Biology subjects

Liu, F.

Publications and source records attributed to Liu, F..

At least 19 recordsLinked to original sources

bioRxiv2026

CellMethMarker provides an integrated database of human cell- and tissue-type-specific DNA methylation markers

Cell- and tissue-type-specific DNA methylation markers provide epigenetic signatures of cellular identity and are widely used to infer cellular origin from bulk and single-cell methylomes. Existing resources mainly emphasize disease-associated biomarkers, methylome atlases, genomic annotations or RNA-based cell markers, leaving an unmet need for an integrated region-level resource dedicated to such markers. Here we present CellMethMarker (http://gu-zhanglab.hfcas.ac.cn/CellMethMarker), a curated database integrating 347,514 de novo markers derived from uniformly processed whole-genome and reduced-representation bisulfite sequencing datasets, 2,203,507 literature-derived marker records and harmonized metadata for 2,810 samples. CellMethMarker enables cell- and tissue-centered marker retrieval, coordinate-based search, genome-browser visualization, interactive methylation analysis and data download. In an independent single-cell methylome atlas, these markers recover the expected cell-type-associated methylation patterns, and a platform-matched reference built from them lowers the mean deconvolution error from 0.365 to 0.144. CellMethMarker therefore links region-level DNA methylation variation to cellular identity and supports methylome-based cell-type annotation and deconvolution.

bioinformatics↗

bioRxiv2026

OTTER: Orchestrated Transcriptomic, Tumor-xenograft (PDX/CDX), and Epigenomic Reporting Workflow

Summary: Tumor xenograft sequencing libraries inevitably contain infiltrating murine host reads, but conventional deconvolution tools fail on bisulfite sequencing (BS-seq) because chemical C-to-T deamination collapses sequence entropy and destroys graft recall (< 0.015%). We present OTTER, an automated, compiled multi-omics workflow framework that decouples execution into static domain operators, an immutable reference registry, and a native strand-aware edit-distance engine, restoring bisulfite deconvolution (52%-54% recall across a 0%-99% compositional gradient) while preserving complete decision parity on transcriptomics. Availability and implementation: OTTER is implemented in Go and Rust, runs on x86_64 Linux (including CentOS 7 with glibc 2.17), and is freely available open-source under the MIT License at https://github.com/otterlab-bio/otter; test and validation data are provided at https://huggingface.co/datasets/fallingstar10/otter-data.

bioinformatics↗

bioRxiv2026

Xenograft supervision and joint methylation-fragment-end encoding define a reusable molecular scoring layer for cell-free tumor DNA

Circulating tumor DNA is often scarce in plasma, and regional methylation summaries can obscure informative differences between individual molecules. Here we present ctDNA-BERT, a Transformer that scores individual bisulfite reads without predefined differentially methylated regions by jointly encoding CpG methylation state, nucleotide context and the fragment 3' end. Xenografts provide molecule-level tumor supervision. The resulting frozen scorer supported tumor-fraction estimation in synthetic and patient-derived xenograft mixtures and enriched tumor-concordant methylation and chromatin-accessibility signals in independent hepatocellular carcinoma and stage III pan-cancer plasma without cohort-specific retraining. Features derived from selected reads discriminated stage I cancers from healthy controls in a retrospective cohort of 1,477 specimens, achieving an out-of-fold area under the receiver operating characteristic curve of 0.884. By separating molecular scoring from sample-level inference, ctDNA-BERT provides a reusable read-level scoring layer for cell-free DNA methylation analysis.

bioinformatics↗

bioRxiv2026

An implantable sensor network for large-scale cellular force mapping in living embryos

Mechanical forces generated by cells are fundamental regulators of embryonic development, yet how locally generated forces are integrated across tissues to drive large-scale morphogenesis remains poorly understood. Addressing this question requires direct quantitative mapping of intercellular forces across tissue scale with cellular resolution while preserving native tissue architectures and dynamics, a capability not yet achieved. Here, we introduce FORCENET, an implantable force-sensing network that enables quantitative tissue-scale force mapping at cellular resolution within living embryos. FORCENET consists of a microfabricated network of ultrathin elastic sensors whose three-dimensional deformations are tracked over time and converted into intercellular force maps through physics-based reconstruction. FORCENET covers hundreds of cells while occupying a total volume 6- to 20-fold smaller than that of a single cell. Anatomical measurements, three-dimensional fluorescent imaging, and cell density and speed tracking confirmed that FORCENET seamlessly integrates within developing embryos without perturbing cell motion and proliferation, tissue architecture, and embryonic development. Applied to zebrafish gastrulation, FORCENET revealed that intercellular forces are dynamically coordinated across supracellular length scales of ~30-210 m. Inhibition of fibroblast growth factor signaling accelerated force accumulation and shortened the force-coordination length scales despite only modest changes in cell density and kinematics, demonstrating that FORCENET uncovers information not readily inferred from cell tracking alone. FORCENET establishes a scalable platform for in vivo force mapping and reveals that cell-generated forces are coordinated into supracellular mechanical patterns that are regulated by developmental signaling.

developmental biology↗

bioRxiv2026

A telomere-to-telomere genome of Holstein cattle resolves chromosome-end architecture and the genetic basis of telomere length

Telomeres safeguard chromosome-end integrity, yet population-scale dissection of telomere-length genetics has been largely restricted to humans. Here, we report a 3.01-Gb telomere-to-telomere (T2T) genome of Holstein cattle that resolves repeat-rich chromosome ends and centromeres and enables telomere-length quantification at single-chromosome-end resolution. Holstein chromosome ends show marked telomere-length asymmetry and end-specific variation in telomere variant repeats, subtelomeric tandem repeats, GC/CpG composition, and DNA methylation. Using sequencing-depth-corrected telomere-length phenotypes from 9,591 cows, teloGWAS identifies major loci encompassing RTEL1, CTC1, and TERT, while multi-tissue eQTL, sQTL, TWAS, and co-expression analyses prioritize CTC1 and implicate DNA replication, DNA repair, and stress-response networks. Together, these findings extend population-scale telomere genetics beyond humans and establish a sequence-resolved framework for chromosome-end biology and telomere-informed livestock genomics.

genomics↗

bioRxiv2026

Exploring the activation mechanism of the Mic60 subcomplex governing mitochondrial crista junctions

Crista junctions (CJs) are narrow infoldings of the inner mitochondrial membrane, serving as entry points into the cristae microenvironment. The mitochondrial contact site and cristae organizing system (MICOS) complex is a highly conserved protein machinery controlling CJ biogenesis and architecture, but its assembly mechanism driving CJ formation has remained unclear. By determining a crystal structure of a Chaetomium thermophilum Mic60-Mic19 complex and combining it with modelling and mutagenesis studies, we identify an extended helical region (EHR) of the Mic60 mitofilin domain and a further Mic19 helix as crucial elements of complex formation. In vitro cross-linking data and hydrogen-deuterium exchange mass spectrometry resolve domain assembly and conformational dynamics of the Mic60 Mic19 subcomplex and point to the EHR as a molecular switch controlling Mic60 transition from a closed dimer to a Mic19-bound hetero-octamer. Our data provide a structural model for Mic60 activation and therefore MICOS assembly as a prerequisite for crista junction formation.

molecular biology↗

bioRxiv2026

Early dynamics of a neutrophil interferon program drive immunotherapy resistance and limit durable anti-tumor immunity

Despite the remarkable success of immune checkpoint blockade (ICB), durable clinical benefit remains limited to a subset of patients, highlighting the need for predictive biomarkers and new therapeutic targets. Here, we investigated the early immune dynamics associated with anti-PD1 responsiveness using longitudinal single-cell transcriptomics, spatial transcriptomics, and neutrophil-specific genetic perturbations in preclinical models of triple-negative breast cancer. We identified a conserved neutrophil interferon-stimulated gene (ISG) program that emerges before overt tumor divergence and predicts resistance to anti-PD1 therapy. Successful treatment was associated with an early reduction of IFN-responsive neutrophils in both blood and tumor tissues, whereas persistent neutrophil IFN signaling correlated with therapeutic resistance. Mechanistically, genetic disruption of either type I or type II interferon signaling in neutrophils enhanced anti-PD1 efficacy and promoted durable anti-tumor immune memory. Spatial analyses further revealed an inverse association between IFN-responsive neutrophils and tertiary lymphoid structure-enriched regions during effective therapy. Together, these findings identify IFN-responsive neutrophils as early determinants of immunotherapy outcome and establish dynamic neutrophil interferon programs as candidate blood-based biomarkers and therapeutic targets for cancer immunotherapy.

cancer biology↗

bioRxiv2026

Integrator governs NF-κB dwell time on chromatin to drive inflammatory transcription

NF-{kappa}B must remain bound to chromatin long enough to activate innate immune genes, but what stabilizes this transcriptionally productive state is unknown. Here, we identify the Integrator complex as an essential determinant of NF-{kappa}B chromatin residence in mouse and human cells. Integrator associated with NF-{kappa}B and co-occupied its genomic targets. Single-molecule tracking revealed that Integrator markedly prolonged the chromatin residence of RELA molecules in a low-mobility state. Catalytically inactive INTS11-E203Q fully restored NF-{kappa}B-dependent transcription, separating this chromatin-retention function from RNA cleavage. Conditional Ints11 deletion abolished TLR4-dependent dendritic-cell activation in adult mice and impaired LPS-induced transcription in mouse embryonic fibroblasts. Loss of Integrator in human cancer cells similarly suppressed TNF-induced inflammatory gene expression. These findings uncover a noncatalytic function for Integrator that stabilizes NF-{kappa}B at enhancers, complementing its established catalytic control of RNA polymerase II pause release. By coupling signal recognition at enhancers to productive elongation, Integrator provides a molecular solution to a central challenge of multicellularity: converting transient extracellular cues into coherent gene-expression programs across complex chromatin landscapes.

molecular biology↗

bioRxiv2026

Phosphorylation-dependent binding of the Adenomatous Polyposis Coli protein to β-TrCP1 regulates β-catenin destruction

Wnt signaling controls cellular development by regulating levels of {beta}-catenin, a dual transcription factor and adhesion protein. The tumor suppressor gene Adenomatous Polyposis coli (APC) is a negative regulator of Wnt signaling that acts by interacting with multiple proteins in the destruction complex to drive {beta}-catenin degradation. Mutations in APC cause deregulation of Wnt/{beta}-catenin signaling contributing to the development of several types of cancer, especially colorectal cancers. Tumors are not null mutant for APC - instead they accumulate truncated proteins. Many APC proteins are truncated between the second and third 20-amino acid repeats, a region known as the {beta}-catenin inhibition domain (CID), which is essential for {beta}-catenin destruction, but its mechanism of action is unclear. Here we find that cyclin dependent kinases and GSK3{beta} phosphorylate the CID region of APC in vitro. This allows the APC CID to bind to the E3 ubiquitin ligase component {beta}-TrCP1 in a phosphorylation dependent manner and this in turn regulates the rate of {beta}-catenin ubiquitylation. {beta} TrCP1 binding to the phosphorylated CID favors the retention and stabilization of the SCF {beta}-TrCP1 E3 ligase in the destruction complex and ensures that SCF {beta}-TrCP1 remains available for {beta}-catenin ubiquitylation. These findings provide a mechanism for the vital role of APCs CID region in {beta}-catenin destruction.

biochemistry↗

bioRxiv2026

The ModelSEED Biochemistry Database, 2026 update: grading multi-source thermodynamics

The ModelSEED Biochemistry Database (https://modelseed.org) supplies foundational mass- and charge-balanced reaction networks for metabolic reconstructions. Here we present an update on the biochemistry where the database has been expanded to [~] 46,000 compounds, and [~] 56,000 reactions, featuring [~] 37,000 metabolic structures. We have expanded our approach for handling thermodynamic data, enabling multiple sources of data to be derived, integrated, and presented to the wider research community. We now publish predictions of pKa, reaction energy (and respective uncertainties), and estimates of reaction direction from multiple independent sources. Each reaction is graded gold, silver or bronze according to the strength of the evidence behind it, so that users can weigh its reliability directly. We also release reaction directions predicted by an ensemble of large language models. This multi-source approach exposes agreements and discrepancies between sources for [~] 33,000 reactions. Finally, to ensure data integrity, a new conflict-resolution pipeline reconciles structures across sources, documenting input from curators. Our work is publicly available at https://github.com/ModelSEED/ModelSEEDDatabase.

biochemistry↗

bioRxiv2026

Site-resolved spatial and structural interactome of a human cell

The spatial and structural arrangement of proteins determine virtually every process in human cells. We combined gentle subcellular fractionation by differential ultracentrifugation with cross-linking mass spectrometry to systematically map this cellular proteome architecture with residue-level evidence, identifying 164,146 residue-to-residue links in HEK293 cells. These links capture spatial protein arrangement at a resolution sufficient to pinpoint protein localizations at sub-organelle level, determine protein orientations within cellular membranes, and identify inter-organelle contact sites. The residue-level information provides evidence for 18,074 direct protein-protein interactions (PPIs), which we integrate into AlphaFold-based pipelines to nominate PPI-mediating short linear motifs and generate assembly models of large protein complexes. Guided by these spatial and structural readouts, we discover new PPIs within the endomembrane system that regulate the compartmental localization of trafficking machinery. Leveraging a network topology-driven strategy, we augment our HEK293 dataset with PPI data from different cell lines and methods, expanding the spatial and structural interactome of human cells.

systems biology↗

bioRxiv2026

NLR DNA copy-number expansion outpaces accumulation of predicted coding-intact copies

Whether nucleotide-binding leucine-rich repeat (NLR) DNA copies and predicted coding-intact copies accumulate proportionally within homologous neighbourhoods remains unresolved. We compared these counts across 173 anchor-defined neighbourhoods in 11 Capsicum genomes. After accounting for neighbourhood and genome effects, predicted coding-intact copies increased less than proportionally with DNA copies. DNA-copy doubling corresponded to 1.48-fold and 1.84-fold increases in expected coding counts under strict and inclusive definitions, respectively. The strict association persisted across sequence and sampling controls, with highly expanded arrays and heterogeneous coding recovery affecting interpretation. An independently defined panel of 17 Arabidopsis thaliana accessions reproduced sublinear scaling using curated gene counts. Matched pepper RNA-seq showed a transcript-support gradient across predicted coding states. At DH06, a near-megabase segmental duplication in C. pubescens contained intact and disrupted family pairs. Copy-specific HiFi reads placed the same F396 coding lesions in both physical blocks. Together, these results reveal a recurrent relationship between NLR array size and coding composition in the surveyed plant systems. Interpreting DNA expansion together with coding state provides a more informative basis for comparing NLR repertoires and prioritizing immune-gene candidates.

evolutionary biology↗

bioRxiv2026

Structural insights into MBOAT2 catalysis, product retention, and ligand exchange

MBOAT2 suppresses ferroptosis independently of GPX4 and FSP1 by transferring monounsaturated acyl chains from acyl-CoA donors to lysophospholipid acceptors, but the structural basis of its catalytic cycle remains unclear. Here, we report the first cryo-EM structures of human MBOAT2, capturing endogenous and substrate-induced ligand-bound states. Unexpectedly, as-purified MBOAT2 contains a co-purified phospholipid-like density consistent with a retained product, together with a second density at a putative acyl-donor entry site. Oleoyl-CoA addition reduces the ordered product-like density and reveals donor density, whereas LPE addition increases local heterogeneity near the archway. The inactive H373A mutant contains endogenous donor- and acceptor-like densities along the two access pathways, consistent with substrate preloading. Together, these structures define the catalytic architecture of MBOAT2, support a product-retained, donor-primed working model, and provide templates for structure-guided ligand discovery.

biophysics↗

bioRxiv2026

4-Hydroxybenzaldehyde Attenuates Isoproterenol-induced Cardiac Fibrosis via TGF-β-Smad2/3 Signaling Pathway

This study aims to investigate the cardioprotective effects of 4-Hydroxybenzaldehyde (4-HBA) against isoproterenol (ISO)-induced cardiac fibrosis and to elucidate the underlying mechanisms. In vivo, cardiac fibrosis was induced in C57BL/6 mice by subcutaneous injection of ISO, and the mice were treated with 4-HBA or a TGF-{beta} inhibitor. Assessments using echocardiography, histopathology, and Western blotting demonstrated that 4-HBA significantly alleviated ISO-induced cardiac dysfunction, reduced collagen deposition, and attenuated apoptosis in mice. Mechanistically, 4-HBA inhibited TGF-{beta} expression and Smad2/3 phosphorylation. In vitro, ISO was applied to cardiomyocytes (HL-1) and cardiac fibroblasts (MCFs), with or without 4-HBA or TGF-{beta} inhibitor intervention. The results showed that 4-HBA suppressed HL-1 apoptosis and fibroblast proliferation, and significantly reduced the expression of extracellular matrix genes, TGF-{beta} levels, and Smad2/3 phosphorylation in MCFs. These findings indicate that 4-HBA reduces myocardial injury while targeting the TGF-{beta}/Smad2/3 pathway to attenuate cardiac fibrosis, highlighting its potential as a therapeutic agent for fibrotic cardiomyopathy.This study aims to investigate the cardioprotective effects of 4-Hydroxybenzaldehyde (4-HBA) against isoproterenol (ISO)-induced cardiac fibrosis and to elucidate the underlying mechanisms. In vivo, cardiac fibrosis was induced in C57BL/6 mice by subcutaneous injection of ISO, and the mice were treated with 4-HBA or a TGF-{beta} inhibitor. Assessments using echocardiography, histopathology, and Western blotting demonstrated that 4-HBA significantly alleviated ISO-induced cardiac dysfunction, reduced collagen deposition, and attenuated apoptosis in mice. Mechanistically, 4-HBA inhibited TGF-{beta} expression and Smad2/3 phosphorylation. In vitro, ISO was applied to cardiomyocytes (HL-1) and cardiac fibroblasts (MCFs), with or without 4-HBA or TGF-{beta} inhibitor intervention. The results showed that 4-HBA suppressed HL-1 apoptosis and fibroblast proliferation, and significantly reduced the expression of extracellular matrix genes, TGF-{beta} levels, and Smad2/3 phosphorylation in MCFs. These findings indicate that 4-HBA reduces myocardial injury while targeting the TGF-{beta}/Smad2/3 pathway to attenuate cardiac fibrosis, highlighting its potential as a therapeutic agent for fibrotic cardiomyopathy.

molecular biology↗

bioRxiv2026

A multi-tissue epigenomic atlas links the sheep non-coding genome to domestication and complex traits

Non-coding regulatory variation drives complex traits, domestication, and evolutionary adaptation, yet the sheep genome lacks high-resolution functional annotation. Here we present SheepEpimap, a multi-tissue regulatory atlas harmonizing 516 CUT&Tag histone modifications, ATAC-seq, and RNA-seq datasets across 43 adult tissues in sheep. We annotated 2.93 million cis-regulatory elements, yielding 557,441 enhancer-gene pairs and 145,407 variants with allele-specific effects. By training a sequence-to-function deep-learning model, we decoded the base-pair syntax of chromatin accessibility, annotated transcription factor motif instances genome-wide, and constructed 12,210 tissue-specific gene regulatory networks (GRNs). Integrating this resource with multi-tissue expression quantitative trait loci, selection sweeps, and genome-wide association studies prioritized non-coding variants driving domestication and complex traits. Finally, cross-species analysis revealed that sequence-conserved, tissue-matched enhancers were significantly enriched in the heritability of complex traits and diseases in humans. In summary, SheepEpimap (https://genome.ucsc.edu/s/mengzhu/SheepEpimap) provides an open-access foundational ecosystem for sheep functional genomics, precision breeding, and comparative biology.

genetics↗

bioRxiv2026

The common evolution of fungicide persistence in cryptococcosis patients

Fungicide persistence, the ability of dormant fungal cells to survive lethal drug exposure, undermines treatment efficacy, yet its clinical evolution remains largely unexplored. We assembled a nationwide collection of clinical Cryptococcus neoformans isolates from China and revealed extensive inter strain variation in amphotericin B (AmB) persistence. This variation can arise from common evolutionary events in patients, generating previously undescribed high persistence cryptococcal variants refractory to AmB clearance. Genome wide fitness landscape analysis shows that persistence associated mutations generally impose minimal fitness costs, facilitating persistence evolution even in fungistatic resistant and hypervirulent genetic backgrounds. Machine learning identified deficient ACO2 expression as a key predictor of high persistence clinical isolates. ACO2 deficiency reproduces the high persistence phenotype by promoting POPC accumulation, which competes with AmB for its target. Moreover, the clinical stage antifungal T-2307 effectively eliminates high persistence strains across diverse genetic backgrounds. Collectively, our findings unveil common evolution of fungicide persistence in cryptococcosis patients, representing a previously overlooked clinical concern.

microbiology↗

bioRxiv2026

TEAD1 signaling modulates adrenal chromaffin maturation

Chromaffin cells synthesize and secrete catecholamines to coordinate systemic stress responses and regulate diverse neuroendocrine and metabolic functions. However, the molecular mechanisms governing chromaffin-cell differentiation and their disruption in pheochromocytoma (PC) remain incompletely understood. Here, through integrated analyses of human developmental atlases, patient-derived transcriptomic datasets, genetically engineered mouse models, and chromaffin organoids, we identify TEAD1 signaling as a critical regulator of chromaffin-cell differentiation and function. In vivo studies using a chromaffin cell-specific TEAD1 overexpression mouse model demonstrated that suppression of TEAD signaling markedly compromises chromaffin-cell differentiation and endocrine function. Additionally, compared with other TEAD family members, TEAD1 transcriptional activities are readily affected by sequences near the binding motif. To identify therapeutically actionable regulators of TEAD1 signaling, we established a TEAD activity-based screening platform and identified the serotonin receptor HTR5A antagonist SB699551 as a potent modulator of chromaffin-cell state. SB699551 suppressed PC-cell proliferation in vivo, and remodeled catecholamines synthesis in primary human PC cells. Additionally, application of SB699551 to human PC tumor revealed a subpopulation of primary chromaffin cells sensitive to this compound. Mechanistically, CXXC5 and L1CAM were identified as downstream SB699551-TEAD1 signaling effectors mediating chromaffin-cell proliferation and differentiation. Overall, we demonstrate that TEAD1 signaling is a fundamental mechanism regulating chromaffin cell differentiation and that modulation of TEAD1 signaling via SB699551 offers a new area of investigation in chromaffin cell biology.

molecular biology↗

bioRxiv2026

Tumor-tropic E. coli engineered as living T and NK cell engagers

Despite advances in immunotherapy, most solid tumors remain resistant to treatment. Immune cell engagers redirect cytotoxic lymphocytes against cancer, but limited tumor access, immunosuppressive microenvironments and systemic immune activation limit efficacy. Here we develop live immune modulating engagers (LIME), a modular platform where non-pathogenic, tumor-tropic Escherichia coli display tandem single-chain variable fragments targeting a tumor-associated antigen and an activating receptor on T or natural killer cells. LIME bridged effector and tumor cells, induced transcriptional programs of T cell activation, metabolism and proliferation, and enhanced cytotoxicity across cancer cell lines and patient-derived organoids. In mouse models, LIME safely accumulated in tumors, outperformed tarlatamab in small cell lung cancer, and induced durable immunity in lymphoma. RAS inhibition and PD-L1 blockade enhanced LIME activity in pancreatic cancer and induced humoral responses. Multi-lineage immune modulation remained tumor-confined, without organ toxicity. These findings establish LIME as a versatile living therapeutic platform for programmable, tumor-restricted immune orchestration.

bioengineering↗