Biology subjects

Liu, N.

Publications and source records attributed to Liu, N..

At least 55 records · Page 3Linked to original sources

bioRxiv2026

EOLA1, a novel mitochondria-localized protein critical for heart functions via regulating mitochondrial translation

Mitochondria possess their own mRNA translation system, mediated by specialized mitoribosomes. Dysregulation of mitochondrial translation disrupts metabolic homeostasis and is linked to various pathologies, including metabolic syndromes, neurological disorders, and cardiac diseases. Using CRISPR/Cas9 screening, we identified EOLA1 (endothelial-overexpressed lipopolysaccharide-associated factor 1) as a novel mitochondrial matrix protein essential for metabolic homeostasis. Knockout of Eola1 severely affects mitochondrial translation and consequently the oxidative phosphorylation in mammalian cells. Mechanistically, EOLA1 physically interacts with mitochondrial 12S ribosomal RNA (12S mt-rRNA) and the mitochondrial Tu translation elongation factor (TUFM), facilitating efficient translation elongation of mitochondrial-encoded mRNAs. Furthermore, genetic ablation of Eola1 in mice induced severe cardiac dysfunction, demonstrating its indispensable role in maintaining heart function through mitochondrial translation control. Together, our findings establish EOLA1 as a key regulator of mitochondrial translation via its interactions with 12S mt-rRNA and TUFM, highlighting its importance in cellular metabolism and a potential role in cardiac disease pathogenesis.

molecular biology↗

bioRxiv2025

DOMINO: diffusion-optimised graph learning identifies domain structures with enhanced accuracy and scalability

Spatial transcriptomics enables in situ molecular profiling, allowing to measure the cellular transcriptional output within the tissue. As the tissue architecture is conserved, spatial domains with specific transcriptional patterns can be identified, facilitating the discovery and understanding of functional tissue compartments. Thus, several methods to uncover and identify these spatial domains have been developed. However, most of these existing methods do not scale to rapidly increasing data sizes and focus only on local structure while missing the global view of the tissue. Here, we present DOMINO, a diffusion-optimised contrastive learning framework for spatial domain detection. DOMINO utilises graph diffusion convolution to propagate information beyond immediate neighbours and jointly optimises local and, importantly, global graph structure via contrastive learning. This novel framework yields biologically interpretable domains with clearer boundaries and scales to large datasets, outperforming state-of-the-art methods across healthy and malignant benchmark datasets. We apply DOMINO to a newly generated spatial transcriptomic dataset of endometriosis-associated ovarian cancers, which could not be processed by existing domain detection methods owing to its size. We uncovered conserved proliferative and non-proliferative tumour states that recurred across these tumours and were independently validated in an external clear cell ovarian cancer spatial transcriptomic dataset. Proliferative domains were characterised by elevated expression of EIF4A1 and HSPA8, increased cell cycle activity, reduced mast cell abundance, and coordinated stromal remodelling, including altered fibroblast states and spatial organisation. In parallel, integrative analysis across tumours revealed subtype-specific multicellular ecosystems associated with either endometrioid or clear cell ovarian carcinomas, together with a tumour-excluded stromal domain that could only be resolved through the integration of spatial and transcriptional information. These findings demonstrate how well DOMINO scales up and that it uncovers biologically meaningful spatial programs spanning tumour intrinsic states, tumour microenvironment interactions, and subtype-specific tissue architecture that are not recovered by conventional expression-based clustering approaches.

bioinformatics↗

bioRxiv2025

Synchronized Latency Reversal and Immune Clearance by a Multifunctional Fusion Protein Enables HIV-1 Reservoir Reduction

Strategies that concurrently reactivate latent reservoirs and enhance immune-mediated clearance hold significant promise for achieving an HIV cure. Here, we developed hyperIL-15xsCD4-Fc (15xsCD4-Fc), a fusion protein that integrates latency reactivation, targeted immune engagement, and effector-mediated killing into a single molecule. This agent not only potently reverses HIV-1 latency in CD4+ T cells from people living with HIV-1 (PLWH) through coordinated IL-15 receptor signaling and sCD4-mediated HIV-1 envelope (Env) engagement, but also enhances antigen-specific CD8+ T cell response in PBMCs derived from PLWH. Furthermore, 15xsCD4-Fc enables Env-specific elimination of reactivated latently infected cells by NK cells while preventing off-target cytotoxicity. In PBMCs from PLWH, 15xsCD4-Fc reduced replication-competent HIV-1 DNA by 93.8%. In antiretroviral treated HIV-1-infected humanized mice, the molecule demonstrated both safety and efficacy in diminishing viral reservoir in lymphoid organs. This spatiotemporally coupled approach to reservoir exposure and immune recognition establishes a clinically viable strategy for clearing the HIV-1 reservoir. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=195 SRC="FIGDIR/small/693434v1_ufig1.gif" ALT="Figure 1"> View larger version (44K): org.highwire.dtl.DTLVardef@8f8f0org.highwire.dtl.DTLVardef@10f63f7org.highwire.dtl.DTLVardef@16c1de2org.highwire.dtl.DTLVardef@11e1787_HPS_FORMAT_FIGEXP M_FIG C_FIG

immunology↗

bioRxiv2025

Single-cell transcriptomic dynamics exposes hidden survival trajectory under antibiotic treatment

Heterogeneity plays a major role in bacterial resistance to antibiotic treatment while the mechanism at single-cell level is largely unknown. Here, we employed a robust integration of bulk and bacterial single-cell RNA-seq (scRNA-seq) to uncover how individual cells of Acinetobacter baumannii reorganise the heterogenous transcriptome in response to antibiotic. Using polymyxin as a representative, bulk RNA-seq showed canonical envelope- and efflux-centred responses but obscured underlying heterogeneity. Single-cell profiling resolved these averages into discrete subpopulations whose abundances shifted with concentration and time. Specifically, in early time an envelope-stress programme predominated survival at the low concentration, whereas an outer-membrane repair/efflux programme dominated survival at the high concentration. These patterns revealed structured and time-resolved heterogeneity, highlighting an ingenious bacterial stress responsive strategy. Through trajectory inference, we further revealed a concentration-dependent bifurcation of cell fates: low-concentration treated cells detoured through a transient stress state and rejoined growth, whereas high-concentration treated survivors diverted into a slow-growing, tolerant branch. Perturbing marker genes from these programmes altered fitness eventually and rapidly increased permeability, depolarisation and reactive-oxygen burden, linking state to survival capability. Collectively, we map a dynamic, concentration-structured landscape of antibiotic responses at the single-cell level, revealing diverse survival trajectories that are obscured in conventional population-averaged analyses. Our developed single-cell based framework revealed tolerant bacterial cells with rewiring of the transcriptional landscape, causing emergence of antibiotic resistance. Importantly, these findings urge precision antimicrobial therapy in patients to minimise emergence of antibiotic resistance.

microbiology↗

bioRxiv2025

Disease-associated mutations in the STAT5B SH2 domain reprogram hepatic cholesterol and lipid metabolism

Growth hormone (GH) signaling through STAT5B is a central regulator of hepatic metabolism, yet the functional consequences of disease-associated STAT5B variants remain poorly understood. Here, we analyzed mice carrying STAT5BY665F (gain-of-function) and STAT5BY665H (loss-of-function) variants and dissect their impact on metabolic regulation. STAT5BY665F mice developed hepatic lipid accumulation, hypercholesterolemia, and enhanced insulin sensitivity, whereas STAT5BY665H mice displayed reduced body weight and impaired insulin responsiveness. Transcriptomic analyses revealed that STAT5BY665F activated lipid, cholesterol, and immune transcriptional programs, while STAT5BY665H failed to induce these pathways. Notably, STAT5BY665F substantially feminized male liver gene expression, inducing 77% of female-biased genes while repressing 51% of male-biased genes, thereby mimicking the persistent STAT5B activation characteristic of female livers. ChIP-seq demonstrated extensive STAT5BY665F enhancer occupancy at metabolic and immune loci, contrasting with the minimal chromatin engagement of STAT5BY665H. Beyond the liver, STAT5BY665F broadly reprogrammed adipose tissue gene expression, activating lipid metabolism and immune regulatory networks, whereas STAT5BY665H exerted more restricted effects. Together, these findings illustrate how alterations in STAT5B activity affect enhancer activation and can lead to changes in metabolic function and hepatic sexual dimorphism.

genomics↗

bioRxiv2025

Mechanical Disturbance of Trichomes Enhances Cd2+ Uptake via Malate-Mediated Stomatal Opening in Arabidopsis

Phytoremediation of cadmium-contaminated soils relies on efficient metal uptake and translocation in plants. We previously found that gentle mechanical stimulation of non-glandular trichomes by brushing significantly enhances shoot Cd{superscript 2} accumulation in Arabidopsis thaliana, although the underlying physiological mechanism remained unclear. Here, we demonstrate that trichome brushing specifically induces stomatal opening, elevates transpiration, and promotes Cd{superscript 2} uptake, as evidenced by measurements of stomatal aperture, stomatal conductance, transpiration rate, and Cd{superscript 2} concentration in wild-type and mutant leaves. These responses are absent in the glabrous gl1-1 mutant and are not elicited by brushing epidermal pavement cells, indicating a trichome-specific mechanosensory pathway. Mechanistically, this pathway requires MPK3/MPK6 activity and employs malic acid as a key regulator of stomatal aperture, functioning independently of canonical ABA signaling. Our findings uncover a previously unrecognized trichome-to-stomatal signaling cascade that links trichome mechanostimulation to enhanced heavy metal accumulation.

plant biology↗

bioRxiv2025

DNA methylation reprogramming in marsupial embryos is restricted to the extraembryonic lineage

DNA methylation (5mC) is an epigenetic mark that plays a critical role in defining cell fate. Following fertilisation, DNA methylation inherited from gametes must be reprogrammed to establish totipotency and enable the parental-to-zygotic transition. To accomplish this, non-mammalian vertebrates such as zebrafish and medaka subtly reprogram maternal 5mC profiles while maintaining high methylation levels throughout embryogenesis. In contrast, eutherian mammals such as mouse and human undergo global 5mC erasure in both embryonic and extraembryonic lineages. However, while embryonic 5mC is rapidly re-established to high levels upon implantation, the trophectoderm, which gives rise to the placenta, displays sustained and conserved DNA hypomethylation, suggesting that this drastic 5mC erasure may be functionally linked to complex placentation in mammals. To clarify whether extensive post-fertilisation 5mC erasure co-evolved with placentation, we explored embryonic methylation dynamics in marsupials, a lineage of therian mammals with a short-lived placenta. We produced a near complete telomere-to-telomere (T2T) genome and generated detailed epigenome maps of embryonic development for an Australian marsupial, the fat-tailed dunnart (Sminthopsis crassicaudata). We found the dunnart embryo exhibits genome wide DNA demethylation at the blastocyst stage, but these changes occur in the trophectoderm only, suggesting that 5mC erasure in the placenta is an ancestral state in therian mammals. Furthermore, the T2T-level dunnart genome assembly enabled identification of sex chromosomes, uncovering extensive hypomethylation of the paternally-inherited inactive X chromosome in females and revealing the previously unannotated master regulator of X chromosome inactivation, lncRNA Rsx. Our data indicate that while the use of genome-wide 5mC erasure differs between eutherian and marsupial lineages, 5mC erasure in extraembryonic tissue is ancestral to therian mammals and may be necessary to support placental development. HIGHLIGHTSO_LIFirst embryonic DNA methylation maps in an Australian marsupial C_LIO_LIExtensive global erasure of DNA methylation in the trophectoderm C_LIO_LIMaintenance of high DNA methylation in the embryonic lineage C_LIO_LIHypomethylated paternal X chromosome with methylated escapee genes C_LI

developmental biology↗

bioRxiv2025

SpNeigh: spatial neighborhood and differential expression analysis for high-resolution spatial transcriptomics

Spatial transcriptomics technologies such as Xenium, MERFISH, and Visium HD enable high-resolution profiling of gene expression while preserving tissue architecture. However, most computational methods for spatial analysis do not explicitly model local tissue context, such as boundaries, neighborhoods, or gradients. Here we present SpNeigh, an R package for spatial neighborhood analysis and spatially-aware differential expression modeling. SpNeigh includes tools for boundary detection, spatial neighborhood extraction, distance-based weighting, and gradient-based statistical testing. It supports both region-based differential expression and smooth spatial modeling using spline-based regression, along with a spatial enrichment index that identifies genes enriched near defined spatial features. We demonstrate the utility of SpNeigh across multiple platforms and tissues, including mouse brain, human breast cancer, and human liver, revealing intermediate populations at tissue interfaces, immune microenvironment differences, and spatially zonated gene expression patterns. SpNeigh offers a flexible and interpretable framework for dissecting spatial gene expression dynamics in complex tissues.

bioinformatics↗

bioRxiv2025

Cancer-specific sialylation of insulin-like growth factor 1 receptor impairs therapeutic antibody binding and efficacy

Despite extensive efforts to develop insulin-like growth factor (IGF1R)-targeted therapies for various malignancies, none has received clinical approval in the past two decades. Here, we reveal that N-glycan sialylation significantly decreases recognition by the humanized monoclonal anti-IGF1R antibody ganitumab across various cancer types, reducing its efficacy both in vitro and in vivo. Sialoforms of IGF1R are virtually absent in normal cells, indicating that the modification is tumor-specific. Pharmacological inhibition of sialyltransferases significantly sensitizes metastatic tumors to ganitumab in a ganitumab-resistant ovarian cancer model. Enzymatic removal of sialic acids from tissue sections resulted in marked enhancement in antibody binding to ovarian cancer patient tumors, but not normal tissues. Upregulation of 2-6 sialyltransferase ST6GAL1 in tumor tissues was found to be responsible for sialylation of IGF1R. Consequently, ST6GAL1-high tumors were more likely to benefit from desialylation-mediated enhancement of ganitumab binding. Furthermore, through comprehensive glycoproteomics analysis, structural prediction, and molecular dynamics simulation, we identify Asn-607 (N607) as a crucial site harboring sialylated glycans. Mechanistically, N607 glycosylation destabilizes the IGF1R-ganitumab complex. Overexpression of IGF1R Asn-607-Gln (N607Q) mutant in IGF1R-knockout cancer cells increases ganitumab efficacy compared to wild-type IGF1R in vivo. Taken together, these findings highlight sialylation as a common barrier in IGF1R-targeted therapies and provide crucial insights for therapy enhancement in cancer and patient stratification for future clinical trials. Graphical Abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=99 SRC="FIGDIR/small/682592v1_ufig1.gif" ALT="Figure 1"> View larger version (14K): org.highwire.dtl.DTLVardef@17c6d5corg.highwire.dtl.DTLVardef@1efe2f7org.highwire.dtl.DTLVardef@1dd05aorg.highwire.dtl.DTLVardef@159fb23_HPS_FORMAT_FIGEXP M_FIG C_FIG Synopsis2-6 sialylation of IGF1R Asn-607 by ST6GAL1 is prevalent in cancer. This modification disrupts the interaction of IGF1R with therapeutic mAb ganitumab. Removal of sialylation augments ganitumab efficacy.

cancer biology↗

bioRxiv2025

PTH-Induced Behavioral and Metabolic Alterations in Mouse Models of Hyperparathyroidism

Parathyroid hormone (PTH) is a critical endocrine regulator of calcium homeostasis and bone remodeling and is widely employed in clinical settings through synthetic analogs for the treatment of osteoporosis. Although traditionally considered a peripheral regulator, emerging evidence indicates that PTH also exerts effects through the central nervous system (CNS). This study investigated the neuropsychiatric impact of elevated PTH and explored potential CNS involvement using multiple murine models of hyperparathyroidism (HPT). Distinct behavioral phenotypes were observed across models, indicating that psychiatric symptoms vary depending on disease etiology and progression. The effects of hPTH(1-34), a clinically approved PTH analog, were further assessed in male and female mice. Under pharmacological concentrations, hPTH(1-34) enhanced locomotor activity in males but induced mild anxiety-like behavior in females. These behavioral changes in females were independent of the estrus cycle and were amplified by ovariectomy. Metabolic analysis indicates PTH affects the basic metabolism by inhibiting the respiratory exchange ratio, promotes the energy expenditure and locomotion without affecting the food consumption in a 48hr range. To further investigate the molecular effect of PTH in the brain, a PTH1R-Cre mouse line was generated to map PTH receptor-1 (PTH1R) expression. Widespread expression of PTH1R was detected across the brain, including in both neuronal and non-neuronal cell populations. These findings suggest that PTH may influence behavior through interactions with PTH1R-expressing cells in brain vasculature and circumventricular regions. However, further studies are warranted to define the specific brain nuclei and cell types involved in PTH-driven modulation of neurobehavioral function.

neuroscience↗

bioRxiv2025

Phosphatidylcholine Metabolism Controls Alveolar Progenitor Renewal and Pulmonary Fibrosis

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease marked by alveolar type 2 (AT2) stem cell dysfunction and excessive matrix deposition, with no effective treatments. Recent advances have recognized that AT2 cells act as stem cells, in addition to their role in the production of pulmonary surfactants in the distal alveolar space. We and others have reported a failure of AT2 regeneration and a loss of AT2 cells in IPF. We recently further reported that there is a defect in lipid metabolism in IPF AT2 cells and we discovered a selective loss of lysophosphatidylcholine acyltransferase 1 (LPCAT1) in AT2 cells from IPF, as well as in AT2 cells from bleomycin-injured mice. Pharmacological and genetic experiments confirm that LPCAT1 is required for AT2 cell renewal in 3D organoid assays. AT2 cell-specific Lpcat1 deletion resulted in reduced AT2 renewal, spontaneous lung fibrosis, and heightened susceptibility to bleomycin-induced fibrosis in mice in vivo. Expression-based high-content drug screening with an LPCAT1 knock-in cell line identified several drug families that upregulated LPCAT1 expression. We further confirmed that anti-malarial artesunate and PLA2 inhibitor ONO-RS-082 increased LPCAT1 mRNA expression, promoted AT2 renewal, and attenuated bleomycin-induced lung fibrosis in mice in vivo. Our findings establish LPCAT1 as a critical regulator of AT2 renewal and lipid metabolism in IPF, suggesting that reactivation of LPCAT1 could offer a novel therapeutic strategy for restoring alveolar progenitor function and mitigating lung fibrosis.

cell biology↗

bioRxiv2025

Bioinformatics-based stereochemical elucidation of MM 46115: an unusual antiviral spirotetronate that inhibits clathrin-mediated endocytosis

The influenza virus is a leading cause of respiratory tract infection in humans, with the emergence of antiviral drug resistance posing an ongoing challenge to the treatment of influenza. This underscores the urgent need for effective new antiviral treatments. Spirotetronates are a family of bacterial natural products with a range of potent bioactivities. Some members of this family have antiviral activity. Here, we report the bioinformatics-based stereochemical assignment, antiviral properties, and mechanism of action of the unusual type II spirotetronate MM 46115 (renamed pellemicin). We show that pellemicin is active against both influenza A and B viruses at non-toxic concentrations, and inhibits clathrin-mediated endocytosis, which is required for virus internalisation. Given the need for new treatments for viral infections, the results of our work suggest that pellemicin and related spirotetronates could provide a basis for developing promising alternatives to existing antivirals to combat drug-resistant influenza. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=199 SRC="FIGDIR/small/677008v1_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@177aacforg.highwire.dtl.DTLVardef@16f0b26org.highwire.dtl.DTLVardef@144f9dcorg.highwire.dtl.DTLVardef@16fe673_HPS_FORMAT_FIGEXP M_FIG C_FIG HighlightsO_LIMM 46115 (here renamed pellemicin) produced by a mycetoma pathogen is a promising antiviral C_LIO_LIThe pellemicin biosynthetic gene cluster was identified in Actinomadura pelletieri DSM 43383 C_LIO_LISequence analysis of biosynthetic enzymes enabled full stereochemical assignment C_LIO_LIPellemicin inhibits clathrin-mediated endocytosis, an early stage of the viral life cycle C_LI SignificanceThe influenza virus is a respiratory pathogen with epidemic and pandemic potential, resulting in tens of thousands of deaths each year and causing significant health, social and economic impact. The rise of resistant influenza strains against existing antiviral drugs creates a pressing need for alternative treatments. Natural products - specialised metabolites of bacteria, fungi, and plants that often have antimicrobial activity - are a promising source of therapeutics to treat human disease. Here, we identify a cryptic polyketide biosynthetic gene cluster in the genome sequence of Actinomadura pelletieri DSM 43383, an Actinomycete that causes mycetoma in humans. This is proposed to direct production of the previously reported spirotetronate MM 46115 (here renamed pellemicin), which has activity against the influenza virus. Sequence analyses of a polyketide synthase and Diels-Alderase involved in pellemicin biosynthesis, combined with comparative analysis of NMR data for other spirotetronates, enabled us to fully resolve longstanding stereochemical ambiguities in the structure of pellemicin. This underscores the emerging power of bioinformatics-based approaches, and their complementarity to traditional spectroscopic methods, for natural product structure elucidation. We also report extensive insights into the antiviral properties and mechanism of pellemicin, demonstrating that it exhibits antiviral activity at non-toxic doses for up to eight hours after administration and inhibits clathrin-mediated endocytosis, a process that many viruses exploit to enter cells. Only one other bacterial natural product, ikarugamycin, is known to inhibit clathrin-mediated endocytosis. Ikarugamycin contains a tetramate group, which bears a close structural relationship to the tetronate moiety of pellemicin, suggesting that inhibition of clathrin-mediated endocytosis may be a general mechanism of action for antiviral spirotetronates. Our findings therefore indicate that pellemicin, and related spirotetronate natural products, could form a basis for development of new drugs to combat antiviral resistance, and serve as useful tools to study the process of endocytosis.

microbiology↗

bioRxiv2025

Preserving tissue structure through density-based spatial analysis with scider

In spatial transcriptomics, most existing approaches for spatial domain detection analyze slide-wide gene expression patterns while integrating information from local neighborhoods or nearest neighbors. However, such global strategies can overlook tissue organization and obscure regional heterogeneity. To address this, we present scider, a framework for spatial data analysis to preserve tissue structures. scider defines spatial domains from local cellular organization and distribution, instead of relying on global clustering of gene expression and neighborhood profiles. Kernel density estimation (KDE) is used to characterize the spatial distribution of cells, enabling the robust and unbiased identification of regions of interest (ROIs) beyond histological annotations. We show that ROIs make multi-sample analysis possible and reveal spatial patterns that are undetectable in single-sample analysis. Additionally, KDE-derived contour lines define regions of similar cell density, supporting cell type composition and differential expression analyses along continuous spatial gradients.

bioinformatics↗

bioRxiv2025

Cis-delivering releasable IL-15 superagonist enhances antitumor immunity in cold tumors by invigorating preexisting CD25+CD8+ T cells

Antibody-mediated cis-delivery and trans-delivery both direct cytokines to tumors and have been extensively investigated in clinical trials. However, a comparative analysis of their differential effects on cytokine activity is still lacking. In this study, we initially verify that cis-delivery of cytokine demonstrates a markedly stronger antitumor effect than trans-delivery, but it also exhibits certain drawbacks, including severe toxicity, insufficient activation of CD25+CD8+ T cells, and enhanced stimulation of intratumoral regulatory T cells (Tregs). To further address these issues, we developed a conditionally releasable and cis-delivering IL-15 immunocytokine (termed PMIS), which can selectively release a free IL-15 superagonist within tumors rather than immobilizing IL-15 to PD-1+ Tregs, thereby potently stimulating CD25+CD8+ T cells. Mice treated with PMIS showed significantly reduced systemic toxicities while achieving notably stronger antitumor effects. Administered either alone or in combination with other therapies, PMIS exhibits great potential for inhibiting orthotopic cold tumor and its metastases. Mechanistically, the significant activation of the pre-existing intratumoral CD25+CD8+ T cells and the improved CD25+CD8/Treg ratio contribute to the enhanced antitumor response of PMIS. These findings underscore the indispensable role of CD25+CD8+ T cells in cis-delivering IL-15 and provide a promising strategy for overcoming resistance to therapies and effectively controlling advanced cold tumors.

immunology↗

bioRxiv2025

Differential transcriptomics and metabolomics analyses of the skin of coarse and fine Liaoning cashmere goats

Secondary follicles in cashmere goats determine cashmere yield and quality. The present study investigated the relationship between the regulatory factors and cashmere fiber diameter through transcriptomics and metabolomics methods. Diameters of the fibers of 400 (18 months old) female Liaoning cashmere goats were measured and categorized into coarse and fine hair types (200 goats per category). Six goats were selected as representatives of each group for further analysis. Fiber diameters were significantly different between groups (P < 0.05). Transcriptomic analysis revealed 211 differentially expressed genes between groups, including FGF18, KRT36, KRT79, AWAT2, and MOGAT1, which were enriched in the PPAR and glycerol-lipid metabolism signaling pathways that regulate hair follicle growth and sebum secretion. Metabolomics analysis revealed 50 differentially expressed metabolites in the skin, which regulate cellular ion channels and participate in neurological channels by enriching ABC transporter protein pathways, amino acid biosynthesis and metabolism, and arachidonic acid metabolism. The findings of the present study could facilitate improvement of cashmere quality in cashmere goats.

genetics↗

bioRxiv2025

LeGO-Teknik reveals that the neurogenesis pathway is a clone-specific hallmark of brain metastasis in breast cancer

Breast cancer exhibits substantial inter- and intra-patient heterogeneity. Yet the molecular features underlying this diversity and their roles in tumour progression are not yet fully elucidated. Within a primary tumour, certain clones possess a unique capacity to metastasize to distant organs, such as the brain, and this propensity may be associated with specific gene expression profiles. To investigate this phenomenon, we developed a new optical barcoding library, LeGO-Teknik, compatible with high resolution imaging, flow cytometry, single-cell RNA sequencing and machine learning computational methods. Using this new tool, we systematically assessed the fitness and organ tropism of multiple human breast cancer clones in spontaneous metastasis assays. Linking transcriptomic profiles of individual cancer cells to their clonal identities and metastatic behaviours, we identified that clones predisposed to forming brain metastases exhibit distinct molecular signatures. Notably, individual cells from these clones showed enriched expression of neurogenesis-related genes. Using SCENIC transcription factor analysis, we found that some of these features are driven by the transcription factor SOX4. This hallmark, likely due to a process of cellular reprogramming, is a remarkable example of organ mimicry during clonal selection. Together, this work provides critical insights into brain metastasis and highlights the potential for identifying predictive biomarkers and therapeutic targets for metastatic breast cancer.

cancer biology↗

bioRxiv2025

Activation of the impaired NAMPT/SIRT7/SOD2 axis restores alveolar progenitor cell homeostasis in idiopathic pulmonary fibrosis and reverses pulmonary fibrosis in mice

Alveolar type II (AT2) progenitor cell exhaustion and impaired regenerative capacity are key pathogenic hallmarks in idiopathic pulmonary fibrosis (IPF). Nicotinamide adenine dinucleotide (NAD+) functions as a central regulator of cellular energy metabolism. We have reported that downregulation of NAD+-dependent sirtuin signaling contributes to the impaired progenitor function of IPF AT2s. In this study, we identified that a key NAD+ biosynthesis enzyme, nicotinamide phosphoribosyltransferase (NAMPT), is significantly downregulated in IPF AT2s. NAMPT deficiency impairs AT2 renewal and enhances lung fibrosis through downregulation of SIRT7 and SOD2, which results in increased oxidative stress, mitochondrial dysfunction, induction of pathological transitional gene expression and impaired regenerative capacity to generate alveolar type I (AT1) cell required for gas exchange. Mice with deletion of Nampt in AT2s showed severely impaired AT2 renewal and increased susceptibility to bleomycin lung injury and spontaneous fibrois. Activation of NAMPT by small molecule activators promoted AT2 renewal, restored homeostasis, and reversed lung fibrosis. NAMPT activation could be a therapeutic strategy for restoring AT2 progenitor function and halting or reversing progressive pulmonary fibrosis.

cell biology↗

bioRxiv2025

Super-giga and tiny orchid genomes illuminate evolution of Orchidaceae

Orchidaceae (orchids) is commonly known as one of the largest families of seed plants, and grow in an extensive range of habitats worldwide. In the present study, we generated chromosome-level reference genomes for two orchids using a combination of PacBio, Illumina, and Hi-C sequencing, Cypripedium singchii has the largest genome and chromosomes among the sequenced species so far, with a genome size of 43.19 Gb (1C) with ten chromosomes, and Apostasia fujianica has the smallest known genome and chromosomes in Orchidaceae, with a genome size of 340.90 Mb (1C) with 35 chromosomes. We predicted a total of 32,412 and 21,724 protein-coding genes for C. singchii and A. fujianica, respectively. The overall BUSCO score was 85.01% for C. singchii and 91.80% in A. fujianica. Based on protein-coding sequences from 55 conserved single-copy families across 21 plant species, we constructed a high-confidence phylogenetic tree and estimated the divergence times. The high-quality genomes of super-giga and tiny orchids offer key insight for future evolutionary researches.

genomics↗