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TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

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《医学前沿（英文）》 2015年 第9卷 第3期   页码 322-330 doi: 10.1007/s11684-015-0408-9

摘要：

This study systematically evaluates the TCGA whole-transcriptome sequencing data of hepatocellular carcinoma (HCC) by comparing the global gene expression profiles between tumors and their corresponding non-tumorous liver tissue. Based on the differential gene expression analysis, we identified a number of novel dysregulated genes, in addition to those previously reported. Top-listing upregulated (CENPF and FOXM1) and downregulated (CLEC4G, CRHBP, and CLEC1B) genes were successfully validated using qPCR on our cohort of 65 pairs of human HCCs. Further examination for the mechanistic overview by subjecting significantly upregulated and downregulated genes to gene set enrichment analysis showed that different cellular pathways were involved. This study provides useful information on the transcriptomic landscape and molecular mechanism of hepatocarcinogenesis for development of new biomarkers and further in-depth characterization.

关键词： TCGA     whole-transcriptome sequencing     HCC     liver cancer    

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Exploring the cancer genome in the era of next-generation sequencing

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《医学前沿（英文）》 2012年 第6卷 第1期   页码 48-55 doi: 10.1007/s11684-012-0182-x

摘要：

The emergence of next-generation sequencing technologies has led to dramatic advances in cancer genome studies. The increased efficiency and resolution of next-generation sequencing greatly facilitate the detection of genetic, genomic, and epigenomic alterations, such as single nucleotide mutations, small insertions and deletions, chromosomal rearrangements, copy number variations, and DNA methylation. Comprehensive analysis of cancer genomes through approaches of whole genome, exome, and transcriptome sequencing has significantly improved the understanding of cancer biology, diagnosis, and therapy. The present study briefly reviews the recent pioneering studies on cancer genome sequencing and provides an unprecedented insight into the landscape of genomic alterations in human sporadic cancers.

关键词： next-generation sequencing     cancer genome     whole genome sequencing     exome     transcriptome    

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Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

《医学前沿（英文）》   页码 889-906 doi: 10.1007/s11684-023-0994-x

摘要： Primary central nervous system lymphoma (PCNSL) is an uncommon non-Hodgkin’s lymphoma with poor prognosis. This study aimed to depict the genetic landscape of Chinese PCNSLs. Whole-genome sequencing was performed on 68 newly diagnosed Chinese PCNSL samples, whose genomic characteristics and clinicopathologic features were also analyzed. Structural variations were identified in all patients with a mean of 349, which did not significantly influence prognosis. Copy loss occurred in all samples, while gains were detected in 77.9% of the samples. The high level of copy number variations was significantly associated with poor progression-free survival (PFS) and overall survival (OS). A total of 263 genes mutated in coding regions were identified, including 6 newly discovered genes (ROBO2, KMT2C, CXCR4, MYOM2, BCLAF1, and NRXN3) detected in ≥ 10% of the cases. CD79B mutation was significantly associated with lower PFS, TMSB4X mutation and high expression of TMSB4X protein was associated with lower OS. A prognostic risk scoring system was also established for PCNSL, which included Karnofsky performance status and six mutated genes (BRD4, EBF1, BTG1, CCND3, STAG2, and TMSB4X). Collectively, this study comprehensively reveals the genomic landscape of newly diagnosed Chinese PCNSLs, thereby enriching the present understanding of the genetic mechanisms of PCNSL.

关键词： primary central nervous system lymphoma     whole-genome sequencing     TMSB4X     copy number variation     gene mutation    

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Exome sequencing greatly expedites the progressive research of Mendelian diseases

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《医学前沿（英文）》 2014年 第8卷 第1期   页码 42-57 doi: 10.1007/s11684-014-0303-9

摘要：

The advent of whole-exome sequencing (WES) has facilitated the discovery of rare structure and functional genetic variants. Combining exome sequencing with linkage studies is one of the most efficient strategies in searching disease genes for Mendelian diseases. WES has achieved great success in the past three years for Mendelian disease genetics and has identified over 150 new Mendelian disease genes. We illustrate the workflow of exome capture and sequencing to highlight the advantages of WES. We also indicate the progress and limitations of WES that can potentially result in failure to identify disease-causing mutations in part of patients. With an affordable cost, WES is expected to become the most commonly used tool for Mendelian disease gene identification. The variants detected cumulatively from previous WES studies will be widely used in future clinical services.

关键词： genetics     whole-exome sequencing     Mendelian disease     disease gene    

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Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the

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《医学前沿（英文）》 2018年 第12卷 第1期   页码 23-33 doi: 10.1007/s11684-017-0607-7

摘要：

Two decades have passed since the first bacterial whole-genome sequencing, which provides new opportunity for microbial genome. Consequently, considerable genetic diversity encoded by bacterial genomes and among the strains in the same species has been revealed. In recent years, genome sequencing techniques and bioinformatics have developed rapidly, which has resulted in transformation and expedited the application of strategy and methodology for bacterial genome comparison used in dissection of infectious disease epidemics. Bacterial whole-genome sequencing and bioinformatic computing allow genotyping to satisfy the requirements of epidemiological study in disease control. In this review, we outline the significance and summarize the roles of bacterial genome sequencing in the context of bacterial disease control and prevention. We discuss the applications of bacterial genome sequencing in outbreak detection, source tracing, transmission mode discovery, and new epidemic clone identification. Wide applications of genome sequencing and data sharing in infectious disease surveillance networks will considerably promote outbreak detection and early warning to prevent the dissemination of bacterial diseases.

关键词： genome sequencing     genomic epidemiology     bacteria     surveillance     infectious diseases    

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

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《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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Plastic materials and water sources actively select and shape wastewater plastispheres over time

《环境科学与工程前沿（英文）》 2022年 第16卷 第11期 doi: 10.1007/s11783-022-1580-1

摘要：

● Wastewater MPs exhibited resistomes and therefore health threats.

关键词： Microplastics     Whole-genome metagenomic sequencing     Plastisphere     Plastic degradation     MHETase    

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A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome

《医学前沿（英文）》 2023年 第17卷 第2期   页码 330-338 doi: 10.1007/s11684-022-0933-2

摘要： Clouston syndrome (OMIM #129500), also known as hidrotic ectodermal dysplasia type 2, is a rare autosomal dominant skin disorder. To date, four mutations in the GJB6 gene, G11R, V37E, A88V, and D50N, have been confirmed to cause this condition. In previous studies, the focus has been mainly on gene sequencing, and there has been a lack of research on clinical manifestations and pathogenesis. To confirm the diagnosis of this pedigree at the molecular level and summarize and analyse the clinical phenotype of patients and to provide a basis for further study of the pathogenesis of the disease, we performed whole-exome and Sanger sequencing on a large Chinese Clouston syndrome pedigree. Detailed clinical examination included histopathology, hair microscopy, and scanning electron microscopy. We found a novel heterozygous missense variant (c.134G>C:p.G45A) for Clouston syndrome. We identified a new clinical phenotype involving all nail needling pain in all patients and found a special honeycomb hole structure in the patients’ hair under scanning electron microscopy. Our data reveal that a novel variant (c.134G>C:p.G45A) plays a likely pathogenic role in this pedigree and highlight that genetic testing is necessary for the diagnosis of Clouston syndrome.

关键词： Clouston syndrome     whole exome sequencing     GJB6 gene     novel variant     unique phenotype    

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Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

《农业科学与工程前沿（英文）》 2014年 第1卷 第1期   页码 77-84 doi: 10.15302/J-FASE-2014010

摘要： While the differential responses of trees to changes in climatic and environmental conditions have been demonstrated as they age, the underlying mechanisms and age control of tree growth and development are complex and poorly understood particularly at a molecular level. In this paper, we present a transcriptome analysis of , a deciduous conifer that is widely-grown in the northern hemisphere and of significant ecological and economic value. Using high-throughput RNA sequencing, we obtained about 26 million reads from the stems of 1-, 2-, 5-, 10-, 25- and 50-year-old trees. Combining these with the published Roche 454 sequencing reads and the expressed sequence tags (both mainly from embryogenic cell cultures), we assembled 26670549 reads into 146786 transcripts, of which we annotated 79182 to support investigations of the molecular basis of tree aging and adaption, somatic embryogenesis and wood formation. Using these sequences we also identified many single-nucleotide polymorphisms, simple sequence repeats, and insertion and deletion markers to assist breeding and genetic diversity studies of .

关键词： Larix     transcriptome     age     wood formation     somatic embryogenesis     molecular marker    

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clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

《医学前沿（英文）》 doi: 10.1007/s11684-023-1029-3

摘要： Microbiome subsets determine tumor prognosis and molecular characteristics of clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome data

关键词： tumor prognosis molecular     Microbiome subsets determine     center analysis microbiome     transcriptome data    

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METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

《农业科学与工程前沿（英文）》 2021年 第8卷 第2期

摘要：

Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

 

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Organizational evolution of project management teams over the whole lifecycle of megaprojects: Case study

《工程管理前沿（英文）》   页码 439-454 doi: 10.1007/s42524-022-0211-7

摘要： Project management teams are critical in the implementation of megaprojects, but their evolution throughout the project lifecycle has not been clearly explained. This paper explores the organizational evolution of megaproject management teams through a longitudinal retrospective case study of the Hong Kong–Zhuhai–Macao Bridge (HZMB) project. The organizational evolution is examined in terms of management objectives, management content, and organizational structure. The organizational evolution of the HZMB project management team exhibits stage differentiation with the coexistence of turbulence and stability. Changes in the external environment are the driving force for organizational evolution, whereas a flexible organizational strategy is critical in promoting this evolution. Basing on the HZMB case study, this paper summarizes six critical measures that facilitate the organizational evolution of megaproject management teams. Our findings add value to megaproject management theory and provide a better understanding of the dynamics and complexity of megaproject organizational management.

关键词： megaproject     organizational evolution     whole lifecycle management     project management team    

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Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

《农业科学与工程前沿（英文）》 2018年 第5卷 第2期   页码 214-225 doi: 10.15302/J-FASE-2018219

摘要： Sweet potato, , is a globally important food crop. The purple-fleshed sweet potato, rich in anthocyanins, has great potential for both nutritional and pharmaceutical uses. In this study, we characterized the root transcriptomes of the purple-fleshed sweet potato cv. Jingshu 6 and its mutant JS6-5 with high anthocyanin content by high-throughput RNA sequencing. A total of 22873364 and 27955097 high quality reads were obtained from Jingshu 6 and JS6-5, respectively, and assembled into 35592 unigenes. In all, we obtained 1566 differentially expressed genes (DEGs). Among them, 994 were upregulated and 572 were downregulated in JS6-5 compared to the expression in Jingshu 6. A total of 1436 DEGs were annotated, in which 847 DEGs had gene ontology (GO) terms and 329 DEGs were assigned to 84 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Most importantly, 23 differentially expressed genes and 24 transcription factors were identified as candidate genes involved in anthocyanin biosynthesis. In addition, 2349 SSRs were detected. This study not only provides the candidate genes but also provides insights into the molecular mechanism of anthocyanin biosynthesis in sweet potato.

关键词： anthocyanin     gene expression     mutant     purple-fleshed sweet potato     transcriptome    

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Cell surface protein engineering for high-performance whole-cell catalysts

Hajime Nakatani,Katsutoshi Hori

《化学科学与工程前沿（英文）》 2017年 第11卷 第1期   页码 46-57 doi: 10.1007/s11705-017-1609-3

摘要： Cell surface protein engineering facilitated by accumulation of information on genome and protein structure involves heterologous production and modification of cell surface proteins using genetic engineering, and is important for the development of high-performance whole-cell catalysts. In this field, cell surface display is a major technology by exposing target proteins, such as enzymes, on the cell surface using a carrier protein. The target proteins are fused to the carrier proteins that transport and tether them to the cell surface, as well as to a secretion signal. This paper reviews cell surface display systems for prokaryotic and eukaryotic cells from the perspective of carrier proteins, which determine the number of displayed molecules, and the localization, size, and direction ( or terminal anchoring) of the passengers. We also discuss advanced methods for displaying multiple enzymes and a new method for the immobilization of whole-cell catalysts using adhesive surface proteins.

关键词： cell surface engineering     surface display     whole-cell catalysts     bioprocess    

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单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞 Article

张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟

《工程（英文）》 2022年 第17卷 第10期   页码 161-169 doi: 10.1016/j.eng.2021.05.009

摘要：

了解重症新型冠状病毒肺炎（COVID-19）患者单核细胞的免疫学特征（包括与纤维化相关的特征）对了解疾病的重症化机制和阻止疾病恶化至关重要。本研究共纳入7名COVID-19患者（包括3名重症/危重症患者和4名普通型患者）和6名健康对照者。采集7名COVID-19患者不同疾病时期外周血样本，包括重症/危重症时期血样3例，轻症时期血样4例，康复期血样7例。将以上血样和6例健康对照者血样进行单细胞转录组测序分析。本研究发现在COVID-19重症/危重症时期，单核细胞发生显著变化。单核细胞在外周血单个核细胞中占比增加，多样性却显著降低。同时本研究发现两个新的COVID-19重症疾病特异性单核细胞亚群：Mono 0和Mono 5。这两个亚群表达amphiregulin（AREG）、epiregulin（EREG）和细胞因子基因IL-18，KEGG分析显示富集的ErbB信号通路，这两个亚群可能具有促纤维化和促炎的特征。进一步分析发现Mono 0和Mono 5发生代谢改变，包括糖酵解/糖异生的增加和HIF-1信号通路的增加。本研究同时发现一个疾病重症前期取得的样本显示出与重症/危重症时期样本相似的单核细胞UMAP图谱。本研究发现了两种新的COVID-19重症疾病特异性单核细胞亚群，可作为重症COVID-19的潜在预测因子和治疗靶点。

关键词： COVID-19     重症感染     危重症     单核细胞     纤维化    

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标题 作者 时间 类型 操作

TCGA whole-transcriptome sequencing data reveals significantly dysregulated genes and signaling pathways

null

期刊论文

Exploring the cancer genome in the era of next-generation sequencing

null

期刊论文

Analysis of the genomic landscape of primary central nervous system lymphoma using whole-genome sequencing

期刊论文

Exome sequencing greatly expedites the progressive research of Mendelian diseases

null

期刊论文

Transforming bacterial disease surveillance and investigation using whole-genome sequence to probe the

null

期刊论文

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

null

期刊论文

Plastic materials and water sources actively select and shape wastewater plastispheres over time

期刊论文

A novel variant in the gene in a large Chinese family with a unique phenotype of Clouston syndrome

期刊论文

Transcriptome resources and genome-wide marker development for Japanese larch (

Wanfeng LI,Suying HAN,Liwang QI,Shougong ZHANG

期刊论文

clear-cell renal cell carcinoma: a multi-center integrated analysis of microbiome, metabolome, and transcriptome

期刊论文

METABOLIC AND TRANSCRIPTOME ANALYSIS REVEALS METABOLITE VARIATION AND FLAVONOID REGULATORY NETWORKS IN

期刊论文

Organizational evolution of project management teams over the whole lifecycle of megaprojects: Case study

期刊论文

Comparative transcriptome analysis of purple-fleshed sweet potato provides insights into the molecular

Hongyuan ZHAO, Shanshan ZHANG, Feibing WANG, Ning ZHAO, Shaozhen HE, Qingchang LIU, Hong ZHAI

期刊论文

Cell surface protein engineering for high-performance whole-cell catalysts

Hajime Nakatani,Katsutoshi Hori

期刊论文

单细胞转录组测序鉴定COVID-19外周血重症疾病特异性单核细胞

张研, 王淑婷, 夏鹤, 郭静, 何康信, 黄晨杰, 罗瑞, 陈燕飞, 徐凯进, 高海女, 盛吉芳, 李兰娟

期刊论文