Biology subjects

Chen, X.

Publications and source records attributed to Chen, X..

At least 1,387 records · Page 77Linked to original sources

bioRxiv2020

Tracing the origin of a new organ by inferring the genetic basis of rumen evolution

The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We used 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen origin and evolution. Comparative analyses reveal that the rumen and the first-chamber stomachs of camels and cetaceans shared a common tissue origin from the esophagus. The rumen recruited genes from other tissues/organs and up-regulated many esophagus genes to aquire functional innovations involving epithelium absorption, improvement of the ketone body metabolism and regulation of microbial community. These innovations involve such genetic changes as ruminant-specific conserved elements, newly evolved genes and positively selected genes. Our in vitro experiements validate the functions of one enhancer, one positively selected gene and two newly evolved antibacterial genes. Our study provides novel insights into the origin and evolution of a complex organ.

evolutionary biology↗

bioRxiv2020

Sox17 and β-catenin co-occupy Wnt-responsive enhancers to govern the endodermal gene regulatory network

Lineage specification is governed by gene regulatory networks (GRNs) that integrate the activity of signaling effectors and transcription factors (TFs) on enhancers. Sox17 is a key transcriptional regulator of definitive endoderm development, and yet, its genomic targets remain largely uncharacterized. Here, using genomic approaches and epistasis experiments, we define the Sox17-governed endoderm GRN in Xenopus gastrulae. We show that Sox17 functionally interacts with the canonical Wnt pathway to specify and pattern the endoderm while repressing alternative mesectoderm fates. Sox17 and {beta}-catenin co-occupy hundreds of key enhancers. In some cases, Sox17 and {beta}-catenin synergistically activate transcription independent of Tcfs, whereas on other enhancers, Sox17 represses {beta}-catenin/Tcf-mediated transcription to spatially restrict gene expression domains. Our findings establish Sox17 as a tissue-specific modifier of Wnt responses and point to a novel paradigm where genomic specificity of Wnt/{beta}-catenin transcription is determined through functional interactions between lineage-specific Sox TFs and {beta}-catenin/Tcf transcriptional complexes. Given the ubiquitous nature of Sox TFs and Wnt signaling, this mechanism has important implications across a diverse range of developmental and disease contexts. Key findingsO_LISox17 regulates germ layer segregation by promoting endoderm differentiation while simultaneously repressing mesectoderm fates. C_LIO_LIFunctional interactions between Sox17 and canonical Wnt-signaling is a major feature of the GRN controlling endoderm specification and patterning. C_LIO_LISox17 and {beta}-catenin co-occupy a subset of enhancers to synergistically stimulate transcription in the absence of Tcfs. C_LIO_LISox17 regulates the spatial expression domains of Wnt/{beta}-catenin-responsive transcription in the gastrula. C_LI

developmental biology↗

bioRxiv2020

Agewise mapping of genomic oxidative DNA modification demonstrates oxidative-driven reprogramming of pro-longevity genes

The accumulation of unrepaired oxidatively damaged DNA can influence both the rate of ageing and life expectancy of an organism. Mapping oxidative DNA damage sites at whole-genome scale will help us to recognize the damage-prone sequence and genomic feature information, which is fundamental for ageing research. Here, we developed an algorithm to map the whole-genome oxidative DNA damage at single-base resolution using Single-Molecule Real-Time (SMRT) sequencing technology. We sequenced the genomic oxidative DNA damage landscape of C. elegans at different age periods to decipher the potential impact of genomic DNA oxidation on physiological ageing. We observed an age-specific pattern of oxidative modification in terms of motifs, chromosomal distribution, and genomic features. Integrating with RNA-Seq data, we demonstrated that oxidative modification in promoter regions was negatively associated with the expression of pro-longevity genes, denoting that oxidative modification in pro-longevity genes may exert epigenetic potential and thus affect lifespan determination. Together, our study opens up a new field for exploration of "oxigenetics," that focuses on the mechanisms of redox-mediated ageing. SummaryO_LIWe developed an algorithm to map the oxidative DNA damage at single-base resolution. C_LIO_LIOxidative DNA damage landscape in C. elegans illustrated an age-specific pattern in terms of motifs, chromosomal distribution, and genomic features. C_LIO_LIOxidative modification in older worms occurred higher frequency at the sex chromosome, with the preference for promoter and exon regions. C_LIO_LIOxidative modification in promoter regions of pro-longevity genes was negatively associated with their expression, suggesting the oxidative-driven transcript reprogramming of pro-longevity genes in physiological ageing. C_LI

genetics↗

bioRxiv2020

Single Chlamydomonas reinhardi (C. reinhardtii) cell separation from bacterial cells and auto-fluorescence tracking with a nano-sieve device

A planar, transparent, and adaptable nano-sieve device is developed for efficient microalgae/bacteria separation. In our strategy, a sacrificial layer is applied in the dual photolithography patterning to achieve a one-dimensional channel with a very low aspect ratio (1:10,000). Microalgae/bacteria mixture is then introduced into the deformable polydimethylsiloxane (PDMS) nano-channel. The hydrodynamic deformation of the nano-channel is regulated to allow the bacteria cells to pass through while leaving the microalgae cells trapped in the device. At a flow rate of 4 l/min, ~100% of the microalgae cells are trapped in the device. Additionally, this device is capable of immobilizing single cells in a transparent channel for auto-fluorescence tracking. These microalgae cells demonstrate minimal photo-bleaching over 250 s laser exposure and can be used to monitor hazardous compounds in the sample with a continuous flow fashion. Our method will be valuable to purify microalgae samples containing contaminations and study single cell heterogeneity.

bioengineering↗

bioRxiv2020

Genomic study of oral lichen planus and oral microbiome with RNAseq

Oral lichen planus (OLP) is a common chronic inflammatory disease affecting the oral mucosa. The pathogenesis of OLP is incompletely understood but is thought to be related to the immune system. As the oral cavity is a major reservoir and transmission gateway for bacteria, viruses, and fungi, the microbial composition of the oral cavity could play a role in the pathogenesis of OLP. However, due to limitations of analytic technology and incomplete knowledge of the microbial community in the oral cavity, it is not yet clear which pathogens are associated with OLP. Next-generation sequencing (NGS) is a powerful tool that can help to identify pathogens for many infectious diseases. In this study, we compared host cell gene expression profiles and microbial profiles from OLP patients and matched healthy individuals. We identified activation of the hepatocyte nuclear factor alpha (HNF4A) network in OLP patients and potential pathogens, including Corynebacterium matruchotii, Fusobacterium periodonticum, Streptococcus intermedius, Streptococcus oralis, and Prevotella denticola. P. denticola is capable of activating the HNF4A gene network. Our findings shed light on the previously elusive association of OLP with various diseases like hepatitis, and indicate that OLP is a T-helper type 17 (Th17)-mediated mucosal inflammatory process. The molecular pathways and microbes identified here can inform future investigations into OLP pathogenesis and development of novel therapeutics for OLP treatment.

molecular biology↗

bioRxiv2020

Low bias DNA for sustainable and efficient data storage

In DNA data storage, the massive sequence complexity creates challenges in repeatable and efficient information readout. Here, our study clearly demonstrated that canonical polymerase chain reaction (PCR) created significant DNA amplification biases, which greatly hinder fast and stable data retrieving from hundred-thousand synthetic DNA sequences encoding over 2.85 megabyte (MB) digital data. To mitigate the amplification bias, we adapted an isothermal DNA amplification for low-bias amplification of DNA pool with massive sequence complexity, and named the new method isothermal DNA reading (iDR). By using iDR, we were able to robustly and repeatedly retrieve the data stored in DNA strands attached on magnetic beads (MB) with significantly decreased sequencing reads, compared with the PCR method. Therefore, we believe that the low-bias iDR method provides an ideal platform for robust DNA data storage, and fast and reliable data readout.

synthetic biology↗

bioRxiv2020

Altered Temporal Variability of Local and Large-scale Resting-state Brain Functional Connectivity Patterns in Schizophrenia and Bipolar Disorder

Schizophrenia and bipolar disorder share some common clinical features and are both characterized by aberrant resting-state functional connectivity (FC). However, little is known about the common and specific aberrant features of the dynamic FC patterns in these two disorders. In this study, we explored the differences in dynamic FC among schizophrenia patients (n = 66), type I bipolar disorder patients (n = 53) and healthy controls (n = 66), by comparing temporal variabilities of FC patterns involved in specific brain regions and large-scale brain networks. Compared with healthy controls, both patient groups showed significantly increased regional FC variabilities in subcortical areas including the thalamus and basal ganglia, as well as increased inter-network FC variability between the thalamus and sensorimotor areas. Specifically, more widespread changes were found in the schizophrenia group, involving increased FC variabilities in sensorimotor, visual, attention, limbic and subcortical areas at both regional and network levels, as well as decreased regional FC variabilities in the default-mode areas. The observed alterations shared by schizophrenia and bipolar disorder may help to explain their overlapped clinical features; meanwhile, the schizophrenia-specific abnormalities in a wider range may support that schizophrenia is associated with more severe functional brain deficits than bipolar disorder.

neuroscience↗

bioRxiv2020

MiRNAs profiling and degradome sequencing between the CMS-line N816S and its maintainer line Ning5m during anther development in pepper (Capsicum annuum L.)

Utilization of cytoplasmic male sterility (CMS) is significant for agriculture. MiRNAs are a class of endogenously non-coding small RNAs (21-24 nt) that play key roles in the regulation of various growth and developmental processes in plants. The knowledge miRNA-guided CMS regulation is rather limited in pepper. To better understand the miRNAs involvement and regulatory mechanism of CMS, miRNA libraries from anther of CMS-line N816S and its maintainer line Ning5m were generated by miRNAome sequencing in pepper. A total of 76 differentially expressed miRNAs were detected, of which 18 miRNAs were further confirmed by quantitative real-time PCR (qRT-PCR). In addition, miRNA targets were identified by degradome sequencing. The result showed that 1292 targets that were potentially cleaved by 321 miRNAs (250 conserved miRNAs and 71 novel miRNAs). Gene Ontology (GO) and KEGG pathway analysis indicated that 35 differentially expressed miRNAs might play roles in the regulation of CMS sterility, by cleaving 77 target transcripts, such as MYBs, SPLs, and AFRs, of which targeted by miR156, miR167, miRNA858 family. Nineteen miRNA-cleaved targets were selectively examined by qRT-PCR, and the results showed that there were mostly negative correlations between miRNAs and their targets on the expression level. These findings provide a valuable information to understand miRNAs mechanism during anther development and CMS occurrence in pepper.

plant biology↗

bioRxiv2020

Clinically applicable histopathological diagnosis system for gastric cancer detection using deep learning

Gastric cancer is among the most malignant tumours with the highest incidence and mortality rates. The early detection and accurate histopathological diagnosis of gastric cancer are essential factors that can help increase the chances of successful treatment. While the worldwide shortage of pathologists has imposed burdens on current histopathology services, it also offers a unique opportunity for the use of artificial intelligence assistance systems to alleviate the workload and increase diagnostic accuracy. To the best of our knowledge, there has not been a clinically applicable histopathological assistance system with high accuracy that can generalize to whole slide images created with diverse digital scanner models from different hospitals. Here, we report a clinically applicable artificial intelligence assistance system developed at the Chinese PLA General Hospital, China, using a deep convolutional neural network trained with 2,123 pixel-level annotated H&E-stained whole slide images. The model achieved a sensitivity near 100% and an average specificity of 80.6% on a real-world test dataset, which included 3,212 whole slide images digitalized with three scanner models. We showed that the system could aid pathologists in improving diagnostic accuracy and preventing misdiagnoses. Moreover, we demonstrated that our system could perform robustly with 1,582 whole slide images from two other medical centres. Our study suggests the feasibility and benefits of using histopathological artificial intelligence assistance systems in routine practice scenarios.Competing Interest StatementXiaoqing Zhang is the founder of Thorough Images. Shuhao Wang is the co-founder and chief technology officer (CTO) of Thorough Images. Calvin Ku, Cancheng Liu, Zhuo Sun, Gang Xu, Yuefeng Wang are algorithm researchers of Thorough Images. All remaining authors have declared no conflicts of interest.View Full Text

pathology↗

bioRxiv2020

A variant in SMOC2, inhibiting BMP signaling by competitively binding to BMPR1B, causes multiple epiphyseal dysplasia

Previously study showed that SMOC, a matricellular protein, inhibits BMP signaling downstream of its receptor via activation of mitogen-activated protein kinase (MAPK) signaling. In our study, exome sequencing revealed a missense mutation (c.1076T>G, p.Leu359Arg) in EC domain of SMOC2 in a Chinese family with multiple epiphyseal disease (MED). The pathogenicity of this SMOC2 variant was verified by Smoc2L359R/L359R knock-in mice. Of note, decreasing phosphorylation of SMAD1/5/9 was detected in growth plates and primary chondrocytes from Smoc2L359R/L359R mice. Furthermore, binding affinity of mutant SMOC2 with collagen IX and HSPG in the extracellular matrix of cartilage were reduced while binding affinity with BMPRIB was intact. In addition, in contrast to previously results, that SMOC2 cannot antagonize BMP activity in the presence of a constitutively activated BMP receptor. These results support that SMOC2 with p.Leu359Arg variant act as an antagonist of canonical BMP pathway by competitively binding with BMP receptors.

genomics↗

bioRxiv2020

Bcl6 Preserves the Suppressive Function of Regulatory T Cells during Tumorigenesis

During tumorigenesis, tumor infiltrating regulatory T (Treg) cells restrict the function of effector T cells in tumor microenvironment and thereby promoting tumor growth. The anti-tumor activity of effector T cells can be therapeutically unleashed, and is now being exploited for the treatment of various types of human cancers. However, the immune suppressive function of Treg cells remains a major hurdle to broader effectiveness of tumor immunotherapy. In this article, we reported that the deletion of Bcl6 specifically in Treg cells led to stunted tumor growth, which was caused by impaired Treg cell responses. Notably, Bcl6 is essential in maintaining the lineage stability of Treg cells in tumor microenvironment. Meanwhile, we found that the absence of follicular regulatory T (Tfr) cells, which is a result of Bcl6 deletion in Foxp3+ cells, was dispensable for tumor control. Importantly, the increased Bcl6 expression in Treg cells is associated with poor prognosis of human colorectal cancer and lymph node metastasis of skin melanoma. Furthermore, Bcl6 deletion in Treg cells exhibits synergistic effects with immune checkpoint blockade therapy. Collectively, these results indicate that Bcl6 actively participates in regulating Treg cell immune responses during tumorigenesis and can be exploited as a therapeutic target of anti-tumor immunity.

immunology↗

bioRxiv2020

Hesperetin inhibits foam cell formation in macrophages via activating LXRα signal in an AMPK dependent manner

Cholesterol efflux from macrophages is the first step of cholesterol reverse transport (RCT), whose increase inhibits cholesterol accumulation and foam cell formation to suppress atherogenesis. Liver X receptor alpha (LXR) and adenosine monophosphate activated protein kinases (AMPK) both have the pivotal role in cholesterol homeostasis. However the association between these two molecules in cell model of atherosclerosis is poorly understood. Hesperetin has been reported to possess several protective effects for cardiovascular diseases, while little is known about the role of hesperetin and its underlying mechanism on macrophage foam cell formation. In this study, we sought to investigate the potential effects of hesperetin in cholesterol efflux by using human macrophage derived foam cells, focusing on liver X receptor alpha (LXR) and adenosine monophosphate activated protein kinases (AMPK) implication. Hesperetin treatment concentration-dependently reduced foam cell formation, intracellular cholesterol level and cholesterol esterification rate, and enhanced cholesterol efflux in THP-1 macrophages. Hesperetin upregulated the protein levels of LXR and its targets including ABCA1, ABCG1 as well as SR-BI, and phosphorylated-AMPK. Meanwhile, hesperetin-induced upregulation of LXR expression was enhanced by AMPK agonist and inhibited by AMPK inhibitor. Furthermore, hesperetin increased mRNA level of LXR and its target genes, all which were depressed by AMPK1/2 small interfering RNA (siRNA) transfection. In conclusion, we founded for the first time that hesperetin could active AMPK. And this activation upregulated LXR and its targets including ABCA1, ABCG1 and SR-BI, which significantly inhibited foam cell formation and promoted cholesterol efflux in THP-1 macrophages. Our results highlight the therapeutic potential of hespretin for the possible reduction in foam cell formation. This new mechanism could contribute the anti-atherogenic effects of hesperetin.

pharmacology and toxicology↗

bioRxiv2020

Genome-wide discovery of lupus genetic risk variant allelic regulatory activity

Genome-wide association studies of Systemic Lupus Erythematosus (SLE) nominate 3,073 genetic variants at 91 risk loci. To systematically screen these variants for allelic transcriptional enhancer activity, we constructed a massively parallel reporter assay (MPRA) library comprising 12,396 DNA oligonucleotides containing the genomic context around every allele of each SLE variant. Transfection into the Epstein-Barr virus-transformed B cell line GM12878 revealed 482 variants with enhancer activity, with 51 variants showing genotype-dependent (allelic) enhancer activity at 27 risk loci. Comparison of MPRA results in GM12878 and Jurkat T cell lines highlights shared and unique allelic transcriptional regulatory mechanisms at SLE risk loci. In-depth analysis of allelic transcription factor (TF) binding at and around allelic variants identifies one class of TFs whose DNA-binding motif tends to be directly altered by the risk variant and a second, larger class of TFs that bind allelically without direct alteration of their motif by the variant. Collectively, our approach provides a blueprint for the discovery of allelic gene regulation at risk loci for any disease and offers insight into the transcriptional regulatory mechanisms underlying SLE.

genomics↗

bioRxiv2020

Fully Automated Peptide Mapping Protocol for Multi-Attribute Method by Liquid Chromatography-Tandem Mass Spectroscopy with a High-Throughput Robotic Liquid Handling System

The multi-attribute method (MAM) based on liquid chromatography-tandem mass spectroscopy is emerging as a powerful tool to directly monitor multiple product quality attributes simultaneously. Preparation of samples for MAM, however, is labor intensive, involving protein denaturation, disulfide bond reduction, free cysteine alkylation, and enzymatic digestion steps, which require significant analyst hands-on time while limiting result turnaround. Such complexity can also render nontrivial variations across analysts and laboratories. We describe the development of a fully automated peptide mapping procedure with a high-throughput robotic liquid handling system to improve sample handling capability and outcome reproducibility while saving analyst hands-on time. The automated procedure is completely hands-free, and setup requires the analyst only to prenormalize the sample concentrations and load buffers and reagents at their designated positions on the robotic deck. The robotic liquid handler performs all the subsequent preparation steps and stores the digested samples on a chiller unit to await retrieval. The convenience and flexibility provided by this automated peptide mapping method provides substantial benefits over manual sample preparation protocols. The optimized, automated procedure showed good reproducibility and results that were comparable to those of the manual procedure with respect to sequence coverage, digestion completeness, and quantification of posttranslational modifications. With this increased throughput, coupled with fast MAM analysis, more comprehensive characterization can be achieved.

biochemistry↗

bioRxiv2020

Circadian Rhythm Is Disrupted by ZNF704 in Breast Carcinogenesis

Copy number gain in chromosome 8q21 is considered as the prototype of genetic abnormalities associated with development of breast cancer, yet the oncogenic potential underlying this amplicon in breast carcinogenesis remains to be delineated. We report here that ZNF704, a gene mapped to 8q21, is recurrently amplified in various malignancies including breast cancer. We found that ZNF704 acts as transcription repressor and interacts with the transcription corepressor SIN3A complex. Genome-wide interrogation of the transcriptional targets identifies that the ZNF704/SIN3A complex represses a panel of genes including PER2 that are critically involved in the function of circadian clock. Indeed, ZNF704 overexpression prolongs the period and dampens the amplitude of circadian clock. We showed that ZNF704 promotes the proliferation and invasion of breast cancer cells in vitro and accelerates the growth and metastasis of breast cancer in vivo. Consistently, the level of ZNF704 expression is inversely correlated with that of PER2 in breast carcinomas, and high level of ZNF704 correlates with advanced histological grades, lymph node positivity, and poor prognosis of breast cancer patients, especially those with HER2+ and basal-like subtypes. These results indicate that ZNF704 is an important regulator of circadian clock and a potential driver for breast carcinogenesis.

cancer biology↗

bioRxiv2020

Cell autonomous versus systemic Akt isoform deletions uncovered new roles for Akt1 and Akt2 in breast cancer

Studies in three mouse models of breast cancer identified profound discrepancies between cell autonomous and systemic Akt1 or Akt2 deletion on breast cancer tumorigenesis and metastasis. First, unlike systemic Akt1 deletion, which inhibits metastasis, cell autonomous Akt1 deletion does not. Second, systemic Akt2 deletion does not inhibit mammary tumorigenesis and metastasis, but cell autonomous Akt2 deletion eliminates ErbB2 expressing cells in the mammary gland and prevents tumorigenesis. However, the elevation in insulin by Akt2 systemic deletion hyperactivates tumor Akt, enabling ErbB2 expression, and exacerbates mammary tumorigenesis. Decreasing insulin level inhibits accelerated tumorigenesis by systemic Akt2 deletion. Single cell mRNA sequencing revealed that systemic Akt1 deletion maintains the pro-metastatic cluster within primary tumors but ablates pro-metastatic neutrophils. Systemic Akt1 deletion inhibits metastasis by impairing the survival and mobilization of tumor-associated neutrophils. Importantly, neutrophil-specific deletion of Akt1 is sufficient to exert resistance to metastasis. The results underscore the importance of determining systemic effects rather than cell autonomous effects as a proof of concept for cancer therapy.

cancer biology↗

bioRxiv2020

Identifying strategies to target the metabolic flexibility of tumours.

Plasticity of cancer metabolism can be a major obstacle for efficient targeting of tumour-specific metabolic vulnerabilities. Here, we identify and quantify the compensatory mechanisms following the inhibition of major pathways of central carbon metabolism in c-MYC-induced liver tumours. We find that glutaminase isoform Gls2, expressed in normal liver, compensates for the deletion of Gls1 isoform expressed in tumours. Inhibiting both glutaminases significantly delays tumourigenesis but does not completely block glutamine catabolism through the Krebs cycle. We reveal that glutamine catabolism is then driven by amidotransferases. Consistently, the synergistic effect of glutaminase and amidotransferase inhibitors on proliferation of mouse and human tumour cells is observed in vitro and in vivo. Furthermore, when Gls1 is deleted the Krebs cycle activity and tumour formation can also be significantly affected if glycolysis is co-inhibited (Gls1KO/Hk2KO). Finally, the inhibition of either serine (Psat1KO) or fatty acid (FasnKO) biosynthesis can be compensated by uptake of circulating nutrients. Thus, removing these nutrients from the diet produces synergistic effects on suppression of tumourigenesis. These results highlight the high flexibility of tumour metabolism and demonstrate how targeting compensatory mechanisms can improve a therapeutic outcome.

cancer biology↗

bioRxiv2020

An Active Chemo-mechanical Model to Predict Adhesion and Microenvironmental Regulation of 3D Cell Shapes

Cell shapes are known to regulate cytoskeletal organization, stiffness and the ability of cells to migrate and proliferate. Yet a quantitative understanding of the fundamental biochemical and biophysical mechanisms that determine the cell shapes is currently not available. In this study, we developed a chemo-mechanical feedback model to predict how adhesions and the properties of the 3D microenvironment regulate cell shapes. We find that the cells in 3D collagen matrices remain round or adopt an elongated shape depending on the density of active integrins, the level of contractility regulated by mechanosensitive signaling pathways and the density and mechanics of the matrix. While the formation of actin fibers that run along the cell body mediated by integrins and matrix stiffness drive elongation of cells, the cortical and membrane tension resist elongation. Based on the competition between these mechanisms, we derive phase diagrams for cell shape in the space spanned by the density of active adhesions and the level of biochemical signaling that controls contractility. Our predictions are validated by studying the shapes of HT1080 cells cultured in collagen gels of varying densities and using pharmacological treatments to regulate adhesions and contractility. The predictions of the model are found to be in excellent agreement with our experiments and data reported on a number of cell types in the literature.

biophysics↗