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期刊论文 10

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MS-CETSA 1

免疫球蛋白 G 1

抗疟 1

消化道癌症 1

糖基化 1

诊断生物标志物 1

转录组学 1

青蒿素 1

靶标鉴定 1

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Mutation profiling of 16 candidate genes in

Yang Zhang, Fang Wang, Xue Chen, Wenjing Liu, Jiancheng Fang, Mingyu Wang, Wen Teng, Panxiang Cao, Hongxing Liu

《医学前沿（英文）》 2019年 第13卷 第2期   页码 229-237 doi: 10.1007/s11684-018-0616-1

摘要： This retrospective analysis aimed to investigate the mutation profile of 16 common mutated genes in acute myeloid leukemia (AML) patients. A total of 259 patients who were diagnosed of AML were enrolled in this study. Mutation profiling of 16 candidate genes were performed in bone marrow samples by using Sanger sequencing. We identified at least 1 mutation in 199 of the 259 samples (76.8%), and 2 or more mutations in 31.7% of samples. was the most common mutated gene (16.2%, 42/259), followed by (15.1%, 39/259), (14.7%, 38/259), and (13.5%, 35/259). Concurrence was observed in 97.1% of the mutated cases and in 29.6% of the double mutated cases. Distinct patterns of co-occurrence were observed for different hotspot mutations within the gene: mutations were associated with and/or mutations, whereas mutations co-occurred with mutations only. Concurrence was also observed in 86.6% of epigenetic regulation genes, most of which co-occurred with mutations. The results showed certain rules in the mutation profiling and concurrence of AML patients, which was related to the function classification of genes. Defining the mutation spectrum and mutation pattern of AML will contribute to the comprehensive assessment of patients and identification of new therapeutic targets.

关键词： leukemia     myeloid     acute     gene     mutation    

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Profiling influences of gene overexpression on heterologous resveratrol production in

Duo Liu,Bingzhi Li,Hong Liu,Xuejiao Guo,Yingjin Yuan

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 117-125 doi: 10.1007/s11705-016-1601-3

摘要： Metabolic engineering of heterologous resveratrol production in faces challenges as the precursor L-tyrosine is stringently regulated by a complex biosynthetic system. We overexpressed the main gene targets in the upstream pathways to investigate their influences on the downstream resveratrol production. Single-gene overexpression and DNA assembly-directed multigene overexpression affect the production of resveratrol as well as its precursor -coumaric acid. Finally, the collaboration of selected gene targets leads to an optimal resveratrol production of 66.14±3.74 mg·L , 2.27 times higher than the initial production in YPD medium (4% glucose). The newly discovered gene targets expressing phosphoribosylanthranilate isomerase, expressing 3-deoxy-D-arabino-heptulosonate-7-phosphate synthase, and expressing 4-coumaryl-CoA ligase show notable positive impacts on resveratrol production in .

关键词： resveratrol     aromatic amino acid     DNA assembly     metabolic engineering     gene overexpression    

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Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

null

《医学前沿（英文）》 2016年 第10卷 第1期   页码 61-75 doi: 10.1007/s11684-016-0436-0

摘要：

The latent expression pattern of Epstein-Barr Virus (EBV) genes in nasopharyngeal carcinoma (NPC) has been extensively investigated, and the expression of several lytic genes in NPC has been reported. However, comprehensive information through EBV transcriptome analysis in NPC is limited. We performed paired-end RNA-seq to systematically and comprehensively characterize the expression of EBV genes in NPC tissue and C666-1 NPC cell line, which consistently carries EBV. In addition to the transcripts restricted to type II latency infection, the type III latency EBNA3s genes and a substantial number of lytic genes, such as BZLF1, BRLF1, and BMRF1, were detected through RNA-seq and were further verified in C666-1 cells and NPC tissue through real-time PCR. We also performed clustering analysis to classify NPC patient groups in terms of EBV gene expression, which presented two subtypes of NPC samples. Results revealed interesting patterns of EBV gene expression in NPC patients. This clustering was correlated with many signaling pathways, such as those related to heterotrimeric G-protein signaling, inflammation mediated by chemokine and cytokine signaling, ribosomes, protein metabolism, influenza infection, and ECM-receptor interaction. Our combined findings suggested that the expression of EBV genes in NPC is restricted not only to type II latency genes but also to type III latency and lytic genes. This study provided further insights into the potential role of EBV in the development of NPC.

关键词： Epstein-Barr virus     paired-end transcriptome sequencing     latency genes     lytic genes     nasopharyngeal carcinoma    

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Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

《信息与电子工程前沿（英文）》 2015年 第16卷 第2期   页码 135-151 doi: 10.1631/FITEE.1400239

摘要： Accurate and fast performance estimation is necessary to drive design space exploration and thus support important design decisions. Current techniques are either time consuming or not accurate enough. In this paper, we solve these problems by presenting a hybrid method for multimedia multiprocessor system-on-chip (MPSoC) performance estimation. A general coverage analysis tool GNU gcov is employed to profile the execution statistics during the native simulation. To tackle the complexity and keep the analysis and simulation manageable, the orthogonalization of communication and computation parts is adopted. The estimation result of the computation part is annotated to a transaction accurate model for further analysis, by which a gradual refinement of MPSoC performance estimation is supported. The implementation and its experimental results prove the feasibility and efficiency of the proposed method.

关键词： MPSoC     Gradual refinement     Native simulation     Performance estimation     Profiling     Annotation     Gcov    

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Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

《医学前沿（英文）》 2021年 第15卷 第1期   页码 144-154 doi: 10.1007/s11684-020-0792-7

摘要： Oocyte cryopreservation is widely used for clinical and social reasons. Previous studies have demonstrated that conventional slow-freezing cryopreservation procedures, but not storage time, can alter the gene expression profiles of frozen oocytes. Whether vitrification procedures and the related frozen storage durations have any effects on the transcriptomes of human metaphase II oocytes remain unknown. Four women (30–32 years old) who had undergone IVF treatment were recruited for this study. RNA-Seq profiles of 3 fresh oocytes and 13 surviving vitrified-thawed oocytes (3, 3, 4, and 3 oocytes were cryostored for 1, 2, 3, and 12 months) were analyzed at a single-cell resolution. A total of 1987 genes were differentially expressed in the 13 vitrified-thawed oocytes. However, no differentially expressed genes were found between any two groups among the 1-, 2-, 3-, and 12-month storage groups. Further analysis revealed that the aberrant genes in the vitrified oocytes were closely related to oogenesis and development. Our findings indicated that the effects of vitrification on the transcriptomes of mature human oocytes are induced by the procedure itself, suggesting that long-term cryostorage of human oocytes is safe.

关键词： human metaphase II oocyte     vitrification     cryostorage duration     single-cell RNA-Seq     lncRNA    

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Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

null

《医学前沿（英文）》 2013年 第7卷 第2期   页码 157-171 doi: 10.1007/s11684-013-0272-4

摘要：

Non-small-cell lung cancer (NSCLC) is the most common cause of premature death among the malignant diseases worldwide. The current staging criteria do not fully capture the complexity of this disease. Molecular biology techniques, particularly gene expression microarrays, proteomics, and next-generation sequencing, have recently been developed to facilitate effectively its molecular classification. The underlying etiology, pathogenesis, therapeutics, and prognosis of NSCLC based on an improved molecular classification scheme may promote individualized treatment and improve clinical outcomes. This review focuses on the molecular classification of NSCLC based on gene expression microarray technology reported during the past decade, as well as their applications for improving the diagnosis, staging and treatment of NSCLC, including the discovery of prognostic markers or potential therapeutic targets. We highlight some of the recent studies that may refine the identification of NSCLC subtypes using novel techniques such as epigenetics, proteomics, or deep sequencing.

关键词： non-small-cell lung cancer     molecular typing     individualized medicine     molecular-targeted therapy     gene expression profiling    

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Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

《环境科学与工程前沿（英文）》 2023年 第17卷 第1期 doi: 10.1007/s11783-023-1604-5

摘要：

● Metabolomic temporal profiling of cells exposed to xenobiotics.

关键词： Metabolomics     BPA     MCF-7     Temporal profiling     Metabolic adaption     Dysregulation correlation    

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ANTIVIRAL EFFECTS OF BACTERIOCIN AGAINST ANIMAL-TO-HUMAN TRANSMITTABLE MUTATED SARS-COV-2: A SYSTEMATIC REVIEW

《农业科学与工程前沿（英文）》 2021年 第8卷 第4期   页码 603-622 doi: 10.15302/J-FASE -2021397

摘要：

The COVID-19 infections caused by SARS-CoV-2 have resulted in millions of people being infected and thousands of deaths globally since November 2019. To date, no unique therapeutic agent has been developed to slow the progression of this pandemic. Despite possessing antiviral traits the potential of bacteriocins to combat SARS-CoV-2 infection has not been fully investigated. This review summarizes the mechanisms by which bacteriocins can be manipulated and implemented as effective virus entry blockers with infection suppression potential properties to highly transmissible viruses through comprehensive immune modulations that are potentially effective against COVID-19. These antimicrobial peptides have been suggested as effective antiviral therapeutics and therapeutic supplements to prevent rapid virus transmission. This review also provides a new insight into the cellular and molecular alterations which have made SARS-CoV-2 self-modified with diversified infection patterns. In addition, the possible applications of antimicrobial peptides through both natural and induced mechanisms in infection prevention perspectives on changeable virulence cases are comprehensively analyzed. Specific attention is given to the antiviral mechanisms of the molecules along with their integrative use with synthetic biology and nanosensor technology for rapid detection. Novel bacteriocin based therapeutics with cutting-edge technologies might be potential substitutes for existing time-consuming and expensive approaches to fight this newly emerged global threat.

 

关键词： antimicrobial proteins / antiviral profiling of bacteriocins / antiviral therapeutics / immunomodulation / nanosensor technology / mutated SARS-CoV-2    

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通过鉴定关键靶标蛋白探究青蒿素抗疟机制 Article

高鹏, 王建友, 陈嘉鋆, 谷丽维, 王晨, 徐丽婷, Yin Kwan Wong, 张会敏, 徐承超, 戴凌云, 王继刚

《工程（英文）》 2023年 第31卷 第12期   页码 86-97 doi: 10.1016/j.eng.2023.06.001

摘要：

青蒿素（ART）及其衍生物的广泛使用极大地减轻了全球疟疾负担。然而，疟疾仍然对全球健康构成严重威胁。尽管ART抗疟机制的研究在近年已经取得了重大进展，但其最关键治疗靶点蛋白和途径仍然是未知的。当前，在东南亚等地区已经出现了ART耐药性的迹象，因此迫切需要了解ART确切的抗疟机制。在本研究中，我们使用质谱-细胞热转移技术（MS-CETSA）和转录组学分析联用策略来鉴定ART的潜在靶标蛋白。然后对五个潜在靶蛋白进行了一系列验证实验，证明了ART可能通过干扰疟原虫的氧化还原稳态，脂质代谢和蛋白质合成过程来发挥抗疟作用。总之，本研究为ART的抗疟机制研究提供了新的视角，并确定了几种参与寄生虫生存的关键蛋白，这些蛋白可以作为防治疟疾的靶标。

关键词： 青蒿素     抗疟     靶标鉴定     MS-CETSA     转录组学    

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血清免疫球蛋白G N-糖基的高通量分析——一种消化道癌症的非侵入性生物标志物 Article

刘鹏程, 王小兵, 顿爱社, 李昱潼, 李厚强, 王璐, 张怡春, 李灿灿, 张金霞, 张晓雨, 马立兴, 侯海峰

《工程（英文）》 2023年 第26卷 第7期   页码 44-53 doi: 10.1016/j.eng.2023.02.008

摘要：

免疫球蛋白G (Immunoglobulin G, IgG) 的 N-糖基化在炎症性疾病的发展中起着重要作用。本研究旨在评价IgG N-糖基在消化道癌症亚型中的诊断效能。从中国医学科学院肿瘤医院招募749名消化道癌症患者，包括食管癌 (esophageal cancer, EC)、胃癌 (gastric cancer, GC)、结直肠癌 (colorectal cancer, CRC) 和胰腺癌 (pancreatic cancer, PC) 患者。采用亲水交互高效液相色谱-超高效液相色谱（hydrophilic interaction liquid chromatography using ultra-performance liquid chromatography, HILIC-UPLC）分析血浆中IgG的 N-糖基构成。采用Bio-Plex悬液芯片系统检测方法（Bio-Rad）进行炎症因子检测。采用典型相关分析（canonical correlation analysis, CCA）探索糖基和炎症因子之间的相关性。 采用LASSO回归和logistic回归模型，基于检测到的糖基谱建立可用于区分胃肠癌症患者和健康人群诊断模型。与健康对照组相比，EC、GC、CRC和PC患者的唾液酸化和半乳糖基化水平降低，而二等分乙酰葡萄糖胺基化水平在消化道癌症患者中升高。 此外，只有胰腺癌患者具有低水平的岩藻糖基化。消化道癌症组的IL-1β、IL-31和sCD40L水平均高于对照组。IgG N-糖基的组成与炎症因子相关 (r = 0.556)。基于糖基的模型表现出良好的诊断效能，EC、GC、CRC和PC的受试者工作特征曲线下面积(AUC)分别为0.972、0.871、0.867和0.907。这些研究结果表明，IgG N-糖基在调节消化道肿瘤的发病机制中发挥了重要作用。血清IgG N-糖基可以作为潜在的非侵入性辅助消化道癌症临床诊断的方法。

关键词： 消化道癌症     糖基化     免疫球蛋白 G     诊断生物标志物    

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标题 作者 时间 类型 操作

Mutation profiling of 16 candidate genes in

Yang Zhang, Fang Wang, Xue Chen, Wenjing Liu, Jiancheng Fang, Mingyu Wang, Wen Teng, Panxiang Cao, Hongxing Liu

期刊论文

Profiling influences of gene overexpression on heterologous resveratrol production in

Duo Liu,Bingzhi Li,Hong Liu,Xuejiao Guo,Yingjin Yuan

期刊论文

Comprehensive profiling of EBV gene expression in nasopharyngeal carcinoma through paired-end transcriptome

null

期刊论文

Profiling and annotation combined method formultimedia application specificMPSoCperformance estimation

Kai HUANG,Xiao-xu ZHANG,Si-wen XIU,Dan-dan ZHENG,Min YU,De MA,Kai HUANG,Gang CHEN,Xiao-lang YAN

期刊论文

Effects of vitrification and cryostorage duration on single-cell RNA-Seq profiling of vitrified-thawed

Ying Huo, Peng Yuan, Qingyuan Qin, Zhiqiang Yan, Liying Yan, Ping Liu, Rong Li, Jie Yan, Jie Qiao

期刊论文

Molecular classification of non-small-cell lung cancer: diagnosis, individualized treatment, and prognosis

null

期刊论文

Time-dependent metabolomics uncover dynamic metabolic adaptions in MCF-7 cells exposed to bisphenol A

期刊论文

ANTIVIRAL EFFECTS OF BACTERIOCIN AGAINST ANIMAL-TO-HUMAN TRANSMITTABLE MUTATED SARS-COV-2: A SYSTEMATIC REVIEW

期刊论文

通过鉴定关键靶标蛋白探究青蒿素抗疟机制

高鹏, 王建友, 陈嘉鋆, 谷丽维, 王晨, 徐丽婷, Yin Kwan Wong, 张会敏, 徐承超, 戴凌云, 王继刚

期刊论文

血清免疫球蛋白G N-糖基的高通量分析——一种消化道癌症的非侵入性生物标志物

刘鹏程, 王小兵, 顿爱社, 李昱潼, 李厚强, 王璐, 张怡春, 李灿灿, 张金霞, 张晓雨, 马立兴, 侯海峰

期刊论文