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Rice functional genomics:decades'efforts and roads ahead

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Science china(Life sciences) 2022年第1期65卷 33-92页

作者： Rongzhi Chen Yiwen Deng Yanglin Ding Jingxin Guo Jie Qiu bing Wang Changsheng Wang Yongyao Xie Zhihua Zhang Jiaxin Chen Letian Chen Chengcai Chu Guangcun He Zuhua He Xuehui huang Yongzhong Xing Shuhua Yang Daoxin Xie Yaoguang Liu Jiayang Li State Key laboratory of Hybrid Rice College of Life SciencesWuhan UniversityWuhan 430072China national Key laboratory of Plant molecular Genetics CAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology&EcologyChinese Academy of SciencesShanghai 200032China State Key laboratory of Plant Physiology and biochemistry College of Biological SciencesChina Agricultural UniversityBeijing 100193China State Key laboratory of Plant Genomics Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China State Key laboratory for Conservation and Utilization of Subtropical Agro-Bioresources South China Agricultural UniversityGuangzhou 510642China national Center for Gene Research Center of Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200233China Shanghai Key laboratory of Plant molecular sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China national Key laboratory of Crop Genetic Improvement and national Centre of Plant Gene Research Huazhong Agricultural UniversityWuhan 430070China college of Plant Science Jilin UniversityChangchun 130062China MOE laboratory of Bioinformatics School of Life SciencesTsinghua UniversityBeijing 100084China

Rice(Oryza sativa L.)is one of the most important crops in the *** the completion of rice reference genome sequences,tremendous progress has been achieved in understanding the molecular mechanisms on various rice traits and dissecting the underlying regulatory *** this review,we summarize the research progress of rice biology over past decades,including omics,genome-wide association study,phytohormone action,nutrient use,biotic and abiotic responses,photoperiodic flowering,and reproductive development(fertility and sterility).For the roads ahead,cutting-edge technologies such as new genomics methods,high-throughput phenotyping platforms,precise genome-editing tools,environmental microbiome optimization,and synthetic methods will further extend our understanding of unsolved molecular biology questions in rice,and facilitate integrations of the knowledge for agricultural applications.

关键词： rice omics GWAS phytohormone action nutrient use biotic and abiotic responses photoperiodic flowering reproductive development

Junctional and somatic hypermutation-induced CX4C motif is critical for the recognition of a highly conserved epitope on HCV E2 by a human broadly neutralizing antibody

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Cellular & molecular Immunology 2021年第3期18卷 675-685页

作者： Chunyan Yi Jing Xia Lan He Zhiyang Ling Xuesong Wang Yu Yan Jiangjun Wang Xinhao Zhao Weiguo Fan Xiaoyu Sun Ronghua Zhang Sheng Ye Rongguang Zhang Yongfen Xu Liyan Ma Yaguang Zhang Honglin Zhou Zhong huang Junqi Niu Gang Long Junxia Lu Jin Zhong bing Sun State Key laboratory of Cell biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of Sciences/University of Chinese Academy of SciencesShanghaiChina CAS Key laboratory of molecular Virology and Immunology Institut Pasteur of ShanghaiChinese Academy of Sciences/University of Chinese Academy of SciencesShanghaiChina School of Life Science and Technology ShanghaiTech UniversityShanghaiChina CAS Key laboratory of Synthetic Chemistry of Natural Substances Shanghai Institute of Organic ChemistryChinese Academy of SciencesShanghaiChina college of biology Hunan Provincial Key Laboratory of Medical VirologyHunan UniversityChangshaChina national laboratory of Biophysics Institute of BiophysicsChinese Academy of Sciences/University of Chinese Academy of Sciences BdjingBeijingChina Interdisciplinary Innovation Institute of Medicine&Engineering Beijing Advanced Innovation Center for Big Data-Based Precision MedicineSchool of Biological Science and Medical EngineeringBeihang UniversityBeijingChina Nanjing Galaxy Biopharma Co. LtdNanjingChina Hepatology Section First HospitalUniversity of JilinChangchunChina

Induction of broadly neutralizing monoclonal antibodies(bNAbs)that bind to the viral envelope glycoproteins is a major goal of hepatitis C virus(HCV)vaccine *** study of bNAbs arising in natural infection is essential in this *** generated a human antibody,8D6,recognizing the E2 protein of HCV isolated from a chronic hepatitis C *** antibody shows broadly neutralizing activity,which covers a pan-genotypic panel of cell culture-derived HCV virions(HCVcc).Functional and epitope analyses demonstrated that 8D6 can block the interaction between E2 and CD81 by targeting a highly conserved epitope on *** describe how the 8D6 lineage evolved via somatic hypermutation to achieve broad *** found that the V(D)J recombination-generated junctional and somatic hypermutation-induced disulfide bridge(C-C)motif in the CDRH3 is critical for the broad neutralization and binding activity of *** motif is conserved among a series of broadly neutralizing HCV antibodies,indicating a common binding ***,the 8D6 inferred germline(iGL)was reconstructed and tested for its binding affinity and neutralization ***,8D6 iGL-mediated relatively strong inhibition of the 1b genotype PR79L9 strain,suggesting that PR79L9 may serve as a potential natural viral strain that provides E2 sequences that induce ***,our detailed epitope mapping and genetic studies of the HCV E2-specific mAb 8D6 have allowed for further refinement of antigenic sites on E2 and reveal a new mechanism to generate a functional CDRH3,while its iGL can serve as a probe to identify potential HCV vaccine strains.

关键词： Hepatitis C virus neutralizing antibody inferred germline CDRH3 disulfide bridge motif

Applications of atomic force microscopy in immunology

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Frontiers of Medicine 2021年第1期15卷 43-52页

作者： Jiping Li Yuying Liu Yidong Yuan Bo huang beijing Smartchip Microelectronics Technology Company Limited Beijing 100192China department of Immunology&national Key laboratory of medical molecular biology Institute of Basic Medical SciencesChinese Academy of Medical SciencesSchool of Basic Medicine Peking Union Medical CollegeBeijing 100005China Clinical Immunology Center Chinese Academy of Medical SciencesBeijing 100005China School of Microelectronics Tianjin UniversityTianjin 300072China department of biochemistry&molecular biology Tongji Medical CollegeHuazhong University of Science&TechnologyWuhan 430030China

Cellular mechanics,a major regulating factor of cellular architecture and biological functions,responds to intrinsic stresses and extrinsic forces exerted by other cells and the extracellular matrix in the *** mechanics also acts as a fundamental mediator in complicated immune responses,such as cell migration,immune cell activation,and pathogen *** principle of atomic force microscopy(AFM)and its three running modes are introduced for the mechanical characterization of living *** peak force tapping mode provides the most delicate and desirable virtues to collect high-resolution images of morphology and force *** a concrete description of AFM capabilities,three AFM applications are *** applications include the dynamic progress of a neutrophil-extracellular-trap release by neutrophils,the immunological functions of macrophages,and the membrane pore formation mediated by perforin,streptolysin O,gasdermin D,or membrane attack complex.

关键词： cellular mechanics atomic force microscopy neutrophil extracellular trap macrophage phagocytosis pore formation

Plant pan-genomics and its applications

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molecular Plant 2023年第1期16卷 168-186页

作者： Junpeng Shi Zhixi Tian Jinsheng Lai Xuehui huang State Key laboratory of Biocontrol School of AgricultureSun Yat-sen UniversityShenzhen 518107China State Key laboratory of Plant Cell and Chromosome Engineering Institute of Genetics and Developmental BiologyInnovation Academy for Seed DesignChinese Academy of SciencesBeijing 100101China State Key laboratory of Plant Physiology and biochemistry and national Maize Improvement Center Department of Plant Genetics and BreedingChina Agricultural UniversityBeijing 100193China Shanghai Key laboratory of Plant molecular sciences College of Life SciencesShanghai Normal UniversityShanghai 200234China

Plant genomes are so highly diverse that a substantial proportion of genomic sequences are not shared among *** variable DNA sequences,along with the conserved core sequences,compose the more sophisticated pan-genome that represents the collection of all non-redundant DNA in a *** rapid progress in genome sequencing technologies,pan-genome research in plants is now *** we review recent advances in plant pan-genomics,including major driving forces of structural variations that constitute the variable sequences,methodological innovations for representing the pan-genome,and major successes in constructing plant *** also summarize recent efforts toward decoding the remaining dark matter in telomere-to-telomere or gapless plant *** new genome resources,which have remarkable advantages over numerous previously assembled less-than-perfect genomes,are expected to become new references for genetic studies and plant breeding.

关键词： plant pan-genome genome assembly structural variations graph genome T-2-T genome

Genotoxins exaggerate the stressed state of aneuploid embryonic stem cells via activation of autophagy

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Science china(Life sciences) 2020年第7期63卷 1026-1036页

作者： Meili Zhang Rong Xiao Guang Liu Yue huang State Key laboratory of medical molecular biology Institute of Basic Medical SciencesChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100005China department of medical Genetics Institute of Basic Medical SciencesChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100005China

The cellular consequences of aneuploidy are largely dependent on the cell types examined. Aneuploid yeasts and mouse embryonic fibroblasts exhibit cell proliferation defects and can be selectively inhibited by compounds that cause proteotoxic or energy stress. By contrast, most aneuploid pluripotent stem cells proliferate rapidly and reach higher saturation densities. The responses of aneuploid pluripotent stem cells to the stress-inducing compounds remain uncharacterized. Here, we tested the response of aneuploid embryonic stem cells to several compounds that caused proteotoxic, energy and genotoxic stress using previously established mouse embryonic stem cell lines trisomic for chromosome 6, 8, 11, or 15. Not all trisomic embryonic stem cells were selectively inhibited by compounds that cause proteotoxic or energy stress. However, most of these cells exhibited increased sensitivity to genotoxins. They displayed elevated DNA damage response as characterized by increased γH2A.X foci under genotoxic stress. Further investigations indicated that elevated autophagy levels might contribute to the increased cytotoxic effects of genotoxins on trisomic embryonic stem cells. Our study laid the foundation for eliminating aneuploidy that might be an effective approach for controlling cancer progression.

关键词： aneuploidy embryonic stem cells genotoxins autophagy

Recent advances in drug delivery systems for targeting cancer stem cells

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Acta Pharmaceutica Sinica B 2021年第1期11卷 55-70页

作者： Hongxia Duan Yanhong Liu Zhonggao Gao Wei huang State Key laboratory of Bioactive Substance and Function of Natural Medicines Department of PharmaceuticsInstitute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China beijing Key laboratory of Drug Delivery Technology and Novel Formulations Institute of Materia MedicaChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100050China

Cancer stem cells(CSCs)are a subpopulation of cancer cells with functions similar to those of normal stem *** few in number,they are capable of self-renewal,unlimited proliferation,and multi-directional differentiation *** addition,CSCs have the ability to escape immune ***,they play an important role in the occurrence and development of tumors,and they are closely related to tumor invasion,metastasis,drug resistance,and recurrence after ***,specific targeting of CSCs may improve the efficiency of cancer therapy.A series of corresponding promising therapeutic strategies based on CSC targeting,such as the targeting of CSC niche,CSC signaling pathways,and CSC mitochondria,are currently under *** the rapid progression in this field and nanotechnology,drug delivery systems(DDSs)for CSC targeting are increasingly being *** this review,we summarize the advances in CSC-targeted ***,we highlight the latest developmental trends through the main line of CSC occurrence and development process;some considerations about the rationale,advantages,and limitations of different DDSs for CSCtargeted therapies were discussed.

关键词： Cancer stem cells Targeting strategies Drug delivery systems Cancer treatment Niche Biomarker Cellular level molecular level

HTR2A agonists play a therapeutic role by restricting ILC2 activation in papain-induced lung inflammation

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Cellular & molecular Immunology 2023年第4期20卷 404-418页

作者： Zhishuo Wang Chenghua Yan Qizhen Du Yuying huang Xuezhen Li Dan Zeng Ruizhi Mao Rama Krishna Gurram Shipeng Cheng Wangpeng Gu Lin Zhu Weiguo Fan Liyan Ma Zhiyang Ling Ju Qiu Dangsheng Li Enmei Liu Yaguang Zhang Yiru Fang Jinfang Zhu bing Sun state Key laboratory of Cell biology CAS Center for Excellence in Molecular Cell ScienceShanghai Institute of Biochemistry and Cell BiologyChinese Academy of SciencesUniversity of Chinese Academy of Sciences320 Yueyang RoadShanghai 200031China college of Life sciences Jiangxi University of Chinese MedicineNanchang 330004China department of Respiratory Medicine Children's Hospital of Chongqing medical University National Clinical Research Center for Child Health and DisordersMinistry of Education Key Laboratory of Child Development and DisordersChongqing Key Laboratory of PediatricsChongqingChina department of Allergy Chongqing General HospitalChongqingChina Clinical Research Center and Division of Mood Disorders Shanghai Mental Health CenterShanghai Jiao Tong University School of MedicineShanghai 200030China laboratory of Immune System biology National Institute of Allergy and Infectious DiseasesNational Institutes of HealthBethesdaMD 20892USA CAS Key laboratory of Tissue Microenvironment and Tumor Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China CAS Center for Excellence in Brain Science and Intelligence Technology Shanghai 200031China Shanghai Key laboratory of Psychotic Disorders Shanghai 201108China.

Group 2 innate lymphoid cells(ILC2s)are a category of heterogeneous cells that produce the cytokines IL-5 and IL-13,which mediate the type 2 immune ***,specific drug targets on lung ILC2s have rarely been *** studies have shown that type 2 cytokines,such as IL-5 and IL-13,are related to ***,we demonstrated the negative correlation between the depression-associated monoamine neurotransmitter serotonin and secretion of the cytokines IL-5 and IL-13 by ILC2s in individuals with ***,serotonin ameliorates papain-induced lung inflammation by suppressing ILC2 *** data showed that the serotonin receptor HTR2A was highly expressed on ILC2s from mouse lungs and human ***,an HTR2A selective agonist(DOI)impaired ILC2 activation and alleviated the type 2 immune response in vivo and in *** with ILC2-specific depletion of HTR2A(Il5^(cre/+)·Htr2a^(flox/flox)mice)abolished the DOI-mediated inhibition of ILC2s in a papain-induced mouse model of *** conclusion,serotonin and DOI could restrict the type 2 lung immune response,indicating a potential treatment strategy for type 2 lung inflammation by targeting HTR2A on ST2+ILC2s.

关键词： Serotonin(5-HT) HTR2A DOl Group 2 innate lymphoid cell Type 2 lung inflammation

Ubiquitin proteasome system research in gastrointestinal cancer

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World Journal of Gastrointestinal Oncology 2016年第2期8卷 198-206页

作者： Jia-Ling Zhong Chang-Zhi huang Clinical laboratory department Sichuan Academy of Medical Science and Sichuan Provincial People’s HospitalChengdu 610072 Sichuan Province China department of Etiology and Carcinogenesis and State Key laboratory of molecular Oncology Cancer Institute and HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021 China

The ubiquitin proteasome system(UPS) is important for the degradation of proteins in eukaryotic cells. It is involved in nearly every cellular process and plays an important role in maintaining body homeostasis. An increasing body of evidence has linked alterations in the UPS to gastrointestinal malignancies,including esophageal,gastric and colorectal cancers. Here,we summarize the current literature detailing the involvement of the UPS in gastrointestinal cancer,highlighting its role in tumor occurrence and development,providing information for therapeutic targets research and antigastrointestinal tumor drug design.

关键词： Ubiquitin proteasome system Gastrointestinalcancer

GSDME with a moonlighting function in pancreatic ductal adenocarcinoma: a narrative review

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Journal of Pancreatology 2022年第4期5卷 83-104页

作者： Bo huang department of Immunology&national Key laboratory of medical molecular biology Institute of Basic Medical SciencesChinese Academy of Medical Sciences&Peking Union Medical CollegeBeijing 100005China department of biochemistry&molecular biology Tongji Medical CollegeHuazhong University of Science&TechnologyWuhan 430030China

Pancreatic ductal adenocarcinoma(PDAC)originates in the exocrine pancreas and accounts for 95%of pancreatic cancers,with 5-year survival rates of approximately 10%.Multiple factors are involved in PDAC pathogenesis,including internal genetic alterations and external inflammation-related *** of exocrine pancreatic enzymes caused by PDAC obstruction inevitably results in autolysis of surrounding normal cells and extracellular matrix,generating tissue damage-related inflammation;however,this process does not cause autolysis of PDAC *** tumor cells acquire resistance to pancreatic enzymatic digestion has been ignored for a long *** this review,we discuss how PDAC cells mobilize gasdermin E,a pore-forming protein,to achieve resistance to autolysis by pancreatic digestive enzymes.

关键词： PDAC GSDME mucins pancreatic enzymes