Biology subjects

Chen, C.

Publications and source records attributed to Chen, C..

At least 703 records · Page 39Linked to original sources

bioRxiv2019

Structural determinants of protocadherin-15 elasticity and function in inner-ear mechanotransduction

Protocadherin-15 (PCDH15), an atypical member of the cadherin superfamily, is essential for vertebrate hearing and its dysfunction has been associated with deafness and progressive blindness. The PCDH15 ectodomain, made of eleven extracellular cadherin (EC1-11) repeats and a membrane adjacent domain (MAD12), assembles as a parallel homodimer that interacts with cadherin-23 (CDH23) to form the tip link, a fine filament necessary for inner-ear mechanotransduction. Here we report X-ray crystal structures of a PCDH15 + CDH23 heterotetrameric complex and ten PCDH15 fragments that were used to build complete high-resolution models of the monomeric PCDH15 ectodomain. Using molecular dynamics (MD) simulations and validated crystal contacts we propose models for complete PCDH15 parallel homodimers and the tip-link bond. Steered MD simulations of these models predict their strength and suggest conditions in which a multimodal PCDH15 ectodomain can act as a stiff or soft gating spring. These results provide a detailed view of the first molecular steps in inner-ear sensory transduction.

biophysics↗

bioRxiv2019

The common neoantigens in colorectal cancer are predicted and validated to be presented or immunogenic

Colorectal cancer (CRC) is a malignant cancer with high incidence and mortality in the world, as the result of the traditional treatments. Immunotherapy targeting neoantigens can induce durable tumor regression in cancer patients, but is almost limited to individual treatment, resulting from the unique neoantigens. Many shared oncogenic mutations are detected, but whether the common neoantigens can be identified in CRC is unknown. Using the somatic mutations data from 321 CRC patients combined with a filter standard and 7 predicted algorithms, we screened and obtained 25 HLA-A*11:01 restricted common neoantigens with high binding affinity (IC50<50 nM) and presentation score (>0.9). Except the positive epitope KRAS_G12V8-16, 11 out of 25 common neoantigens were proved to be naturally processed and presented on constructed K562 cell surface by mass spectroscopy (MS), and 11 out of 25 common neoantigens specifically induced in vitro pre-stimulated cytotoxic lymphocyte (CTL) to secrete IFN-{gamma}. However, only 2 out of 25 common neoantigens were simultaneously presented and immunogenic. Moreover, using cell-sorting technology combined with single-cell RNA sequencing, the immune repertoire profiles of C1orf170_S418G413-421 and KRAS_G12V8-16-specific CTL were clarified. Therefore, common neoantigens with presentation and immunogenicity could be found in CRC, which would be developed as the universal targets for CRC immunotherapy.

immunology↗

bioRxiv2019

Discovery and Multi-center Verification of Prostate Cancer Protein Biomarkers using Single-shot Short Gradient Microflow SWATH and MRMHR Mass Spectrometry

We report and evaluated a microflow, single-shot, short gradient SWATH MS method intended to accelerate the discovery and verification of protein biomarkers in clinical specimens. The method uses 15-min gradient microflow-LC peptide separation, an optimized SWATH MS window configuration and OpenSWATH software for data analysis.\n\nWe applied the method to a cohort 204 of FFPE prostate tissue samples from 58 prostate cancer patients and 10 prostatic hyperplasia patients. Altogether we identified 27,976 proteotypic peptides and 4,043 SwissProt proteins from these 204 samples. Compared to a reference SWATH method with 2-hour gradient the accelerated method consumed only 27% instrument time, quantified 80% proteins and showed reduced batch effects. 3,800 proteins were quantified by both methods in two different instruments with relatively high consistency (r = 0.77). 75 proteins detected by the accelerated method with differential abundance between clinical groups were selected for further validation. A shortlist of 134 selected peptide precursors from the 75 proteins were analyzed using MRM-HR, exhibiting high quantitative consistency with the 15-min SWATH method (r = 0.89) in the same sample set. We further verified the capacity of these 75 proteins in separating benign and malignant tissues (AUC = 0.99) in an independent prostate cancer cohort (n=154).\n\nOverall our data show that the single-shot short gradient microflow-LC SWATH MS method achieved about 4-fold acceleration of data acquisition with reduced batch effect and a moderate level of protein attrition compared to a standard SWATH acquisition method. Finally, the results showed comparable ability to separate clinical groups.

cancer biology↗

bioRxiv2019

High-throughput proteomic analysis of FFPE tissue samples facilitates tumor stratification

Formalin-fixed, paraffin-embedded (FFPE), biobanked tissue samples offer an invaluable resource for clinical and biomarker research. Here we developed a pressure cycling technology (PCT)-SWATH mass spectrometry workflow to analyze FFPE tissue proteomes and applied it to the stratification of prostate cancer (PCa) and diffuse large B-cell lymphoma (DLBCL) samples. We show that the proteome patterns of FFPE PCa tissue samples and their analogous fresh frozen (FF) counterparts have a high degree of similarity and we confirmed multiple proteins consistently regulated in PCa tissues in an independent sample cohort. We further demonstrate temporal stability of proteome patterns from FFPE samples that were stored between one to 15 years in a biobank and show a high degree of the proteome pattern similarity between two types histological region of small FFPE samples, i.e. punched tissue biopsies and thin tissue sections of micrometer thickness, despite the existence of certain degree of biological variations. Applying the method to two independent DLBCL cohorts we identified myeloperoxidase (MPO), a peroxidase enzyme, as a novel prognostic marker. In summary, this study presents a robust proteomic method to analyze bulk and biopsy FFPE tissues and reports the first systematic comparison of proteome maps generated from FFPE and FF samples. Our data demonstrate the practicality and superiority of FFPE over FF samples for proteome in biomarker discovery. Promising biomarker candidates for PCa and DLBCL have been discovered.

biochemistry↗

bioRxiv2019

MALT1 mediates IL-17 Neural Signaling to regulate C. elegans behavior, immunity and longevity

Besides well-known immune roles, the evolutionarily ancient cytokine interleukin-17 (IL-17) modulates neural circuit function. We investigate how IL-17 signals in neurons, and the extent to which this signaling can alter organismal phenotypes. We combine immunoprecipitation and mass spectrometry to biochemically characterize endogenous signaling complexes that function downstream of IL-17 receptors in C. elegans (Ce) neurons. We identify the Ce ortholog of MALT1 as a critical output of the pathway. MALT1 was not previously implicated in IL-17 signaling or in nervous system function. MALT1 forms a complex with homologs of Act1 and IRAK and functions both as a scaffold for I{kappa}B recruitment, and as a protease. MALT1 is expressed broadly in the Ce nervous system, and neuronal IL-17-MALT1 signaling regulates many phenotypes, including escape behavior, associative learning, immunity and longevity. Our data suggest MALT1 has an ancient role modulating neural function downstream of IL-17 to remodel physiological and behavioral state.

neuroscience↗

bioRxiv2019

Interpretable attention model in transcription factor binding site prediction with deep neural networks

Due to the complexity of the biological factors that may influence the binding of transcription factors to DNA sequences, prediction of the potential binding sites remains a difficult task in computational biology. The attention mechanism in deep learning has shown its capability to learn from input features with long-range dependencies. Until now, no study has applied this mechanism in deep neural network models with input data from massively parallel sequencing. In this study, we aim to build a model for binding site prediction with the combination of attention mechanism and traditional deep learning techniques, including convolutional neural networks and recurrent neural networks. The performance of our methods is evaluated on the ENCODE-DREAM in vivo Transcription Factor Binding Site Prediction Challenge datasets.\n\nThe benchmark shows that our implementation with attention mechanism (called DeepGRN) improves the performance of the deep learning models. Our model achieves better performance in at least 9 of 13 targets than any of the methods participated in the DREAM challenge. Visualization of the attention weights extracted from the trained models reveals how those weights shift when binding signal peaks move along the genomic sequence, which can interpret how the predictions are made. Case studies show that the attention mechanism helps to extract useful features by focusing on regions that are critical to successful prediction while ignoring the irrelevant signals from the input.

bioinformatics↗

bioRxiv2019

An omnidirectional visualization model of personalized gene regulatory networks

Gene regulatory networks (GRNs) have been widely used as a fundamental tool to reveal the genomic mechanisms that underlie the organisms response to environmental and developmental cues. Standard approaches infer GRNs as holistic graphs of gene co-expression, but such graphs cannot quantify how gene-gene interactions differentiate among organisms and how they alter structurally across spatiotemporal gradients. Here, we develop a generalized framework for inferring informative, dynamic, omnidirectional, and personalized GRNs (idopGRNs) from routine transcriptional experiments. This framework is constructed by a system of quasi-dynamic ordinary differential equations (qdODEs) derived from the combination of ecological and evolutionary theories. We reconstruct idopGRNs from a clinical genomic study and illustrate how network structure and organization affect surgical response to infrainguinal vein bypass grafting and the outcome of grafting. idopGNRs may shed light on genotype-phenotype relationships and provide valuable information for personalized medicine.

bioinformatics↗

bioRxiv2019

Pregnancy reprograms the enhancer landscape of mammary epithelial cells and alters the response to cMYC-driven oncogenesis

Pregnancy leaves a series of cellular and molecular modifications on mammary epithelial cells (MECs). Pregnancy is also known for decreasing the predisposition of rodent and human MECs to oncogenesis. Here, in order to understand the molecular basis for this effect, we analyzed epigenetic changes in the enhancer landscape of murine post-pregnancy MECs, together with their effect on gene regulation, tissue development and oncogenesis. Using in vivo and in vitro analyses, we found that completion of a pregnancy cycle changed the dynamics of cellular proliferation and gene expression in response to a second pregnancy. Our results also demonstrated that post-pregnancy MECs are resistant to the initial molecular programs driven by cMYC overexpression, a response that blocked MEC proliferation but did not perturb the pregnancy-induced epigenomic landscape. Overall, our findings suggest that pregnancy-induced mammary cancer prevention involves the epigenomic changes in MECs brought about by pregnancy.

molecular biology↗

bioRxiv2019

Dynamic Changes of G-CSF etc. Nine Cytokines in Mouse Bloodstream Infection Models of Staphylococcus aureus and Klebsiella pneumoniae and their Clinical Performances

Blood culture has been considered as the gold standard to diagnose the bacterial bloodstream infection, but its long turnaround time gravely obstructed the clinical medication by physicians. Cytokines play an important role in bacterial infection. The purpose of this study was to monitor the kinetic changes of nine cytokines in mouse infection models and to infer their diagnostic value in early infection.\n\nMethodsThe mouse bloodstream infection model of Staphylococcus aureus and the other model of Staphylococcus aureus and Klebsiella pneumoniae were constructed respectively, and the dynamic changes of nine cytokines were monitored within 48 hours after infected with 1/2 LD50 bacterial concentration. Cytokines with significant differences between the two groups and PBS control group from 0 to 6 hours after infection were selected for theoretical proof in patient sera that were clearly diagnosed as bloodstream infection. Receiver operating characteristic (ROC) curve analysis was conducted to determine the clinical differentiation of different cytokines.\n\nResultsTwo models of S.aureus and K. pneumoniae bloodstream infection in mice were constructed successfully. In the two mouse models, six of the nine cytokines monitored were different (P<0.05) in each experimental group. In the 121 patient sera samples, three cytokines, IL-6, IL-12p70 and G-CSF in the infection groups and control group had showed differences. In particular, AUC of G-CSF was 0.9051, the accuracy is better than IL-6 for diagnosing the infection. In addition, only G-CSF was significantly different between the two infection groups and in the analysis of ROC curve, AUC is equal to 0.735.\n\nConclusionsG-CSF can not only judge the bacterial infection and non-infection, but also distinguish the infection of S.aureus from K. pneumoniae.

microbiology↗

bioRxiv2019

Immune-mediated genetic pathways resulting in pulmonary function impairment increase lung cancer susceptibility

Impaired lung function is often caused by cigarette smoking, making it challenging to disentangle its role in lung cancer susceptibility. Investigation of the shared genetic basis of these phenotypes in the UK Biobank and International Lung Cancer Consortium (29,266 cases, 56,450 controls) shows that lung cancer is genetically correlated with reduced forced expiratory volume in one second (FEV1: rg=0.098, p=2.3x10-8) and the ratio of FEV1 to forced vital capacity (FEV1/FVC: rg=0.137, p=2.0x10-12). Mendelian randomization analyses demonstrate that reduced FEV1 increases squamous cell carcinoma risk (odds ratio (OR)=1.51, 95% confidence intervals: 1.21-1.88), while reduced FEV1/FVC increases the risk of adenocarcinoma (OR=1.17, 1.01-1.35) and lung cancer in never smokers (OR=1.56, 1.05-2.30). These findings support a causal role of pulmonary impairment in lung cancer etiology. Integrative analyses reveal that pulmonary function instruments, including 73 novel variants, influence lung tissue gene expression and implicate immune-related pathways in mediating the observed effects on lung carcinogenesis.

genetics↗

bioRxiv2019

The Urinary Microbiota in Relation to the Reproductive Tract Microbiota

Human urine is traditionally considered to be sterile, and whether the urine harbours distinct microbial communities has been a matter of debate. The potential link between female urine and reproductive tract microbial communities is currently not clear. Here we collected the urine samples from 147 Chinese women of reproductive age, and explored the nature of colonization by 16S rRNA gene amplicon sequencing, real-time qPCR and live bacteria culture. To demonstrate utility intra-individual Spearmans correlation was used to explore the relationship between urine and multi-sites of the reproductive tract. PERMANOVA was also performed to explore potential correlations between the lifestyle and various clinical factors and urinary bacterial communities. Our data demonstrated distinct bacterial communities in urine, indicative of a non-sterile environment. Types of diverse, Streptococcus-dominated, and Lactobacillus-dominated were the three most common types in the cohort. Detailed comparison of the urinary microbiota to the multi-sites of reproductive tract microbiota demonstrated the urinary microbiota was more similar to the microbiota in the cervix and uterine cavity instead of vagina in the same women. Our data demonstrates the potential connectivity of the microbiota in the female urogenital system and provided insight into the exploration of urethra and genital tract diseases.

microbiology↗

bioRxiv2019

Spatial genome re-organization between fetal and adult hematopoietic stem cells

Fetal hematopoietic stem cells (HSCs) undergo a developmental switch to become adult HSCs. The functional properties of the HSCs change dramatically during this switch, including their cycling behavior, hematopoietic lineage outputs and proliferation rate. The relationship between three-dimensional (3D) genome organization, epigenomic state, and transcriptome is poorly understood during this critical developmental transition. Here we conducted a comprehensive survey of the 3D genome, epigenome and transcriptome of fetal and adult HSCs in mouse. We found that chromosomal compartments and topologically associating domains (TAD) are largely conserved between fetal and adult HSCs. However, there is a global trend of increased compartmentalization and TAD boundary strength in adult HSCs. In contrast, dynamics of intra-TAD chromatin interactions is much higher and more widespread, involving over a thousand gene promoters and distal enhancers. Such dynamic interactions target genes involved in cell cycle, metabolism, and hematopoiesis. These developmental-stage-specific enhancer-promoter interactions appear to be mediated by different sets of transcription factors in fetal and adult HSCs, such as TCF3 and MAFB in fetal HSCs, versus NR4A1 and GATA3 in adult HSCs. Loss-of-function studies of TCF3 confirms the role of TCF3 in mediating condition-specific enhancer-promoter interactions and gene regulation in fetal HSCs. In summary, our data suggest that the fetal-to-adult transition is accompanied by extensive changes in intra-TAD chromatin interactions that target genes underlying the phenotypic differences between fetal and adult HSCs.

molecular biology↗

bioRxiv2019

Angiocrine FSTL1 insufficiency leads to atrial and vein wall fibrosis via SMAD3 activation

Angiocrine factors, mediating the endothelial-mural cell interaction in vascular wall construction as well as maintenance, are incompletely characterized. Here we show that loss of follistatin-like protein 1 (FSTL1) in endothelial cells (Fstl1ECKO) led to an increase of pulmonary vascular resistance, resulting in the heart regurgitation especially with tricuspid valves. However, this abnormality was not detected in mutant mice with Fstl1 deletion in smooth muscle cells or hematopoietic cells. We further showed that there was excessive alpha-smooth muscle actin (SMA) associated with atrial endocardia, heart valves, veins and microvessels after the endothelial FSTL1 deletion. Consistently, there was an increase of collagen deposition as demonstrated in livers of Fstl1ECKO mutants. The SMAD3 phosphorylation was significantly enhanced and pSMAD3 staining was colocalized with SMA in vein walls, suggesting the activation of TGF{beta} signaling in vascular mural cells of Fstl1ECKO mice. The findings imply that endothelial FSTL1 is critical for the homeostasis of atria and veins and its insufficiency may favor cardiovascular fibrosis leading to heart failure.

developmental biology↗

bioRxiv2019

Normal development and fertility of Fut1, Fut2, and Sec1 triple knockout mice

The fucose alpha(1,2) galactose structure (H antigen) is synthesized by 1,2 fucosyltransferases Fut1, Fut2 and Sec1. H antigen has been reported to be involved in cancer progression, neurite migration, synaptic plasticity, host-microbe interaction, blastocyst implantation, and the maintenance of gut microbiome. Genetic depletion of Fut1 or Fut2 only cause defects of alpha1,2 fucosylation in limited tissues because of enzyme redundancy. In this study, we generated mice with deficiencies in Fut1, Fut2, and Sec1 genes to deplete H antigen through BAC Engineering for the generation of ES Cell-Targeting construct. The homogenous triple knockout mice showed no significant decrease of viability or development. Mass spectrometry and Western blot analysis confirmed the absence of H blood group antigen in multiple organs. These results indicate normal development and fertility of mice devoid of blood group H. The fine pathophysiological alterations in these mice remain to be carefully studied, and they may serve as valuable tools to study gut microbiome and host-microbe interactions.

biochemistry↗

bioRxiv2019

Pan-genomic and Polymorphic Driven Prediction of Antibiotic Resistance in Elizabethkingia

The Elizabethkingia are a genetically diverse genus of emerging pathogens that exhibit multidrug resistance to a range of common antibiotics. Two representative species, Elizabethkingia bruuniana and Elizabethkingia meningoseptica, were phenotypically tested to determine minimum inhibitory concentrations for five antibiotics. Ultra-long read sequencing with Oxford Nanopore Technologies and subsequent de novo assembly produced complete, gapless circular genomes for each strain. Alignment based annotation with Prokka identified 5,480 features in E. bruuniana and 5,203 features in E. meningoseptica, where none of these identified genes or gene combinations corresponded to observed phenotypic resistance values. Pan-genomic analysis, performed with an additional 19 Elizabethkingia strains, identified a core-genome size of 2,658,537 bp, 32 uniquely identifiable intrinsic chromosomal antibiotic resistance core-genes and 77 antibiotic resistance pan-genes. Using core-SNPs and pan-genes in combination with six machine learning algorithms, binary classification of clindamycin and vancomycin resistance achieved f1 scores of 0.94 and 0.84 respectively. Performance on the more challenging multiclass problem for fusidic acid, rifampin and ciprofloxacin resulted in f1 scores of 0.70, 0.75 and 0.54 respectively.

bioinformatics↗

bioRxiv2019

Extension of the in vivo haploid induction system from diploid maize to hexaploid wheat

Doubled haploid breeding technology has been one of the most important techniques for accelerating crop breeding. In compare to in vivo haploid induction in maize, which is efficient and background independent, wheat haploid production by interspecific hybridization pollinated with maize is influenced by genetic background and requires rescue of young embryos. Here, we analyzed the homologues of maize haploid induction gene MTL/ZmPLA1/NLD in several crop species systematically, the homologues are highly conserved in sorghum, millet and wheat etc. Since wheat is a very important polyploidy crop, as a proof of concept, we demonstrated that the in vivo haploid induction method could be extended from diploid maize to hexaploid wheat by knocking out the wheat homologues (TaPLAs). Result showed that double knock-out mutation could trigger wheat haploid induction at ~ 2%-3%, accompanied by 30% - 60% seed setting rate. The performance of haploid wheat individual showed shorter plant, narrower leaves and male sterile. Our results also revealed that knockout of TaPLA-A and TaPLA-D do not affect pollen viability. This study not only confirmed the function of the induction gene and explored a new approach for haploid production in wheat, but also provided an example that the in vivo haploid induction could be applied in more crop species with different ploidy levels. Furthermore, by combining with gene editing, it would be a fast and powerful platform for traits improvement in polyploidy crops breeding.

plant biology↗

bioRxiv2019

piNET: a versatile web platform for downstream analysis and visualization of proteomics data

Large proteomics data, including those generated by mass spectrometry, are being generated to characterize biological systems at the protein level. Computational methods and tools to identify and quantify peptides, proteins and post-translational modifications (PTMs) that are captured in modern mass spectrometers have matured over the years. On the other hand, tools for downstream analysis, interpretation and visualization of proteomics data sets, in particular those involving PTMs, require further improvement and integration to accelerate scientific discovery and maximize the impact of proteomics studies by connecting them better with biological knowledge across not only proteomics, but also other Omics domains. With the goal of addressing these challenges, the piNET server has been developed as a versatile web platform to facilitate mapping, annotation, analysis and visualization of peptide, PTM, and protein level quantitative data generated by either targeted, shotgun or other proteomics approaches. Building on our experience with large scale analysis of gene and protein expression profiles as part of the Library of Integrated Network Cellular Signatures (LINCS) project, piNET has been designed as a fast, versatile and easy to use web-based tool with three modules that provide mapping from peptides (with PTMs) to proteins, from PTM sites to modifying enzymes that target those sites, and finally from proteins (with PTMs) to pathways, and for further mechanistic insights to LINCS signatures of chemical and genetic perturbations. piNET is freely available at http://www.pinet-server.org.

bioinformatics↗

bioRxiv2019

CD4 T-cell transcriptome expression reversal of the lncRNA-mRNA co-expression network in elite controller vs. normal-process HIV patients

Elite controller refers to a patient with human imunodeficienvcy virus infection with an undetected viral load without anti-viral treatment. Studies on gene expression and regulation in these individuals are limited but significant. We enrolled 196 patients and collected CD4 T-cell samples from two elite controllers, two normal-process infected patients, and two healthy controls to perform second-generation transcriptome sequencing. Using the Cuffdiff model, we identified differentially expressed mRNAs and long non-coding RNAs with corrected P value < 0.05, and constructed a protein-protein interaction network as well a long non-coding RNA-mRNA co-expression network based on the Pearson correlation coefficient. Interestingly, some interactions within the networks were identified as associated with viral infections and immune responses. This was the first study to examine gene transcription in elite controllers and to study their functional relationships. Our results provide a reference for subsequent functional verification at the molecular or cellular level.\n\nAuthor SummarySome individuals can spontaneously inhibit HIV replication after infection with HIV, and thus lack any symptoms. Studies on these patients, termed elite controllers (ECs) will help researchers and clinicians to understand the interrelationship between HIV and the host. In the present study, we focused on the interactions and functional relationships between significantly differentially expressed long non-coding RNAs (lncRNAs) and mRNAs in ECs vs. normal-process patients (NPs). RNA-sequencing was performed for six representative samples of CD4 T-cells. Using the Pearson correlation test, an lncRNA-mRNA co-expression network was constructed. Several new regulatory relationships between transcripts were revealed that might be closely related to the ability of ECs to maintain a low viral load for long periods without anti-viral treatment. For example, lncRNA C3orf35 was upregulated in ECs vs. NPs and was positively related to downregulation of GNG2 mRNA (encoding G protein subunit gamma 2), which functions in chemokine signaling pathways and HIV-1 infection. Overall, we identified certain interesting genetic interactions that will provide information about the mechanism of host suppression of viral replication.

bioinformatics↗