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Screening for metastasis-related genes in mouse melanoma cells through sequential tail vein injection

Biophysics Reports 2024年第1期10卷 15-21页

作者： Qinggang Hao Rui Dong Weiyu Bai Dong Chang Xinyi Yao Yingru Zhang Huangying Xu Huiyan Li Xiang Kui Feng Wang Yan Wang Chengqin Wang Yujie Lei Yan Chen Junling Shen Lei Sang Yan Bai Jianwei Sun Center for Life sciences Yunnan Key Laboratory of Cell Metabolism and Diseases State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan School of Life Sciences Yunnan University Key Laboratory of Tumor Immunological Prevention and Treatment of Yunnan Province Yan'an Hospital Affiliated to Kunming Medical University Shandong Provincial Key Laboratory of Animal Resistance Biology Collaborative Innovation Center of Cell Biology in Universities of Shandong Center for Cell Structure and Function Institute of Biomedical Science College of Life Sciences Shandong Normal University Department of Pathology The Second Affiliated Hospital of Kunming Medical University State Key Laboratory of Bioactive Molecules and Druggability Assessment Institute of Genomic Medicine College of Pharmacy Jinan University Department of Pathology School of Basic Medicine Qingdao University Department of Thoracic Surgery Yunnan Cancer Hospital & The Third Affiliated Hospital of Kunming Medical University & Yunnan Cancer Center

Tumor metastasis, responsible for approximately 90% of cancer-associated mortality, remains poorly understood. Here in this study, we employed a melanoma lung metastasis model to screen for metastasis-related genes. By sequential tail vein injection of mouse melanoma B16F10 cells and the subsequently derived cells from lung metastasis into BALB/c mice, we successfully obtained highly metastatic B16F15 cells after five rounds of in vivo screening. RNA-sequencing analysis of B16F15 and B16F10 cells revealed a number of differentially expressed genes, some of these genes have previously been associated with tumor metastasis while others are novel discoveries. The identification of these metastasis-related genes not only improves our understanding of the metastasis mechanisms, but also provides potential diagnostic biomarkers and therapeutic targets for metastatic melanoma.

关键词： Melanoma Lung metastasis model Gene screening Tail vein injection

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Single-nucleus transcriptomics uncovers a geroprotective role of YAP in primate gingival aging

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Protein & Cell 2024年第8期15卷 612-632页

作者： Qinchao Hu Bin Zhang Yaobin Jing Shuai Ma Lei Hu jingyi Li Yandong Zheng Zijuan Xin Jianmin Peng Si Wang Bin Cheng Jing Qu Weiqi zhang Guang-Hui Liu Songlin Wang State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Hospital of Stomatology Guanghua School of StomatologyGuangdong Provincial Key Laboratory of StomatologySun Yat-sen UniversityGuangzhou 510060China Salivary Gland Disease Center and Beijing Key Laboratory of Tooth Regeneration and Function Reconstruction Beijing Laboratory of Oral Health and Beijing Stomatological HospitalCapital Medical UniversityBeijing 100050China Department of Biochemistry and Molecular Biology School of Basic Medical SciencesCapital Medical UniversityBeijing 100069China CAS Key Laboratory of genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China Institute for Stem Cell and Regeneration Chinese Academy of SciencesBeijing 100101China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China Advanced Innovation Center for Human Brain Protection and National Clinical Research Center for Geriatric Disorders Xuanwu Hospital Capital Medical UniversityBeijing 100053China Aging Translational Medicine Center Intermational Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuan Wu HospitalCapital Medical UniversityBeijing 100053China Intemational Center for Aging and Cancer Hainan Medical UniversityHaikou 571199China Aging Biomarker Consortium Beijing 100101China

Aging has a profound impact on the gingiva and significantly increases its susceptibility to periodontitis,a worldwide prevalent inflammatory ***,a systematic characterization and comprehensive understanding of the regulatory mechanism underlying gingival aging is still ***,we systematically dissected the phenotypic characteristics of gingiva during aging in primates and constructed the first single-nucleus transcriptomic landscape of gingival aging,by which a panel of cell type-specific signatures were *** cells were identified as the most affected cell types by aging in the *** analyses pinpointed the crucial role of YAP in epithelial self-renew and homeostasis,which declined during aging in epithelial cells,especially in basal *** decline of YAP activity during aging was confrmed in the human gingival tissues,and downregulation of YAP in human primary gingival keratinocytes recapitulated the major phenotypic defects observed in the aged primate gingiva while overexpression of YAP showed rejuvenation *** work provides an in-depth understanding of gingival aging and serves as a rich resource for developing novel strategies to combat aging-associated gingival diseases,with the ultimate goal of advancing periodontal health and promoting healthy aging.

关键词： single-nucleus RNA-sequencing primate gingiva aging YAP

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The genome-wide meiotic recombination landscape in ciliates and its implications for crossover regulation and genome evolution

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Journal of Genetics and genomics 2024年第3期51卷 302-312页

作者： Lu Fu Chen Gu Kazufumi Mochizuki Jie Xiong Wei Miao Guangying Wang Key Laboratory of Aquatic Biodiversity and Conservation Institute of HydrobiologyChinese Academy of SciencesWuhanHubei 430072China University of Chinese Academy of sciences Beijing 100049China Institute of Human Genetics(IGH) CNRSUniversity of Montpellier34396 MontpellierFrance Key Laboratory of Breeding Biotechnology and Sustainable Aquaculture Chinese Academy of SciencesWuhanHubei 430072China Key Laboratory of Lake and Watershed Science for Water Security Chinese Academy of SciencesNanjingJiangsu 210008China

Meiotic recombination is essential for sexual reproduction and its regulation has been extensively studied in many ***,genome-wide recombination landscape has not been reported in ciliates and it remains unknown how it is affected by the unique features of ciliates:the synaptonemal complex(SC)-independent meiosis and the nuclear ***,we show the recombination landscape in the model ciliate Tetrahymena thermophila by analyzing single-nucleotide polymorphism datasets from 38 hybrid *** detect 1021 crossover(CO)events(35.8 per meiosis),corresponding to an overall CO rate of 9.9 cM/***,gene conversion by non-crossover is rare(1.03 per meiosis)and not biased towards G or C *** with the reported roles of SC in CO interference,we find no obvious sign of CO *** tends to occur within germ-soma common genomic regions and many of the 44 identified CO hotspots localize at the centromeric or subtelomeric *** ontology analyses show that CO hotspots are strongly associated with genes responding to environmental *** discuss these results with respect to how nuclear dimorphism has potentially driven the formation of the observed recombination landscape to facilitate environmental adaptation and the sharing of machinery among meiotic and somatic recombination.

关键词： Meiotic recombination Hotspot Crossover interference Adaptive evolution

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Telomere-to-telomere genome of the allotetraploid legume Sesbania cannabina reveals transposon-driven subgenome divergence and mechanisms of alkaline stress tolerance

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Science China(Life sciences) 2024年第1期67卷 149-160页

作者： Haofei Luo Xiaofei Wang Changqing You Xuedan Wu Duofeng Pan Zhiyao Lv Tong Li Dongmei Zhang Zhongbao Shen Xiaodong Zhang Guodao Liu Kaixuan He Qingtong Ye Yajun Jia Qinghua Zhao Xian Deng Xiaofeng Cao Xianwei Song Gai Huang State Key Laboratory of Plant genomics and National Center for Plant Gene Research Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China Hainan Yazhou Bay Seed Lab Sanya 572025China University of Chinese Academy of sciences Beijing 100049China Institute of Forage and Grassland sciences Heilongjiang Academy of Agricultural SciencesHarbin 150086China Shandong Academy of Agricultural sciences Jinan 250100China National Center of Technology Innovation for Comprehensive Utilization of Saline-Alkali Land Dongying 257345China Shandong Green Manure Ecological Technology Co. LtdDongying 257345China State Key Laboratory of Tropical Crop Breeding Chinese Academy of Tropical Agricultural SciencesHaikou 571101China

Alkaline soils pose an increasing problem for agriculture worldwide,but using stress-tolerant plants as green manure can improve marginal ***,we show that the legume Sesbania cannabina is very tolerant to alkaline conditions and,when used as a green manure,substantially improves alkaline *** understand genome evolution and the mechanisms of stress tolerance in this allotetraploid legume,we generated the first telomere-to-telomere genome assembly of *** spanning~2,087 *** assembly included all centromeric regions,which contain centromeric satellite repeats,and complete chromosome ends with telomeric *** genome analysis distinguished A and B subgenomes,which diverged approximately 7.9 million years *** genomic analysis revealed that the chromosome homoeologs underwent large-scale inversion events(>10 Mb)and a significant,transposon-driven size expansion of the chromosome 5A *** further identified four specific alkali-induced phosphate transporter genes in ***;these may function in alkali tolerance by relieving the deficiency in available phosphorus in alkaline *** work highlights the significance of *** as a green tool to improve marginal lands and sheds light on subgenome evolution and adaptation to alkaline soils.

关键词： Sesbania cannabina alkaline stress telomere-to-telomere genome legume green manure phosphate transporter allotetraploid

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Evolutionary mechanisms and practical significance of reproductive success and clonal diversity in unisexual vertebrate polyploids

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Science China(Life sciences) 2024年第3期67卷 449-459页

作者： Meng Lu Li Zhou Jian-Fang Gui State Key Laboratory of Freshwater Ecology and Biotechnology Hubei Hongshan Laboratorythe Innovation Academy of Seed DesignInstitute of HydrobiologyChinese Academy of SciencesWuhan 430072China University of Chinese Academy of sciences Beijing 100049China

Unisexual reproduction is generally relevant to polyploidy, and unisexual vertebrates are often considered an evolutionary “dead end” due to the accumulation of deleterious mutations and absence of genetic diversity. However, some unisexual polyploids have developed strategies to avoid genomic decay, and thus provide ideal models to unveil unexplored evolutionary mechanisms, from the reproductive success to clonal diversity creation. This article reviews the evolutionary mechanisms for overcoming meiotic barrier and generating genetic diversity in unisexual vertebrates, and summarizes recent research advancements in the polyploid Carassius complex. Gynogenetic gibel carp(Carassius gibelio) is a unique amphitriploid that has undergone a recurrent autotriploidy and has overcome the bottleneck of triploid sterility via gynogenesis. Recently, an efficient strategy in which ploidy changes, including from amphitriploid to amphitetraploid, then from amphitetraploid to novel amphitriploid, drive unisexual-sexual-unisexual reproduction transition and clonal diversity has been *** on this new discovery, multigenomic reconstruction biotechnology has been used to breed a novel strain with superior growth and stronger disease resistance. Moreover, a unique reproduction mode that combines both abilities of ameiotic oogenesis and sperm-egg fusion,termed as ameio-fusiongensis, has been discovered, and it provides an efficient approach to synthesize sterile allopolyploids. In order to avoid ecological risks upon escape and protect the sustainable property rights of the aquaculture seed industry, a controllable fertility biotechnology approach for precise breeding is being developed by integrating sterile allopolyploid synthesis and gene-editing *** review provides novel insights into the origin and evolution of unisexual vertebrates and into the attempts being made to exploit new breeding biotechnologies in aquaculture.

关键词： unisexual vertebrates polyploidy reproduction transition clonal diversity precise breeding genomic reconstruction controllable fertility

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Plant genomic resources at National genomics Data Center:assisting in data-driven breeding applications

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aBIOTECH 2024年第1期5卷 94-106页

作者： Dongmei Tian Tianyi Xu Hailong Kang Hong Luo Yanqing Wang Meili Chen Rujiao Li Lina Ma Zhonghuang Wang Lili Hao Bixia Tang Dong Zou Jingfa Xiao Wenming Zhao Yiming Bao Zhang Zhang Shuhui Song National genomics Data Center Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China CAS Key Laboratory of Genome sciences and Information Beijing Institute of GenomicsChinese Academy of Sciences&China National Center for BioinformationBeijing 100101China University of Chinese Academy of sciences Beijing 100049China

genomic data serve as an invaluable resource for unraveling the intricacies of the higher plant systems,including the constituent elements within and among *** various efforts in genomic data archiving,integrative analysis and value-added curation,the National genomics Data Center(NGDC),which is a part of the China National Center for Bioinformation(CNCB),has successfully established and currently maintains a vast amount of database *** dedicated initiative of the NGDC facilitates a data-rich ecosystem that greatly strengthens and supports genomic research ***,we present a comprehensive overview of central repositories dedicated to archiving,presenting,and sharing plant omics data,introduce knowledgebases focused on variants or gene-based functional insights,highlight species-specific multiple omics database resources,and briefly review the online application *** intend that this review can be used as a guide map for plant researchers wishing to select effective data resources from the NGDC for their specific areas of study.

关键词： Plant-omics data Data repositories Data integration Knowledgebase Plant genomics

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Long-term prognosis and its associated predictive factors in patients with eosinophilic gastroenteritis

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World Journal of Gastroenterology 2024年第2期30卷 146-157页

作者： Kai-Wen Li Ge-Chong Ruan Shuang Liu Tian-Ming Xu Ye Ma Wei-Xun Zhou Wei Liu Peng-Yu Zhao Zhi-Rong Du Ji Li Jing-Nan Li Department of Gastroenterology Chinese Academy of Medical Sciences and Peking Union Medical College HospitalBeijing 100730China Department of Allergy Chinese Academy of Medical Sciences and Peking Union Medical College HospitalBeijing 100730China Department of Pathology Chinese Academy of Medical Sciences and Peking Union Medical College HospitalBeijing 100730China Department of Radiology Chinese Academy of Medical Sciences and Peking Union Medical College HospitalBeijing 100730China Affairs Office Chinese Academy of Medical Sciences and Peking Union Medical College Hospital(West campus)Beijing 100032China

BACKGROUND Eosinophilic gastroenteritis(EGE)is a chronic recurrent disease with abnormal eosinophilic infiltration in the gastrointestinal *** remain the most common treatment ***,disease relapse and glucocorticoid dependence remain notable *** date,few studies have illuminated the prognosis of EGE and risk factors for disease *** To describe the clinical characteristics of EGE and possible predictive factors for disease relapse based on long-term *** This was a retrospective cohort study of 55 patients diagnosed with EGE admitted to one medical center between 2013 and *** records were collected and ***-Meier curves and log-rank tests were conducted to reveal the risk factors for long-term relapse-free survival(RFS).RESULTS EGE showed a median onset age of 38 years and a slight female predominance(56.4%).The main clinical symptoms were abdominal pain(89.1%),diarrhea(61.8%),nausea(52.7%),distension(49.1%)and vomiting(47.3%).Forty-three(78.2%)patients received glucocorticoid treatment,and compared with patients without glucocorticoid treatments,they were more likely to have elevated serum immunoglobin E(IgE)(86.8%vs 50.0%,P=0.022)and descending duodenal involvement(62.8%vs 27.3%,P=0.046)at *** a median follow-up of 67 mo,all patients survived,and 56.4%had at least one *** variables at baseline might have been associated with the overall RFS rate,including age at diagnosis24 kg/m^(2)(HR 0.3922,95%CI:0.1916-0.8027,P=0.014),disease duration from symptom onset to diagnosis>3.5 mo(HR 2.4725,95%CI:1.220-5.0110,P=0.011),vomiting(HR 3.1259,95%CI:1.5246-6.4093,P=0.001),total serum IgE>300 KU/L at diagnosis(HR 0.2773,95%CI:0.1204-0.6384,P=0.022)and glucocorticoid treatment(HR 6.1434,95%CI:2.8446-13.2676,P=0.003).CONCLUSION In patients with EGE,younger onset age,longer disease c

关键词： Eosinophilic gastroenteritis Prognosis Relapse Glucocorticoid Glucocorticoid dependence

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Aging hallmarks of the primate ovary revealed by spatiotemporal transcriptomics

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Protein & Cell 2024年第5期15卷 364-384页

作者： Huifen Lu Ying Jing Chen Zhang Shuai Ma Weiqi Zhang Daoyuan Huang Bin Zhang Yuesheng Zuo Yingying Qin Guang-Hui Liu Yang Yu Jing Qu Si Wang Advanced Innovation Center for Human Brain Protection National Clinical Research Center for Geriatric DisordersXuanwu Hospital Capital Medical UniversityBeijing 100053China State Key Laboratory of Stem Cell and Reproductive Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Translational Medicine Center International Center for Aging and CancerBeijing Municipal Geriatric Medical Research CenterXuanwu HospitalCapital Medical UniversityBeijing 100053China State Key Laboratory of Membrane Biology Institute of ZoologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of sciences Beijing 100049China Beijing Institute for Stem Cell and Regenerative Medicine Beijing 100101China CAS Key Laboratory of genomic and Precision Medicine Beijing Institute of GenomicsChinese Academy of SciencesBeijing 100101China Institute for Stem cell and Regeneration CASBeijing 100101China China National Center for Bioinformation Beijing 100101China The Fifth People’s Hospital of Chongqing Chongqing 400062China Sino-Danish College University of Chinese Academy of SciencesBeijing 101408China Sino-Danish Center for Education and Research Beijing 101408China Department of Obstetrics and Gynecology Center for Reproductive MedicinePeking UniversityThird HospitalBeijing 100191China Clinical Stem Cell Research Center Peking UniversityThird HospitalBeijing 100191China Center for Reproductive Medicine Cheeloo College of MedicineShandong UniversityJinan 250012China Key Laboratory of Reproductive Endocrinology of Ministry of Education National Research Center for Assisted Reproductive Technology and Reproductive GeneticsShandong Key Laboratory of Reproductive MedicineShandong Provincial Clinical Research Center for Reproductive HealthJinan 250012China Key Laboratory of Organ Regeneration and Reconstruction Institute of ZoologyChinese Academy of SciencesBeijing 100101China Aging Biomarker Consortium Beijing 100101China

The ovary is indispensable for female reproduction,and its age-dependent functional decline is the primary cause of ***,the molecular basis of ovarian aging in higher vertebrates remains poorly ***,we apply spatiotemporal transcriptomics to benchmark architecture organization as well as cellular and molecular determinants in young primate ovaries and compare these to aged primate *** a global view,somatic cells within the non-follicle region undergo more pronounced transcriptional fluctuation relative to those in the follicle region,likely constituting a hostile microenvironment that facilitates ovarian ***,we uncovered that inflammation,the senescent-associated secretory phenotype,senescence,and fibrosis are the likely primary contributors to ovarian aging(PCOA).Of note,we identified spatial co-localization between a PCOA-featured spot and an unappreciated MT2(Metallothionein 2)highly expressing spot(MT2^(high))characterized by high levels of inflammation,potentially serving as an aging hotspot in the primate ***,with advanced age,a subpopulation of MT2^(high)accumulates,likely disseminating and amplifying the senescent signal *** study establishes the first primate spatiotemporal transcriptomic atlas,advancing our understanding of mechanistic determinants underpinning primate ovarian aging and unraveling potential biomarkers and therapeutic targets for aging and age-associated human ovarian disorders.

关键词： spatial transcriptome primate ovary aging senescence inflammation

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Genetic analysis and candidate gene identification of salt tolerancerelated traits in maize

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Journal of Integrative Agriculture 2024年第7期23卷 2196-2210页

作者： Hui Fang Xiuyi Fu Hanqiu Ge Mengxue Jia Jie Ji Yizhou Zhao Zijian Qu Ziqian Cui Aixia Zhang Yuandong Wang Ping Li Baohua Wang Scientific Observing and Experimental Station of Maize in Plain Area of Southern Region Ministry of Agriculture and Rural Affairs/School of Life SciencesNantong UniversityNantong 226019China Maize Research Institute Beijing Academy of Agriculture and Forestry Sciences(BAAFS)Beijing 100097China

Soil salinization poses a threat to maize production worldwide,but the genetic mechanism of salt tolerance in maize is not well ***,identifying the genetic components underlying salt tolerance in maize is of great *** the current study,a teosinte-maize BC2F7 population was used to investigate the genetic basis of 21 salt tolerance-related *** total,125 QTLs were detected using a high-density genetic bin map,with one to five QTLs explaining 6.05–32.02%of the phenotypic variation for each *** total phenotypic variation explained(PVE)by all detected QTLs ranged from 6.84 to 63.88%for each *** all 125 QTLs,only three were major QTLs distributed in two genomic regions on chromosome 6,which were involved in three salt tolerance-related *** addition,10 pairs of epistatic QTLs with additive effects were detected for eight traits,explaining 0.9 to 4.44%of the phenotypic ***,18 QTL hotspots affecting 3–7 traits were *** one hotspot(L5),a gene cluster consisting of four genes(ZmNSA1,SAG6,ZmCLCg,and ZmHKT1;2)was found,suggesting the involvement of multiple pleiotropic ***,two important candidate genes,Zm00001d002090 and Zm00001d002391,were found to be associated with salt tolerance-related traits by a combination of linkage and marker-trait association ***00001d002090 encodes a calcium-dependent lipid-binding(CaLB domain)family protein,which may function as a Ca^(2+)sensor for transmitting the salt stress signal downstream,while Zm00001d002391 encodes a ubiquitin-specific protease belonging to the C19-related *** findings provide valuable insights into the genetic basis of salt tolerance-related traits in maize and a theoretical foundation for breeders to develop enhanced salt-tolerant maize varieties.

关键词： maize salt tolerance-related traits QTL mapping region-based association analysis

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Unsynchronized butyrophilin molecules dictate cancer cell evasion of Vγ9Vδ2 T-cell killing

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Cellular & Molecular Immunology 2024年第4期21卷 362-373页

作者： Zeguang Wu Qiezhong Lamao Meichao Gu Xuanxuan Jin Ying Liu Feng Tian Ying Yu Pengfei Yuan Shuaixin Gao Thomas S.Fulford Adam P.Uldrich Catherine C.L Wong Wensheng Wei Biomedical Pioneering Innovation Center Peking-Tsinghua Center for Life SciencesPeking University Genome Editing Research CenterState Key Laboratory of Protein and Plant Gene ResearchSchool of Life SciencesPeking University100871BeijingChina EdiGene Inc. Life Science ParkChangping District102206BeijingChina Center for Precision Medicine Multi-Omics Research Peking University Health Science CenterPeking University100191BeijingChina Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity The University of MelbourneParkvilleVIC3010Australia Cancer Immunology program Peter MacCallum Cancer CentreMelbourneVICAustralia State Key Laboratory for Complex Severe and Rare DiseasesClinical Research InstitutePeking Union Medical College HospitalChinese Academy of Medical Science&Peking Union Medical CollegePeking-Tsinghua Center for Life Sciences100871BeijingChina

Vγ9Vδ2 T cells are specialized effector cells that have gained prominence as immunotherapy agents due to their ability to target and kill cells with altered pyrophosphate *** our effort to understand how cancer cells evade the cell-killing activity of Vγ9Vδ2 T cells,we performed a comprehensive genome-scale CRISPR screening of cancer *** found that four molecules belonging to the butyrophilin(BTN)family,specifically BTN2A1,BTN3A1,BTN3A2,and BTN3A3,are critically important and play unique,nonoverlapping roles in facilitating the destruction of cancer cells by primary Vγ9Vδ2 T *** coordinated function of these BTN molecules was driven by synchronized gene expression,which was regulated by IFN-γsignaling and the RFX ***,an enzyme called QPCTL was shown to play a key role in modifying the N-terminal glutamine of these BTN proteins and was found to be a crucial factor in Vγ9Vδ2 T cell killing of cancer *** our research,we offer a detailed overview of the functional genomic mechanisms that underlie how cancer cells escape Vγ9Vδ2 T ***,our findings shed light on the importance of the harmonized expression and function of gene family members in modulating T-cell activity.

关键词： Butyrophilin Vγ9Vδ2 T-cell Cancer-specific immune evasion Glutaminyl-peptide cyclotransferase-like Pyrophosphate metabolite Immunotherapy

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