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| 1 | Single-cell transcriptomic analysis defines the interplay between tumor cells,viral infection,and the microenvironment in nasopharyngeal carcinoma显示文摘Nasopharyngeal carcinoma(NPC)is an Epstein-Barr virus(EBV)-associated malignancy with a complex tumor ecosystem.How the interplay between tumor cells,EBV,and the microenvironment contributes to NPC progression and immune evasion remains unclear.Here we performed single-cell RNA sequencing on^104,000 cells from 19 EBV^+NPCs and 7 nonmalignant nasopharyngeal biopsies,simultaneously profiling the transcriptomes of malignant cells,EBV,stromal and immune cells.Overall,we identified global upregulation of interferon responses in the multicellular ecosystem of NPC.Notably,an epithelial–immune dual feature of malignant cells was discovered and associated with poor prognosis.Functional experiments revealed that tumor cells with this dual feature exhibited a higher capacity for tumorigenesis.Further characterization of the cellular components of the tumor microenvironment(TME)and their interactions with tumor cells revealed that the dual feature of tumor cells was positively correlated with the expression of co-inhibitory receptors on CD8^+tumor-infiltrating T cells.In addition,tumor cells with the dual feature were found to repress IFN-γproduction by T cells,demonstrating their capacity for immune suppression.Our results provide new insights into the multicellular ecosystem of NPC and offer important clinical implications. | Shanzhao Jin Ruoyan Li Ming-Yuan Chen Chao Yu Lin-Quan Tang Yan-Min Liu Jiang-Ping Li Yi-Na Liu Yi-Ling Luo Yifan Zhao Yu Zhang Tian-Liang Xia Shang-Xin Liu Qi Liu Guan-Nan Wang Rui You Jing-Yun Peng Jiang Li Feng Han Jianwei Wang Qiu-Yan Chen Li Zhang Hai-Qiang Mai Benjamin E.Gewurz Bo Zhao Lawrence S.Young Qian Zhong Fan Bai Mu-Sheng Zeng | 2020 | Cell Research2020，30，11： | 16 |
| 2 | Phylogenetic Analysis of the Dengue Virus Strains Causing the 2019 Dengue Fever Outbreak in Hainan,China显示文摘Dengue virus is an arthropod-borne pathogen that is transmitted to humans primarily by Aedes spp.mosquitos,causing the acute infectious disease,dengue fever(DF).Until 2019,no dengue outbreak had been reported in Hainan Province for over 20 years.However,in early September of 2019,an increasing number of infected cases appeared and the DF outbreak lasted for over one month in Haikou City,Hainan Province.In our study,we collected 97 plasma samples from DF patients at three hospitals,as well as 1585 mosquito larvae samples from puddles in different areas of Haikou.There were 49(50.5%)plasma samples found to be strongly positive and 9(9.3%)plasma samples were weakly positive against the NS1 antigen.We discovered DENV both in the patient's plasma samples and mosquito larvae samples,and isolated the virus from C6/36 cells inoculated with the acute phase serum of patients.Phylogenetic analysis revealed that the new strains were the most closely related to the epidemic strain in the southern regions of China,belonging to lineageⅣ,genotypeⅠ,DENV-1.Compared to the seven closest strains from neighboring countries and provinces,a total of 18 amino acid mutations occurred in the coding sequences(CDS)of the new isolated strain,DENV1 HMU-HKU-2.Our data shows that dengue virus is re-emerged in Hainan,and pose new threats for public health.Thus regular molecular epidemiological surveillance is necessary for control and prevention of DENV transmission. | Jiang Du Liyuan Zhang Xiaoyuan Hu Ruoyan Peng Gaoyu Wang Yi Huang Wenqi Wang Kunliang Wu Qiang Wang Haoxiang Su Fan Yang Yun Zhang Chuanning Tang Xiuji Cui Lina Niu Gang Lu Meifang Xiao Yongguo Du Feifei Yin | 2021 | Virologica Sinica2021，36，4： | 2 |
| 3 | Metagenomic insights into responses of microbial population and key functional genes to fulvic acid during partial nitritation显示文摘The long-term impact of fulvic acid(FA)on partial nitritation(PN)systemwas initially examined in this study.The obtained results revealed that the FA lower than 50 mg/L had negligible effect on the nitrite accumulation rate(NAR nearly 100%)and ammonium removal rate(ARR 56.85%),while FA over 50 mg/L decreased ARR from 56.85%to 0.7%.Sludge characteristics analysis found that appropriate FA(<50 mg/L)exposure promoted the settling performance and granulation of PN sludge by removing Bacteroidetes and accumulating Chloroflexi.The analysis of metagenomics suggested that the presence of limited FA(0-50 mg/L)stimulated the generation of NADH,which favors the denitrification and nitrite reduction.The negative impact of FA on the PN system could be divided into two stages.Initially,limited FA(50-120 mg/L)was decomposed by Anaerolineae to stimulate the growth and propagation of heterotrophic bacteria(Thauera).Increasing heterotrophs competed with AOB(Nitrosomonas)for dissolved oxygen,causing AOB to be eliminated and ARR to declined.Subsequently,when FA dosage was over 120 mg/L,Anaerolineae were inhibited and heterotrophic bacteria reduced,resulting in the abundance of AOB recovered.Nevertheless,the ammonium transformation pathway was suppressed because genes amoABC and hao were obviously reduced,leading to the deterioration of reactor performance.Overall,these results provide theoretical guidance for the practical application of PN for the treatment of FA-containing sewage. | Li Zhang Shuang Lan Quanhao Dou Shiwei Hao Yueping Wang Xiaoxuan Wang Ruoyan Zhang Yongzhen Peng Jiachun Yang | 2023 | Journal of Environmental Sciences2023，，2： | 1 |
| 4 | In Silico analysis and linking of metabolism-related genes with the immune landscape in head and neck squamous cell carcinoma显示文摘Metabolic reprogramming and immunologic suppression are two critical characteristics promoting the progression of head and neck squamous cell carcinoma(HNSCC).The integrative analysis of all the metabolismrelated genes(MRGs)in HNSCC is lacking and the interaction between the metabolism and the immune characteristics also requires more exploration to uncover the potential mechanisms.Therefore,this study was designed to establish a prognostic signature based on all the MRGs in HNSCC.Genes of HNSCC samples were available from the TCGA and GEO databases while the MRGs were retrieved from a previous study.Ultimately 4 prognostic MRGs were selected to construct a model possessing robust prognostic value and accuracy in TCGA cohorts.The favorable reproducibility of this model was confirmed in validation cohorts from GEO databases.The risk score calculated by this model was an independent prognostic factor that further classified these HNSCC patients into high-/low-risk groups.GSEA analyses and somatic mutations indicated the low-risk group could activate several anti-tumor pathways and possessed lower TP53 mutation.The results of ESTIMATE,single-sample GSEA,CIBERSORT,and some immune-related molecules analyses suggested the low-risk group exhibited lower metabolic activities and higher immune characteristics.The Spearman correlation test implied most metabolic pathways with tumor-promoting function were negatively correlated with the immune activity,indicating a plausible approach of combining the anti-metabolism and the immunotherapy drugs in the high-risk group to enhance therapeutic effects than applied separately.In conclusion,this prognostic signature linking MRGs with the immune landscape could promote the individualized treatment for HNSCC patients. | JIAYU ZHANG RUOYAN CAO JIANMIN PENG QINCHAO HU JUAN XIA BIN CHENG | 2022 | BIOCELL2022，46，1： | 0 |
| 5 | 基因组和转录组测序整合分析揭示混合型肝癌的不同分子亚型显示文摘文章简介原发性肝癌每年造成全球约70万病人死亡且过半死亡病例来自中国,其致死率在所有癌种中高居第二。肝癌主要分为3种类型:肝细胞癌(约80%)、肝内胆管癌(约15%)和混合型肝癌(约5%)。混合型肝癌兼具肝细胞癌和胆管细胞癌两种成分,是预后最差的一种肝癌。 | 薛瑞栋 陈璐 张冲 藤田征志 Ruoyan Li Shu-Mei Yan Choon Kiat Ong Xiwen Liao Qiang Gao Shota Sasagawa Yanmeng Li Jincheng Wang Hua Guo Qi-Tao Huang Qian Zhong Jing Tan Lisha Qi Wenchen Gong Zhixian Hong Meng Li Jingmin Zhao Tao Peng Yinying Lu Kiat Hon Tony Lim Arnoud Boot Atushi Ono Kazuaki Chayama Zemin Zhang Steve George Rozen Bin Tean Teh Xin Wei Wang Hidewaki Nakagawa 曾木圣 白凡 张宁 | 2020 | 科学新闻2020，，2： | 0 |
| 6 | Diversity and independent evolutionary profiling of rodent-borne viruses in Hainan,a tropical island of China显示文摘The risk of emerging infectious diseases(EID)is increasing globally.More than 60%of EIDs worldwide are caused by animal-borne pathogens.This study aimed to characterize the virome,analyze the phylogenetic evolution,and determine the diversity of rodent-borne viruses in Hainan Province,China.We collected 682 anal and throat samples from rodents,combined them into 28 pools according to their species and location,and processed them for next-generation sequencing and bioinformatics analysis.The diverse viral contigs closely related to mammals were assigned to 22 viral families.Molecular clues of the important rodent-borne viruses were further identified by polymerase chain reaction for phylogenetic analysis and annotation of genetic characteristics such as arenavirus,coronavirus,astrovirus,pestivirus,parvovirus,and papillomavirus.We identified pestivirus and bocavirus in Leopoldoms edwardsi from Huangjinjiaoling,and bocavirus in Rattus andamanensis from the national nature reserves of Bangxi with low amino acid identity to known pathogens are proposed as the novel species,and their rodent hosts have not been previously reported to carry these viruses.These results expand our knowledge of viral classification and host range and suggest that there are highly diverse,undiscovered viruses that have evolved independently in their unique wildlife hosts in inaccessible areas. | Youyou Li Chuanning Tang Yun Zhang Zihan Li Gaoyu Wang Ruoyan Peng Yi Huang Xiaoyuan Hu Henan Xin Boxuan Feng Xuefang Cao Yongpeng He Tonglei Guo Yijun He Haoxiang Su Xiuji Cui Lina Niu Zhiqiang Wu Jian Yang Fan Yang Gang Lu Lei Gao Qi Jin Meifang Xiao Feifei Yin Jiang Du | 2023 | Virologica Sinica2023，38，5： | 0 |
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