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| 1 | Effect of human umbilical cord-derived mesenchymal stem cells on lung damage in severe COVID-19 patients:a randomized,double-blind,placebo-controlled phase 2 trial显示文摘Treatment of severe Coronavirus Disease 2019(COVID-19)is challenging.We performed a phase 2 trial to assess the efficacy andsafety of human umbilical cord-mesenchymal stem cells(UC-MScs)to treat severe coViD-19 patients with lung damage,based onour phase 1 data.In this randomized,double-blind,and placebo-controlled trial,we recruited 101 severe coVID-19 patients withlung damage.They were randomly assigned at a 2:1 ratio to receive either UC-MSCs(4×10^(7)cells per infusion)or placebo on day 0,3,and 6.The primary endpoint was an altered proportion of whole lung lesion volumes from baseline to day 28.Other imagingoutcomes,6-minute walk test(6-MWT),maximum vital capacity,diffusing capacity,and adverse events were recorded and analyzed.In all,100 COVID-19 patients were finally received either UC-MSCs in=65)or placebo(n=35).UC-MSCs administrationexerted numerical improvement in whole lung lesion volume from baseline to day 28 compared with the placebo(the mediandifference was-13.31%,95%Cl-29.14%,2.13%,P=0.08).UC-MSCs significanty reduced the proportions of solid componentlesion volume compared with the placebo(median difference:-15.45%;95%CI-30.82%,-0.39%;P=0.043).The 6-MWT showedan increased distance in patients treated with UC-MSCs(difference:27.00 m;95%CI 0.00,57.00;P=0.057).The incidence of adverseevents was similar in the two groups.These results suggest that UC-MSCs treatment is a safe and potentially effective therapeuticapproach for COVID-19 patients with lung damage.A phase 3 trial is required to evaluate effects on reducing mortality andpreventing long-term pulmonary disability. | Lei Shi Hai Huang Xuechun Lu Xiaoyan Yan Xiaojing Jiang Ruonan Xu Siyu Wang Chao Zhang Xin Yuan Zhe Xu Lei Huang Jun-Liang Fu Yuanyuan Li Yu Zhang Wei-Qi Yao Tianyi Liu Jinwen Song Liangliang Sun Fan Yang Xin Zhang Bo Zhang Ming Shi Fanping Meng Yanning Song Yongpei Yu Jiqiu Wen Qi Li Qing Mao Markus Maeurer Alimuddin Zumla Chen Yao Wei-Fen Xie Fu-Sheng Wang | 2021 | Signal Transduction and Targeted Therapy2021，6，3： | 13 |
| 2 | The circFASN/miR-33a pathway participates in tacrolimusinduced dysregulation of hepatic triglyceride homeostasis显示文摘Dyslipidemia exhibits a high incidence after liver transplantation,in which tacrolimus,a widely used immunosuppressant,plays a fundamental role.MicroRNAs and related circRNAs represent a class of noncoding RNAs that have been recognized as important regulators of genes associated with lipid metabolism.However,their transcriptional activities and functional mechanisms in tacrolimus-related dyslipidemia remain unclear.In this study,we observed that tacrolimus could induce triglyceride accumulation in hepatocytes by stimulating sterol response element-binding proteins(SREBPs)and miR-33a.Our in silico and experimental analyses identified miR-33a as a direct target of circFASN.Tacrolimus could downregulate circFASN and result in elevated miR-33a in vivo and in vitro.Overexpression of circFASN or silencing of miR-33a decreased the promoting effects of tacrolimus on triglyceride accumulation.Clinically,the incidence of dyslipidemia in liver transplant recipients with elevated serum miR-33a after liver transplantation was higher than that in patients without elevated serum miR-33a(46.3%vs.18.8%p=0.012,n=73).Our results showed that the circFASN/miR-33a regulatory system plays a distinct role in tacrolimus-induced disruption of lipid homeostasis.MiR-33a is likely a risk factor for tacrolimus-related dyslipidemia,providing a potential therapeutic target to combat tacrolimus-induced dyslipidemia after liver transplantation. | Chenzhi Zhang Kangchen Chen Rongli Wei Guanghan Fan Xuechun Cai Li Xu Beini Cen Jianguo Wang Haiyang Xie Shusen Zheng Xiao Xu | 2020 | Signal Transduction and Targeted Therapy2020，5，1： | 2 |
| 3 | Pyrolysis Characteristics and Kinetics of Methyl Oleate Based on TG-FTIR Method显示文摘The thermal decomposition characteristics of methyl oleate were preliminarily investigated under nitrogen atmosphere by a thermogravimetric analyzer when the ester was heated at a heating rate of 10 ℃/min from room temperature to 600 ℃. Furthermore, the pyrolytic and kinetic characteristics of methyl oleate were intensively studied at different heating rates. The gaseous species obtained during thermal decomposition were also identified by the TG-FTIR coupling analysis. The results showed that the pyrolysis of methyl oleate proceeded in three stages, viz. the drying stage, the main pyrolysis stage and the residual pyrolysis stage. The initial decomposition temperature, the maximum weight loss temperature, the peak decomposition temperature and the rate of maximum weight loss of methyl oleate increased with the increasing heating rates. Gaseous CO, CO2 and H2 O were the typical decomposition products from pyrolysis of methyl oleate. In addition, a kinetic model for thermal decomposition of methyl oleate was built up based on the experimental results using the CoatsRedfern integral method and the multiple-linear regression method. The activation energy, the pre-exponential factor, the reaction order and the kinetic equation for thermal decomposition of methyl oleate were obtained. Comparison of the experimental data with the calculated ones and analysis of statistical errors of pyrolysis ratios demonstrated that the kinetic model was reliable for studying the pyrolysis of methyl oleate. Finally, the kinetic compensation effect between the preexponential factors and the activation energy in the pyrolysis of methyl oleate was also confirmed. | Wang Xuechun Fang Jianhua Chen Boshui Wang Jiu Wu Jiang | 2015 | China Petroleum Processing & Petrochemical Technology2015，17，2： | 2 |
| 4 | BDE-47 disrupts axonal growth and motor behavior in developing zebrafish显示文摘 | Xiaojuan Chen Changjiang Huang Xuechun Wang Jiangfei Chen Chenglian Bai Yuanhong Chen Xiangping Chen Qiaoxiang Dong Dongren Yang | 2012 | Aquatic Toxicology2012，，： | 1 |
| 5 | Analysis of adverse events following the treatment of autologous cytokine-induced killer cells for adoptive immunotherapy in malignant tumour sufferers显示文摘 | Yajing Zhang Lei Xia Yan Zhang Yao Wang Xuechun Lu Fengxia Shi Yang Liu Meixia Chen Kaixhao Feng Wenying Zhang Xiaobing Fu Weidong Han | 2015 | Expert Opinion on Biological Therapy2015，，： | 1 |
| 6 | Development of a Wireless-Controlled LED Array for the Tunable Optogenetic Control of Cellular Activities显示文摘1.Introduction In order to decipher a complex biological process,tools are required to perturb the various players involved to gain information about the important parameters.Optogenetic modules are genetically encoded molecular reagents that,when expressed in cells,allow a specific biological process to be precisely controlled by light in a spatiotemporal manner[1].Optogenetics thus offers cell biologists an unprecedented new way to perturb cellular activities.The application of optogenetic approaches in cellular biology and synthetic biology research has evolved tremendously in the last few years[2–4]. | Yuankai Qi Junye Chen Xuechun Liu Xiaoxu Zhou Jiannan Fan Ping Shentu Olof Idevall-Hagren Yingke Xu | 2018 | Engineering2018，4，6： | 1 |
| 7 | Pathogenesis of premature coronary artery disease:Focus on risk factors and genetic variants显示文摘The development of premature coronary artery disease(PCAD)is dependent on both genetic predisposition and traditional risk factors.Strategies for unraveling the genetic basis of PCAD have evolved with the advent of modern technologies.Genome-wide association studies(GWASs)have identified a considerable number of common genetic variants that are associated with PCAD.Most of these genetic variants are attributable to lipid and blood pressure-related single-nucleotide polymorphisms(SNPs).The genetic variants that predispose individuals to developing PCAD may depend on race and ethnicity.Some characteristic genetic variants have been identified in Chinese populations.Although translating this genetic knowledge into clinical applications is still challenging,these genetic variants can be used for CAD phenotype identification,genetic prediction and therapy.In this article we will provide a comprehensive review of genetic variants detected by GWASs that are predicted to contribute to the development of PCAD.We will highlight recent findings regarding CAD-related genetic variants in Chinese populations and discuss the potential clinical utility of genetic variants for preventing and managing PCAD. | Haiming Wang Zifan Liu Junjie Shao Min Jiang Xuechun Lu Lejian Lin Lin Wang Qiang Xu Haomin Zhang Xin Li Jingjing Zhou Yundai Chen Ran Zhang | 2022 | Genes & Diseases2022，9，2： | 1 |
| 8 | BDE-47 disrupts axonal growth and motor behavior in developing zebrafish显示文摘 | Xiaojuan Chen Changjiang Huang Xuechun Wang Jiangfei Chen Chenglian Bai Yuanhong Chen Xiangping Chen Qiaoxiang Dong Dongren Yang | 2012 | Aquatic Toxicology2012，，： | 1 |
| 9 | Theoretical Analysis of Random Scattering Induced by Microlensing显示文摘Theoretical investigations into the deflection angle caused by microlenses offer a direct path to uncovering principles of the cosmological microlensing effect.This work specifically concentrates on the the probability density function(PDF)of the light deflection angle induced by microlenses.We have made several significant improvements to the widely used formula from Katz et al.First,we update the coefficient from 3.05 to 1.454,resulting in a better fit between the theoretical PDF and our simulation results.Second,we developed an elegant fitting formula for the PDF that can replace its integral representation within a certain accuracy,which is numerically divergent unless arbitrary upper limits are chosen.Third,to facilitate further theoretical work in this area,we have identified a more suitable Gaussian approximation for the fitting formula. | Wenwen Zheng Hou-Zun Chen Xuechun Chen Guoliang Li | 2023 | Research in Astronomy and Astrophysics2023，23，8： | 0 |
| 10 | Conductive PS inverse opals for regulating proliferation and differentiation of neural stem cells显示文摘The development of neural tissue engineering has brought new hope to the treatment of spinal cord injury(SCI).Up to date,various scaffolds have been developed to induce the oriented growth and arrangement of nerves to facilitate the repair after injury.In this work,a conductive and anisotropic inverse opal substrate was presented by modifying polystyrene(PS)inverse opal films with carbon nanotubes and then stretching them to varying degrees.The film had good biocompatibility,and neural stem cells(NSCs)grown on the film displayed good orientation along the stretching direction.In addition,benefiting from the conductivity and anisotropy of the film,NSCs differentiated into neurons significantly.These results suggest that the conductive and anisotropic PS inverse opal substrates possess value in nerve tissue engineering regeneration. | Yangnan Hu Han Zhang Hao Wei Menghui Liao Xiaoyan Chen Jiayue Xing Lian Duan Cuntu Cheng Weicheng Lu Xuechun Yang Peina Wu Huan Wang Jingdun Xie Renjie Chai | 2023 | Engineered Regeneration2023，4，2： | 0 |
| 11 | Deciphering bioactive compounds of complex natural products by tandem mass spectral molecular networking combined with an aggregation-induced emission based probe显示文摘Natural products are great treasure troves for the discovery of bioactive components.Current bioassay guided fractionation for identification of bioactive components is time-and workload-consuming.In this study,we proposed a robust and convenient strategy for deciphering the bioactive profile of natural products by mass spectral molecular networking combined with rapid bioassay.As a proof-of-concept,the strategy was applied to identify angiotensin converting enzyme(ACE)inhibitors of Fangjihuangqi decoction(FJHQD),a traditional medicine clinically used for the treatment of heart failure.The chemical profile of FJHQD was comprehensively revealed with the assistance of tandem mass spectral molecular networking,and a total of 165 compounds were identified.With characterized constituents,potential clinical applications of FJHQD were predicted by Bioinformatics Analysis Tool for Molecular mech ANism of Traditional Chinese Medicine,and a range of cardiovascular related diseases were significantly enriched.ACE inhibitory activities of FJHQD and its constituents were then investigated with an aggregation-induced emission based fluorescent probe.FJHQD exhibited excellent ACE inhibitory effects,and a bioactive molecular network was established to elucidate the ACE inhibitory profile of constituents in FJHQD.This bioactive molecular network provided a panoramic view of FJHQD’s ACE inhibitory activities,which demonstrated that flavones from Astragali Radix and Glycyrrhizae Radix et Rhizoma,saponins from Astragali Radix,and sesquiterpenoids from Atractylodis Macrocephalae Rhizoma were principal components responsible for this effect of FJHQD.Among them,four novel ACE inhibitors were the first to be reported.Our study indicated that the proposed strategy offers a useful approach to uncover the bioactive profile of traditional medicines and provides a pragmatic workflow for exploring bioactive components. | Zhenzhong Yang Jun Li Xuechun Chen Xiaoping Zhao Yi Wang | 2022 | Journal of Pharmaceutical Analysis2022，12，1： | 0 |
| 12 | Rapid and mass manufacturing of soft hydrogel microstructures for cell patterns assisted by 3D printing显示文摘Micro-/nano-patterns on hydrogels are widely used in cell patterning.However,manufacturing molds with traditional lithography is time-consuming and expensive.In addition,the excessive demolding force can easily damage patterns since biocompatible hydrogels are ultra-soft or brittle.Here,we presented a novel method for rapid and mass fabrication of cell patterns.High-precision three-dimensional(3D)printing was used to manufacture a mold with a resolution of 2µm,and the gelatin-based hydrogel was cured by thermal–photo-crosslinking so that the low-concentration and low-substitutionrate hydrogel could be demolded successfully.We found that pre-cooling before illumination made gelatin-based hydrogels resilient due to the partial regain of triple-helix structures.With this method,arbitrarily customized hydrogel patterns with a feature size of 6–80µm can be fabricated stably and at low cost.When cardiomyocytes were seeded on ultra-soft hydrogels with parallel groove structures,a consistent and spontaneous beating with 216 beats per minute(BPM)could be observed,approaching the natural beating rate of rat hearts(300 BPM).Overall,this work provides a general scheme for manufacturing cell patterns which has great potential for cell ethology and tissue repair. | Chaofan He Xuechun Chen Yuan Sun Mingjun Xie Kang Yu Jing He Jinwei Lu Qing Gao Jing Nie Yi Wang Yong He | 2022 | Bio-Design and Manufacturing2022，5，4： | 0 |
| 13 | Two cases on primary bone marrow lymphoma显示文摘Managing Editor:Peng Lyu Primary bone marrow lymphoma(PBML)is a rare lymphoma accounting for 1.23%of non-Hodgkin lymphoma(NHL)cases.It is characterized by tumor cells invading only the bone marrow without systemic lymphadenopathy or extranodal organ involvement.Owing to the lack of standardized treatment regimens,most patients are treated using rituximab with cyclophosphamide,doxorubicin,vincristine,and prednisone(R-CHOP)regimens;however,their efficacy needs to be further investigated. | Zining Wang Lu Sun Yue Wang Haoran Chen Hongbin Pu Bo Yang Xuechun Lu | 2024 | Cancer Pathogenesis and Therapy2024，2，1： | 0 |
| 14 | Bioinformatics analysis of SARS-CoV-2 infectionassociated immune injury and therapeutic prediction for COVID-19显示文摘Background:Severe acute respiratory syndrome coronavirus 2 is a highly contagious viral infection,without any available targeted therapies.The high mortality rate of COVID-19 is speculated to be related to immune damage.Methods:In this study,clinical bioinformatics analysis was conducted on transcriptome data of coronavirus infection.Results:Bioinformatics analysis revealed that the complex immune injury induced by coronavirus infection provoked dysfunction of numerous immune-related molecules and signaling pathways,including immune cells and toll-like receptor cascades.Production of numerous cytokines through the Th17 signaling pathway led to elevation in plasma levels of cytokines(including IL6,NF-kB,and TNF-a)followed by concurrent inflammatory storm,which mediates the autoimmune response.Several novel medications seemed to display therapeutic effects on immune damage associated with coronavirus infection.Conclusions:This study provided insights for further large-scale studies on the target therapy on reconciliation of immunological damage associated with COVID-19. | Haomin Zhang Haoran Chen Jundong Zhang Ximeng Chen Bin Guo Peng Zhi Zhuoyang Li Geliang Liu Bo Yang Xiaohua Chi Yixing Wang Feng Cao Jun Ren Xuechun Lu | 2021 | Emergency and Critical Care Medicine2021，1，1： | 0 |
| 15 | Targeting Hypoxic Tumors with Hybrid Nanobullets for Oxygen-Independent Synergistic Photothermal and Thermodynamic Therapy显示文摘Hypoxia is a feature of solid tumors and it hinders the therapeutic efficacy of oxygen-dependent cancer treatment.Herein,we have developed all-organic oxygen-independent hybrid nanobullets ZPA@HA-ACVA-AZ for the“precise strike”of hypoxic tumors through the dual-targeting effects from surface-modified hyaluronic acid(HA)and hypoxia-dependent factor carbonic anhydrase IX(CA IX)-inhibitor acetazolamide(AZ).The core of nanobullets is the special zinc(II)phthalocyanine aggregates(ZPA)which could heat the tumor tissues upon 808-nm laser irradiation for photothermal therapy(PTT),along with the alkyl chain-functionalized thermally decomposable radical initiator ACVA-HDA on the side chain of HA for providing oxygen-independent alkyl radicals for ablating hypoxic cancer cells by thermodynamic therapy(TDT).The results provide important evidence that the combination of reverse hypoxia hallmarks CA IX as targets for inhibition by AZ and synergistic PTT/TDT possess incomparable therapeutic advantages over traditional(reactive oxygen species(ROS)-mediated)cancer treatment for suppressing the growth of both hypoxic tumors and their metastasis. | Di Gao Ting Chen Shuojia Chen Xuechun Ren Yulong Han Yiwei Li Ying Wang Xiaoqing Guo Hao Wang Xing Chen Ming Guo Yu Shrike Zhang Guosong Hong Xingcai Zhang Zhongmin Tian Zhe Yang | 2021 | Nano-Micro Letters2021，13，6： | 0 |
| 16 | Wave effect of gravitational waves intersected with a microlens field:A new algorithm and supplementary study显示文摘The increase in gravitational wave(GW) events has allowed receiving strong lensing image pairs of GWs. However, the wave effect(diffraction and interference) due to the microlens field contaminates the parameter estimation of the image pair, which may lead to a misjudgment of strong lensing signals. To quantify the influence of the microlens field, researchers need a large sample of statistical research. Nevertheless, due to the oscillation characteristic, the Fresnel-Kirchhoff diffraction integral’s computational time hinders this aspect’s study. Although many algorithms are available, most cannot be well applied to the case where the microlens field is embedded in galaxy/galaxy clusters. This work proposes a faster and more accurate algorithm for studying the wave optics effect of microlenses embedded in different types of strong lensing images. Additionally, we provide a quantitative estimation criterion for the lens plane boundary for the Fresnel-Kirchhoff diffraction integral. This algorithm can significantly facilitate the study of wave optics, particularly in the case of microlens fields embedded in galaxy/galaxy clusters. | Xikai Shan Guoliang Li Xuechun Chen Wenwen Zheng Wen Zhao | 2023 | Science China(Physics,Mechanics & Astronomy)2023，66，3： | 0 |
| 17 | Crystal structure of the GDSL family esterase EstL5 in complex with PMSF reveals a branch channel of the active site pocket显示文摘Esterases/lipases from the GDSL family have potential applications in the hydrolysis and synthesis of important esters of pharmaceutical,food,and biotechnical interests.However,the structural and functional understanding of GDSL enzymes is still limited.Here,we report the crystal structure of the GDSL family esterase EstL5 complexed with PMSF at 2.34Åresolution.Intriguingly,the PMSF binding site is not located at the active site pocket but is situated in a surface cavity.At the active site,we note that there is a trapped crystallization solvent 1,6-hexanediol,which mimics the bound ester chain,allowing for further definition of the active site pocket of EstL5.The most striking structural feature of EstL5 is the presence of a unique channel,which extends approximately 18.9Å,with a bottleneck radius of 6.8Å,connecting the active-site pocket and the surface cavity.Replacement of Ser205 with the bulk aromatic residue Trp or Phe could partially block the channel at one end and perturb its access.Reduced enzymatic activity is found in the EstL5 S205W and EstL5 S205F mutants,suggesting the functional relevance of the channel to enzyme catalysis.Our study provides valuable information regarding the properties of the GDSL-family enzymes for designing more efficient and robust biocatalysts. | Runsha Chen Xuechun Gao Ting Nie Jinhong Wu Lin Wang Ali Osman Yan Feng Xianghong Li Yong Zhang | 2023 | Acta Biochimica et Biophysica Sinica2023，55，11： | 0 |
| 18 | Mirror-like tongue is an important predictor of acute heart failure:a cohort study of acute heart failure in Chinese patients显示文摘OBJECTIVE:To reveal that mirror-like tongue,observed via a noninvasive inspection,is a powerful indicator of the severity and prognosis of patients with acute heart failure(AHF).METHODS:This was an observational,prospective study.A total of 408 patients who met the inclusion criteria and were diagnosed with AHF for the first time at Taicang Traditional Chinese Medicine Hospital Affiliated to Nanjing University of Chinese Medicine from August 2019 to January 2021 were selected as the research subjects.According to their tongue fur,the patients were divided into group A(mirror-like tongue group)and group B(non-mirror-like tongue group).The clinical characteristics and incidence of major adverse cardiovascular events(MACEs)within 1 year of follow-up were systematically compared between the two groups.RESULTS:Sixty-five patients were included in group A,and 343 patients were included in group B.There were 32 males and 33 females in group A and 168 males and 175 females in group B.The average age of the overall population was 64 years old,and the average age of group A was significantly higher than that of group B(74 vs 62 years,P<0.001).Compared with that in group B,the left ventricular ejection fraction(LVEF)in group A was significantly lower(35%vs 42%,P<0.001),and the log N-terminal pro B-type natriuretic peptide(NT-proBNP)level was significantly higher(4.0 vs 3.4,P<0.001).The proportion of the combined application of vasoactive drugs in group A was significantly higher than that in group B(64%vs 38%,P<0.001).Group B had a higher proportion of coronary angiography(29.5%vs 16.9%,P=0.038).Group A was more inclined to require mechanical ventilation than group B(33.9%vs 22.5%,P=0.049).The length of hospital stay in group A was significantly longer than that in group B(13.1 vs 7.6,P<0.001).The incidence of MACEs,such as recurrence of AHF,new myocardial infarction and stroke,in group A within one year was higher than that in group B(P=0.007,0.009,<0.001).The incidence of cumulative MACEs in group A was significantly higher than that in group B[hazard ratio=2.76,95%confidence interval(1.73,4.41),P<0.001].Univariate and multivariate Cox regression analyses showed that mirror-like tongue,age,length of stay,LVEF and log NT-proBNP were independent predictors of MACEs in patients with AHF within one year.CONCLUSIONS:Noninvasive tongue inspection technology can be used as a powerful tool for assessing the severity of illness and predicting prognosis in patients with AHF.A mirror-like tongue is an independent risk factor for MACEs in patients with AHF during the first year and has a combination effect with age,length of hospital stay,ejection fraction and NT-proBNP on the occurrence of MACEs. | CHEN Yunhu YIN Moqing FAN Lihua JIANG Xuechun ZHANG Tao ZHU Xingyu XU Hongfeng | 2023 | Journal of Traditional Chinese Medicine2023，43，6： | 0 |
| 19 | 1.2 kW all-fiber narrow-linewidth picosecond MOPA system显示文摘Achieving an all-fiber ultra-fast system with above kW average power and mJ pulse energy is extremely challenging.This paper demonstrated a picosecond monolithic master oscillator power amplifier system at a 25 MHz repetition frequency with an average power of approximately 1.2 kW,a pulse energy of approximately 48μJ and a peak power of approximately 0.45 MW.The nonlinear effects were suppressed by adopting a dispersion stretched seed pulse(with a narrow linewidth of 0.052 nm)and a multi-mode master amplifier with an extra-large mode area;then an ultimate narrow bandwidth of 1.32 nm and a moderately broadened pulse of approximately 107 ps were achieved.Meanwhile,the great spatio-temporal stability was verified experimentally,and no sign of transverse mode instability appeared even at the maximum output power.The system has shown great power and energy capability with a sacrificed beam propagation product of 5.28 mm·mrad.In addition,further scaling of the peak power and pulse energy can be achieved by employing a lower repetition and a conventional compressor. | Jiexi Zuo Haijuan Yu Shuzhen Zou Zhiyong Dong Chaojian He Shuang Xu Chaoyu Ning Xuechun Chen Xinyao Li Xuechun Lin | 2023 | High Power Laser Science and Engineering2023，11，2： | 0 |
| 20 | CRISPR-detector:fast and accurate detection,visualization,and annotation of genome-wide mutations induced by genome editing events显示文摘The leading-edge CRISPR/CRISPR-associated technology is revolutionizing biotechnologies through genome editing.To track on/off-target events with emerging new editing techniques,improved bioinformatic tools are indispensable.Existing tools suffer from limitations in speed and scalability,especially with whole-genome sequencing(WGS)data analysis.To address these limitations,we have developed a comprehensive tool called CRISPR-detector,a web-based and locally deployable pipeline for genome editing sequence analysis.The core analysis module of CRISPR-detector is based on the Sentieon TNscope pipeline,with additional novel annotation and visualization modules designed to fit CRISPR applications.Co-analysis of the treated and control samples is performed to remove existing background variants prior to genome editing.CRISPR-detector offers optimized scalability,enabling WGS data analysis beyond Browser Extensible Data file-defined regions,with improved accuracy due to haplotype-based variant calling to handle sequencing errors.In addition,the tool also provides integrated structural variation calling and includes functional and clinical annotations of editing-induced mutations appreciated by users.These advantages facilitate rapid and efficient detection of mutations induced by genome editing events,especially for datasets generated from WGS.The web-based version of CRISPR-detector is available at http://gffzz984746bd41ee48d7subwvbf5fnn0c6ucq.ffgz.tsg.suse.edu.cn/crispr-detector,and the locally deployable version is available at http://gffzz188fe103f8f1460asubwvbf5fnn0c6ucq.ffgz.tsg.suse.edu.cn/hlcas/CRISPR-detector. | Lei Huang Dan Wang Haodong Chen Jinnan Hu Xuechen Dai Chuan Liu Anduo Li Xuechun Shen Chen Qi Haixi Sun Dengwei Zhang Tong Chen Yuan Jiang | 2023 | Journal of Genetics and Genomics2023，50，8： | 0 |
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