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Mapping of de novo mutations in primary biliary cholangitis to a disease-specific co-expression network underlying homeostasis and metabolism

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Journal of Genetics and Genomics 2022年第2期49卷 145-154页

作者： Lu Wang Jinchen Li Chan Wang Ruqi Tang Jialong Liang Yuhua Gong Yaping Dai Ningling Ding Jian Wu Na Dai Lei Liu Yi Zhao Youlin Shao Weifeng Zhao Peng Jiang Xingjuan Shi Weichang Chen Ye Tian Xiangdong Liu Xiong Ma Zhongsheng Sun Key Laboratory of Developmental Genes and Human Diseases Institute of Life SciencesSoutheast University2 Sipailou RoadNanjingJiangsu 210096China Beijing Institutes of Life Science Chinese Academy of SciencesNo.1 West Beichen RoadChaoyang DistrictBeijing 100101China Department of Gastroenterology and Hepatology Shanghai Institute of Digestive DiseasesShanghai Jiao Tong University School of Medicine Afﬁliated Renji Hospital145 Shandong Middle RoadShanghai 200001China Department of Laboratory Medicine The Third People’s Hospital of Zhenjiang300 DaijiamenZhenjiangJiangsu 212021China Department of Laboratory Medicine The Fifth People’s Hospital of Wuxi1215 Guangrui RoadWuxiJiangsu 214000China Department of Hepatology The Fifth People’s Hospital of SuzhouSoochow University10 Guangqian RoadSuzhouJiangsu 215131China Department of Rheumatology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology Jiangsu University Afﬁliated Kunshan Hospital91 Qianjin West RoadKunshanJiangsu 215300China Department of Gastroenterology Yixing People’s Hospital75 Tongzhenguan RoadYixinJiangsu 214200China Department of Gastrointestinal Endoscopy Eastern Hepatobiliary Surgery Hospital700 Moyu North RoadShanghai 201800China Department of Hepatology The Third People’s Hospital of Changzhou300 Lanling North RoadChangzhouJiangsu 213001China Department of Infectious Diseases First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Gastroenterology First Afﬁliated Hospital of Soochow University188 Shizi RoadSuzhouJiangsu 215006China Department of Radiology Second Afﬁliated Hospital of Soochow University1055 Sanxiang RoadSuzhouJiangsu 215004China Institute of Genomic Medicine Wenzhou Medical UniversityUniversity TownChashanWenzhouZhejiang 325035China

Primary biliary cholangitis(PBC) is an autoimmune disease involving dysregulation of a broad array of homeostatic and metabolic processes. Although considerable single-nucleotide polymorphisms have been unveiled, a large fraction of risk factors remains enigmatic. Candidate genes with rare mutations that tend to confer more deleterious effects need to be identified. To help pinpoint cellular and developmental mechanisms beyond common noncoding variants, we integrate whole exome sequencing with integrative network analysis to investigate genes harboring de novo mutations. Prominent convergence has been revealed on a network of disease-specific co-expression comprised of 55 genes associated with homeostasis and metabolism. The transcription factor gene MEF2 D and the DNA repair gene PARP2 are highlighted as hub genes and identified to be up-and down-regulated, respectively, in peripheral blood data set. Enrichment analysis demonstrates that altered expression of MEF2 D and PARP2 may trigger a series of molecular and cellular processes with pivotal roles in PBC pathophysiology. Our study identifies genes with de novo mutations in PBC and suggests that a subset of genes in homeostasis and metabolism tend to act in synergy through converging on co-expression network, providing novel insights into the etiology of PBC and expanding the pool of molecular candidates for discovering clinically actionable biomarkers.

关键词： Primary biliary cholangitis de novo mutations Whole exome sequencing Transcriptional networks co-expression

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combinatorial co-expression of xanthine dehydrogenase and chaperone XdhC from Acinetobacter baumannii and Rhodobacter capsulatus and their applications in decreasing purine content in food

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Food Science and Human Wellness 2023年第4期12卷 1343-1350页

作者： Chenghua Wang Ran Zhang Yu Sun You Wen Xiaoling Liu Xinhui Xing college of Light Industry and Food Engineering Guangxi UniversityNanning 530004China Key Laboratory of Industrial Biocatalysis Ministry of EducationInstitute of Biochemical EngineeringDepartment of Chemical EngineeringTsinghua UniversityBeijing 100084China

This study investigated the combinatorial expression of xanthine dehydrogenase(XDH)and chaperone XdhC from Acinetobacter baumannii and Rhodobacter capsulatus and their applications in decreasing purine content in the beer,beef and yeast.Naturally occurring xdhABC gene clusters of A.baumannii CICC 10254 and R.capsulatus CGMCC 1.3366 as well as two refactored clusters constructed by exchanging their xdhC genes were overexpressed in Escherichia coli and purified to near homogeneity.RcXDH chaperoned by AbXdhC showed nearly the same catalytic performance as that by RcXdhC,except for the decreased substrate affinity.While the AbXDH co-expressed with RcXdhC displayed enhanced acidic adaptation but weakened catalytic activity.All the XDHs degraded purines in beer,beef and yeast extract effectively,indicating potential applications in low-purine foods to prevent hyperuricemia and gout.The study also presents a method for exploiting the better chaperone XdhC and novel XDHs by functional complement activity using existing XdhCs such as RcXdhC.

关键词： co-expression Low purine food Uric acid Xanthine dehydrogenase XdhC

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Whole miRNome-wide Differential co-expression of MicroRNAs

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Genomics, Proteomics & Bioinformatics 2012年第5期10卷 285-294页

作者： cord F.Stehler Andreas Keller Petra Leidinger Christina Backes Anoop Chandran Jerg Wischhusen Benjamin Meder Eckart Meese Siemens Healthcare Strategy Department of Human Genetics Saarland University Interdisciplinary Center for Clinical Research University of Wuerzburg Department of Internal Medicine III Heidelberg University

co-regulation of genes has been extensively analyzed, however, rather limited knowledge is available on co-regulations within the miRNome. We investigated differential co-expression of microRNAs （miRNAs） based on miRNome profiles of whole blood from 540 individuals. These include patients suffering from different cancer and non-cancer diseases, and unaffected controls. Using hierarchi- cal clustering, we found 9 significant clusters of co-expressed miRNAs containing 2-36 individual miRNAs. Through analyzing multiple sequencing alignments in the clusters, we found that co-expression of miRNAs is associated with both sequence similarity and genomic co-localization. We calculated correlations for all 371,953 pairs of miRNAs for all 540 individuals and identified 184 pairs of miRNAs with high correlation values. Out of these 184 pairs of miRNAs, 16 pairs （8.7%） were differentially co-expressed in unaffected controls, cancer patients and patients with non-cancer diseases. By computing correlated and anti-correlated miRNA pairs, we constructed a net- work with 184 putative co-regulations as edges and 100 miRNAs as nodes. Thereby, we detected specific clusters of miRNAs with high and low correlation values. Our approach represents the most comprehensive co-regulation analysis based on whole miRNome-wide expression profiling. Our findings further decrypt the interactions of miRNAs in normal and human pathological processes.

关键词： co-expression Microarray MicroRNA Network analysis

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co-expression and Immunity of Legionella pneumophila mip Gene and Immunoadjuvant ctxB Gene

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Acta Biochimica et Biophysica Sinica 2005年第3期37卷 199-204页

作者： Tao WANG Jian-Ping CHEN Hong LI Ke-Qian ZHI Lei ZHANG Chun-Lei YANG Da-Chang TAO School of Precliaical and Forensic Medicine of West China,Sichuan University,Chengdu 610041,China School of Stomatolngy,Xi’an Jiaotong University,Xi’an 710004,China School of Life Science,Sichuan University,Chengdu 610041,China School of Preclinical and Forensic Medicine of West China Sichuan University Chengdu 610041 China Nuclear Physics Institute Academy of Sciences of the Czech Republic Rez Czech Republic

The mip gene of Legionella pneumophila and the ctxB gene of Vibrio cholerae were amplifiedby PCR respectively.The amplified cDNA was ligated to the pcDNA3.1(+)vector.The recombinant plasmidspcDNA3,1-mip and pcDNA3.1-ctxB were identified by restriction analysis and PCR,and further confirmedby sequencing analysis.NIH3T3 cells were transfected with pcDNA3.1-mip and pcDNA3.1-ctxB accordingto the Lipofection method.Transient and stable products of the co-expression of the mip gene and ctxB genewere detected by immunofluorescence and Western blotting.The results showed that NIH3T3 cells weresuccessfully transfected,and that the transiently and stably co-expressed products can be detected in thetransfected cells.To detect the humoral and cellular immune response in immunized mice induced by the co-immunization of the mip and ctxB genes,female BALB/c mice were immunized intramuscularly with pcDNA3.1-mip and pcDNA3.1-ctxB.The results showed that the specific antibody titer and the cytotoxic T-lymphocyteresponse for pcDNA3,1-mip immunization and co-immunization were increased compared with that ofpcDNA3.1(+) immunization.Furthermore,the specific antibody titer and cytotoxic T-lymphocyte responsefor co-immunization were increased compared with that of pcDNA3.1-mip immunization.Statistical analysisusing one-way analysis of variance(ANOVA)showed that there was a significant difference between thegroups(P<0.01).The results indicated that the ctxB gene enhanced the humoral and cellular immune responseto the mip gene immunization.These findings provide experimental evidence to support the development ofthe L.pneumophila DNA vaccine.

关键词： Legionella pneumophila co-expression humoral immunity cellular immunity

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Identification of Key Modules and Hub Genes in Glioblastoma Multiforme Based on co-expression Network Analysis

Identification of Key Modules and Hub Genes in Glioblastoma ...

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第十四届中国医师协会神经外科医师年会

作者： Long Gu Jian Zhou Jianhua Peng Jinwei Pang Lifang Zhang Ligang Chen Yong Jiang Department of Neurosurgery the Affiliated Hospital of Southwest Medical University

Purpose: Glioblastoma multiforme（GBM） is the most malignant primary tumor in the central nervous system. The molecular mechanism of its pathogenesis remains unclear. Our goal is to identify key modules and hub genes involved in the pathogenesis of GBM by constructing a gene co-expression network. Methods: Dataset GSE50161 was used to construct a co-expression network for Weighted Gene co-expression Network Analysis（WGCNA）. Key modules were obtained by correlating module eigengenes and the disease status. Gene Oncology（GO） and Kyoto Encyclopedia of Genes and Genomes（KEGG） enrichment analysis were performed. Hub genes were screened by survival analysis in The Cancer Genome Atlas（TCGA） and The Human Protein Atlas（HPA） database. The expression level and translational level of hub genes were also verified. Results: The brown and turquoise modules were found to have the strongest correlation with GBM. Functional enrichment analysis indicated that the brown module was involved with cell cycle, DNA replication and pyrimidine metabolism. The turquoise module is primarily related to circadian rhythm entrainment, glutamatergic synapses and axonal guidance. The eight hub genes（NUSAP1, SHCBP1, KNL1, SULT4 A1, SLC12 A5, NUF2, NAPB and GARNL3） were identified by survival analysis in TCGA, and verified at both expression and translational levels. conclusion: In this study, we identified two modules and eight hub genes that are strongly related to GBM. These two modules provide new insights into the molecular mechanism of GBM. Meanwhile, the hub genes can be the potential biomarkers and therapeutic targets for the accurate diagnosis and management of GBM.

关键词： Glioblastoma multiforme WGCNA co-expression Hub gene

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Multi-gene co-expression can improve comprehensive resistance to multiple abiotic stresses in Brassica napus L.

Multi-gene co-expression can improve comprehensive resistanc...

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中国作物学会油料作物专业委员会第八次会员代表大会暨学术...

作者： WANG Zai-qing YANG Cui-ling CHEN Hao WANG Pei WANG Peng-tao SONG Chun-peng ZHANG Xiao WANG Dao-jie Key Laboratory of Plant Stress Biology State Key Laboratory of Cotton BiologySchool of Life SciencesSchool of Mathematics and StatisticsHenan University

Rapeseed(Brassica napus L.) is an important oil crop worldwide.For current B.napus production,it is urgent to develop new varieties with higher seed productivity and increased stress tolerance for better adaptation to abiotic stresses as a result of global climate change.Genetic engineering,to some extent,can overcome limitations of genetic exchange in conventional breeding.consequendy,it considered as an effective method for improving modern crop breeding for B.napus.Since crop stress resistance is a complex polygenic trait,only multi-gene synergistic effects can effectively achieve the comprehensive stress resistance.Hence,in present study,5 stress resistance genes,NCED3,ABAR,CBF3,L0 S5 and ICE1 were transferred into B.napus.compared with wild type(WT) plants,multi-gene transformants K15 exhibited pronounced growth advantage under bodi normal growdi and stress conditions.Additionally,K15 plants also showed significantly higher resistance response to multiple stresses at seed germination and seedling stages than WT plants.Furthermore,K15 plants had significantly higher leaf temperature lower stomatal aperture and water loss rate than WT plants,which indicated that water-holding capacity of K15 plants was significantly superior to that of WT plants after stress treatment.In addition,K15 plants had significantly higher abscisic acid(ABA) content and remarkably lower malondialdehyde(MDA) content than WT plants.In conclusion,the above results suggested that multi-gene co-expression could rapidly trigger plant stress resistance,reduce the stress injury and synergistically improve comprehensive resistance of B.napus.

关键词： Brassica napus L. abiotic stress co-expression comprehensive stress resistance multi-genes transformation

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co-expression of Clostridium perfringens α and ε Toxins and Their Immunogenicity

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Animal Husbandry and Feed Science 2015年第2期7卷 74-77页

作者： Han Guangwei Li Zhaocai Gong Xiaowei Chen Qiwei Cao Xiaoan Zheng Fuying Zhang Xiaoying Zhou Jizhang State Key Laboratory of Veterinary Etiological Biology / Lanzhou Veterinary Research Institute Chinese Academy of Agricultural Science Lanzhou Animal Health Inspection Institute

The genc CPA and ETX encoding α and e toxins were amplified from the standard strain C60-2 of type D Clostridium perfingens by PCR, and then they were inserted into pet-Duct-1 vecto, respectively for the construction of co-expression plasmid pETDoet-1-CPA-ETX. The co-expression plasmid was transformed into BL21 （DE3） competent cells, at and e toxins proteins were induced by IPTG before analysis by SDS-PAGE. As a result, both of α and e toxins were detected at 43 and 34 KU by western-blot. Mice immunized with the co-expressed α and e toxins proteins produced high titers of neutralizing antibodies in the serum, which protected the mice against the attack of type D C. perfringens culture filtrate. In addition, mice immunized with the produced co-expressed α and e toxins proteins showed significantly higher surviving rate than with ε toxins protein alone when infected with culture filtrate of type D C. perfringens . These results indicated that co-expression of α and e toxins proteins could be used as a new method to prepare vaccines against the pathogens of multiple serotypes.

关键词： Clostridium perfingens α toxins ε toxins co-expression

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construction and secretory co-expression of Amylase and Cellulase in Lactobacillus Casei

Construction and secretory Co-expression of Amylase and Cell...

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中国畜牧兽医学会动物微生态学分会第十一次全国学术研讨会...

作者： DING Ke YU Zu-hua Li Wang Li Yuan-xiao CHENG Xiang-chao ZHANG Chun-jie Jia Yan-yan He Lei Hongxiang Biological Feed Laboratory of Henan University of Science and Technology Animal Disease and Public Security Academician Workstation of Henan Province Military Veterinary Institute.Academy of Military Medical Sciences

This study is to construct a recombinant vector co-expressing amylase and cellulase,and examine the enzyme activities in Lactobacillus.The signal peptide gene SP,amylase and cellulase genes were cloned by PCR method,respectively,and inserted into plasmid pIlac according to special order to obtain the recombinant expressive vector pIlac-SP-AMY-CEL.Then this recombinant plasmid was transformed into Lactobacillus casei CECT5276 by electroporation methods.The gene sequences,enzyme activities,and hereditary stability were studied.The signal peptide gene,amylase gene and cellulase gene were 100%,98.9%and 99.6% similar to the GenBank corresponding sequences.SDS-PAGE indicated there was a special band at 114 kDa in both supemant and cell samples of recombinant Lactobacillus casei CECT5276/ pllac-SP- AMY-CEL.The total enzymes activity of amylase and cellulase were 35.65U/mL and 0.91U/mL in positive transformants,and its secretion rate was 70%.The recombinant Lactobacillus appeared more hereditary stability when they were blind cultured 50 generations under erythromycin selective pressure.The results revealed that the secretive fusion expression system of amylase and cellulase was constructed successfully,the amylase and cellulase could be produced in supernatant of the recombinant Lactobacilus,This recombinant Lactobacillus has a number promising properties that make it candidate for application as a probiotic additive in farm industry.

关键词： co-expression amylase cellulase Lactobacillus casei

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co-expression of TRAIL and Smac delivered by an E1B-55K deleted oncolytic adenovirus containing a caspase-8 cleavage site (IETD) elicits complete elimination of hepatocellular carcinoma xenograft

Co-expression of TRAIL and Smac delivered by an E1B-55K dele...

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2012年浙江省血液病学年会

作者： Shibing Wang Yuan Tan Wen Lei Yigang Wang Xiumei Zhou Kangjian Zhang Liang Chu Xinyuan Liu Wenbin Qian Xinyuan Institute of Medicine and Biotechnology School of Life Science Zhejiang Sci-Tech University Institute of Hematology The First Affiliated Hospital College of Medicine Zhejiang University Laboratory of Molecular Cell Biology Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences

combination target therapy is necessary for cancer treatment because tumors are genetically diverse. In our current study, we generated a novel E1B-55K deleted oncolytic adenovirus that harbors both TRAIL and Smac genes (ZD55-TRAIL-IETD-Smac). In this vector, a caspase-8 cleavage site (IETD) was introduced between the genes, which allows the production of TRAIL and Smac, respectively, within virusinfected cells after activation of caspase-8. In our system, treatment with ZD55-TRAIL-IETD-Smac produced equal expression of TRAIL and Smac, and resulted in significant cytotoxicity against various cancer cells with stronger efficacy than that of ZD55-TRAIL or ZD55-Smac alone. The expression of these two therapeutic genes in the infected cells was downregulated by a caspase-8 inhibitor (Z-IETD-FMK) and upregulated by 5-FU (a activator of caspase-8), suggesting that cleavage of TRAIL-IETD-Smac fusion protein by activation of caspase-8. In a s.c. xenograft hepatocellular carcinoma (HCC) model, the antitumor effect of ZD55-TRAIL-IETD-Smac was significantly stronger than that of ZD55-TRAIL and ZD55-Smac, respectively. Importantly, intratumoral injection of ZD55-TRAIL-IETD-Smac eliminated all xenograft tumors established from a human HCC cell line Bel-7404, resulting in long-term, tumor-free survival. In conclusion, our data suggest that oncolytic adenovirus incorporating two different therapeutic genes by introduction of the IETD sequence may be attractive candidates for clinical application in treatment of cancer.

关键词： TRAIL Smac co-expression IETD virotherapy genetherapy

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co-expression with RadA and the characterization of stRad55B, a RadA paralog from the hyperthermophilic crenarchaea Sulfolobus tokodaii

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Science China(Life Sciences) 2008年第1期51卷 60-65页

作者： SHENG DuoHong, LI MingFeng, JIAO JianDong, NI JinFeng & SHEN YuLong State Key Laboratory of Microbial Technology, Shandong University, Jinan 250100, China State Key Laboratory of Microbial Technology Shandong University Jinan 250100 China

ST0838 (designed stRad55B) is one of the four RadA paralogs (or Rad55 homologues) in the genome of the hyperthermophilic crenarchaeon Sulfolobus tokodaii. The gene is induced by UV irradiation, sug-gesting that it is involved in DNA recombinational repair in this organism. However, this protein could not be expressed normally in vitro. In this study, thermostable and soluble stRad55B was obtained by co-expression with S. tokodaii RadA (stRadA) in E. coli, and the enzymatic properties were examined. It was found that stRad55B bound ssDNA preferentially and had a very weak ATPase activity that was not stimulated by DNA. The recombinant protein inhibited the strand exchange activity promoted by stRadA, indicating that stRad55B might be an inhibitor to the homologous recombination in this ar-chaeon. The results will be helpful for further functional and interaction analysis of RadA paralogs and for the understanding of the mechanism of recombinational repair in archaea.

关键词： Archaea recombinational repair RadA Rad55 co-expression

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