Biology subjects

Qin, J.

Publications and source records attributed to Qin, J..

At least 73 records · Page 4Linked to original sources

bioRxiv2020

The transcriptional and splicing changes caused by hybridization can be globally recovered by genome doubling during allopolyploidization

Allopolyploidization, which involves hybridization and genome doubling, is a key driving force in higher plant evolution. The transcriptome reprogramming that accompanies allopolyploidization can cause extensive phenotypic variations, and thus confers allopolyploids higher evolutionary potential than their diploid progenitors. Despite many studies, little is known about the interplay between hybridization and genome doubling in transcriptome reprogramming during allopolyploidization. Here, we performed genome-wide analyses of gene expression and splicing changes during allopolyploidization in wheat and brassica lineages. Our results indicated that both hybridization and genome doubling can induce genome-wide transcriptional and splicing changes. Notably, the gene transcriptional and splicing changes caused by hybridization can be largely recovered to parental levels by genome doubling in allopolyploids. Since transcriptome reprogramming is an important contributor to heterosis, our results revealed that only part of the heterosis in hybrids can be fixed in allopolyploids through genome doubling. Therefore, our findings update the current understanding of the permanent fixation of heterosis in hybrids through genome doubling. In addition, our results indicated that a large proportion of the transcriptome reprogramming in interspecific hybrids was not caused by the merging of two parental genomes, providing novel insights into the mechanism of heterosis.

evolutionary biology↗

bioRxiv2020

SUMOylation- and GAR1-dependent regulation of dyskerin nuclear and subnuclear localization

Dyskerin, a telomerase-associated protein and H/ACA ribonucleoprotein complex component plays an essential role in human telomerase assembly and activity. The nuclear and subnuclear compartmentalization of dyskerin and the H/ACA complex is an important though incompletely understood aspect of H/ACA ribonucleoprotein function. The posttranslational modification, SUMOylation, targets a wide variety of proteins, including numerous RNA-binding proteins, and most identified targets reported to date localize to the nucleus. Four SUMOylation sites were previously identified in the C-terminal Nuclear/Nucleolar Localization Signal (N/NoLS) of dyskerin, each located within one of two lysine-rich clusters. We found that a cytoplasmic localized C-terminal truncation variant of dyskerin lacking most of the C-terminal N/NoLS and both lysine-rich clusters represents an under-SUMOylated variant of dyskerin compared to wildtype dyskerin. We demonstrate that mimicking constitutive SUMOylation of dyskerin using a SUMO3-fusion construct can drive nuclear accumulation of this variant, and that the SUMO site K467 in this N/NoLS is particularly important for the subnuclear localization of dyskerin to the nucleolus in a mature H/ACA complex assembly- and SUMO-dependent manner. We also characterize a novel SUMO-interacting motif in the mature H/ACA complex component GAR1 that mediates the interaction between dyskerin and GAR1. Mislocalization of dyskerin, either in the cytoplasm or excluded from the nucleolus, disrupts dyskerin function and leads to reduced interaction of dyskerin with the telomerase RNA. These data indicate a role for dyskerin C-terminal N/NoLS SUMOylation in regulating the nuclear and subnuclear localization of dyskerin, which is essential for dyskerin function as both a telomerase-associated protein and as an H/ACA ribonucleoprotein involved in rRNA and snRNA biogenesis.

cell biology↗

bioRxiv2020

Modeling SARS-CoV-2 infection in vitro with a human intestine-on-chip device

Coronavirus disease 2019 (COVID-19) caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) has given rise to a global pandemic. The gastrointestinal symptoms of some COVID-19 patients are underestimated. There is an urgent need to develop physiologically relevant model that can accurately reflect human response to viral infection. Here, we report the creation of a biomimetic human intestine infection model on a chip system that allows to recapitulate the intestinal injury and immune response induced by SARS-CoV-2, for the first time. The microengineered intestine-on-chip device contains human intestinal epithelium (co-cultured human intestinal epithelial Caco-2 cells and mucin secreting HT-29 cells) lined in upper channel and vascular endothelium (human umbilical vein endothelial cells, HUVECs) in a parallel lower channel under fluidic flow condition, sandwiched by a porous PDMS membrane coated with extracellular matrix (ECM). At day 3 post-infection of SARS-CoV-2, the intestine epithelium showed high susceptibility to viral infection and obvious morphological changes with destruction of intestinal villus, dispersed distribution of mucus secreting cells and reduced expression of tight junction (E-cadherin), indicating the destruction of mucous layer and the integrity of intestinal barrier caused by virus. Moreover, the endothelium exhibited abnormal cell morphology with disrupted expression of adherent junction protein (VE-cadherin). Transcriptional analysis revealed the abnormal RNA and protein metabolism, as well as activated immune responses in both epithelial and endothelial cells after viral infection (e.g., up-regulated cytokine genes, TNF signaling and NF-kappa B signaling-related genes). This bioengineered in vitro model system can mirror the human relevant pathophysiology and response to viral infection at the organ level, which is not possible in existing in vitro culture systems. It may provide a promising tool to accelerate our understanding of COVID-19 and devising novel therapies.

bioengineering↗

bioRxiv2020

Rbx1 Cullin-Ring ligase E3 and Ube2m neddylation E2 differentially governs the fitness of Treg cells

Cullin-RING Ligases (CRLs) are a family of multi-unit E3 ubiquitin ligases with two members of RING family proteins, acting as the catalytic subunit: RING-box 1 (Rbx1) couples with CRLs1-4, whereas RING-box 2 (Rbx2/Sag) couples mainly with CRL5.1-4 Activity of CRLs requires neddylation on their Cullin subunit, catalyzed by neddylation enzyme cascades E1, E2 and E3. Ube2m and Ube2f are two neddylation E2s responsible for neddylation of Cullins in CRLs1-4 or CRL5, respectively.5-6 Regulatory T cells (Treg cells) are specialized immunosuppressive CD4+ T lymphocytes, that play pivotal roles in maintaining immune homeostasis in vivo.7-10 Whether and how Rbx1-Rbx2/CRLs and Ube2m-Ube2f/neddylation regulate Treg cell homeostasis and function are currently unknown. Here we show that while mice with a Treg-specific deletion of Rbx2/Sag showed no obvious phenotype, mice with Rbx1 deletion in Treg cells developed an early-onset fetal inflammatory disorders and death at day ~25 after birth (~p25), with disrupted homeostasis and functions of Treg cells, indicating Rbx1 as a prominent regulator of Treg cells. Single cell transcriptome assay showed that Rbx1 is essential for the maintenance of the effector subpopulations in Treg cells. The whole genome transcriptome and proteomics analysis revealed that Rbx1 regulates several inflammatory pathways, such as T-cell receptor, IL-17, TNF, NF{kappa}B, chemokine, cytokine-cytokine receptor interaction, as well as energy and purine metabolisms. Accumulation of Acly, Fto and Nfkbib proteins, upon Rbx1 depletion suggests that these are likely the novel substrates of CRLs1-4 in Treg cells. Consistently, while Ube2f deletion showed no obvious phenotype, mice with Ube2m deletion in Treg cells also suffers from inflammatory disorders, but to a much lesser severity with a 50% of death rate at ~150 days of age. Since Rbx1 is a dual E3 as a component of CRLs1-4 ligase and as a neddylation co-E3, downstream of Ube2m E2 for neddylation activation of CRLs1-45, much severe phenotypes in Foxp3cre;Rbx1fl/fl mice suggests Rbx1 may have additional function independent of neddylation activation in Treg cells. Indeed, unbiased transcriptome comparison between Rbx1-deficient and Ube2m-deficient Treg cells, revealed that the former had greater as well as unique alteration in the signaling pathways controlling the inflammatory responses. Collectively, our study shows that the Ube2m-Rbx1 axis of the neddylation-CRL is required for the maintenance of homeostasis and functional fitness of Treg cells in the fine control of immune tolerance; with implication that targeting the neddylation/CRLs, such as a small molecule inhibitor pevonedistat11, currently in the Phase II clinic trial for anticancer therapy, may have novel application in the treatment of human diseases associated with overactivated Treg cells.

immunology↗

bioRxiv2020

A human disease model of SARS-CoV-2-induced lung injury and immune responses with a microengineered organ chip

Coronavirus disease 2019 (COVID-19) is a global pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that seriously endangers human health. There is an urgent need to build physiological relevant human models for deep understanding the complex organ-level disease processes and facilitating effective therapeutics for COVID-19. Here, we first report the use of microengineered alveolus chip to create a human disease model of lung injury and immune responses induced by native SARS-CoV-2 at organ-level. This biomimetic system is able to reconstitute the key features of human alveolar-capillary barrier by co-culture of alveolar epithelial and microvascular endothelial cells under microfluidic flow. The epithelial cells on chip showed higher susceptibility to SARS-CoV-2 infection than endothelial cells identified by viral spike protein expression. Transcriptional analysis showed distinct responses of two cell types to SARS-CoV-2 infection, including activated type I interferon (IFN-I) signaling pathway in epithelium and activated JAK-STAT signaling pathway in endothelium. Notably, in the presence of circulating immune cells, a series of alveolar pathological changes were observed, including the detachment of endothelial cells, recruitment of immune cells, and increased production of inflammatory cytokines (IL-6, IL-8, IL-1{beta} and TNF-). These new findings revealed a crucial role of immune cells in mediating lung injury and exacerbated inflammation. Treatment with antiviral compound remdesivir could suppress viral copy and alleviate the disruption of alveolar barrier integrity induced by viral infection. This bioengineered human organ chip system can closely mirror human-relevant lung pathogenesis and immune responses to SARS-CoV-2 infection, not possible by other in vitro models, which provides a promising and alternative platform for COVID-19 research and preclinical trials.

bioengineering↗

bioRxiv2020

Rapid detection of SARS-CoV-2 and other respiratory viruses by using LAMP method with Nanopore Flongle workflow

The ongoing novel coronavirus (COVID-19) outbreak as a global public health emergency infected by SARC-CoV-2 has caused devastating loss around the world. Currently, a lot of diagnosis methods have been used to detect the infection. The nucleic acid (NA) testing is reported to be the clinical standard for COVID-19 infection. Evidence shows that a faster and more convenient method to detect in the early phase will control the spreading of SARS-CoV-2. Here, we propose a method to detect SARC-Cov-2 infection within two hours combined with Loop-mediated Isothermal Amplification (LAMP) reaction and nanopore Flongle workflow. In this approach, RNA reverse transcription and nucleic acid amplification reaction with one step in 30 minutes at 60-65{degrees}C constant temperature environment, nanopore Flongle rapidly adapter ligated within 10 minutes. Flongle flow cell sequencing and analysis in real-time. This method described here has the advantages of rapid amplification, convenient operation and real-time detection which is the most important for rapid and reliable clinical diagnosis of COVID-19. Moreover, this approach not only can be used for SARS-CoV-2 detection but also can be extended to other respiratory viruses and pathogens.

microbiology↗

bioRxiv2020

Global Screening of Sentrin-Specific Protease Family Substrates in SUMOylation

Post-translational modification of proteins by the addition of small ubiquitin-related modifier (SUMO) is a dynamic process, in which deSUMOylation is carried out by members of the Sentrin/SUMO-specific protease (SENP) family. While identification of SUMOylation sites at global scale has made great progress, much less effort has been made on the SENP family-dependent deSUMOylation. Here we report a dataset of 3,763 high confident SUMO1 modification sites and their dependence on the 6 members of SENP proteins. Interrogation of the dataset led to the discovery that SENP3 regulates the innate immune response via deSUMOylation of DHX15 and PCBP2 and recruitment of inflammatory molecules. Collectively, this dataset presents a site-resolved network of the SUMO-SENP system, providing information for potential substrates of the SENP proteins.

biochemistry↗

bioRxiv2020

Global multi-environment resistance QTL for foliar late blight resistance in tetraploid potato with tropical adaptation

The identification of environmentally stable and globally predictable resistance to potato late blight is challenged by the crops clonal and polyploid nature and the pathogens rapid evolution. Genome-wide analysis (GWA) of multi-environment trials can add precision to breeding for complex traits. A diversity panel of tetraploid potato germplasm bread for multiple resistance and quality traits was genotyped by genotyping by sequencing (GBS) and phenotyped for late blight resistance in a trait observation network spanning three continents addressed by the International Potato Centers (CIPs) breeding program. The aims of this study were to (i) identify QTL underlying resistance in and across environments and (ii) develop prediction models to support the global deployment and use of promising resistance sources in local breeding and variety development programs. Health-indexed in vitro plants of 380 clones and varieties were distributed from CIP headquarters in Peru to China and Ethiopia and tuber seed was produced centrally in each country. Phenotypes were recorded as rAUDPC following field exposure to local isolates of Phytophthora infestans, Stringent filtering for individual read depth >60 resulted in 3,239 tetraploid SNPs. Meanwhile, 55,748 diploid SNPs were identified using diploidized data and individual read depth>17. The kinship matrix was utilized to obtain BLUP and identify best performing germplasm in each and all environments. Genotypes with high levels of resistance in all environments were identified from the B3, LBHT and B3-LTVR populations. GWA identified stable QTL for late blight resistance in chromosome 9 and environment specific QTL in chromosomes 3, 5, 6 and 10.

genomics↗

bioRxiv2019

Mining the human tonsillar microbiota as autoimmune modulator

Palatine tonsils are important lymphoid organs featuring constant cross-talks between the commensal microorganisms and immune system, and have been implicated as critical autoimmunity origins for immune-related diseases, including rheumatoid arthritis (RA), a common autoimmune disorder. However, there was no evidence to show link between tonsillar microbiota and RA. Here, we identified a significant dysbiosis of RA tonsillar microbiota, with loss of Streptococcus salivarius and its functional molecules salivaricins (a type of antibacterial peptides). Consistent with the niche-preference, S. salivarius and salivaricins administrated intranasally or intraorally conferred prophylactic and therapeutic efficacies against experimental arthritis. Moreover, we demonstrated, for the first time, that S. salivarius and salivaricins exerted immunosuppressive capacities via inhibiting CD4+effector T cell subsets and autoantibody production in mice and human. These results uncover a communication between tonsillar microbiota and host autoimmunity, and identify the active components from tonsillar microbes in modulating immune homeostasis.\n\nOne sentence summaryTonsillar microbiota regulate host autoimmunity via antibacterial peptides

microbiology↗

bioRxiv2019

More Severe Loss-of-Function Sodium Channel induced by Compound SCN5A R965C and R1309H Mutants lead to Complex Familial Arrhythmia Syndrome.

[Abstract]O_ST_ABSObjectiveC_ST_ABSA complex familial arrhythmia syndrome was identified in a Chinese Han family, characterized by sick sinus syndrome, progressive conduction block, atrial fibrillation, atrial standstill and Brugada syndrome. The underlying mechanism associated with the genetic mutation was investigated.\n\nMethodsGenetic analysis was conducted for probands in the coding and splicing regions of genes susceptible to cardiac arrhythmia diseases. The stable cell lines overexpressing wild-type (WT) or mutant SCN5A gene were generated in HEK293T cells and electrophysiological recordings were performed to evaluate the functional changes of mutant NaV1.5 channels.\n\nResultsWe identified a rare double R965C and R1309H mutations in NaV1.5 channel, as a heterozygous and compound pattern, locating in the same chromosome. Compared to WT, a single mutation of R965C or R1309H, the compound mutations of R965C-R1309H most dramatically reduced the peak current of NaV1.5 channel with testing potentials ranging from -35 mV to 25 mV. Notably, the maximal peak current of NaV1.5 channel carrying R1309H only and R965C-R1309H mutations displayed significant decreases by 31.5% and 73.34%, respectively, compared to WT. Additionally, compared to single mutations of R965C or R1309H, the R965C-R1309H mutations resulted in more obviously depolarization-shifted activation and hyperpolarization-shifted inactivation, also caused most significantly changed time constant, V1/2 and slope factor of activation and inactivation.\n\nConclusionsThe compound mutations of R965C-R1309H led to more dramatically reduced current density of Nav1.5 channel, as well as more depolarization-shifted activation and hyperpolarization-shifted inactivation than single mutation of R965C or R1309H, which may provide more understanding on the molecular mechanisms underlying the familial arrhythmia syndrome.\n\nAuthor summarySeveral limited types of research about the interaction of compound mutations and the mechanism of interaction remains controversial. Here we report a novel compound mutation R965C-R1309H in SCN5A gene.The compound mutations of R965C-R1309H markedly reduced the Na+ current density of Nav1.5 channel and caused significant depolarization-shifted activation and hyperpolarization-shifted inactivation, suggesting that R965C mutation aggravated the pore gating changes of sodium channel containing R1309H mutation. The R965C located in the S4-like region in the intracellular loop between DII and DIII, and the R1309H located in the S4 helix of DIII as voltage sensor, which thus potentially had synergistic and interacting effects on pore gating properties of the sodium channel. Additionally, the complex familial arrhythmia syndrome simultaneously complicated of early young onset of arrhythmia and harmful prognosis of recurrent ischemic cerebral stroke, even though effective Warfarin anticoagulation.

genetics↗

bioRxiv2019

Branched-Chain Amino Acid Metabolic Reprogramming Orchestrates Drug Resistance to EGFR Tyrosine Kinase Inhibitors

Drug resistance is a significant hindrance to effective cancer treatment. Although resistance mechanisms of epidermal growth factor receptor (EGFR)-mutant cancer cells to lethal EGFR tyrosine kinase inhibitors (TKI) treatment have been investigated intensively, how cancer cells orchestrate adaptive response under sublethal drug challenge remains largely unknown. Here we find that 2-hour sublethal TKI treatment elicits a transient drug-tolerant state in EGFR-mutant lung cancer cells. Continuous sublethal treatment reinforces this tolerance and eventually establishes long-term TKI resistance. This adaptive process involves H3K9 demethylation-mediated epigenetic upregulation of branched-chain amino acid aminotransferase 1 (BCAT1) and subsequent metabolic reprogramming, which promotes TKI resistance through attenuating reactive oxygen species (ROS) accumulation. Combinational treatment with TKI and ROS-inducing reagents overcomes this drug resistance in preclinical mouse models. Clinical information analyses support the correlation of BCAT1 expression with EGFR TKI response. Collectively, our findings reveal the importance of epigenetically regulated BCAT1-engaged metabolism reprogramming in TKI resistance in lung cancer.\n\nHIGHLIGHTSSublethal EGFR TKI treatment induces transient drug-tolerant state and long-term resistance in EGFR-mutant lung cancer cells\n\nEpigenetically regulated BCAT1-mediated metabolic reprogramming orchestrates EGFR TKI-induced drug resistance\n\nCombinational treatment with TKI and ROS-inducing agents overcomes the drug resistance induced by EGFR TKI treatment

cancer biology↗

bioRxiv2019

The Role of the Public Health Service Equalization Program in the Control of Hypertension in China: Results from a Cross-sectional Health Interview Survey

ObjectivesNon-communicable diseases (NCDs) have become the main cause of mortality in China. In 2009, the Chinese government introduced the Public Health Service Equalization (PHSE) program to restore the primary healthcare system in both essential medical care and public health service provision. This study evaluates the impact of management on hypertension control and evaluate how the program works.\n\nMethodsThe China National Health Development Research Centre (CNHDRC) undertook the Cross-sectional Health Service Interview Survey (CHSIS) of 62,097 people from primary healthcare reform pilot areas, across 17 provinces from eastern, central and western parts of China in 2014. This study is based on CHSIS survey responses from 9,607 participants, who had been diagnosed with hypertension. Regression analysis was used to estimate the impact of management provided under PHSE on hypertension control adjusting for the effects of other known determinants of hypertension control.\n\nFindingsUncontrolled hypertension was markedly lower among respondents, whose hypertension had been managed (22.4% in managed patients versus 31.1% in unmanaged patients, p<0.001). The interaction between PHSE management and the geographical region was highly significant in the model (p<0.001), suggesting that the PHSE program was not equally effective in all regions. Further analysis suggested that approximately 10% of regional variability was attributed to differences in administrative systems, as there was a significant association (P=0.014) between the presence of established regional Information Management Systems (IMS) and increased PHSE effectiveness. Insurance ({chi}2(5)=4.4, p=0.496) and Hukou ({chi}2(1)=2.4, p=0.121), which denote social security and urban rural differences, respectively, were not significant predictor of hypertension control.\n\nConclusionActive management of hypertension through the PHSE program was effective with 7.31 million more patients receiving hypertension control and equalization of service delivery was reflected to some extent. The link between established IMS and regional variability in the impact of PHSE highlights the importance of effective management of patient referrals and follow-up. Further investigation is needed to explore the factors that influence the effectiveness of PHSE.

scientific communication and education↗

bioRxiv2019

Mechanically Resolved Imaging of Bacteria using Expansion Microscopy

Imaging dense and diverse microbial communities has broad applications in basic microbiology and medicine, but remains a grand challenge due to the fact that many species adopt similar morphologies. While prior studies have relied on techniques involving spectral labeling, we have developed an expansion microscopy method (ExM) in which cells are physically expanded prior imaging and their expansion patterns depend on the structural and mechanical properties of their cell walls, which vary across species and conditions. We use this phenomenon as a quantitative and sensitive phenotypic imaging contrast orthogonal to spectral separation in order to resolve bacterial cells of different species or in distinct physiological states. Focusing on host-microbe interactions that are difficult to quantify through fluorescence alone, we demonstrate the ability of ExM to distinguish species within a dense community through in vivo imaging of a model gut microbiota, and to sensitively detect cell-envelope damage caused by antibiotics or previously unrecognized cell-to-cell phenotypic heterogeneity among pathogenic bacteria as they infect macrophages.

biophysics↗

bioRxiv2019

Large-scale Lassa fever outbreaks in Nigeria: quantifying the association between disease reproduction number and local rainfall

BackgroundLassa fever (LF) is increasingly recognized as an important rodent-borne viral hemorrhagic fever presenting a severe public health threat to sub-Saharan West Africa. In 2018, LF caused an unprecedented outbreak in Nigeria, and the situation was worse in 2019. This work aims to study the epidemiological features of outbreaks in different Nigerian regions and quantify the association between reproduction number (R) and local rainfall by using modeling analysis.\n\nMethodsWe quantify the infectivity of LF by the reproduction numbers estimated from four different growth models: the Richards, three-parameter logistic, Gompertz, and Weibull growth models. LF surveillance data are used to fit the growth models and estimate the Rs and epidemic turning points ({tau}) in different regions at different time periods. Cochrans Q test is further applied to test the spatial heterogeneity of the LF epidemics. A linear random-effect regression model is adopted to quantify the association between R and local rainfall with various lag terms.\n\nFindingsOur estimated Rs for 2017-18 (1.33 with 95% CI: [1.29, 1.37]) and 2018-19 (1.29 with 95% CI: [1.27, 1.32]) are significantly higher than those for 2016-17 (1.23 with 95% CI: [1.22, 1.24]). We report spatial heterogeneity in the Rs for outbreaks in different Nigerian regions. For the association between rainfall and R, we find that a one unit (mm) increase in average rainfall over the past 7 months could cause a 0.62% (95% CI: [0.20%, 1.05%]) rise in R.\n\nConclusionThere is significant spatial heterogeneity in the LF epidemics in different Nigerian regions. We report clear evidence of rainfall impacts on LF outbreaks in Nigeria and quantify the impact.

epidemiology↗

bioRxiv2019

Prevalence of HIV-1 infection among foreign applicant to residency in Shanghai, China, 2005-2016

BackgroundShanghai is one of the biggest cities which have the highest number of entry travelers from all over the world. The HIV(human immunodeficiency virus) infection status of this population can reflect global trends of HIV prevalence to a certain extent. MethodsA retrospective cohort study was conducted to reveal the prevalence and characteristics of HIV-1 infection among entry travelers who applied to residency in Shanghai. The HIV-1 infection rate was estimated based on the detection of HIV-1 antibody. ResultsAmong 50830 entry travelers who applied to residency in Shanghai(2005-2016), 245 were determined HIV-1 positive with an infection rate of 0.48%. The detection rate of HIV was significantly higher in male (P<0.0001). Those aged 18-30 years, 31-40 years and >40years accounted for 34.3%,39.6% and 26.1% respectively of the infected population. Although there was no trend of increase in HIV-1 prevalence rates (Cochran-Armitage Z =2.543, P =0.111),proportions of individuals infected through homosexual transmission increased over the study period (Cochran-Armitage Z =5.41, P<0.001), while the proportions infected through heterosexual(Cochran-Armitage Z=3.38, P=0.001). ConclusionThe rate and characteristics of HIV-1 infection among foreign applicant to residency in Shanghai were revealed in the study. The results could provide the necessary epidemiological data for monitoring the HIV-1 epidemic among entry international travelers and to further contribute to the establishment of relevant policies and regulations for HIV control and prevention.

epidemiology↗

bioRxiv2019

Deep protein methylation profiling by combined chemical and immunoaffinity approaches reveals novel PRMT1 targets

Protein methylation has been implicated in many important biological contexts including signaling, metabolism, and transcriptional control. Despite the importance of this post-translational modification, the global analysis of protein methylation by mass spectrometry-based proteomics has not been extensively studied due to the lack of robust, well-characterized techniques for methyl peptide enrichment. Here, to better investigate protein methylation, we optimized and compared two methods for methyl peptide enrichment: immunoaffinity purification (IAP) and high pH strong cation exchange (SCX). Comparison of these methods revealed that they are largely orthogonal for monomethyl arginine (MMA), suggesting that the usage of both techniques is required to provide a global view of protein methylation. Using both IAP and SCX, we investigated changes in protein methylation downstream of protein arginine methyltransferase 1 (PRMT1) and quantified [~]1,000 methylation sites on 407 proteins. Of these methylation sites, PRMT1 knockdown resulted in significant changes to 97 arginine methylation sites on 59 proteins. In contrast, zero lysine methylation sites were significantly changed upon PRMT1 knockdown. In PRMT1 knockdown cells, 84 MMA sites were either significantly downregulated or upregulated. PRMT1 knockdown also induced significant changes in both asymmetric dimethyl arginine (ADMA) and symmetric dimethyl arginine (SDMA), suggesting that loss of PRMT1 activity allows scavenging of PRMT1 substrates by other PRMTs. Using neutral loss fragmentation ions unique to ADMA and SDMA, we annotated dimethylarginines as either ADMA or SDMA. Through integrative analysis of methyl forms, we identified 12 high confidence PRMT1 substrates, 43 putative PRMT1 substrates, and 17 methylation sites that are scavenged by other non-PRMT1 arginine methyltransferases in the absence of PRMT1 activity. Taken together, our results suggest that deep protein methylation profiling by mass spectrometry requires orthogonal enrichment techniques to identify novel PRMT1 methylation targets and highlight the dynamic interplay between methyltransferases in mammalian cells.

systems biology↗

bioRxiv2018

Study of the binding mechanisms between palytoxin and its aptamer by docking and molecular simulation

This paper provides a feasible model for aptamer and its target in molecular structure analysis and interaction mechanism. In this study, modeling and dynamic simulation of ssDNA aptamer (P-18S2) and target (Palytoxin, PTX) were performed separately. Then, the combination mechanism of DNA and PTX were predicted, and docking results showed that PTX can combine steadily in the groove at the top of DNA model trough strong hydrogen-bonds and electrostatic interaction. Therefore, we have further truncated and optimized to P-18S2 by simulating, at the same time, we also confirmed the reliability of simulative results by experimenting. Combining with the experimental and computational results, we provide a more reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX and offer the basis for aptamer development in molecular diagnostics and therapeutic application.\n\nAuthor summaryIn order to further study the complex structure and interaction of P-18S2 and PTX, a series of molecular modeling program were designed, including modeling, traditional dynamics simulation and molecular docking. Modeling results reveal that the structure of P-18S2 is a DNA G-quadruplex. Meanwhile, the 3D structure of PTX with lowest total energy after equilibrium was selected to use for the subsequent simulations. Then, based on the DNA with G-quadruplex structure, the combination model of DNA and PTX were predicted, and docking results showed that PTX can combine steadily in the groove at the top of DNA model trough strong hydrogen-bonds and electrostatic interaction. Futhermore, we compared the affinity of 6 optimized aptamers by computer simulating to primary P-18S2 bind to PTX respectively, the results showed no significant difference. Therefore, we have further truncated and optimized to P-18S2. In addition, this paper further refined research method based on our previous study[17], the instability of the target structure was considered and optimized, and the biological experiments were used to confirm the veracity of the simulative results. Combining with the experimental and computational methods, we obtained a reasonable interpretation for the high affinity and specific binding of P-18S2 and PTX. In summary, we established a feasible model for aptamer and its target in molecular structure analysis and interaction mechanism, and offer the basis for the study of aptamer development in molecular diagnostics and therapeutic application.

molecular biology↗

bioRxiv2018

‘Chromatic’ Neuronal Jamming in a Primitive Brain

Jamming models developed in inanimate matter have been widely used to describe cell packing in tissues1-7, but predominantly neglect cell diversity, despite its prevalence in biology. Most tissues, animal brains in particular, comprise a mix of many cell types, with mounting evidence suggesting that neurons can recognize their respective types as they organize in space8-11. How cell diversity revises the current jamming paradigm is unknown. Here, in the brain of the flatworm planarian Schmidtea mediterranea, which exhibits remarkable tissue plasticity within a simple, quantifiable nervous system12-16, we identify a distinct packing state, chromatic jamming. Combining experiments with computational modeling, we show that neurons of distinct types form independent percolating networks barring any physical contact. This jammed state emerges as cell packing configurations become constrained by cell type-specific interactions and therefore may extend to describe cell packing in similarly complex tissues composed of multiple cell types.

biophysics↗