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Hu, S.

Publications and source records attributed to Hu, S..

At least 55 records · Page 3Linked to original sources

Post-replicative initial expression of the cell fate regulator PAX6 during neuroectoderm differentiation

The development of multicellular organisms requires precise coordination between cell division and differentiation. Cell division generates the necessary number of cells, while differentiation creates distinct cell identities, forming tissues and organs. The transcription factors SOX2 and PAX6 specify neuroepithelial cells, the earliest neural progenitor cells (NPCs) during brain development. How lineage specification is coordinated with the cell cycle is not fully understood. Here, we show that PAX6 expression occurs during a narrow time window--between 48 and 72 hours--after neural induction of human embryonic stem cells (ESCs). Flow cytometry analyses and time-lapse imaging further show that PAX6 expression starts during the G2 phase of the cell cycle. We identify a novel 500-bp PAX6 promoter that drives its G2-specific expression. PAX6 expression is independent of known regulators of cell-cycle-dependent transcription, suggesting the existence of a novel mechanism. S-phase block by hydroxyurea prevents PAX6 expression and differentiation into NPC. Thus, NPC fate specification is coupled to cell cycle progression and occurs after the completion of DNA replication. This post-replicative lineage commitment ensures the creation of two daughter cells of identical cell fate following cell division.

cell biology↗

Molecular insights into nucleocapsid assembly and transport in Marburg and Ebola viruses

Live-cell imaging enables visualization of the spatiotemporal dynamics of signals in cells. The intracytoplasmic movement of nucleocapsids is crucial during the lifecycle of enveloped viruses, but the molecular mechanisms governing their assembly and transport are not fully understood. Using a MARV live-cell imaging system, we identified three nucleocapsid proteins--NP, VP35, and VP24--that are necessary and sufficient to form transport-competent nucleocapsid-like structures (NCLSs). These findings are consistent with observations in Ebola virus (EBOV). Interestingly, despite incompatibility among these proteins, VP30 interacts with nucleocapsid proteins from both MARV and EBOV, supporting viral transcription and replication in heterologous systems. Furthermore, we show that the conserved PPxPxY motif at the C-terminus of NP regulates NP-VP30 interactions in both homologous and heterologous contexts, and is crucial for VP30 association with NCLSs. Because this motif is conserved across filoviruses, it represents a promising target for antiviral development. Our findings advance the understanding of nucleocapsid formation and offer new avenues for therapeutic intervention against MARV and EBOV.

microbiology↗

Boundary-guided cell alignment drives mouse epiblast maturation

Symmetry breaking and pattern formation are critical events that occur throughout embryonic development. In early mouse development, a mass of non-polarized epiblast (EPI) cells in the blastocyst forms the egg-cylinder, while cells become apico-basally polarized and build a radial configuration. Yet, what drives the formation of this tissue architecture remains unclear. Here, we demonstrate that orientational patterning of EPI cells is dictated by heterogeneous tissue boundaries, which then defines central lumen positioning. We show that EPI cells progressively orient perpendicular to the visceral endoderm (VE) boundary enriched with laminin and active integrin {beta}1, but parallel to the extraembryonic ectoderm interface. These orientation dynamics are consistent with general boundary-induced alignment effects in polar materials, with a topological defect predicting the position where the pro-amniotic cavity nucleates. Knockout of laminin {gamma}1 and integrin {beta}1 confirms the essential role of adhesion at the EPI-VE-boundary. The established EPI pattern, in turn, facilitates ERK activation to ensure proper EPI maturation. Together, these findings present the mechanistic basis and functional significance of EPI tissue patterning.

developmental biology↗

Construction of Complete Telomere-to-Telomere Genome Assembly of the Rabbit Using Haploid Embryonic Stem Cells

The rabbit owns commercial importance in meat and fur production, and also has long served as a valuable animal model in biomedical research. Yet, the complete assembly of a high-quality rabbit reference genome has not been established. Here, we present a telomere-to-telomere (T2T) genome assembly of the New Zealand White (NZW) rabbit, the most complete and accurate rabbit genome to date. Using a haploid embryonic stem cells (haESCs) to overcame the challenges of homologous sequence interference and structural variation, we generate a genome with a contig N50 of 137.71 Mb, anchoring all chromosomes with only three gaps, through integrating long-read sequencing (PacBio HiFi, Oxford Nanopore), Hi-C, and Illumina data. Quality assessments reveal near-complete coverage of the BUSCO mammalian gene set, with 99.61% completeness. Notably, this complete assembly allowed for the first comprehensive annotation of the rabbit immunoglobulin loci and major histocompatibility complex region, which were previously unresolved in earlier genome versions. The NZW-T2T assembly based on haESCs not only provides a critical resource for advancing rabbit-based research, but also set a new benchmark for de novo genome assembly for other animals with complex genome.

genomics↗

WDR81 represses IKK mediated expression of pro-survival genes to regulate apoptosis

Apoptosis is a common host response to virus infection. The extent and timing of apoptosis following infection is controlled by the balance between the strength of signals that activate death signaling and those that promote the survival of cells. In many cell types, infection with Mammalian orthoreovirus (reovirus) results in induction of cell death by apoptosis late in infection. In this study, we uncovered that WD repeat-containing protein 81 (WDR81) is required for apoptosis induction after reovirus infection. The requirement for WDR81 for apoptosis induction is not unique to reovirus because cells lacking WDR81 are also resistant to apoptosis induced by other agonists that trigger the extrinsic apoptotic pathway. We find that in cells deficient in WDR81, expression of several pro-survival genes is upregulated. The expression of these genes is controlled by the inhibitor of kB kinase complex (IKK)-Nuclear Factor of kB (NF{kappa}B) signaling pathway. When IKK signaling is blocked in WDR81-deficient cells, pro-survival gene expression is restored to normal levels and the cells regain their susceptibility to reovirus-induced death receptor-triggered apoptosis. Our work uncovers a new function for WDR81 in controlling apoptosis. Additionally, it reveals a previously unknown link between endosomally localized protein WDR81 and IKK-NF{kappa}B signaling. Author SummaryVirus infection often results in death of the infected cells. Cell death prior to generation of virus progeny limits the spread of infection to neighboring cells and therefore can be beneficial to the host. However, cell death might also cause tissue destruction and could contribute to viral disease. It is therefore important to understand how cell death is controlled. Here, we uncover a cell death regulating role for WDR81 - a cellular protein that has not been previously implicated in affecting cell death. We find that when this protein is absent, cells express a much greater level of survival signals. These survival signals prevent efficient induction of cell death. By investigating how these survival signals are expressed, we reveal a new link between WDR81 and NF{kappa}B, a well-known cellular survival pathway.

microbiology↗

Homoharringtonine Promotes FTO Degradation to Suppress LILRB4-Mediated Immune Evasion in Acute Monocytic Leukemia

Acute monocytic leukemia (AML-M5), a subtype of acute myeloid leukemia, is a highly aggressive malignancy characterized by a poor prognosis, primarily due to the ability of leukemic cells to evade immune surveillance. In this study, we demonstrate that homoharringtonine (HHT), an FDA-approved therapeutic agent for chronic myeloid leukemia (CML), inhibits this immune evasion by targeting the FTO/m6A/LILRB4 signaling pathway in monocytic AML. Utilizing RNA sequencing (RNA-seq) and various functional assays, we reveal that HHT treatment significantly reduces LILRB4 expression at both the RNA and protein levels, suggesting that the effects of HHT on LILRB4 are distinct from its well-established role as a protein synthesis inhibitor. Mechanistically, HHT treatment markedly increases global levels of RNA m6A in THP-1 cells by promoting the degradation of FTO, which subsequently diminishes the expression of its downstream targets, MLL1 and LILRB4. Furthermore, in vitro and in vivo analyses employing monocytic AML cell lines, mouse-derived AML xenograft models, and patient samples collectively support the conclusion that HHT suppresses immune evasion in monocytic AML by reducing LILRB4 expression. Importantly, the downregulation of LILRB4 resulting from HHT treatment enhances the susceptibility of THP-1 cells to CD8+ T cell cytotoxicity, accompanied by increased markers of immune activation. Overall, our findings position HHT as a promising clinical agent for enhancing CD8+ T cell-based cancer immunotherapy by mitigating immune evasion in monocytic AML. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=147 HEIGHT=200 SRC="FIGDIR/small/643466v1_ufig1.gif" ALT="Figure 1"> View larger version (20K): org.highwire.dtl.DTLVardef@e72e5dorg.highwire.dtl.DTLVardef@19519aeorg.highwire.dtl.DTLVardef@1c8f786org.highwire.dtl.DTLVardef@f2a963_HPS_FORMAT_FIGEXP M_FIG C_FIG

cancer biology↗

KcatNet: advancing genome-wide enzyme turnover number prediction through structural enzymatic characterization

Enzyme turnover numbers (Kcat) are fundamental kinetic constants that quantify enzymatic efficiency. Systematic studies of Kcat are essential for characterizing the mechanisms underlying proteomic composition and cellular metabolism. However, experimental measurements of Kcat remain limited and prone to noise. To address this, we present KcatNet, a geometric deep learning model designed for high-throughput prediction of Kcat in metabolic enzymes across all organisms, leveraging paired enzyme sequence and substrate representations. KcatNet consistently outperforms existing predictors, particularly for enzymes with high catalytic efficiency, and demonstrates strong generalization to enzymes that are dissimilar to those in the training set. Furthermore, KcatNet uncovers structural mechanisms and interaction patterns within enzyme-substrate complexes, providing insights into architectural principles that are inaccessible with existing methods by harnessing the representational power of large-scale protein language models. We applied KcatNet to genome-scale Kcat prediction across diverse yeast species, improving proteome allocation predictions by integrating its outputs into metabolic models. Experimental validation further confirmed the models ability to identify enzyme mutants with enhanced activity. By bridging the gap between sequence, structure, and function, KcatNet establishes a robust foundation for advancing understanding of molecular-level mechanisms and accelerating enzyme engineering efforts.

bioinformatics↗

FveTRM5 plays a critical role in regulating fruit shape in woodland strawberry

Cultivated strawberry is a globally important fruit crop with high economic value. Fruit shape contributes to fruit quality and diversity and is a target for breeding, but very few regulatory genes have been reported in strawberry. Here, we identified an ethyl methanesulfonate (EMS) round fruit (rf) mutant that produces round or flat fruits in woodland strawberry. The primary candidate point mutation is located in the second exon of FvH4_2g22810, causing a premature stop codon at residue 266. This gene encodes a protein with a high similarity to TON1 RECRUITING MOTIF 5 (TRM5) and has therefore been named FveTRM5. Transformation of FveTRM5pro:FveTRM5 into rf could rescue the round fruit phenotype, suggesting that FveTRM5 is responsible for rf. Overexpression of FveTRM5 produced elongated organs in both Arabidopsis and woodland strawberry, suggesting a conserved role in different species. FveTRM5 is ubiquitously expressed with higher levels in developing organs. Observation of cell shape showed that FveTRM5 promotes cell elongation and inhibits cell division in the medial-lateral direction in the receptacle. The FveTRM5 protein localized to microtubules. In conclusion, our results suggest that FveTRM5 plays an essential role in regulating strawberry fruit shape by influencing cell elongation and cell division, providing an excellent target gene for breeding new fruit shape cultivars.

plant biology↗

Epithelial-mesenchymal transition couples with cell cycle arrest at various stages

Numerous computational approaches have been developed to infer cell state transition trajectories from snapshot single-cell data. Most approaches first require projecting high-dimensional data onto a low-dimensional representation; however, this can distort the dynamics of the system. Using epithelial-to-mesenchymal transition (EMT) as a test system, we show that both biology-guided low-dimensional representations and trajectory simulations in high-dimensional state space, not representations obtained with brute force dimensionality-reduction methods, reveal two broad paths of TGF-{beta} induced EMT. The paths arise from the coupling between cell cycle and EMT at either the G1 or G2/M phase, contributing to cell-cycle related EMT heterogeneity. Subsequent multi-plex immunostaining studies confirmed the multiple predicted paths at the protein level. The present study highlights the heterogeneity of EMT paths, emphasizes that caution should be taken when inferring transition dynamics from snapshot single-cell data in two- or three-dimensional representations, and shows that incorporating dynamical information can improve prediction accuracy.

systems biology↗

Leopard Cats Occupied Human Settlements in China for 3,500 years before the Arrival of Domestic cats in 600-900 CE around the Tang Dynasty

The earliest cats in human settlements in China were not domestic cats (Felis catus), but native leopard cats (Prionailurus bengalensis). To trace when and how domestic cats arrived in East Asia, we analyzed 22 feline bones from 14 sites across China spanning 5,000 years. Nuclear and mitochondrial genomes revealed that leopard cats began occupying anthropogenic scenes around 5,400 years ago and last appeared in 150 CE. Following several centuries gap of archeological feline remains, the first known domestic cat (706-883 CE) in China was identified in Shaanxi during the Tang Dynasty. Genomic analysis suggested a white or partially white coat and a link to a contemporaneous domestic cat from Kazakhstan, indicating a likely dispersal route via the Silk Road. The two felids once independently occupied ancient anthropogenic environments in China but followed divergent paths and reached different destinations in human-animal interactions.

evolutionary biology↗

Solubilization of Membrane Proteins using designed protein WRAPS

The development of therapies and vaccines targeting integral membrane proteins has been complicated by their extensive hydrophobic surfaces, which can make production and structural characterization difficult. Here we describe a general deep learning-based design approach for solubilizing native membrane proteins while preserving their sequence, fold, and function using genetically encoded de novo protein WRAPs (Water-soluble RFdiffused Amphipathic Proteins) that surround the lipid-interacting hydrophobic surfaces, rendering them stable and water-soluble without the need for detergents. We design WRAPs for both beta-barrel outer membrane and helical multi-pass transmembrane proteins, and show that the solubilized proteins retain the binding and enzymatic functions of the native targets with enhanced stability. Syphilis vaccine development has been hindered by difficulties in characterizing and producing the outer membrane protein antigens; we generated soluble versions of four Treponema pallidum outer membrane beta barrels which are potential syphilis vaccine antigens. A 4.0 [A] cryo-EM map of WRAPed TP0698 is closely consistent with the design model. WRAPs should be broadly useful for facilitating biochemical and structural characterization of integral membrane proteins, enabling therapeutic discovery by screening against purified soluble targets, and generating antigenically intact immunogens for vaccine development.

biochemistry↗

Food pairing independently associated with cardiometabolic traits beyond dietary patterns across western and eastern populations

Cardiometabolic health is closely linked to diet. Both specific food choices and dietary indices are commonly used to guide cardiometabolic protection strategies. However, the balance between foods may also significantly impact cardiometabolic health. Here, we explore the balance and imbalance in long-term dietary food intake to quantify food pairing patterns (FPs), providing insights beyond conventional dietary indices and single-food intake frequencies. Using data from our GGMP (n = 6,994) and the NHANES (n = 7,350) cohorts, we observed that long-term food pairing patterns are independent of single food intake frequency and dietary indices. We identified 1,759 and 306 cardiometabolic-related long-term food pairing patterns from two cohorts (FDR < 0.05), respectively. Notably, around 80% of these pairing foods not individually associated with cardiometabolic traits, and food pairing pattern associations with cardiometabolic traits at hyper food group level were consistent across Eastern and Western populations. Besides, mediation analysis revealed that 72.7% of long-term food pairing patterns affected cardiometabolic traits through 31 microbial genera, with Clostridiumsensustricto1 playing a predominant role. Moreover, multi-step mediation analysis found that microbes mediated the impact of long-term food pairing patterns on cardiometabolic traits primarily through their metabolic pathways, such as pyruvate fermentation to propanoate and ergothioneine biosynthesis pathways. Our data suggest that balance between dietary foods is broadly associated with cardiometabolic traits by modulating gut microbial functionalities, in contrast to the lower occurrence when considering individual foods in isolation. These results offer a novel perspective for designing personalized dietary strategies beyond present dietary indices to enhance cardiometabolic health.

microbiology↗

The genetic diversity and populational specificity of the human gut virome at single nucleotide resolution

Large-scale characterization of gut viral genomes provides strain-resolved insights into host-microbe interactions. However, existing viral genomes are mainly derived from Western populations, limiting our understanding of global gut viral diversity and functional variations necessary for personalized medicine and addressing regional health disparities. Here, we introduce the Chinese Gut Viral Reference (CGVR) set, consisting of 120,568 viral genomes from 3,234 deeply sequenced fecal samples collected nationwide, covering 72,751 viral species-level clusters (VSCs), nearly 90% of which are absent from current databases. Analysis of single nucleotide variations (SNVs) in 233 globally prevalent VSCs revealed that 18.9% showed significant genetic stratification between Chinese and non-Chinese populations, potentially linked to bacterial infection susceptibility. The predicted bacterial hosts of population-stratified viruses exhibit distinct genetic components associated with health-related functions, including multidrug resistance. Additionally, viral strain diversity at the SNV level correlated with human phenotypic traits, such as age and gastrointestinal issues like constipation. Our analysis also indicates that the human gut bacteriome is specifically shaped by the virome, which mediates associations with human phenotypic traits. This foundational resource underscores the unique genetic makeup of the gut virome across populations and emphasizes the importance of recognizing gut viral genetic heterogeneity for deeper insights into regional health implications.

microbiology↗

Deficiency of DDI2 suppresses liver cancer progression byworsening cell survival conditions

The levels of reactive oxygen species (ROS) and the extent of ensuing DNA damage significantly influence cancer initiation and progression. Of crucial importance, the aspartate protease DDI2 has been proposed to play a pivotal role in monitoring intracellular ROS levels (to trigger oxidative eustress or distress), as well as in the oxidative DNA damage repair, through redox homeostasis-determining factor Nrf1 (encoded by NFE2L1). However, the specific role of DDI2 in the multi-step process resulting in the development and progression of liver cancer remains elusive to date. In the present study, we employed the CRISPR/Cas9 gene editing system to create two nuanced lines of DDI2 knockout (i.e., DDI2-/- and DDI2insG/-) from liver cancer cells. Subsequent experiments indicate that the knockout of DDI2 leads to increased ROS levels in hepatoma cells by downregulating two major antioxidant transcription factors Nrf1 and Nrf2 (encoded by NFE2L2), exacerbating endogenous DNA damages caused by ROS and not-yet-identified factors, thereby inhibiting cell proliferation and promoting apoptosis, and ultimately hindering in vivo malignant growth of xenograft tumor cells. Conversely, the restoration of DDI2 expression reverses the accumulation of ROS and associated DNA damage caused by DDI2 knockout, eliminating the subsequent inhibitory effects of DDI2 deficiency on both in vitro and in vivo growth of liver cancer cells. Collectively, these findings demonstrate that DDI2 deficiency impedes liver tumor growth by disrupting its survival environment, suggesting that DDI2 may serve as a novel therapeutic target for anti-cancer strategies aimed at modulating ROS or DNA damage processes.

cancer biology↗

UltimateSynth: MRI Physics for Pan-Contrast AI

Magnetic resonance imaging (MRI) is commonly used in healthcare for its ability to generate diverse tissue contrasts without ionizing radiation. However, this flexibility complicates downstream analysis, as computational tools are often tailored to specific types of MRI and lack generalizability across the full spectrum of scans used in healthcare. Here, we introduce a versatile framework for the development and validation of AI models that can robustly process and analyze the full spectrum of scans achievable with MRI, enabling model deployment across scanner models, scan sequences, and age groups. Core to our framework is UltimateSynth, a technology that combines tissue physiology and MR physics in synthesizing realistic images across a comprehensive range of meaningful contrasts. This pan-contrast capability bolsters the AI development life cycle through efficient data labeling, generalizable model training, and thorough performance benchmarking. We showcase the effectiveness of UltimateSynth by training an off-the-shelf U-Net to generalize anatomical segmentation across any MR contrast. The U-Net yields highly robust tissue volume estimates, with variability under 4% across 150,000 unique-contrast images, 3.8% across 2,000+ low-field 0.3T scans, and 3.5% across 8,000+ images spanning the human lifespan from ages 0 to 100.

bioinformatics↗

The mechanisms by which miRNAs critically contribute to differential roles of Nrf1 and Nrf2 in modulating the epithelial-mesenchymal transformation of hepatocellular carcinoma

Accumulation of various genetics and epigenetics alterations are accepted to result in the initiation and progression of hepatocellular carcinoma (HCC), and its high metastasis is viewed as a critical bottleneck leading to its treatment failure. Amongst them, the abnormal expression of several microRNAs arising from lack of antioxidant transcription factor Nrf2 (encoded by Nfe2l2) leads to cancer metastasis. However, much less known is about regulation of microRNAs by Nrf1 (encoded by Nfe2l1), even though it acts as an essential determinon of cell homeostasis by governing the transcriptional expression of those driver genes contributing to the epithelial-mesenchymal transition (EMT) involved in its metastasis. In this study, distinctive EMT phenotypes were unveiled to result from specific knockout of Nrf1 and Nrf2 in HepG2 cells, as accompanied by differential migratory and invasive capabilities. The Nrf1-/--leading EMT results from a significantly decrease in the epithelial CDH1 expression, plus another increased expression of the mesenchymal CDH2. Such distinct phenotypes of Nrf1-/- from Nrf2-/- cell lines were also attributable to differential regulation of two key microRNAs, i.e., miR3187-3P and miR1247-5p. Further experiments unraveled that Nrf1 activates the expression of miR-3187-3p, directly targeting for the inhibition of SNAI1, leading to CDH1 activation but CDH2 inhibition insomuch as to prevent the process of EMT. By contrast, Nrf2 inhibits the expression of miR1247-5p, relieving its inhibitory effect on MMP15 and MMP17 to promote the EMT. Collectively, these demonstrate that the EMT of liver cancer cells is likely prevented by Nrf1 via the miR3187-3P signaling to the SNAI1-CDH1/2 axis, but conversely promoted by Nrf2 through the miR1247-5p-MMP15/17 signaling axis.

molecular biology↗

In situ Membrane Protein Expression by Efficient Recruitment of mRNA to the Membranes of Synthetic Cells

The synthesis of artificial cells is crucial for understanding the origins of life. In synthetic cells, however, the absence of membrane-bound organelles and auxiliary proteins severely limits the efficient expression and precise localization of membrane proteins using cell-free expression systems. Here we introduce a robust method that significantly enhances membrane protein synthesis by recruiting mRNA to phospholipid membranes. This is achieved through the use of cholesterol-modified, single-stranded DNA that anchors to the membrane and pairs with the mRNAs untranslated region. This strategic placement facilitates the assembly of protein expression machinery, promoting direct co-translational folding at the membrane. Our approach not only ensures correct protein topology and functionality but also demonstrates broad applicability for the in situ expression of various membrane proteins. It effectively addresses the challenges of membrane protein localization and assembly in synthetic cells, showcasing its versatility for synthesizing a wide array of membrane proteins.

synthetic biology↗

SPP1+ tumor-associated macrophages induce radioresistance of nasopharyngeal carcinoma through crosstalk with the tumor microenvironment

The function and phenotype of tumor-associated macrophages (TAMs) influence the efficacy of radiotherapy. However, the effect of different subsets of TAMs on the radioresistance in nasopharyngeal carcinoma (NPC) still needs to be further explored. This study utilized single-cell RNA sequencing (scRNA-seq) to analyze 120,579 cells obtained from 15 NPC samples. Cell annotation, cell-cell communication analysis, and functional annotation were used to investigate the impact of TAMs on the effectiveness of radiotherapy in NPC patients. Additionally, we employed RNA-seq data and clinical information from many patients, including 24 NPC samples from Zhujiang Hospital, 3,934 samples from patients with a history of radiotherapy, for further validation. We identified a hub TAM subpopulation, SPP1+ TAMs, that induced radioresistance in NPC based on single-cell RNA sequencing (scRNA-seq) data. We combined many public datasets to confirm their prognostic value in radiotherapy patients. We found that SPP1+ TAMs had stronger protumorigenic and immunosuppressive effects in the postradiotherapy recurrent tumor (PRRT) group. SPI1 transcription factor efficiently regulates the expression level of SPP1 in macrophages. In addition, we validated the underlying mechanisms by molecular docking, multiplex immunofluorescence and cellular experiments. In conclusions, by forming an immunosuppressive microenvironment and promoting tumor cell proliferation, SPP1+ TAMs leading to radioresistance and poor clinical prognosis in NPC patients. Targeting SPP1+ TAMs could provide new insights into improving the efficacy of radiotherapy in NPC patients.

cancer biology↗