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Clinical and molecular significance of homologous recombination deficiency positive non-small cell lung cancer in Chinese population:An integrated genomic and transcriptional analysis

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Chinese Journal of Cancer Research 2024年第3期36卷 282-297页

作者： Yifei Wang Yidan Ma Lei He Jun Du Xiaoguang Li Peng Jiao Xiaonan Wu Xiaomao Xu Wei Zhou Li Yang Jing Di Changbin Zhu Liming Xu Tianlin Sun Lin Li Dongge Liu Zheng Wang Department of Pathology Department of Minimally Invasive Tumor Therapies Center Department of Thoracic Surgery Department of Oncology Department of Respiratory and Critical Care Medicine Beijing HospitalNational Center of GerontologyInstitute of Geriatric MedicineChinese Academy of Medical SciencesBeijing 100730China Amoy Diagnostics Co. Ltd.Xiamen 361027China

Objective:The clinical significance of homologous recombination deficiency(HRD)in breast cancer,ovarian cancer,and prostate cancer has been established,but the value of HRD in non-small cell lung cancer(NSCLC)has not been fully *** study aimed to systematically analyze the HRD status of untreated NSCLC and its relationship with patient prognosis to further guide clinical ***:A total of 355 treatment-naïve NSCLC patients were retrospectively *** status was assessed using the AmoyDx Genomic Scar Score(GSS),with a score of≥50 considered ***,transcriptomic,tumor microenvironmental characteristics and prognosis between HRD-positive and HRDnegative patients were ***:Of the patients,25.1%(89/355)were *** to HRD-negative patients,HRDpositive patients had more somatic pathogenic homologous recombination repair(HRR)mutations,higher tumor mutation burden(TMB)(Ptranscriptional characteristics were found in HRD-positive *** prognosis and poor response to EGFR-TKIs and immunotherapy were observed in HRD-positive *** study highlights potential actionable alterations in HRD

关键词： Non-small cell lung cancer homologous recombination deficiency genetic alterations transcriptional analysis tumor microenvironment prognosis

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transcriptional analysis of Pseudomonas stutzeri A1501 Associated with Host Rice

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Advances in Microbiology 2016年第3期6卷 210-221页

作者： Khandakar Mohiul Alam Tao Zhang Yonglian Yan Wei Zhang Min Lin Wei Lu Bangladesh Sugarcrop Research Institute Ishurdi Bangladesh Biotechnology Research Institute Chinese Academy of Agricultural Sciences Beijing China

Pseudomonas stutzeriA1501, associative and endophytic nitrogen-fixing bacterium showed the capacity of colonization in the rice roots and considered as the good colonizer in the rice plant. The experiment was conducted to study the expression of genes potentiality relevant to the association of nitrogen fixing Pseudomonas stutzeri with host rice and reveal the molecular mechanism by which underlying interaction between bacteria and host rice. The bacteria were shown to be uniformly distributed on the rhizoplane of the root and the density of bacteria was found at the intercellular junction and micro colony developed on the surface of the epidermal cells and on the cellular junctions. Root exudates of rice were the major components of carbon and energy sources for bacteria. RT-PCR analyses of pilK, metE, rpoN and fdhE genes expression of P. stutzeri A1501 were performed at positive and negative (control) conditions. After 1 h, it was found that pilK, metE and rpoN transcription were increased 5.7, 6.4 and 3.4-fold, respectively, whereas in the fdhE gene has no expression. Consequently, after 4 h pilk, fdhE, metE and rpoN were decreased -1.9, -4.4, -0.2 and -0.8-fold, respectively. The gene pilK, expression was up-regulation after 1 h and down-regulation after 4 h that has twitching motility to convey the bacterial cell to point of attachment in to host plant. The gene expressions of the bacteria, pilK, metE, rpoN and fdhE were up- and down-regulated during the influence of root exudates which regulated the colonization of bacteria during plant-microbe interaction.

关键词： Rice Pseudomonas stutzeri A1501 transcriptional analysis Root Exudates Colonization

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transcriptional analysis of different mulberry cultivars responsive to Ralstonia solanacearum

Transcriptional analysis of different mulberry cultivars res...

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中国植物病理学会2015年学术年会

作者： Dai Fan-Wei Wang Zhen-Jiang Luo Guo-Qing Tang Cui-Ming Sericultural & Agri-Food Research Institute Guangdong Academy of Agricultural Sciences

Bacterial wilt caused by Rabtonia solanacearum is a major disease of the mulberry(Morus atropurpurea),resulting in severe yield and quality ***,little is known about the molecular mechanisms of *** the RNA sequencing technique,we identified early transcriptional changes in resistant(KQIO and YS283) and susceptible(YSDIO) mulberry cultivars in response to *** *** observed that 798 genes were differentially and specifically regulated in both resistant cultivars but not in the susceptible cultivar after infection with ***,including 5O upregulated and 296 downregulated *** the differentially expressed genes,31 encode transcription factors and 48 encode protein ***,we found that a large number of genes(61) associated with cell-wall modification were differentially and specifically regulated in the resistant *** genes could be divided into ten major *** largest group is the glucosyltransferase family,followed by the pectinesterase inhibitor,glucanase,and glycoprotein families,suggesting that cell-wall modifications may play an improtant role in resistance levels in *** transcriptional analysis paves the way for elucidating the molecular mechanisms of the resistance response to *** in mulberry.

关键词： mulberry transcriptional analysis disease resistance Ralstonia solanacearum cell wall

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transcriptional analysis of porcine circovirus-like virus P1

Transcriptional analysis of porcine circovirus-like virus P1

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第七届中国畜牧科技论坛

作者： Wen libin Wang fengzhi He kongwang Li bin Wang xiaomin Guo rong-li Xie jianping Jiangsu Academy of Agricultural Sciences·Key Laboratory of Veterinary Biological Engineering and Technology Ministry of Agriculture·National Center for Engineering Research of Veterinary Bio-productsInstitute of Veterinary Medicine

Background Recently identified porcine circovirus-like virus P1 has the smallest DNA viral *** this study,we identified the viral genes and their corresponding mRNA ***;The RNAs of P1,synthesized in porcine kidney cells,were examined with northern blotting and PCR *** virus-specific RNAs were *** mRNAs(open reading frames(ORFs) 1,2,4,and 5) are encoded by the viral(-) strand and four(ORFs 3,6,7,and 8) are encoded by the viral(+) *** proteins encoded by the ORFs of the P1 virus are less than 50 amino acids in length,except that encoded by ORF1(113 amino acids).Conclusions:We show a very complex viral transcription pattern in P1-infected cells.

关键词： Porcine circovirus like virus P1 transcriptional analysis Northernblotting,RACE

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Profiling biotoxicities of hexafluoropropylene oxide trimer acid with human embryonic stem cell-based assays

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Journal of Environmental Sciences 2022年第6期34卷 34-42页

作者： Shengxian Liang Guoqiang Liang Yue Zhang Xiufang Zhang Li Zhong Institute of Life Sciences and Green Development College of Life SciencesHebei UniversityBaoding 071000China Western University of Health Sciences PomonaCalifornia 91766USA

Hexafluoropropylene oxide trimer acid(HFPO-TA), an emerging replacement of perfluorooctanoic acid(PFOA), has recently been reported to be a potential environmental *** to the similar structure to PFOA, HFPO-TA may cause comparable adverse effects on human health. Therefore, evaluating the toxic profiles of HFPO-TA has become an urgent *** this study, we investigated the cytotoxicity and hepatoxicity of HFPO-TA using human embryonic stem cell(h ESC)-based assays. Results showed that HFPO-TA reduced h ESCs’ viability in a dose dependent manner, and the calculated IC50 for 24, 48 and 72 hr were 222.8,167.4, and 80.6 μmol/L, respectively. Significant intracellular ROS accumulation and mitochondrion membrane potential reduction were detected with HFPO-TA exposure, and increased apoptotic/necrotic cells were also observed in high dose of HFPO-TA treated ***, HFPO-TA at noncytotoxic concentrations also significantly impaired the functions of induced hepatocytes by diminishing cell glycogen storage ability and deregulating specific functional genes. Transcriptome sequencing analysis identified a set of hepatic associated biological processes responding to HFPO-TA exposure. PPAR was the most significantly enriched pathway. Genes including FGA, FGB, FGG, AHSG, HRG, ITIH2, ALB were characterized as hub genes by cyto Hubba plug-in. These data indicated that HFPO-TA is a potential hepatotoxicant, and may not be a safe replacement for PFOA.

关键词： Hexafluoropropylene oxide trimer acid(HFPO-TA) Stem cell toxicology Hepatoxicity transcriptional analysis

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Transcriptomics-based identification and characterization of genes related to sugar metabolism in‘Hongshuijing’pitaya

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Horticultural Plant Journal 2022年第4期8卷 450-460页

作者： Zhike Zhang Yemiao Xing Muthusamy Ramakrishnan Canbin Chen Fangfang Xie Qingzhu Hua Jianye Chen Rong Zhang Jietang Zhao Guibing Hu Yonghua Qin State Key Laboratory for Conservation and Utilization of Subtropical Agrobioresources/Guangdong Provincial Key Laboratory of Postharvest Science of Fruits and Vegetables/Key Laboratory of Biology and Genetic Improvement of Horticultural Crops(South China) Ministry of Agriculture and Rural AffairsCollege of HorticultureSouth China Agricultural UniversityGuangzhou 510642China Co-Innovation Center for Sustainable Forestry in Southern China Nanjing Forestry UniversityNanjing 210037China Bamboo Research Institute Nanjing Forestry UniversityNanjing 210037China

Sugar composition not only affects fruit flavor but is also an important determinant of fruit taste and consumer *** this study,changes in the sugar content and sugar-metabolizing enzymes were investigated from different sections of various fruit development phases of‘Hongshuijing’pitaya(Hylocereus monacanthus).Genes related to sugar metabolism were also screened by transcriptome *** results indicated that glucose was the major sugar in mature pitaya fruit,and was mainly regulated by vacuolar acid invertase(VAI)and sucrose synthase(SS)(degradative direction).Sugar accumulation varied in pulp between different sections of the pitaya ***,neutral invertase(NI)and SS(degradative direction)are crucial enzymes for sugar accumulation in *** expression of 17 genes related to sucrose metabolism obtained from seven databases[NCBI non-redundant protein database(Nr),NCBI non-redundant nucleotide sequence database(Nt),EuKaryotic Orthologous Groups(KOG),The Protein Families(Pfam),Kyoto Encyclopedia of Genes and Genomes(KEGG),Swiss-prot,and Gene Ontology(GO)]were analyzed in different pitaya pulp ***1 had the highest relative expression level on the 29th day after pollination(DAP).Positive correlations were found between HpVAI1 expression and VAI activity;HpNI4 and NI activity;HpSS2,HpSS5,and SS activity(synthetic direction),indicating that HpVAI1,HpNI4,and HpSS2 and HpSS5 were involved in the regulation of VAI,NI,and SS(synthetic direction),***1 and HpNI4 regulated sucrose degradation and the accumulation of glucose and fructose,while HpSS2 and HpSS5 regulated sucrose *** results suggest that HpVAI1 plays a key role in sugar metabolism during fruit development of‘Hongshuijing’*** results of this study provide new information about sugar metabolism in pitaya fruit that could help improve fruit quality and the breeding of new cultivars.

关键词： Hylocereus monacanthus transcriptional analysis Sugar metabolism qRT-PCR Expression analysis

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Characterization and Pathogenicity of Pseudopestalotiopsis vietnamensis Causing Gray Blight of Wuyi Rock Tea(Camellia sinensis)in China and Specific Mechanisms of Disease Infection

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Phyton-International Journal of Experimental Botany 2023年第1期92卷 131-147页

作者： Guangheng Wu Lu Rui Xiang Lu Libo Han Gan Lv Xianyu Fu Jinxian Liu Nong Zhou Chuanhai Zhang Fujian Provincial Key Laboratory of Eco-Industrial Green Technology College of Ecology and Resources EngineeringWuyi UniversityWuyishan354300China Key Laboratory of Ministry of Education for Genetics Breeding and Multiple Utilization of CropsPlant Immunity CenterFujian Agriculture and Forestry UniversityFuzhou350002China Chongqing Engineering Laboratory of Green Planting and Deep Processing of Famous-Region Drug in the Three Gorges Reservoir Region College of Biology and Food EngineeringChongqing Three Gorges UniversityChongqing404120China State Key Laboratory of Crop Gene Exploration and Utilization in Southwest China Sichuan Agricultural UniversityChengdu611130China College of Tea and Food Science Wuyi UniversityWuyishan354300China

Gray blight disease(GBD)causes significant losses in tea production in *** genes and biological processes involved in resistance to fungal disease in tea plants have been identified,specific mechanisms of the GBD infection process remain *** this study,morphological and multi-gene(TEF-TUB-ITS)phylogenetic characteristics were used to identify isolate CLBB1 of Pseudopestalotiopsis *** tests confirmed that isolate CLBB1 from tea leaves caused GBD in the susceptible tea cultivar Wuyi Rock(Camellia sinensis *** ***).Spores began to germinate 24 h after infection(hai),and after 48 h,elongated fungal hyphae formed from a single *** analysis revealed that 482,517,and 369 genes were differentially expressed at 24,48,and 72 hai,respectively,in Wuyi Rock tea *** CLBB1 infection elicited phenotype-related responses and activated defense-related pathways,including plant–pathogen interaction,MAPK signaling,and plant hormone signal transduction,suggesting a possible mechanism underlying phenotype-based susceptibility to ***,a new *** strain causing GBD in the tea cultivar‘Shuixian’was discovered in this *** analysis indicated that pathogen invasion activated chitin-related MAPK pathways and that tea plants required a hormone to restrict CLBB1.

关键词： Chitin-related MAPK pathways gray blight disease Pseudopestalotiopsis tea transcriptional analysis

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Global transcriptional Profile of Tranosema rostrale Ichnovirus Genes in Infected Lepidopteran Hosts and Wasp Ovaries

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Virologica Sinica 2009年第5期24卷 478-492页

作者： Asieh Rasoolizadeh Frédéric Dallaire Don Stewart Catherine Béliveau Renée Lapointe Michel Cusson Natural Resources Canada Canadian Forest Service Laurentian Forestry Centre 1055 du PEPS P.O. Box 10380 Stn. Ste-Foy Québec QC G1V 4C7 Canada Département de biologie Université Laval Québec QC G1V 0A6 Canada Département de biochimie et microbiologie Université Laval Québec QC G1V 0A6 Canada

The ichnovirus TrIV, transmitted by the endoparasitic wasp Tranosema rostrale to its lepidopteran host during oviposition, replicates asymptomatically in wasp ovaries and causes physiological dysfunctions in parasitized caterpillars. The need to identify ichnoviral genes responsible for disturbances induced in lepidopteran hosts has provided the impetus for the sequencing and annotation of ichnovirus genomes, including that of TrIV. In the latter, 86 putative genes were identified, including 35 that could be assigned to recognized ichnoviral gene families. With the aim of assessing the relative importance of each TrIV gene, as inferred from its level of expression, and evaluating the accuracy of the gene predictions made during genome annotation, the present study builds on an earlier qPCR quantification of transcript abundance of TrIV rep ORFs, in both lepidopteran and wasp hosts, extending it to other gene families as well as to a sample of unassigned ORFs. We show that the majority (91%) of putative ORFs assigned to known gene families are expressed in infected larvae, while this proportion is lower (67%) for a sample taken among the remaining ORFs. Selected members of the TrV and rep gene families are shown to be transcribed in infected larvae at much higher levels than genes from any other TrIV gene family, pointing to their likely involvement in host subjugation. In wasp ovaries, the transcriptional profile is dominated by a rep gene and a member of a newly described gene family encoding secreted proteins displaying a novel cysteine motif, which we identified among previously unassigned ORFs.

关键词： Polydnavirus Ichnovirus Choristoneura fumiferana Tranosema rostrale transcriptional analysis

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A primarily study on Duck Enteritis Virus (DEV) dUTPase

A primarily study on Duck Enteritis Virus (DEV) dUTPase

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第四届第九次全国学术研讨会暨饲料和动物源食品安全战略论坛

作者： Zhao Li-chan An-chun Cheng Ming-shu Wang Gui-ping Yuan Ren-yong Jia (Key Laboratory of Animal Disease and Human Health,Avian Disease Research Center,College of Veterinary Medicine,Sichuan Agricultural University,Yaan,Sichuan,625014,China (Analytical & Testing Center,Sichuan Univerisity,Chengdu,610000,China)

dUTPase is a ubiquitous and important enzyme which hydrolyzes dUTP to *** viruses encode virus specific dUTPase that play an essential role in maintaining the integrity of the viral DNA both by reducing the dUTP levels and by providing the substrate for the thymidylate synthase.A 1344bp gene of Duck Enteritis Virus (DEV),which is homologous to dUTPase,was first identified (GenBank accession number DQ486149) and has been *** gene encodes a protein of 477aa with a predicted molecular mass of 49.7 *** comparisons and multiple alignments showed the conserved motifs of this protein which define the Class 2 dUTPases subfamily with 3-1-2-4-5 motif array,and suggested that DEV dUTPase was quite similar to other identified *** analysis showed that the DEV dUTPase was genetically close to the avian ***,RNA Dot-blot and Western blot,as well as immunofluorescence analysis,indicated that the enzyme is expressed at early and late stages of *** also confirmed that DEV dUTPase localized in the cytoplasm of DEV-infected duck embryo fibroblast as early as 4 hours post infection (hpi),and then the enzyme transferred from cytoplasm to nucleus at 8 hpi then the enzyme expression reached a peak at 12 hpi and it is localized both in the cytoplasm and ***,the expression of DEV dUTPase at both early and late times suggested DEV dUTPase gene might be an early viral gene in DEV vitro infection and played a role in ensuring the fidelity of genome replication.

关键词： Duck Enteritis Virus (DEV) Bioinformatics analysis transcriptional analysis subcellular localization

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