Biology subjects

Cui, T.

Publications and source records attributed to Cui, T..

34 records · Page 2Linked to original sources

bioRxiv2023

RealSeq2: a software integrated with UMI identification, error correction, and methylation modifications storing

High-throughput UMI technology sequencing is widely used in early tumor screening, detection, recurrence monitoring, etc. Detecting extremely low-frequency mutations is especially important for monitoring tumor recurrence, so high-precision data, as well as high-quality data, are required. We developed RealSeq2, a new integrated data-preprocessing software based on fastp and gencore, to achieve adapter removal, quality control, UMI identification, and generate consensus reads by clustering and error correction using multithreading in high-throughput next-generation sequencing background. RealSeq2 also supports methylation data of 5-methylcytosine bisulfite-free sequencing. RealSeq2 defined a new tag in SAM for storing methylation information, which is beneficial for co-identifying methylation sites and mutation sites for downstream analysis. RealSeq2 includes three submodules: ReadsProfiler, ReadsCleaner, and ReadsRecycler. In addition, the output format file (BAM or SAM) is universal for downstream analyses. RealSeq2 is the preferred upstream analysis software for the co-detection of ultra-low frequency mutations and bisulfite-free methylation data. The error profile provides data support for downstream analysis. Additionally, XM tags will become a standard protocol for recording methylation signals.

bioinformatics↗

bioRxiv2023

SeMOE allows for quantitative glycan perception and exhibits anti-cancer potentiality

Metabolic oligosaccharide engineering (MOE) is a classical chemical approach to perturb, profile and perceive glycans in physiological systems, but probes upon bioorthogonal reaction require accessibility and background signal readout makes it challenging to achieve absolute glycan quantification. Here we develop SeMOE, a selenosugar-based metabolic oligosaccharide engineering strategy that combines elemental analysis and MOE to enable the absolute quantification and mass spectrometric imaging of glycome in a concise procedure. We demonstrate that SeMOE probes allow for perception, absolute quantification and visualization of glycans in diverse biological contexts. We demonstrate that chemical reporters on conventional MOE can be integrated into a bifunctional SeMOE probe to provide multimodality signal readouts. We further show the anti-cancer potentiality of SeMOE probes. SeMOE thus provides a convenient and simplified method to "see more" of the glyco-world.

bioengineering↗

bioRxiv2023

Decoding human in vitro terminal erythropoiesis originating from umbilical cord blood mononuclear cells and pluripotent stem cells

Ex vivo RBC production generates unsatisfactory expansion, {beta}-globin expression, and maturation of erythroid cells. The underlying mechanisms behind these limitations and ex vivo terminal erythropoiesis from different origins are largely unexplained. In this study, we mapped an atlas of ex vivo terminally differentiated cells from umbilical cord blood mononuclear cells (UCBMNs) and pluripotent stem cells (PSCs), and observed the differential regulatory dynamics of erythropoiesis from these two origins at a single-cell resolution. We detected the presence of hematopoietic stem progenitor cells (HSPCs), erythroid progenitor (e.g., CFU-E), and non-erythroid cells (e.g., macrophages) in the terminal populations. We observed that UCBMN-derived erythropoiesis is more active than PSC-derived erythropoiesis in terms of the cell cycle, stress erythropoiesis, and autophagy at single cell resolution, which may provide new insights into the limitations in cell expansion, globin expression, and maturation in ex vivo RBC production, respectively. We verified that a stress-erythropoiesis-related gene, TRIB3, increases the expression of globin genes in ex vivo erythropoiesis. As the major unexpected component detected in terminally differentiated cells, CFU-E were further characterized as having high- or low- expansion capacity based on CD99 expression, which generally decreased over erythropoiesis. By inhibiting CD99 gene expression using antagonists, we increased reticulocyte production in the population. Heterogeneous CFU-Es also exist in bone marrow. Moreover, decreased CD99 expression mediates the interactions between macrophages and CFU-E during ex vivo erythropoiesis. Overall, our results provide a reference for facilitating the development of strategies to improve ex vivo RBC regeneration. HighlightsO_LIWe performed scRNA-seq and cell typing of late stage UCBMN- and PSC-derived cells C_LIO_LIStress erythropoiesis, autophagy and cell cycle related gene expression different in two origins C_LIO_LICD99high progenitor cells are a proliferating colony forming unit erythroid subpopulation C_LI

cell biology↗

bioRxiv2023

The SARS-CoV-2 Spike protein induces long-term transcriptional perturbations of mitochondrial metabolic genes, causes cardiac fibrosis, and reduces myocardial contractile in obese mice

BackgroundAs the pandemic evolves, post-acute sequelae of CoV-2 (PACS) including cardiovascular manifestations have emerged as a new health threat. This study aims to study whether the Spike protein plus obesity can exacerbate PACS-related cardiomyopathy. MethodsA Spike protein-pseudotyped (Spp) virus with the proper surface tropism of SARS-CoV-2 was developed for viral entry assay in vitro and administration into high fat diet (HFD)-fed mice. The systemic viral loads and cardiac transcriptomes were analyzed at 2 and 24 hrs, 3, 6, and 24 weeks post introducing (wpi) Spp using RNA-seq or real time RT-PCR. Echocardiography was used to monitor cardiac functions. ResultsLow-density lipoprotein cholesterol enhanced viral uptake in endothelial cells, macrophages, and cardiomyocyte-like H9C2 cells. Selective cardiac and adipose viral depositions were observed in HFD mice but not in normal-chow-fed mice. The cardiac transcriptional signatures in HFD mice at 3, 6, and 24 wpi showed systemic suppression of mitochondria respiratory chain genes including ATP synthases and nicotinamide adenine dinucleotide:ubiquinone oxidoreductase gene members, upregulation of stress pathway-related crucial factors such as nuclear factor-erythroid 2-related factor 1 and signal transducer and activator of transcription 5A, and increases in expression of glucose metabolism-associated genes. As compared with the age-matched HFD control mice, cardiac ejection fraction and fractional shortening were significantly decreased, while left ventricular end-systolic diameter and volume were significantly elevated, and cardiac fibrosis was increased in HFD mice at 24 wpi. ConclusionOur data demonstrated that the Spike protein could induce long-term transcriptional suppression of mitochondria metabolic genes and cause cardiac fibrosis and myocardial contractile impairment, providing mechanistic insights to PACS-related cardiomyopathy.

microbiology↗

bioRxiv2022

Inactivation of Vascular Stem Cells Suppresses Intimal Hyperplasia in Vein Grafts

Chronic vein graft (VG) failure (VGF) is associated with VG intimal hyperplasia characterized by abnormal proliferation and accumulation of vascular smooth muscle cells (SMCs), which are derived predominantly from pre-existing vascular SMCs via a process of vascular SMC dedifferentiation.1 Therapeutic approaches focused on vascular SMCs, however, have not changed chronic VGF rates,2 indicating additional and yet unrecognized causes of chronic VGF. Herein, we uncover a novel diagram in which after transplantation, recipient vascular stem cells (VSCs) expressing Sca1 are activated and accumulated in the adventitia of VGs, and they do not differentiate into SMCs but promote intimal hyperplasia via paracrine enforcement of medial SMC dedifferentiation into synthetic SMCs in VGs, suggesting that VSCs may be a novel target for the treatment of chronic VGF.

cell biology↗

bioRxiv2022

The Spike protein of SARS-CoV-2 impairs lipid metabolism and increases susceptibility to lipotoxicity: implication for a role of Nrf2

Background/objectivesCoronavirus disease 2019 (COVID-19) patients exhibit lipid metabolic alterations, but the mechanism remains unknown. In this study, we aimed to investigate whether the Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) impairs lipid metabolism in host cells. MethodsA Spike cell line in HEK293 was generated using the pcDNA vector carrying the Spike gene expression cassette. A control cell line was generated using the empty pcDNA vector. Gene expression profiles related to lipid metabolic, autophagic, and ferroptotic pathways were investigated. Palmitic acid (PA)-overload was used to assess lipotoxicity-induced necrosis. ResultsAs compared with controls, the Spike cells showed a significant increase in lipid depositions on cell membranes as well as dysregulation of expression of a panel of molecules involved lipid metabolism, autophagy, and ferroptosis. The Spike cells showed an upregulation of nuclear factor erythroid 2-related factor 2 (Nrf2), a multifunctional transcriptional factor, in response to PA. Furthermore, the Spike cells exhibited increased necrosis in response to PA-induced lipotoxicity compared to control cells in a time- and dose-dependent manner via ferroptosis, which could be attenuated by the Nrf2 inhibitor trigonelline. ConclusionsThe Spike protein impairs lipid metabolic and autophagic pathways in host cells, leading to increased susceptibility to lipotoxicity via ferroptosis which can be suppressed by a Nrf2 inhibitor. This data also suggests a central role of Nrf2 in Spike-induced lipid metabolic impairments. HighlightsO_LIThe Spike protein increases lipid deposition in host cell membranes C_LIO_LIThe Spike protein impairs lipid metabolic and autophagic pathways C_LIO_LIThe Spike protein exaggerates PA-induced lipotoxicity in host cells via ferroptosis C_LIO_LINrf2 inhibitor Trigonelline can mitigate the Spike protein-induced necrosis C_LI

cell biology↗

bioRxiv2021

Improving Neural Networks for Genotype-Phenotype Prediction Using Published Summary Statistics

Phenotype prediction is a necessity in numerous applications in genetics. However, when the size of the individual-level data of the cohort of interest is small, statistical learning algorithms, from linear regression to neural networks, usually fail due to insufficient data. Fortunately, summary statistics from genome-wide association studies (GWAS) on other large cohorts are often publicly available. In this work, we propose a new regularization method, namely, main effect prior (MEP), for making use of GWAS summary statistics from external datasets. The main effect prior is generally applicable for machine learning algorithms, such as neural networks and linear regression. With simulation and real-world experiments, we show empirically that MEP improves the prediction performance on both homogeneous and heterogeneous datasets. Moreover, deep neural networks with MEP outperform standard baselines even when the training set is small.

bioinformatics↗

bioRxiv2021

Gene-Gene Interaction Detection with Deep Learning

We do not know the extent to which genetic interactions affect the observed phenotype in diseases, because the current interaction detection approaches are limited: they only consider interactions between the top SNPs of each gene, and only simple forms of interaction. We introduce methods for increasing the statistical power of interaction detection by taking into account all SNPs and complex interactions between them, beyond only the currently considered multiplicative relationships. In brief, the relation between SNPs and a phenotype is captured by a gene interaction neural network (NN), and the interactions are quantified by the Shapley score between hidden nodes, which are gene representations that optimally combine information from all SNPs in the gene. Additionally, we design a new permutation procedure tailored for NNs to assess the significance of interactions. The new approach outperformed existing alternatives on simulated datasets, and in a cholesterol study on the UK Biobank it detected six interactions which replicated on an independent FINRISK dataset, four of them novel findings.

bioinformatics↗

bioRxiv2021

Reconstructing human early embryogenesis in vitro with pluripotent stem cells

Understanding human development is of fundamental biological and clinical importance. Yet despite its significance, insights into early developmental events in humans still remain largely unknown. While recent advances show that stem cells can mimic embryogenesis1-9 to unravel hidden developmental mechanisms, a stem cell-based model of early human embryogenesis is lacking. Here, we use human extended pluripotent stem cells10to reconstitute early human development in 3-dimensions and recapitulate early embryo-like events. We first perform a systematic characterisation to reveal unique signalling requirements for building the human pre-implantation blastocyst. Further, we show that these in vitro stem cell-derived blastocyst-like structures are able to undertake spatiotemporal self-organisation to mimic peri-implantation remodelling in which a polarised rosette opens up the amniotic cavity within a developing disc. The hallmarks of human early development displayed by this stem cell-based in vitro model mimics features of embryonic day 3 to day 9/10 of natural development. Thus, this platform represents a tractable model system to contribute to the basic understanding of cellular and molecular mechanisms governing early embryonic events in humans and to provide valuable insights into the design of differentiation protocols for human stem cells in clinical applications.

developmental biology↗

bioRxiv2020

Spike Protein of SARS-CoV-2 Activates Macrophages and Contributes to Induction of Acute Lung Inflammations in Mice

BackgroundCoronavirus disease 2019 (COVID-19) patients exhibit multiple organ malfunctions with a primary manifestation of acute and diffuse lung injuries. The Spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is crucial to mediate viral entry into host cells; however, whether it can be cellularly pathogenic and contribute to pulmonary hyper-inflammations in COVID-19 is not well known. Methods and FindingsIn this study, we developed a Spike protein-pseudotyped (Spp) lentivirus with the proper tropism of SARS-CoV-2 Spike protein on the surface and tracked down the fate of Spp in wild type C57BL/6J mice receiving intravenous injection of the virus. A lentivirus with vesicular stomatitis virus glycoprotein (VSV-G) was used as the control. Two hours post-infection (hpi), Spp showed more than 27-75 times more viral burden in the lungs than other organs; it also exhibited about 3-5 times more viral burden than VSV-G lentivirus in the lungs, liver, kidney and spleen. Acute pneumonia was evident in animals 24 hpi. Spp lentivirus was mainly found in LDLR+ macrophages and pneumocytes in the lungs, but not in MARC1+ macrophages. IL6, IL10, CD80 and PPAR-{gamma} were quickly upregulated in response to infection of Spp lentivirus in the lungs in vivo as well as in macrophage-like RAW264.7 cells in vitro. We further confirmed that forced expression of the Spike protein in RAW264.7 cells could significantly increase the mRNA levels of the same panel of inflammatory factors. ConclusionsOur results demonstrate that the Spike protein of SARS-CoV-2 alone can induce cellular pathology, e.g. activating macrophages and contributing to induction of acute inflammatory responses.

pathology↗

bioRxiv2020

The consensus Nglyco-X-S/T motif and a previously unknown Nglyco-N -linked glycosylation are necessary for growth and pathogenicity of Phytophthora

Asparagine (Asn, N) -linked glycosylation within the glycosylation motif (Nglyco-X-S/T; X=P) is a ubiquitously distributed post-translational modification that participates in diverse eukaryotic cellular processes. However, little is known about the characteristic features and roles of N-glycosylation in oomycetes. In this work, it found that 2.5 g/ml tunicamycin (N-glycosylation inhibitor) completely inhibited Phytophthora sojae growth, suggesting that N-glycosylation is necessary for oomycete development. We conducted a glycoproteomic analysis of P. sojae to identify and map all N-glycosylated proteins and to quantify differentially expressed glycoproteins associated with mycelia, asexual cysts, and sexual oospores. A total of 355 N-glycosylated proteins were found, containing 496 glycosites that likely participate in glycan degradation, carbon metabolism, glycolysis, or other central metabolic pathways. To verify the glycoproteomic results and further examine the function of N-glycosylation in P. sojae, two proteins were selected for PNGase F deglycosylation assays and CRISPR/Cas9-mediated site-directed mutagenesis, including a GPI transamidase protein (GPI16) up-regulated in cysts, with the consensus Nglyco-X-S/T motif at Asn 94, and a heat shock protein 70 (HSP70) up-regulated in cysts and oospores with a previously unknown Nglyco-N motif at Asn 270. We demonstrated that the GPI16 and HSP70 are both N-glycosylated proteins, confirming that the Nglyco-N motif is a target site for asparagine - oligosaccharide N-glycosidic linkage. Glycosite mutations of Asn 94 in the GPI16 led to impaired cyst germination and pathogenicity, while HSP70 mutants exhibited decreased cyst germination and oospore production. This work describes an integrated map of oomycete N-glycoproteomes and advances our understanding of N-glycosylation in oomycetes. Moreover, we confirm that the consensus Nglyco-X-S/T and the Nglyco-N -linked glycosites are both essential for the growth of Phytophthora sojae, indicating that there are multiple N-glycosylation motifs in oomycetes.

microbiology↗

bioRxiv2019

The Calcineurin-TFEB-p62 Pathway Mediates the Activation of Cardiac Macroautophagy by Proteasomal Malfunction

RationaleThe ubiquitin-proteasome system (UPS) and the autophagic-lysosomal pathway (ALP) are pivotal to proteostasis. Targeting these pathways is emerging as an attractive strategy for treating cancer. However, a significant proportion of patients who receive a proteasome inhibitor-containing regime for example, show cardiotoxicity. Moreover, UPS and ALP defects are implicated in the pathogenesis of a large subset of heart disease. Hence, a better understanding of the cross-talk between the two catabolic pathways should help advance cardiac pathophysiology and medicine. ObjectiveSystemic pharmacological proteasome inhibition (PSMI) was shown to increase p62/SQSTM1 expression and induce myocardial macroautophagy. The present study investigates whether cardiomyocyte-restricted PSMI activates myocardial ALP and, more importantly, how proteasome malfunction activates the ALP in the heart. Methods and ResultsMyocardial macroautophagy, transcription factor EB (TFEB) expression and activity, and p62 expression were markedly increased in mice with either cardiomyocyte-restricted ablation of Psmc1 (a 19S proteasome subunit gene) or pharmacological PSMI. In cultured cardiomyocytes, PSMI-induced increases in TFEB activation and p62 expression were blunted markedly by calcineurin inhibition (cyclosporine A) and by siRNA-mediated Molcn1 silence. PSMI induced remarkable increases in myocardial autophagic flux in wild type mice but not p62 null mice. In cultured wild type, but not p62-null, mouse cardiomyocytes, PSMI induced increases in LC3-II flux and in the lysosomal removal of ubiquitinated proteins. Myocardial TFEB activation by PSMI as reflected by TFEB nuclear localization and target gene expression was strikingly less in p62 null mice compared with wild type mice. Conclusions(1) The activation of cardiac macroautophagy by proteasomal malfunction is mediated by the Mocln1-calcineurin-TFEB-p62 pathway; (2) both Mocln1 and p62 form a feed-forward loop with TFEB during TFEB activation by proteasome malfunction; and (3) targeting the Mcoln1-calcineurin-TFEB-p62 pathway may provide new means to intervene cardiac ALP activation in a proteasome malfunction setting.

cell biology↗

bioRxiv2019

An upstream open reading frame represses translation of chicken PPARγ transcript variant 1

Peroxisome proliferator-activated receptor {gamma} (PPAR{gamma}) is a master regulator of adipogenesis. The PPAR{gamma} gene produces various transcripts with different 5'-untranslated regions (5' UTRs) because of alternative promoter usage and splicing. The 5' UTR plays important roles in posttranscriptional gene regulation. However, to date, the regulatory role and underlying mechanism of 5' UTRs in the posttranscriptional regulation of PPAR{gamma} expression remain largely unclear. In this study, we investigated the effects of 5' UTRs on posttranscriptional regulation using reporter assays. Our results showed that the five PPAR{gamma} 5' UTRs exerted different effects on reporter gene activity. Bioinformatics analysis showed that chicken PPAR{gamma} transcript 1 (PPAR{gamma}1) possessed an upstream open reading frame (uORF) in its 5' UTR. Mutation analysis showed that a mutation in the uORF led to increased Renilla luciferase activity and PPAR{gamma} protein expression, but decreased Renilla luciferase and PPAR{gamma}1 mRNA expression. mRNA stability analysis using real-time RT-PCR showed that the uORF mutation did not interfere with mRNA stability, but promoter activity analysis of the cloned 5' UTR showed that the uORF mutation reduced promoter activity. Furthermore, in vitro transcription/translation assays demonstrated that the uORF mutation markedly increased the translation of PPAR{gamma}1 mRNA. Collectively, our results indicate that the uORF represses the translation of chicken PPAR{gamma}1 mRNA.

molecular biology↗

bioRxiv2019

Structural characterization of the N-terminal domain of the Dictyostelium discoideum mitochondrial calcium uniporter

The mitochondrial calcium uniporter (MCU) plays a critical role in the mitochondrial calcium uptake into the matrix. In metazoans, the uniporter is a tightly regulated multi-component system including the pore-forming subunit MCU and several regulators (MICU1, MICU2, EMRE). The calcium-conducting activity of metazoan MCU requires the single-transmembrane protein EMRE. Dictyostelium discoideum (Dd), however, developed a simplified uniporter for which the pore-forming MCU (DdMCU) alone is necessary and sufficient for calcium influx. Here, we report a crystal structure of the N-terminal domain (NTD) of DdMCU at 1.7 [A] resolution. The DdMCU-NTD contains four helices and two strands arranged in a fold that is completely different from the known structures of other MCU-NTD homologs. Biochemical and biophysical analyses of DdMCU-NTD in solution indicated that the domain exists as oligomers, most probably as a pentamer or hexamer. Mutagenesis showed that the acidic residues Asp60, Glu72 and Glu74, which appeared to mediate the parallel interface as observed in the crystal structure, participated in the self-assembly of DdMCU-NTD. Intriguingly, the oligomeric complex readily dissociated to lower-order oligomers in the presence of calcium. We propose that the calcium-triggered dissociation of NTD regulates the channel activity of DdMCU by a yet unknown mechanism.

biophysics↗

bioRxiv2018

Genome-wide CNV study and functional evaluation identified CTDSPL as tumour suppressor gene for cervical cancer

We have investigated copy number variations (CNVs) in relation to cervical cancer by analyzing 731,422 single-nucleotide polymorphisms (SNPs) in 1,034 cervical cancer cases and 3,948 controls, followed by replication in 1,396 cases and 1,057 controls. We found that a 6367bp deletion in intron 1 of the CTD small phosphatase like gene (CTDSPL) was associated with 2.54-fold increased risk of cervical cancer (odds ratio =2.54, 95% confidence interval =2.08-3.12, P=2.0x10-19). This CNV is one of the strongest genetic risk variants identified so far for cervical cancer. The deletion removes the binding sites of zinc finger protein 263, binding protein 2 and interferon regulatory factor 1, and hence downregulates the transcription of CTDSPL. HeLa cells expressing CTDSPL showed a significant decrease in colony-forming ability. Compared with control groups, mice injected with HeLa cells expressing CTDSPL exhibited a significant reduction in tumour volume. Furthermore, CTDSPL-depleted immortalized End1/E6E7 could form tumours in NOD-SCID mice.

cancer biology↗

bioRxiv2017

Evolution of Hominin Polyunsaturated Fatty Acid Metabolism: From Africa to the New World

BackgroundThe metabolic conversion of dietary omega-3 and omega-6 18 carbon (18C) to long chain (> 20 carbon) polyunsaturated fatty acids (LC-PUFAs) is vital for human life. Fatty acid desaturase (FADS) 1 and 2 catalyze the rate-limiting steps in the biosynthesis of LC-PUFAs. The FADS region contains two haplotypes; ancestral and derived, where the derived haplotypes are associated with more efficient LC-PUFA biosynthesis and is nearly fixed in Africa. In addition, Native American populations appear to be nearly fixed for the lesser efficient ancestral haplotype, which could be a public health problem due to associated low LC-PUFA levels, while Eurasia is polymorphic. This haplotype frequency distribution is suggestive of archaic re-introduction of the ancestral haplotype to non-African populations or ancient polymorphism with differential selection patterns across the globe. Therefore, we tested the FADS region for archaic introgression or ancient polymorphism. We specifically addressed the genetic architecture of the FADS region in Native American populations to better understand this potential public health impact.\n\nResultsWe confirmed Native American ancestry is nearly fixed for the ancestral haplotype and is under positive selection. The ancestral haplotype frequency is also correlated to Siberian populations geographic location further suggesting the ancestral haplotype s role in cold weather adaptation and leading to the high haplotype frequency within Native American populations. We also find that the Neanderthal is more closely related to the derived haplotypes while the Denisovan clusters closer to the ancestral haplotypes. In addition, the derived haplotypes have a time to the most recent common ancestor of 688,474 years ago which is within the range of the modern-archaic hominin divergence.\n\nConclusionsThese results support an ancient polymorphism forming in the FADS gene region with differential selection pressures acting on the derived and ancestral haplotypes due to the old age of the derived haplotypes and the ancestral haplotype being under positive selection in Native American ancestry populations. Further, the near fixation of the less efficient ancestral haplotype in Native American ancestry suggests the need for future studies to explore the potential health risk of associated low LC-PUFA levels in Native American ancestry populations.

evolutionary biology↗