Biology subjects

Sun, M.

Publications and source records attributed to Sun, M..

At least 73 records · Page 4Linked to original sources

bioRxiv2024

Osteoporosis with different causation exhibits different changes in bone tissue mineral and organic matrix

Osteoporosis (OP) which is a common skeletal disease with different causation is prevalent in aging population. Postmenopause women generally suffer from OP with bone loss due to estrogen deficiency. Diabetes are also associated with OP by complex metabolic mechanisms. Bone qualities of OP caused by aging were compared with the ovariectomy (OVX) model and the Type 2 diabetic model using Sprague-Dawley (SD) rats in our study. Combining with micro-computed tomography (-CT) and solid-state NMR (SSNMR) methods, this research studied bone changes in SD rats from tissue level to the molecular level. The studies revealed bone loss was most significant for cancellous bones, but not for cortical bones in OP rats. However, at the molecular level, the content of HAP in cortical bone increased with aging, contributing to the brittleness of the bone. Triglyceride, as a senescence maker of osteocyte in cortical bone, was also identified to be closely associated with OP in aging and OVX rats, but not in diabetic rats. This research suggests differing bone qualities in molecular level of OP with various causes more objectively reflect the bone tissue reconstruction rather than bone loss in -CT analysis.

biochemistry↗

bioRxiv2024

Independence of centromeric and pericentromeric chromatin stability on CCAN components

The chromatin of the centromere provides the assembly site for the mitotic kinetochore that couples microtubule attachment and force production to chromosome movement in mitosis. The chromatin of the centromere is specified by nucleosomes containing the histone H3 variant CENP-A. The constitutive centromeric-associated network (CCAN) and kinetochore are assembled on CENP-A chromatin to enable chromosome separation. CENP-A chromatin is surrounded by pericentromeric heterochromatin and bound by the sequence specific binding protein CENP-B. We performed mechanical experiments on mitotic chromosomes while tracking CENP-A and CENP-B to observe the centromeres stiffness and the role of the CCAN. We degraded CENP-C and CENP-N using auxin-inducible degrons, which we verified compromises the CCAN via observation of CENP-T loss. Chromosome stretching revealed that the CENP-A domain does not visibly stretch, even in the absence of CENP-C and/or CENP-N. Pericentromeric chromatin deforms upon force application, stretching approximately 3-fold less than the entire chromosome. CENP-C and/or CENP-N loss has no impact on pericentromere stretching. Chromosome-disconnecting nuclease treatments showed no structural effects on CENP-A. Our experiments show that the core-centromeric chromatin is more resilient and likely mechanically disconnected from the underlying pericentromeric chromatin, while the pericentric chromatin is deformable yet stiffer than the chromosome arms.

cell biology↗

bioRxiv2024

Physical-aware model accuracy estimation for protein complex using deep learning method

With the breakthrough of AlphaFold2 on monomers, the research focus of structure prediction has shifted to protein complexes, driving the continued development of new methods for multimer structure prediction. Therefore, it is crucial to accurately estimate quality scores for the multimer model independent of the used prediction methods. In this work, we propose a physical-aware deep learning method, DeepUMQA-PA, to evaluate the residue-wise quality of protein complex models. For the input complex model, the residue-based contact area and orientation features were first constructed using Voronoi tessellation, representing the potential physical interactions and hydrophobic properties. Then, the relationship between local residues and the overall complex topology as well as the inter-residue evolutionary information are characterized by geometry-based features, protein language model embedding representation, and knowledge-based statistical potential features. Finally, these features are fed into a fused network architecture employing equivalent graph neural network and ResNet network to estimate residue-wise model accuracy. Experimental results on the CASP15 test set demonstrate that our method outperforms the state-of-the-art method DeepUMQA3 by 3.69% and 3.49% on Pearson and Spearman, respectively. Notably, our method achieved 16.8% and 15.5% improvement in Pearson and Spearman, respectively, for the evaluation of nanobody-antigens. In addition, DeepUMQA-PA achieved better MAE scores than AlphaFold-Multimer and AlphaFold3 self-assessment methods on 43% and 50% of the targets, respectively. All these results suggest that physical-aware information based on the area and orientation of atom-atom and atom-solvent contacts has the potential to capture sequence-structure-quality relationships of proteins, especially in the case of flexible proteins. The DeepUMQA-PA server is freely available at http://zhanglab-bioinf.com/DeepUMQA-PA/.

bioinformatics↗

bioRxiv2024

A fitness distribution law for amino-acid replacements

The effect of replacing the amino acid at a given site in a protein is difficult to predict. Yet, evolutionary comparisons have revealed highly regular patterns of interchangeability between pairs of amino acids, and such patterns have proved enormously useful in a range of applications in bioinformatics, evolutionary inference, and protein design. Here we reconcile these apparently contradictory observations using fitness data from over 350,000 experimental amino acid replacements. Almost one-quarter of the 20 x 19 = 380 types of replacements have broad distributions of fitness effects (DFEs) that closely resemble the background DFE for random changes, indicating an overwhelming influence of protein context in determining mutational effects. However, we also observe that the 380 pair-specific DFEs closely follow a maximum entropy distribution, specifically a truncated exponential distribution. The shape of this distribution is determined entirely by its mean, which is equivalent to the chance that a replacement of the given type is fitter than a random replacement. In this type of distribution, modest deviations in the mean correspond to much larger changes in the probability of falling in the far right tail, so that modest differences in mean exchangeability may result in much larger differences in the chance of a highly fit mutation. Indeed, we show that under the assumption that purifying selection filters out the vast majority of mutations, the maximum entropy distributions of fitness effects inferred from deep mutational scanning experiments predict the characteristic patterns of amino acid change observed in molecular evolution. These maximum entropy distributions of mutational effects not only provide a tuneable model for molecular evolution, but also have implications for mutational effect prediction and protein engineering.

evolutionary biology↗

bioRxiv2024

LPS binding caspase activation and recruitment domains (CARDs) are bipartite lipid binding modules

Caspase-11 is an innate immune pattern recognition receptor (PRR) that detects cytosolic bacterial lipopolysaccharides (LPS) through its caspase activation and recruitment domain (CARD), triggering inflammatory cell death known as pyroptosis. Caspase-11 also detects eukaryotic (i.e. self) lipids. This observation raises the question of whether common or distinct mechanisms govern the interactions with self and nonself lipids. In this study, using biochemical, computational, and cell-based assays, we report that the caspase-11 CARD functions as a bipartite lipid-binding module. Distinct regions within the CARD bind to phosphate groups and long acyl chains of self and nonself lipids. Self-lipid binding capability is conserved across numerous caspase-11 homologs and orthologs. The symmetry in self and nonself lipid detection mechanisms enabled us to engineer an LPS-binding domain de novo, using an ancestral CARD-like domain present in the fish Amphilophus citrinellus. These findings offer critical insights into the molecular basis of LPS recognition by caspase-11 and highlight the fundamental and likely inseparable relationship between self and nonself discrimination.

immunology↗

bioRxiv2024

Mechanistic Insights into the Stimulation of the Histone H3K9 Methyltransferase Clr4 by Proximal H3K14 Ubiquitination

H3K9 methylation is an evolutionarily conserved hallmark of heterochromatin and plays crucial roles in chromosome segregation, genome stability, and gene expression regulation. Clr4 is the sole histone methyltransferase responsible for catalyzing H3K9 methylation in Schizosaccharomyces pombe. Clr4 K455/K472 automethylation and histone H3K14 ubiquitination (H3K14Ub) are vital activators of the catalytic activity of Clr4, ensuring appropriate heterochromatin deposition and preventing deleterious gene silencing. While the mechanism by which automethylation activates Clr4 was recently elucidated, the mechanism of the significantly pronounced stimulatory effect of H3K14Ub on Clr4 remains unclear. Here we determined the crystal structures of Clr4 bound to ubiquitinated and unmodified H3 peptides at resolutions of 2.60 [A] and 2.39 [A], respectively. Our structures reveal a synergistic mechanism underlying the stronger stimulatory effect by H3K14Ub compared to automethylation: site-specific ubiquitination constrained by the H3K14 linkage increases substrate affinity through multivalent interactions between ubiquitin and Clr4. Additionally, H3K14Ub facilitates the allosteric transition of Clr4 from an inactive apo conformation to a hyperactive "catalyzing state", accompanied by conformational changes in the C-SET-insertion (SI) region, complete release of the autoregulatory loop (ARL), and retraction of the {beta}9/10 loop. Finally, we propose a structural model for the Clr4 catalytic-regulatory cycle, depicting varying levels of conformational regulation mediated by automethylation and ubiquitination. This work provides structural insights into the interplay between different histone modifications and their collective impact on epigenetic regulation.

molecular biology↗

bioRxiv2024

Leveraging large language models for metabolic engineering design

Establishing efficient cell factories involves a continuous process of trial and error due to the intricate nature of metabolism. This complexity makes predicting effective engineering targets a challenging task. Therefore, it is vital to learn from the accumulated successes of previous designs for advancing future cell factory development. In this study, we developed a method based on large language models (LLMs) to extract metabolic engineering strategies from research articles on a large scale. We created a database containing over 29006 metabolic engineering entries, 1210 products and 751 organisms. Using this extracted data, we trained a hybrid model combining deep learning and mechanistic approaches to predict engineering targets. Our model outperformed traditional metabolic engineering target prediction algorithms, excelled in predicting the effects of gene modifications, and generalized well to out-of-distribution products and multiple gene combinations. Our study provides a valuable dataset, a chatbot, and an engineering target prediction model for the metabolic engineering field and exemplifies an efficient method for leveraging existing knowledge for future predictions.

systems biology↗

bioRxiv2024

Epigenetic regulation of global proteostasis dynamics by RBBP5 ensures mammalian organismal health

Proteostasis is vital for cellular health, with disruptions leading to aging, neurodegeneration and metabolic disorders. Traditionally, proteotoxic stress responses were studied as acute reactions to various noxious factors; however, recent evidence reveals that many proteostasis genes exhibit [~]12h ultradian rhythms under physiological conditions in mammals, driven by an XBP1s-dependent 12h oscillator. By examining the chromatin landscape of this oscillator, we identified RBBP5 as an essential epigenetic regulator of global proteostasis dynamics. Mechanistically, as the core subunit of the SET1/COMPASS complex, RBBP5 co-activates XBP1s to facilitate dynamic proteostasis gene expression by marking promoter-proximal H3K4me3, which further recruits the Integrator Complex and SWI/SNF chromatin remodelers. Functionally, RBBP5 is indispensable for regulating both the 12h oscillator and acute transcriptional response to various proteotoxic stresses, including ER stress and nutrient deprivation. RBBP5 ablation causes increased susceptibility to proteotoxic stress, chronic inflammation, and hepatic steatosis in mice, along with impaired autophagy and reduced cell survival in vitro. In humans, lower RBBP5 expression is associated with reduced adaptive stress-response gene expression and hepatic steatosis. Our findings not only highlight a previously unrecognized epigenetic timing mechanism distinct from circadian regulation but also establish RBBP5 as a central regulator of proteostasis, essential for cellular resilience and organismal health. One sentence summaryRBBP5 regulates global mammalian proteostasis.

cell biology↗

bioRxiv2024

Characterization the gene editing with miniature nucleases TnpB, IscB and enIscB in Escherichia coli strains

DNA nucleases TnpB and IscB were regarded as new antibacterial strategy to combat the drug-resistant bacteria represented by Escherichia coli due to its specificity in targeting DNA and smallest size, but the genome-editing of TnpB/IscB in E. coli remains unclear. This study characterized the genome-editing of TnpB/IscB in E. coli strains. First, the toxicity and cleavage results showed TnpB only worked in E. coli MG1655, while IscB and enIscB could perform in ATCC9637 and BL21(DE3). Next, TnpB-based genome-editing tool was established in MG1655, while IscB/enIscB achieved in ATCC9637/BL21(DE3). The copy number of TnpB/IscB/enIscB were changed to explore the impact of editing efficiency. Moreover, the editing plasmids were successfully cured. Finally, the escaping mechanism of E. coli under editing of TnpB/IscB was revealed. Overall, this study successfully applied TnpB/IscB/enIscB to genome-editing in E. coli, which will broaden genetic manipulation toolbox in E. coli and facilitate the development of new antimicrobial drugs.

microbiology↗

bioRxiv2024

Yeast-MetaTwin for Systematically Exploring Yeast Metabolism through Retrobiosynthesis and Deep Learning

Underground metabolism plays a crucial role in understanding enzyme promiscuity, cellular metabolism, and biological evolution, yet experimental exploration of underground metabolism is often sparse. Even though yeast genome-scale metabolic models have been reconstructed and curated for over 20 years, more than 90% of the yeast metabolome is still not covered by these models. To address this gap, we have developed a workflow based on retrobiosynthesis and deep learning methods to comprehensively explore yeast underground metabolism. We integrated the predicted underground network into the yeast consensus genome-scale model, Yeast8, to reconstruct the yeast metabolic twin model, Yeast-MetaTwin, covering 16,244 metabolites (92% of the total yeast metabolome), 2,057 metabolic genes and 59,914 reactions. We revealed that Km parameters differ between the known and underground network, identified hub molecules connecting the underground network and pinpointed the underground percentages for yeast metabolic pathways. Moreover, the Yeast-MetaTwin can predict the by-products of chemicals produced in yeast, offering valuable insights to guide metabolic engineering designs.

synthetic biology↗

bioRxiv2024

Modulation of blood-tumor barrier transcriptional programs improves intra-tumoral drug delivery and potentiates chemotherapy in GBM

Glioblastoma (GBM) is the most common malignant primary brain tumor. GBM has an extremely poor prognosis and new treatments are badly needed. Efficient drug delivery to GBM is a major obstacle as the blood-brain barrier (BBB) prevents passage of the majority of cancer drugs into the brain. It is also recognized that the blood-brain tumor barrier (BTB) in the growing tumor represents a challenge. The BTB is heterogeneous and poorly characterized, but similar to the BBB it can prevent therapeutics from reaching effective intra-tumoral doses, dramatically hindering their potential. Here, we identified a 12-gene signature associated with the BTB, with functions related to vasculature development, morphogenesis and cell migration. We identified CDH5 as a core molecule in this set and confirmed its over-expression in GBM vasculature using spatial transcriptomics of GBM patient specimens. We found that the indirubin-derivative, 6-bromoindirubin acetoxime (BIA), could downregulate CDH5 and other BTB signature genes, causing endothelial barrier disruption in endothelial monolayers and BBB 3D spheroids in vitro. Treatment of tumor-bearing mice with BIA enabled increased intra-tumoral accumulation of the BBB non-penetrant chemotherapeutic drug cisplatin and potentiated cisplatin-mediated DNA damage by targeting DNA repair pathways. Finally, using an injectable BIA nanoparticle formulation, PPRX-1701, we significantly improved the efficacy of cisplatin in patient-derived GBM xenografts and prolonged their survival. Overall, our work reveals potential targets at the BTB for improved chemotherapy delivery and the bifunctional properties of BIA as a BTB modulator and potentiator of chemotherapy, supporting its further development.

cancer biology↗

bioRxiv2024

Haplotype-resolved genome assembly of upland switchgrass provides insights into cold tolerance

Switchgrass (Panicum virgatum L.) is a bioenergy and forage crop. Upland switchgrass exhibits superior cold tolerance than lowland ecotype, but the underlying molecular mechanisms remain unclear. Here, we presented a high-quality haplotype-resolved genome of the upland ecotype Jingji31 and conducted multi-omics analysis to understand its cold tolerance. The divergence between upland and lowland ecotypes of switchgrass occurred after the differentiation of the two subgenomes (K and N). Under cold stress, the K subgenome has more differentially expressed genes (DEGs). Transcriptome analysis revealed ecotype-specific differential expressions among members of the cold-responsive (COR) gene families. Specifically, certain members of the AFB1, ATL80, HOS10, and STRS2 gene families exhibited opposite expression changes between the two ecotypes, potentially contributing to their differential cold tolerance. By using haplotype-resolved genome, we identified more cold-induced allele-specific expressions (ASEs) in the upland ecotype, and these ASEs were significantly enriched in the COR gene families. Genome-wide association study detected an association signal on Chr3K related to overwintering rate, which overlapped with a selective sweep region and contained a cytochrome P450 (CYP450) gene highly expressed under cold stress. Heterologous overexpression of CYP450 in rice alleviated leaf wilting and improved cold tolerance. Our study provides a high-quality haplotype-resolved genome of upland switchgrass, to advance conceptual understanding of plant cold tolerance for breeding crops with enhanced cold adaptation.

genomics↗

bioRxiv2024

A Self-Assembling Immune-Featured Osteosarcoma Patient/PDX Derived Organoid Model and Biobank for Personalized Immune Therapy

Osteosarcoma (OS) exhibit intra- and inter-heterogeneity, complicating the exploration of effective therapeutic strategies. Traditional in vitro and in vivo models are limited in inheriting biological and genomic heterogeneities of OS patients, even in inheriting the features on tumor microenvironment. The prolonged generation time of current models makes the drug development of OS slow and is not suitable to clinically rapid timing. Here, we introduce methods for generating and biobanking patient/PDX-derived osteosarcoma organoids (OS PD(X)Os) that recapitulate the histological, biological and genomic features of their paired OS patients. OS PD(X)Os can be generated quickly with high reliability in vitro or transplanted to immunodeficient mice. We further demonstrate an immune-featured OS PD(X)O (named iOS) model and its method for testing personalized chemotherapy response, personalized immune therapeutic strategy and target drug development, such as a novel PRMT5MTA inhibitor ARPN2169 on MTAP-deleted OS. Our studies show that iOS models maintain many typical features of OS and could be rapidly employed to investigate patient-specific therapeutic strategies. Additionally, our biobank establishes a rich resource for basic, translational and even clinical OS researches.

cancer biology↗

bioRxiv2024

Wheat TaNADPO promotes spot blotch resistance

Bipolaris sorokiniana is a common soil-borne fungal pathogen that can infect various organs of wheat (Triticum aestivum L.), causing diseases such as spot blotch, common root rot, head blight, and black point. The genetic basis of wheat resistance to B. sorokiniana is not yet fully understood. In this study, a natural population of 1,302 global common wheat germplasms was established and inoculated with B. sorokiniana at the seedling stage in a greenhouse. Resistance to spot blotch was assessed, revealing that only about 3.8% of the germplasms exhibited moderate or higher resistance levels. A genome-wide association study (GWAS) using high-density 660K single nucleotide polymorphism (SNP) data identified a region on chromosome 1BL (621.2-674.0 Mb) with 9 SNPs significantly associated (p < 10e-4) with spot blotch resistance, designated as Qsb.hebau-1BL. RNA sequencing and qRT-PCR assays showed that the gene TraesCS1B02G410300, encoding nicotinamide-adenine dinucleotide phosphate-binding oxidoreductase (TaNADPO), was significantly induced by B. sorokiniana. Five SNP variations were found in the promoter region of TaNADPO in wheat lines with or without Qsb.hebau-1BL. Transient expression of TaNADPO in Nicotiana benthamiana leaves showed a cytoplasmic subcellular localization of the fusion protein with a green fluorescent protein (GFP) tag. Wheat transgenic lines overexpressing TaNADPO exhibited significantly enhanced resistance to spot blotch compared to wildtype plants, with higher accumulation of reactive oxygen species (ROS). The knockout EMS mutant of Triticum turgidum NADPO (tdnadpo-K2561, Gln125*) showed significantly reduced resistance to spot blotch and lower ROS accumulation compared to wildtype plants. In summary, TaNADPO has been identified as a crucial gene for resistance to B. sorokiniana, providing valuable insights for developing spot blotch-resistant wheat varieties through molecular breeding techniques.

genetics↗

bioRxiv2024

A multimodal fMRI dataset unifying naturalistic processes with a rich array of experimental tasks

Cognitive neuroscience has advanced significantly due to the availability of openly shared datasets. Large sample sizes, large amounts of data per person, and diversity in tasks and data types are all desirable, but are difficult to achieve in a single dataset. Here, we present an open dataset with N = 101 participants and 6 hours of scanning per participant, with 6 multifaceted cognitive tasks including 2 hours of naturalistic movie viewing. This datasets combination of ample sample size, extensive data per participant, more than 600 iso hours worth of data, and a wide range of experimental conditions -- including cognitive, affective, social, and somatic/interoceptive tasks -- positions it uniquely for probing important questions in cognitive neuroscience.

neuroscience↗

bioRxiv2024

Neuronal DNA repair reveals strategies to influence CRISPR editing outcomes

Genome editing is poised to revolutionize treatment of genetic diseases, but poor understanding and control of DNA repair outcomes hinders its therapeutic potential. DNA repair is especially understudied in nondividing cells like neurons, which must withstand decades of DNA damage without replicating. This lack of knowledge limits the efficiency and precision of genome editing in clinically relevant cells. To address this, we used induced pluripotent stem cells (iPSCs) and iPSC-derived neurons to examine how postmitotic human neurons repair Cas9-induced DNA damage. We discovered that neurons can take weeks to fully resolve this damage, compared to just days in isogenic iPSCs. Furthermore, Cas9-treated neurons upregulated unexpected DNA repair genes, including factors canonically associated with replication. Manipulating this response with chemical or genetic perturbations allowed us to direct neuronal repair toward desired editing outcomes. By studying DNA repair in postmitotic human cells, we uncovered unforeseen challenges and opportunities for precise therapeutic editing.

molecular biology↗

bioRxiv2024

Functional imaging of whole mouse embryonic development in utero

Despite significant advances in structural and genetic studies, investigations of early embryonic functions, such as brain activity, have long been constrained by technical challenges. Functional ultrasound (fUS) has emerged as a breakthrough modality, enabling real-time monitoring of brain activity with exceptional spatial and temporal resolution and offering unprecedented opportunities for studying functional embryonic development. In this study, we used fUS to monitor whole-embryo activity in mice from embryonic days E8.5 to E18.5, revealing patterns of neural activity throughout embryogenesis. This approach provides new opportunities to explore brain development dynamically as it unfolds. Moreover, we observed embryo responses to external stimuli, including sound, in both mice and cynomolgus macaques, offering insights into early sensory processing and neural maturation. In summary, our study establishes fUS as a powerful tool for studying embryonic brain functional development, with significant implications for scientific research, especially in non- human primate models, and clinical applications.

developmental biology↗

bioRxiv2024

Asymmetric binding of coactivator SRC1 to FXR-RXR and allosteric communication within the complex

Farnesoid X receptor (FXR) is a promising target for treatment of metabolic associated fatty liver disease (MAFLD). In this study, we employed an integrative approach to investigate the interaction between FXR-RXR-hSHP-1 complex and the entire coactivator SRC1-NRID (nuclear receptor interaction domain). We constructed a multi-domain model of FXR120-RXR98-hSHP-1, highlighting the interface between FXR-DBD and LBD. Using HDX-MS, XL-MS, and biochemical assays, we revealed the allosteric communications in FXR-RXR-hSHP-1 upon agonist and DNA binding. We then demonstrated that SRC1 binds only to the coactivator binding surface of FXR within the FXR-RXR heterodimer, with the NR-box2 and NR-box3 of SRC1 as the key binding motifs. Our findings, which provide the first model of SRC1-NRID in complex with FXR-RXR-hSHP-1, shed light on the molecular mechanism through which the coactivator asymmetrically interacts with nuclear receptors and provide structural basis for further understanding the function of FXR and its implications in diseases.

biophysics↗