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Genetic variants in C1GALT1 are associated with gastric cancer risk by influencing immune infiltration

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Journal of Biomedical Research 2024年第4期38卷 348-357页

作者： Mengfan Guo Jingyuan Liu Yujuan Zhang Jingjing Gu Junyi Xin Mulong Du haiyan chu Meilin Wang Hanting Liu Zhengdong Zhang Departments of Environmental Genomics and Genetic Toxicology the Key Laboratory of Modern Toxicology of Ministry of EducationCenter for Global HealthJiangsu Key Laboratory of Cancer BiomarkersPrevention and TreatmentCollaborative Innovation Center for Cancer Personalized MedicineSchool of Public Health/Institute of Clinical Researchthe Affiliated Taizhou People's Hospital of Nanjing Medical UniversityNanjing Medical UniversityNanjingJiangsu 211166China Departments of Environmental Genomics and Genetic Toxicology the Key Laboratory of Modern Toxicology of Ministry of EducationCenter for Global HealthJiangsu Key Laboratory of Cancer BiomarkersPrevention and TreatmentCollaborative Innovation Center for Cancer Personalized MedicineSchool of Public HealthNanjing Medical UniversityNanjingJiangsu 211166China Department of Bioinformatics School of Biomedical Engineering and InformaticsNanjing Medical UniversityNanjingJiangsu 211166China Department of Biostatistics Center for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingJiangsu 211166China

Core 1 synthase glycoprotein-N-acetylgalactosamine 3-β-galactosyltransferase 1(C1GALT1)is known to play a critical role in the development of gastric cancer,but few studies have elucidated associations between genetic variants in C1GALT1 and gastric cancer *** using the genome-wide association study data from the database of Genotype and Phenotype(dbGAP),we evaluated such associations with a multivariable logistic regression model and identified that the rs35999583 G>C in C1GALT1 was associated with gastric cancer risk(odds ratio,0.83;95% confidence interval[CI],0.75-0.92;P=3.95×10^(-4)).C1GALT1 mRNA expression levels were significantly higher in gastric tumor tissues than in normal tissues,and gastric cancer patients with higher C1GALT1 mRNA levels had worse overall survival rates(hazards ratio,1.33;95%CI,1.05-1.68;P_(log-rank)=1.90×10^(-2)).Furthermore,we found that C1GALT1 copy number differed in various immune cells and that C1GALT1 mRNA expression levels were positively correlated with the infiltrating levels of CD4^(+)T cells and *** results suggest that genetic variants of C1GALT1 may play an important role in gastric cancer risk and provide a new insight for C1GALT1 into a promising predictor of gastric cancer susceptibility and immune status.

关键词： O-glycosylation genetic variants immune status gastric cancer

加强气候变化背景下植物病原真菌控制技术的创新和突破

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农业环境科学学报 2024年第3期43卷 473-475页

作者：姚彦坡朱永官褚海燕农业农村部环境保护科研监测所天津300191 中国科学院生态环境研究中心北京100085 中国科学院南京土壤研究所南京210008

全球气候变化是现代农业生态系统目前面临的主要威胁之一。一方面,气候变化正在重塑植物与微生物的互作,诱导某些共生微生物转变为病原微生物,提升植物真菌病害发生的频率和程度;另一方面,气候变化降低植物的免疫力和抗病性,导致植物更... 详细信息

全球气候变化是现代农业生态系统目前面临的主要威胁之一。一方面,气候变化正在重塑植物与微生物的互作,诱导某些共生微生物转变为病原微生物,提升植物真菌病害发生的频率和程度;另一方面,气候变化降低植物的免疫力和抗病性,导致植物更严重的真菌病害。本文将重点讨论气候变化如何影响共生真菌与作物的互作,如何驱动植物真菌病害的发生和传播,以及采取何种调控措施从源头上预防病原真菌的危害。

关键词：气候变化主要作物条件致病菌生态调控

Bladder cancer epidemiology and genetic susceptibility

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The Journal of Biomedical Research 2013年第3期27卷 170-178页

作者： haiyan chu Meilin Wang Zhengdong Zhang Department of Environmental Genomics Jiangsu Key Laboratory of Cancer BiomarkersPrevention and TreatmentCancer CenterNanjing Medical University Department of Genetic Toxicology the Key Laboratory of Modern Toxicology of Ministry of EducationSchool of Public HealthNanjing Medical University

Bladder cancer is the most common malignancy of the urinary system. The incidence of bladder cancer of men is higher than that of women （approximately 4：1）. Here, we summarize the bladder cancer-related risk factors, in- cluding environmental and genetic factors. In recent years, although the mortality rate induced by bladder cancer has been stable or decreased gradually, the public health effect may be pronounced. The well-established risk fac- tors for bladder cancer are cigarette smoking and occupational exposure. Genetic factors also play important roles in the susceptibility to bladder cancer. A recent study demonstrated that hereditary non-polyposis colorectal cancer is associated with increased risk of bladder cancer. Since 2008, genome-wide association study （GWAS） has been used to identify the susceptibility loci for bladder cancer. Further gene-gene or gene-environment interaction stud- ies need to be conducted to provide more information for the etiology of bladder cancer.

关键词： bladder cancer molecular epidemiology risk factors genetic susceptibility

Lowered water table causes species substitution while nitrogen amendment causes species loss in alpine wetland microbial communities

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Pedosphere 2021年第6期31卷 912-922页

作者： Yuntao LI Jin-Sheng HE Hao WANG Jizhong ZHOU Yunfeng YANG haiyan chu State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of Sciences71 East Beijing RoadNanjing 210008(China) University of Chinese Academy of Sciences Beijing 100049(China) Department of Ecology College of Urban and Environmental SciencesPeking UniversityBeijing 100871(China) State Key Laboratory of Grassland Agro-Ecosystems College of Pastoral Agriculture Science and TechnologyLanzhou UniversityLanzhou 730000(China) State Key Joint Laboratory of Environment Simulation and Pollution Control School of EnvironmentTsinghua UniversityBeijing 100084(China) Institute for Environmental Genomics Department of Microbiology and Plant Biology and School of Civil Engineering and Environmental SciencesUniversity of OklahomaNorman OK 73019(USA) Earth Science Division Lawrence Berkeley National LaboratoryBerkeley CA 94270(USA)

Alpine wetlands are hotspots of carbon(C)storage and methane emission,and they could be key contributors to global *** recent years,rapid warming has lowered the water table in alpine wetlands on the Tibetan Plateau,concurrent with intensified nitrogen(N)deposition via anthropogenic *** carried out a field experiment to investigate the ecological impacts of these two factors on soil bacterial and functional communities,which are essential drivers of greenhouse gas *** amendment alone decreased the phylogenetic alpha-diversity of bacterial communities which could be offset by lowered water *** contrast,microbial functional alpha-diversity,revealed by a high-throughput microarray,remained *** bacterial and functional beta-diversity responded to lowered water table,but only bacterial community responded to N *** alpha-Proteobacteria,beta-Proteobacteria,and Bacteroidetes were the major responsive bacterial lineages,and C degradation,methanogenesis,alkaline shock,and phosphorus oxidation were the major responsive functional *** analysis revealed that N amendment changed bacterial community structure mainly via species loss processes but did not affect bacterial functional communities,with soil pH and ammonium as the key factors influencing changes in bacterial community ***,lowered water table altered bacterial and functional communities through species substitution processes linked to soil pH and soil *** to our results,the response mechanisms of microbial communities to lowered water table and N amendment are fundamentally different in alpine wetlands.

关键词： alpha-diversity bacterial community beta-diversity microbial functional community N amendment water table lowering

Biological functions and potential implications of circular RNAs

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The Journal of Biomedical Research 2023年第2期37卷 89-99页

作者： Lan Ma haiyan chu Meilin Wang Zhengdong Zhang Department of Genetic Toxicology The Key Laboratory of Modern Toxicology of Ministry of EducationCenter for Global HealthSchool of Public HealthNanjing Medical UniversityNanjingJiangsu 211166China Department of Environmental Genomics Jiangsu Key Laboratory of Cancer BiomarkersPrevention and TreatmentCollaborative Innovation Center for Cancer Personalized MedicineNanjing Medical UniversityNanjingJiangsu 211166China.

Circular RNAs(circRNAs) are characterized by a covalent closed-loop structure with an absence of both 5′ cap structure and 3′ polyadenylated tail. Numerous studies have found that circRNAs play an important role in various diseases and have a variety of biological regulatory mechanisms, including acting as microRNA sponges,interacting with proteins, modulating the expression of related genes and translating into peptides or *** have also been used as biomarkers for a number of diseases, which could improve clinical *** review summarizes the most recent advances in biogenesis and knowledge of the biological functions of circRNAs as well as the related bioinformatics databases. We specifically describe developments in understanding of circRNA functions in the field of environmental exposure-induced diseases. Finally, we focus on potential clinical implications of circRNAs to facilitate their clinical transformation into disease treatment.

关键词： circular RNAs biogenesis mechanisms database biomarkers

Environmental similarity is more important than distance in the community structuring processes of ammonia-oxidizing archaea in agricultural soils

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Pedosphere 2023年第6期33卷 819-827页

作者： Dorsaf KERFAHI Yu SHI Baozhan WANG Hokyung SONG haiyan chu Jonathan M.ADAMS School of Natural Sciences Department of Biological SciencesKeimyung UniversityDaegu 42601Korea State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475001China State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008China Key Lab of Miboyrgriculural Eonment MintryfgrculureCllege of Life SciencesNanjing Agricultural Univery Nanjing 21008China Department of Earth and Environmental Sciences The University of ManchesterManchester M139PLUK University of Chinese Academy of Sciences Beijing 101408China School of Geography and Oceanography Nanjing UniversityNanjing 210008China

Ammonia-oxidizing archaea(AOA) are important in converting ammonia into nitrate in soils. While many aspects of their community structure have been studied, the relative importance of stochastic versus deterministic processes has poorly been understood. We compared AOA communities across the North China Plain, targeting the amoA gene. A phylogenetic null modelling approach was used to calculate the beta nearest taxon index to quantify the influence of stochastic and deterministic processes. We found that spatial distance between samples predicted the perceived processes involved in community structuring, with stochastic processes dominating at local scales. At greater distances, stochasticity became weaker. However, soil pH, which was also the strongest determinant of AOA community, was a much stronger predictor of community structuring, leaving the distance effect redundant as an explanation of community structuring processes. The communities of AOA differing by less than 1 pH unit differed mainly stochastically in terms of operational taxonomic unit composition. At larger pH differences, deterministic processes based on heterogeneous selection between clades became increasingly dominant. It appears that AOA community composition is largely determined by the environment. However, very similar pH environments are the exception. In environments with very close pH values, stochastic effects dominantly cause differences in community composition, whether spatially near or far.

关键词： amoA gene ammonia-oxidizing bacteria assembly processes beta nearest taxon index community structure operational taxonomic unit

Molecular epidemiology of DNA repair gene polymorphisms and head and neck cancer

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The Journal of Biomedical Research 2013年第3期27卷 179-192页

作者： Meilin Wang haiyan chu Zhengdong Zhang Qingyi Wei Department of Genetic Toxicology the Key Laboratory of Modern Toxicology of Ministry of EducationSchool of Public HealthNanjing Medical University Department of Environmental Genomics Jiangsu Key Laboratory of Cancer BiomarkersPrevention and TreatmentCancer CenterNanjing Medical University Department of Epidemiology the University of Texas M. D. Anderson Cancer Center

Although tobacco and alcohol consumption are two common risk factors of head and neck cancer （HNC）, other specific etiologic causes, such as viral infection and genetic susceptibility factors, remain to be understood. Hu- man DNA is often damaged by numerous endogenous and exogenous mutagens or carcinogens, and genetic vari- ants in interaction with environmental exposure to these agents may explain interindividual differences in HNC risk. Single nucleotide polymorphisms （SNPs） in genes involved in the DNA damage-repair response are reported to be risk factors for various cancer types, including HNC. Here, we reviewed epidemiological studies that have assessed the associations between HNC risk and SNPs in DNA repair genes involved in base-excision repair, nucleotide-excision repair, mismatch repair, double-strand break repair and direct reversion repair pathways. We found, however, that only a few SNPs in DNA repair genes were found to be associated with significantly in- creased or decreased risk of HNC, and, in most cases, the effects were moderate, depending upon locus-locus in- teractions among the risk SNPs in the pathways. We believe that, in the presence of exposure, additional pathway- based analyses of DNA repair genes derived from genome-wide association studies （GWASs） in HNC are needed.

关键词： DNA repair molecular epidemiology head and neck cancer genetic variation genome-wide asso-ciation study

Perception field based imitation learning for unlabeled multi-agent pathfinding

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Science China(Information Sciences) 2024年第5期67卷 115-135页

作者： Wenjie chu Ailun YU Wei ZHANG haiyan ZHAO Zhi JIN School of Computer Science Peking University Key Laboratory of High-Confidence Software Technologies (Peking University) Ministry of Education

This paper proposes an imitation learning method to learn a universal agent policy for unlabeled multi-agent pathfinding(unlabeled MAPF) in grid environments. The method transforms the unlabeled MAPF problem into a series of temporal-independent homogeneous classification problems for each *** on this transformation, a neural network is designed to imitate a distance-optimal expert *** neural network consists of two successive modules: perception field learner and field integrating *** former refines and encodes the current system state into a perception field for each agent by combining a set of learnable field-generating functions. The latter takes an agent's perception field as input and decides the agent's next action based on a triplet cross-attention mechanism. We evaluate our method on a diverse set of unlabeled MAPF tasks. Compared with state-of-the-art counterparts, the experimental results manifest the superiority of the proposed method in both generalization ability and scalability.

关键词： unlabeled multi-agent pathfinding perception field triplet cross-attention multi-agent imitation learning learning-based planning

Effect of long-term fertilization on bacterial communities in wheat endosphere

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Pedosphere 2021年第4期31卷 538-548页

作者： Yuying MA Pamela WEISENHORN Xisheng GUO Daozhong WANG Teng YANG Yu SHI Huanchao ZHANG haiyan chu Co-Innovation Center for the Sustainable Forestry in Southern China College of ForestryNanjing Forestry UniversityNanjing 210037(China) State Key Laboratory of Soil and Sustainable Agriculture Institute of Soil ScienceChinese Academy of SciencesNanjing 210008(China) Biosciences Division Argonne National LaboratoryArgonneIL 60439(USA) Key Laboratory of Nutrient Cycling and Resources Environment of Anhui Province Soil and Fertilizer Research InstituteAnhui Academy of Agricultural SciencesHefei 230031(China) University of Chinese Academy of Sciences Beijing 100049(China)

Fertilization has been shown to exert a significant influence on soil microorganisms and directly and indirectly influences plant growth and survival in agroecosystems. However, it is unknown whether fertilization affects endophytic microbial communities, which are ubiquitous and intimately associated with plant growth and health. Herein, we investigated endophytic bacterial communities in wheat leaves and roots under different long-term fertilization regimes,including NPK chemical fertilizer and NPK chemical fertilizer combined with wheat straw, pig manure, or cow manure. Endophytic bacterial community composition considerably differed in leaves and roots. Although different fertilization treatments did not affect the endophytic bacterial species richness or phylogenetic diversity in either leaves or roots, the community composition was significantly altered, particularly in roots. The endophytic bacterial co-occurrence network in leaves was more complex and stable than that in roots. Furthermore, many of the keystone species that were identified by their topological positions in the co-occurrence networks of leaves and roots were involved in plant growth and fitness. The total relative abundance of keystone species was the highest in the NPK plus cow manure treatment in both leaves and roots. Overall, our results suggest that different fertilization regimes can strongly affect endophytic bacterial communities, and the combination of NPK fertilizer and cow manure promoted the relative abundance of the key endophytic bacterial microbiota in both leaves and roots, which might be beneficial for plants in agroecosystems.

关键词： co-occurrence network endophytic bacterial community key microbiota long-term fertilization organic matter