomitant dysregulation of circulating lipid metabolites-upregulation of PC(16:0/9:0 (CHO)) and arachidonic acid alongside downregulation of cholesterol sulfate. By integrating multiomics data and applying various feature selection methods, we subsequently identified six key biomarkers. The final constructed combined model robustly distinguished patients with T2DM complicated by ACS from those with T2DM alone (AUC = 0.983), outperforming the other single omics models. Our study revealed that the gut microbiota and related serum metabolites serve as key mediators in the onset and progression of ACS among patients with T2DM, and demonstrated their potential value as noninvasive biomarkers for the early diagnosis of T2DM complicated by ACS. Clinical PerspectiveO_ST_ABSWhat Is New?C_ST_ABSWe combined 16S rRNA sequencing with untargeted LC-MS metabolomics to dissect the gut-serum axis in patients with T2DM complicated by newly diagnosed ACS. We identified distinct gut microbial and serum metabolic signatures that distinguish ACS progression within the T2DM population. A multiomics classifier integrating clinical, microbial, and metabolic variables achieved robust diagnostic performance (AUC = 0.983) and outperformed single omics models. What Are the Clinical Implications?Integrated multiomics biomarkers facilitate the early identification of ACS progression in patients with T2DM, offering novel avenues for precision prevention, dynamic clinical surveillance, and individualized therapeutic strategies. Dysregulations of the gut microbiota and serum metabolome may play an important role in the development and progression of ACS in patients with T2DM.

microbiology↗

bioRxiv2026

Synergistic integration of inducible RNA switches enhances the manipulation of vector expression

Precise manipulation of gene expression is pivotal for gene function studies and the optimization of gene therapy. RNA-based gene switches are attractive tools due to their robust tunability by FDA-approved small molecules, the absence of exogenous immunogenic proteins, and the small size for gene delivery vectors such as adeno-associated virus (AAV). However, existing RNA switches only target a single step of gene expression such as transcription or RNA splicing, exhibiting intrinsic limitations in gene regulation. To overcome this issue, this study integrated the aptamer-based polyA regulator (pA), the drug-elicitable alternative splicing module (DreAM) and an engineered translation modulator with conditional upstream open reading frames (uORFs) to construct the DreAM-plus RNA switch. The pA-DreAM concatenation led to 1.5[~]5.0-fold and 1.2[~]4.4-fold increase of inducible fold changes than pA and DreAM, respectively. The uORF module further enhanced the switching performance by 1.4[~]6.3-fold. DreAM-plus-mediated transient transgene expression demonstrated a temporal resolution of about 24 hours and high tissue specificity to liver or heart. Critically, DreAM-plus achieved transient expression of an array of gene editors (SpCas9, SaCas9, Un1Cas12f1, OsCas12f1, AcCas12n, IsDra2 TnpB etc.) that significantly mitigated off-target effects by 1.4[~]2.8 folds in plasmids, lentivirus and AAV. In a new mouse model with lipid-nanoparticle-delivered pre-existing immunity, DreAM-plus attenuated AAV-delivered Cas-specific CD8 T cell immune toxicity in the liver and the heart. Therefore, multiple RNA switches could be synergistically integrated to build more sophisticated genetic cassettes for enhanced manipulation of gene expression.

bioengineering↗

bioRxiv2026

Reconciling Cooperativity Definition in PROTACs and Molecular Glues: Thermodynamic Dissection into PPI and Ligand Entropic Contributions

Douglass Cooperativity and Ciullis Cooperativity in induced-proximity systems, remains controversial with paradoxes such as path-dependent metrics and apparent universal negative Cooperativity. We noticed that in "partial-embedded" model, a substantial portion of giant ligand remains exposed outside and does not engage with the host proteins force field. It incurs an entropic cost due to the restriction of translational/rotational degrees of freedom. This large, mass-dependent unfavorable ligand entropy penalty normally shifts binding affinity to 104[~]108-fold. ITC thermodynamic cycles analysis confirmed the dramatic entropy loss among reaction pair. This reconciles the conflicting Cooperativity definitions, yielding true path-independent positive PPI Cooperativity from observed entropy loss subtracting ligand entropy penalty. ITC data showed rigid linkers appear superior to flexible linkers with respect to both oral bioavailability and safety profile in PROTAC design. "ligand entropy barrier wall/Cooperativity ladder" pair is not only impact induced-proximity systems but also constitute the physical basis for all biosystems.

biochemistry↗

bioRxiv2026

An AI/ML-Powered Workflow for End-to-End Cell Line Development

The generation of clonal CHO cell lines is foundational to biologics manufacturing; however, labor-intensive cell culture workflows predominate in the field. We created the CLAIRE (Cell Line AI Recognition and Evaluation) tool to streamline end-to-end cell line development by integrating deep-learning image analysis with automated liquid handling. We benchmarked three object detection models for monoclonality verification and found DETR provides superior accuracy (>0.90 F1-score) in identifying single cells. To quantify the outgrowth of cell lines, we evaluated multiple zero-shot SAM2 segmentation models against a feature-based estimation method. Feature-based detection successfully identified diverse cell colony types while less robust performance was observed for SAM2 models, particularly for sparse density colonies. The pre-trained DETR and feature-based detection models were wrapped in a task-focused user interface that outputs cell line hitpick lists compatible with a Lynx LM1800 liquid handler in addition to custom scripts automating cell passaging and sampling. This approach yielded an end-to-end 36 day CLD workflow capable of generating high-titer cell lines for multiple complex antibody structures. Here, we open-access our trained models, user interface, and Lynx automation scripts to provide a modular toolkit useful for clonal cell line engineering projects. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=153 SRC="FIGDIR/small/703387v1_ufig1.gif" ALT="Figure 1"> View larger version (51K): org.highwire.dtl.DTLVardef@1f72e70org.highwire.dtl.DTLVardef@109c54dorg.highwire.dtl.DTLVardef@7867b1org.highwire.dtl.DTLVardef@dfa61e_HPS_FORMAT_FIGEXP M_FIG C_FIG

cell biology↗

bioRxiv2026

The kinetics of ribonucleoprotein granules

Ribonucleoprotein (RNP) granules are biomolecular condensates composed of diverse RNAs and RNA-binding proteins that play essential roles in regulating multiple aspects of RNA biology. As complex biological systems, the condensate functions of RNP granules emerge from the higher-order kinetic assembly of individual molecules. Here, we develop an in vitro single-molecule approach--termed SMART (group single-molecule assay for ribonucleoprotein granules)--that enables direct and quantitative measurements of RNP granule assembly and disassembly kinetics across nanoscale to mesoscale regimes. Using SMART, we reveal that RNP granule assembly is strongly pathway dependent. In parallel, we develop a minimal two-state mathematical model that faithfully reproduces these kinetic behaviors. This model enables quantification of multivalent interaction timescales, reconstruction of the underlying free-energy landscape governing RNP granule dynamics, and demonstrates that this assembly process is intrinsically non-equilibrium. Understanding the condensate functions of RNP granules suggests new strategies for their rational manipulation in health and disease.

biophysics↗

bioRxiv2026

Every Cell Counts: Tomato Root Responses to Nitrogen at Single-Cell Resolution

The heterogeneity of cell-types in plant roots provides the structural and mechanistic basis for root responses to developmental and environmental signals, including the availability of the major mineral nutrient nitrogen (N) in the soil. To date, single-cell-resolution analyses of transcriptional responses to external nitrogen supply remain limited in plant and crop species. Here, we performed single-cell multiomic profiling of tomato (Solanum lycopersicum) roots treated with different nitrogen conditions, generating a high-resolution map of root responses to environmental nitrogen availability. We identified root cell types important for nitrogen response, discovered transcriptional regulators and nitrogen-responsive genes in a cell-type-specific manner, and generated a gene regulatory network across nitrogen conditions that can be used to investigate transcriptional circuits in specific cell types. This single-cell-resolution nitrogen-responsive map of the tomato roots provides a valuable knowledge base for identifying candidate genes to improve nitrogen use efficiency in horticultural crop species.

plant biology↗

bioRxiv2026

Structural basis of canonical TIR-NLR activation in plant innate immunity

In plants, intracellular NLRs (nucleotide-binding leucine-rich repeat receptors) detect pathogen effector proteins, form oligomeric resistosomes, and activate ETI (effector-triggered immunity). NLRs contain N-terminal signaling, central NB-ARC (nucleotide-binding) and C-terminal LRR (leucine-rich repeat) domains. NLRs with N-terminal TIR (Toll/interleukin-1 receptor) domains (TNLs) hydrolyze NAD+ (nicotinamide adenine dinucleotide) to generate signaling molecules. We determined cryo-EM structures of flax M, a canonical non C-JID (C-terminal jellyroll/Ig-like domain) TNL, in both monomeric autoinhibited conformation, and tetrameric resistosome after activation by its rust fungal effector AvrM-A. AvrM-A homodimers dissociate into monomers to bind directly to the LRR and NB-ARC domains in the M resistosome. The resistosome structure includes a non-hydrolyzable NAD+ analogue, revealing the substrate NAD+ recognition mechanism by the TIR domains. M cleaves NAD+ and generates the same signaling compounds as the related flax TNL, L6. Our findings explain the mechanism of TNL signaling, and provide a basis for rational engineering of disease-resistant crops.

plant biology↗

bioRxiv2026

Decomposing multi-scale dynamic regulation from single-cell multiomics with scMagnify

Deciphering the highly coupled regulatory circuits that drive cellular dynamics remains a fundamental goal in biology. However, capturing the multi-scale time-lagged dynamics and combinatorial regulatory logic of gene regulation remains computationally challenging. Here we present scMagnify, a deep-learning-based framework that leverages multiomic single-cell assays of chromatin accessibility and gene expression via nonlinear Granger causality to reconstruct and decompose multi-scale gene regulatory networks (GRNs). Benchmarking on both simulated and real datasets demonstrates that scMagnify achieves superior performance. scMagnify employs tensor decomposition to systematically identify combinatorial TF modules and their activation profiles across different time-lags. It enables a hierarchical dissection of the regulatory landscape-- from the activity of individual regulator to the combinatorial logic of regulatory modules and intercellular communications. We applied scMagnify to human hematopoiesis and mouse pancreas development, where it successfully recovered known lineage-driving regulators and provided novel insights into the combinatorial logic that governs cell fate decisions. Furthermore, in the context of kidney injury, scMagnifys intracellular communication module mapped key signaling-to-transcription cascades linking microenvironment cues to pathological epithelial cell changes. In summary, scMagnify provides a powerful and versatile computational framework for dissecting the multi-scale regulatory logic that governs complex biological processes in development and disease.

bioinformatics↗

bioRxiv2026

The genetic repertoire of the deep sea: from sequence to structure and function

The deep sea as the largest and maybe most hostile environment on Earth is still underexplored especially regarding its genetic repertoire. Yet, previous work has revealed significant habitat-specific deep-sea biodiversity. Here, we present an integrated deep-sea genetic dataset comprising 502 million nonredundant genes from 2,138 samples and 2.4 million predicted structures, and used it to link specific protein structures with genetic variants associated with life in the deep sea and to assess their biotechnology potential. Combining global sequence analysis with biophysical and biochemical measurements revealed unprecedented sequence diversity, yet substantial structural conservation of proteins. Especially proteins involved in replication, recombination, and repair were identified to be under rapid evolution and with specialized properties. Among these, a structurally divergent helicase exhibited advantages in controlling nanopore sequencing speed. Thus, our work positions the deep sea as a unique evolutionary engine that generates and hosts genetic diversity and bridges genetic knowledge with biotechnology.

bioinformatics↗

bioRxiv2026

Downregulation of Satb1 is required to prevent autoimmunity by maintaining Tfh homeostasis

T follicular helper (Tfh) cells are a specialized subset of CD4 T cells that localize to germinal centers (GC), where they provide critical help to B cells through the delivery of IL-21 and other cytokines. Here, we demonstrate that the tight control of the chromatin remodeler Special AT-rich sequence-binding protein 1 (Satb1) is key for this process, as overexpression of Satb1 drives lymphoproliferation and expansion of the T cell and B cell compartments in secondary lymphoid organs. Specifically, Satb1 overexpression induces a pronounced shift towards Tfh cell differentiation and increased GC formation accompanied by an increase in non-classed switched GC B cells and auto-antibody secretion. These findings highlight the importance of the precise regulation of Satb1 in fine-tuning CD4 T cells and B cells responses and suggest a potential role for dysregulation of Satb1 in the pathogenesis of autoimmune disease such as systemic lupus erythematodes (SLE).

immunology↗

bioRxiv2026

Distinct neural dynamics in prefrontal and premotor cortex during flexibleperceptual decisions

The neural mechanisms underlying flexible perceptual decisions, where the mapping between sensory input and motor action changes depending on context, remain unclear. Here we show that prefrontal and premotor cortex use distinct neural dynamics to implement different computations during flexible decisions. We trained monkeys to discriminate the dominant color of a red-green checkerboard and report their decision by choosing one of two targets1;2. By randomizing the target configuration on a trial-by-trial basis, we ensured a flexible mapping between color (red vs. green) and action choice (left vs. right), necessitating a nonlinear exclusive- or (XOR) computation3-5. We found that neural dynamics in dorsolateral prefrontal cortex (DLPFC) led to higher-dimensional population representations than those in dorsal premotor cortex (PMd). Neural activity in DLPFC first separated by target configuration, then by color choice and action choice after stimulus onset, reflecting the XOR computation. In contrast, neural dynamics in PMd led to lower-dimensional representations that only reflected action choice, the output of the XOR computation. These higher-dimensional representations in DLPFC enabled earlier decoding of both color choice and action choice compared to PMd, and were strongest in anterior and ventral DLPFC6. These findings reveal distinct computations by neural dynamics: prefrontal cortex implements flexible sensorimotor mappings through high-dimensional representations while dorsal premotor cortex reflects only the selected action.

neuroscience↗

bioRxiv2026

Critical assessment of intratumor and low-biomass microbiome using long-read sequencing

The detection of low-biomass microbial DNA in human tissues is often confounded by contamination, as demonstrated in the debates over the existence of microbiomes in the placenta, brain, blood, and tumors. Here we show that genomic DNA fragment length serves as a discriminator: while genuine microbiome genomes have long genomic DNA fragments, contaminant DNA is typically short. Using germ-free mouse tissues with bacterial spike-ins and human cell lines, we developed a metric that normalizes microbial read length to host read length. Across multiple human tumor and normal tissues, we found genuine microbiome signals are largely limited to tissues with natural microbial exposure (e.g., gastrointestinal tract, cervix, vagina, skin), while other tissues (e.g. kidney, brain, blood, and placenta) showed no evidence of resident microbiome. These findings support DNA fragment length as a metric for quality controlling low-biomass microbiome profiling, clarifying the debates and strengthen future studies of resident microbiome in tissues.

genomics↗

bioRxiv2026

Thermodynamic Insights into the WT and Y220C TP53 DBDs Reveals that the Oncogenic Y220C Variant is a Loss of Function Mutation for Zn2+-binding at Physiological Temperature

We present evidence of previously unrecognized allosteric connectivity across the TP53 DNA binding domain (DBD). Specifically, we have found evidence of explicit influence on the Zn2+-binding site from the region surrounding the hotspot Y220C mutation. This allosteric connectivity is intertwined with a temperature-dependent destabilization of Zn2+ binding in both the WT and Y220C DBDs. Our studies indicate that the Y220C mutation exacerbates this temperature-dependent destabilization of Zn2+-binding to result in overall destabilization of the Y220C variant. We provide detailed thermodynamic evidence that Rezatapopt, a small molecule reactivator of the Y220C DBD, engages Y220C through two distinct thermodynamic pathways and restores WT-level Zn2+-affinity to this oncogenic variant. A series of thermodynamic models describing the WT and Y220C conformational landscapes, as well as the Rezatapopt binding mechanisms, are proposed.

biochemistry↗

bioRxiv2026

Functional Annotation of the Major Histocompatibility Complex Locus

The human major histocompatibility complex (MHC) locus has the greatest density of disease-associations in the human genome, including links to over 100 polygenic disorders. Its complex haplotype structure, rich gene density, and high degree of linkage disequilibrium combine to make deciphering the gene regulatory logic of the MHC locus extremely challenging. Employing complementary high-throughput CRISPR interference (CRISPRi) and activation (CRISPRa) epigenetic screens coupled with single-cell transcriptome profiling across three distinct human cell types, we identified hundreds of new connections between cis-regulatory elements (CREs) and their target genes in this locus. These CRE-gene links are largely cell type-specific and act as enhancers. Additionally, some CREs have complex features, including harboring both active and repressive histone marks, lacking chromatin accessibility, targeting multiple genes, or acting as silencers. Computational methods fail to predict a majority of these CRE-gene connections. These findings emphasize the potential for functional perturbation experiments to dissect complex loci and reveal shared and cell type-specific regulatory mechanisms relevant to genomics of complex diseases. Collectively, this study provides a unique resource for understanding the complex regulatory landscape within the MHC locus and supports the need for creating new models that encompass CRE-gene interactions, cell type-specific gene expression, and disease genetics in the noncoding genome.

genomics↗

bioRxiv2026

Molecular Mechanism of Condensin II auto-repression by NCAPD3 and activation by M18BP1

Human condensin II is a constitutively nuclear molecular motor that initiates chromosome organization in early mitosis. How condensin II is activated specifically in mitosis remains unknown. Here, we describe the molecular mechanism underlying condensin II auto-repression and activation. By determining multiple structural states of condensin II, we discovered that an autoinhibitory tail within the NCAPD3 subunit (NCAPD3Tail) holds the complex in a conformation that is incompatible with DNA capture. Deletion of NCAPD3Tail spontaneously activates condensin II in cells, illuminating its autoinhibitory role in vivo. We further show this translates to increased loop DNA formation by condensin II in vitro. Direct competition for the NCAPD3Tail binding site on condensin II enables the putative activator protein M18BP1 to liberate a key DNA-binding element in the NCAPH2 N-terminus, enabling DNA capture. Unexpectedly, M18BP1 not only relieves autoinhibition but also directly contributes to DNA organization by forming a positively charged loop that enhances DNA-anchoring by condensin II. Together, these findings reveal a bipartite activation mechanism wherein M18BP1 relieves autorepression, and renders condensin II biochemically competent to form stable DNA loops, ensuring highly stringent regulation of mitotic chromosome formation.

biochemistry↗

bioRxiv2026

Bicarbonate Efflux induces GABAergic Excitation and Seizures through pH Regulation

GABAergic signaling can paradoxically excite neurons and initiate seizures, but the underlying mechanisms remain unclear. We developed a computational model integrating pH regulation into neural dynamics to investigate GABAergic excitation. Our results show that GABA-induced bicarbonate efflux causes intracellular acidification and charge accumulation, which enhances neuronal excitability and can trigger seizure-like discharges through bifurcations in the neurodynamic system. Furthermore, we demonstrate that active pH-regulating transporters effectively counteract GABA-induced acidification to maintain neural stability. This work elucidates a novel pH-regulating mechanism for excitatory GABA responses, explaining how impaired pH regulation or excessive GABA stimulation may predispose neurons to seizures and suggesting new therapeutic targets for epilepsy.

neuroscience↗

bioRxiv2026

Novel repressors of cambium activity in Arabidopsis

Wood is the greatest reservoir of terrestrial biomass and an essential carbon sink. Formed of xylem, it is derived from the cambium, a meristematic zone within plant stems from which phloem also forms. In Arabidopsis, cell division within the cambium is promoted by three major factors: auxin, cytokinin, and the TDIF-PXY ligand-receptor pair. Meristems and other stem cell populations are typically regulated by a balance between cell division-promoting factors and those that repress cell division to control meristem size, however few factors with cambium-repressing activity are known. Here we combined transcriptomics and transcriptional network analysis, which led to identification of related homeodomain zinc-finger transcription factors, ATHB23, ATHB30, and ATHB34, that repress cambium activity. These factors inhibit cambium activity by directly binding of promoters from a subset of auxin, cytokinin and TDIF-PXY transcriptional target genes, resulting in attenuation of their transcription. Our findings thus reveal a new mechanism underpinning balanced cambium activity.

plant biology↗