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Dear-DIA^(XMBD): Deep Autoencoder Enables Deconvolution of Data-Independent Acquisition Proteomics

Research 2024年第1期6卷 707-720页

作者： Qingzu He Chuan-Qi Zhong Xiang Li Huan guo Yiming Li Mingxuan Gao Rongshan Yu Xianming Liu Fangfei Zhang Donghui guo Fangfu Ye tiannan guo Jianwei Shuai Jiahuai Han Department of Physics and Fujian Provincial Key Laboratory for Soft Functional Materials ResearchXiamen UniversityXiamen 361005China Oujiang Laboratory(Zhejiang Lab for Regenerative Medicine Vision and Brain Health)and Wenzhou InstituteUniversity of Chinese Academy of SciencesWenzhouZhejiang 325001China School of Life Sciences Xiamen UniversityXiamen 361102China State Key Laboratory of Cellular Stress Biology Innovation Center for Cell Signaling NetworkXiamen 361102China Department of Computer Science Xiamen UniversityXiamen 361005China National Institute for Data Science in Health and Medicine School of MedicineXiamen UniversityXiamen 361102China Bruker(Beijing)Scientific Technology Co.Ltd. BeijingChina Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhou 310024China Westlake Omics Ltd. Yunmeng Road 1HangzhouChina Department of Electronic Engineering Xiamen UniversityXiamen 361005China

Data-independent acquisition(DIA)technology for protein identification from mass spectrometry and related algorithms is developing *** spectrum-centric analysis of DIA data without the use of spectra library from data-dependent acquisition data represents a promising *** this paper,we proposed an untargeted analysis method,Dear-DIA^(XMBD),for direct analysis of DIA ***-DIA^(XMBD) first integrates the deep variational autoencoder and triplet loss to learn the representations of the extracted fragment ion chromatograms,then uses the k-means clustering algorithm to aggregate fragments with similar representations into the same classes,and finally establishes the inverted index tables to determine the precursors of fragment clusters between precursors and peptides and between fragments and *** show that Dear-DIA^(XMBD) performs superiorly with the highly complicated DIA data of different species obtained by different instrument platforms.

关键词： Deep Auto Independent

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Alzheimer’s disease early diagnostic and staging biomarkers revealed by large-scale cerebrospinal fluid and serum proteomic profiling

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The Innovation 2024年第1期5卷 118-126页

作者： Qing-Qing Tao Xue Cai Yan-Yan Xue Weigang Ge Liang Yue Xiao-Yan Li Rong-Rong Lin guo-Ping Peng Wenhao Jiang Sainan Li Kun-Mu Zheng Bin Jiang Jian-Ping Jia tiannan guo Zhi-Ying Wu Department of Neurology and Research Center of Neurology in the Second Affiliated Hospital and Key Laboratory of Medical Neurobiology of Zhejiang Province Zhejiang University School of MedicineHangzhou 310009China Liangzhu Laboratory Zhejiang UniversityHangzhou 311100China Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzho 310024China Department of Neurology First Affiliated HospitalZhejiang University School of MedicineHangzhou 310009China Department of Neurology First Affiliated HospitalSchool of MedicineXiamen UniversityXiamen 361009China Innovation Center for Neurological Disorders and Department of Neurology Xuanwu HospitalCapital Medical UniversityNational Clinical Research Center for Geriatric DiseasesBeijing 100053China MOE Frontier Science Center for Brain Science and Brain-machine Integration School of Brain Science and Brain MedicineZhejiang UniversityHangzhou 310058China CAS Center for Excellence in Brain Science and Intelligence Technology Shanghai 200031China

Amyloid-b,tau pathology,and biomarkers of neurodegeneration make up the core diagnostic biomarkers of Alzheimer disease(AD).However,these proteins represent only a fraction of the complex biological processes underlying AD,and individuals with other brain diseases in which AD pathology is a comorbidity also test positive for these diagnostic *** ADspecific early diagnostic and disease staging biomarkers are *** this study,we performed tandem mass tag proteomic analysis of paired cerebrospinal fluid(CSF)and serum samples in a discovery cohort comprising 98 *** biomarkers were validated by parallel reaction monitoring–based targeted proteomic assays in an independent multicenter cohort comprising 288 *** quantified 3,238 CSF and 1,702 serum proteins in the discovery cohort,identifying 171 and 860 CSF proteins and 37 and 323 serum proteins as potential early diagnostic and staging biomarkers,*** the validation cohort,58 and 21 CSF proteins,as well as 12 and 18 serum proteins,were verified as early diagnostic and staging biomarkers,*** 19-protein CSF and an 8-protein serum biomarker panels were built by machine learning to accurately classify mild cognitive impairment(MCI)due to AD from normal cognition with areas under the curve of 0.984 and 0.881,*** 19-protein CSF biomarker panel also effectively discriminated patients with MCI due to AD from patients with other neurodegenerative ***,we identified 21 CSF and 18 serum stage-associated proteins re-flecting AD *** findings provide a foundation for developing bloodbased tests for AD screening and staging in clinical practice.

关键词： cerebrospinal Alzheimer fluid

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Towards a one-stop solution for large-scale proteomics data analysis

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Science China(Life Sciences) 2018年第3期61卷 351-354页

作者： Yi Zhu tiannan guo Institute of Basic Medical Sciences Westlake Institute for Advanced Study Hangzhou 310024 China Westlake University Hangzhou 310024 China

When China started to push for proteome research in 2010, Dr. John Bergeron from McGill University had just final- ized with colleagues a report from a Human Proteome Or- ganization （HUPO） test sample working group, which had sent an equimolar mixture of 20 highly purified proteins to 27 proteomics laboratories around the world, and asked the proteomists the question： What proteins can you identify with your mass spectrometers （Bell et al., 2009）？ Surpris- ingly, results showed that only seven out of the 27 laborato- ries identified this simple protein mixture correctly. How- ever, after John and colleagues re-analyzed the mass spec- trometry data using their standardized software tools, they found that all the 27 laboratories had correctly identified all the proteins （Bell et al., 2009）. Therefore, he warned the enthusiastic Chinese proteomists in an interview, ＂data analysis is the heart of proteomics＂（Cyranoski, 2010）.

关键词： proteomics 数据分析 proteome Proteome 蛋白质期末考试高度净化软件工具

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Gene Expression Pattern of Signal Transduction in Chronic Myeloid Leukemia

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Wuhan University Journal of Natural Sciences 2006年第3期11卷 732-736页

作者： LI Huiyu JIE Shenghua guo tiannan HUANG Shi＇ang Union Hospital of Tongji Medical College Huazhong University of Science and Technology Wuhan 430022Huhei China

To explore the transcriptional gene expression profiles of signaling pathway in Chronic myeloid leukemia （CML）, a series of cDNA microarray chips were tested. The results showed that differentially expressed genes related to singal transduction in CML were screened out and the genes involved in Phosphoinositide 3-kinases （PI3K）, Ras-MAPK （mitogen-activated protein kinase） and other signaling pathway genes simultaneously. The results also showed that most of these genes were up-expression genes , which suggested that signal transduction be overactivated in CML. Further analysis of these differentially expressed signal transduction genes will be helpful to understand the molecular mechanism of CML and find new targets of treatment.

关键词： signal transduction cDNA microarray gene expression parterre chronic myeloid leukemia bcr-abl

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Diffuse midline glioma treated with epigenetic agent-based immunotherapy

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Signal Transduction and Targeted Therapy 2023年第2期8卷 365-368页

作者： Linkai Jing Zhihong Qian Qiang Gao Rui Sun Zili Zhen Guihuai Wang Xuejun Yang Haitao Li tiannan guo Wei Zhang Department of Neurosurgery Beijing Tsinghua Changgung HospitalTsinghua UniversityBeijingPeople’s Republic of China Department of Basic Medical Sciences School of MedicineTsinghua UniversityBeijingPeople’s Republic of China School of Clinical Medicine Tsinghua UniversityBeijingPeople’s Republic of China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityZhejiangPeople’s Republic of China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyZhejiangPeople’s Republic of China Ministry of Education Key Laboratory of Protein Sciences Beijing Advanced Innovation Center for Structural BiologyBeijing Frontier Research Center for Biological StructureDepartment of Basic Medical SciencesSchool of MedicineTsinghua UniversityBeijingPeople’s Republic of China Tsinghua-Peking Center for Life Sciences Tsinghua UniversityBeijingPeople’s Republic of China IDG/McGovern Institute for Brain Research School of Life SciencesTsinghua UniversityBeijingPeople’s Republic of China

Dear Editor,Diffuse midline glioma,H3K27-altered(DMG),is a pediatric-type high-grade diffuse glioma that preferentially localizes to the brainstem or pons,thalamus,and spinal *** resection is challenging and biopsy is often performed in most *** date,no conventional,targeted or immune therapy has been convincingly shown to improve patients’overall survival(OS).

关键词： glioma immunotherapy brainstem

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sRAGE alleviates SARS-CoV-2-induced pneumonia in hamster

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Signal Transduction and Targeted Therapy 2022年第3期7卷 610-612页

作者： Xiuqin Zhang Dan Li Rui Sun Xinli Hu Zhiqi Song Xiaotian Ni Hua Zhu tiannan guo Chuan Qin Rui-Ping Xiao Institute of Molecular Medicine College of Future TechnologyPeking UniversityBeijingChino Key Laboratory of Human Disease Comparative Medicine of National Health Commission of the People’s Republic of China Beijing Key Laboratory for Animal Models of Emerging and Remerging Infectious DiseasesInstitute of Laboratory Animal ScienceChinese Academy of Medical Sciences and Comparative Medicine CenterPeking Union Medical CollegeBeijingChina Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhouChina

Dear Editor Since last year,the most demanding task of the global pharmaceutical community has been focused on the development of strategies to treat coronavirus disease 2019(COVID-19).To date,several vaccines have been developed and already demonstrated their efficacy in reducing the incidence of COVID-19.1 However,the development of drugs treating COVID-19 is lagging far behind,and all the current treatment regimens have their limitations.

关键词： drugs regimen pneumonia

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约4900年前东亚和东南亚枢纽地区狩猎采集向农业的转变

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Science Bulletin 2024年第1期69卷 103-113页

作者：马敏敏卢敏霞孙瑞朱忠华 Dorian Q.Fuller 郭健新何光林杨晓敏谭玲玲芦永秀董佳佳刘睿良杨继帅李波郭天南李小瑞赵东月张颖王传超董广辉 Key Laboratory of Western China’s Environmental Systems(Ministry of Education) College of Earth and Environmental SciencesLanzhou UniversityLanzhou 730000China Zhaotong University Zhaotong 657000China Westlake Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake UniversityHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China Yunnan Provincial Institute of Cultural Relics and Archaeology Kunming 650118China Institute of Archaeology University College LondonLondon WC1H 0PYUK School of Cultural Heritage Northwest UniversityXi’an 710069China State Key Laboratory of Cellular Stress Biology School of Life SciencesXiamen UniversityXiamen 361102China Department of Anthropology and Ethnology Institute of AnthropologySchool of Sociology and AnthropologyXiamen UniversityXiamen 361005China State Key Laboratory of Marine Environmental Science Xiamen UniversityXiamen 361102China Westlake Omics(Hangzhou)Biotechnology Co. Ltd.Hangzhou 310024China The Department of Asia British MuseumLondon WC1E 7JWUK Tonghai Cultural Relics Management Yuxi 652700China Group of Alpine Paleoecology and Human Adaptation Institute of Tibetan Plateau ResearchChinese Academy of SciencesBeijing 100101China State Key Laboratory of Tibetan Plateau Earth System Resources and EnvironmentBeijing 100101China Ministry of Education Key Laboratory of Contemporary Anthropology Department of Anthropology and Human GeneticsSchool of Life SciencesFudan UniversityShanghai 200433China

The southward expansion of East Asian farmers profoundly influenced the social evolution of Southeast Asia by introducing cereal ***,the timing and routes of cereal expansion in key regions are unclear due to limited empirical *** we report macrofossil,microfossil,multiple isotopic(C/N/Sr/O)and paleoproteomic data directly from radiocarbon-dated human samples,which were unearthed from a site in Xingyi in central Yunnan and which date between 7000 and 3300 a *** isotopes reveal the earliest arrival of millet ca.4900 a BP,and greater reliance on plant and animal agriculture was indicated between 3800 and 3300 a *** dietary differences between hunter-gatherer and agricultural groups are also evident in the metabolic and immune system proteins analysed from their skeletal *** results of paleoproteomic analysis indicate that humans had divergent biological adaptations,with and without *** combined application of isotopes,archaeobotanical data and proteomics provides a new approach to documenting dietary and health changes across major subsistence transitions.

关键词： Isotopes Proteomics Yunnan Millet Agricultural origins Human health

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Longitudinal proteomic investigation of cOVID-19 vaccination

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Protein & Cell 2023年第9期14卷 668-682页

作者： Yingrui Wang Qianru Zhu Rui Sun Xiao Yi Lingling Huang Yifan Hu Weigang Ge Huanhuan Gao Xinfu Ye Yu Song Li Shao Yantao Li Jie Li tiannan guo Junping Shi Marker Lab Westlake Laboratory of Life Sciences and BiomedicineKey Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhou 310024China Research Centerfor Industries of theFuture WestlakeUniversity600D unyu RoadHangzhou 310030China Center for Infectious Disease Research Westlake University18 Shilongshan RoadHangzhou 310024China Westlake Omics(Hangzhou)Biotechnology Co. Ltd.Hangzhou 310024China Department of Translational Medicine Platform The Affiliated Hospital of Hangzhou Normal UniversityHangzhou 310015China The Fourth School of Clinical Medicine Zhejiang Chinese Medical UniversityHangzhou 310053China Medical college of Hangzhou Normal University Hangzhou 311121China Department of Infectious Diseases Nanjing Drum Tower HospitalThe Affiliated Hospital of Nanjing University Medical SchoolNanjing 210008China Institute of Viruses and Infectious Diseases Nanjing UniversityNanjing 210093China Department of Infectious and Hepatology Diseases The Affiliated Hospital of Hangzhou Normal UniversityHangzhou 310015China

Although the development of covID-19 vaccines has been a remarkable success,the heterogeneous individual antibody generation and decline over time are unknown and still hard to *** this study,blood samples were collected from 163 participants who next received two doses of an inactivated COvVID-19 vaccine(CoronaVac)at a 28-day *** TMT-based proteomics,we identified 1,715 serum and 7,342 peripheral blood mononuclear cells(PBMCs)*** proposed two sets of potential biomarkers(seven from serum,five from PBMCs)at baseline using machine learning,and predicted the individual seropositivity 57 days after vaccination(AUC=0.87).Based on the four PBMC's potential biomarkers,we predicted the antibody persistence until 180 days after vaccination(AUC=0.79).Our data highlighted characteristic hematological host responses,including altered lymphocyte migration regulation,neutrophil degranulation,and humoral immune *** study proposed potential blood-derived protein biomarkers before vaccination for predicting heterogeneous antibody generation and decline after coVID-19 vaccination,shedding light on immunization mechanisms and individual booster shot planning.

关键词： COVID-19 vaccination proteomics neutralizing antibodies(NAbs) machine learning

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Gut microbiota,inflammation,and molecular signatures of host response to infection

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Journal of Genetics and Genomics 2021年第9期48卷 792-802页

作者： Wanglong Gou Yuanqing Fu Liang Yue Geng-Dong Chen Xue Cai Menglei Shuai Fengzhe Xu Xiao Yi Hao Chen Yi Zhu Mian-Li Xiao Zengliang Jiang Zelei Miao Congmei Xiao Bo Shen Xiaomai Wu Haihong Zhao Wenhua Ling Jun Wang Yu-Ming Chen tiannan guo Ju-Sheng Zheng College of Life Sciences Zhejiang UniversityHangzhou 310058China Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Center for Infectious Disease Research Westlake Laboratory of Life Sciences and BiomedicineHangzhou 310024China Institute of Basic Medical Sciences Westlake Institute for Advanced StudyHangzhou 310024China Key Laboratory of Structural Biology of Zhejiang Province School of Life SciencesWestlake UniversityHangzhou 310024China Guangdong Provincial Key Laboratory of Food Nutrition and HealthDepartment of EpidemiologySchool of Public HealthSun Yat-sen UniversityGuangzhou 510275China Taizhou Hospital Wenzhou Medical UniversityLinhai 325035China CAS Key Laboratory for Pathogenic Microbiology and Immunology Institute of MicrobiologyChinese Academy of SciencesBeijing 100101China

Gut microbial dysbiosis has been linked to many noncommunicable ***,little is known about specific gut microbiota composition and its correlated metabolites associated with molecular signatures underlying host response to ***,we describe the construction of a proteomic risk score based on 20 blood proteomic biomarkers,which have recently been identified as molecular signatures predicting the progression of the *** demonstrate that in our cohort of 990 healthy individuals without infection,this proteomic risk score is positively associated with proinflammatory cytokines mainly among older,but not younger,*** further discover that a core set of gut microbiota can accurately predict the above proteomic biomarkers among 301 individuals using a machine learning model and that these gut microbiota features are highly correlated with proinflammatory cytokines in another independent set of 366 *** metabolomics analysis suggests potential amino acid-related pathways linking gut microbiota to host metabolism and ***,our multi-omics analyses suggest that gut microbiota composition and function are closely related to inflammation and molecular signatures of host response to infection among healthy *** results may provide novel insights into the cross-talk between gut microbiota and host immune system.

关键词： Gut microbiota Proinflammatory cytokines Proteomic biomarkers COVID-19 Host infection response

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Proteomics profiling of colorectal cancer progression identifies PLOD2 as a potential therapeutic target

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Cancer Communications 2022年第2期42卷 164-169页

作者： Yingkuan Shao Kailun Xu Xi Zheng Biting Zhou Xiuli Zhang Lin Wang Yaoting Sun Dan Li Ting Chen Jian Wang Shaojun Yu Lifeng Sun Xiaoming Xu Shaozhi Dai Huanhuan Gao Guan Ruan Wei Liu Xue Cai Tiansheng Zhu Lina Qi Jiani Chen Wangxiong Hu Xingyue Weng Yi Zhu Xueping Xiang Zhiyuan Hu Jinfan Li Lirong Chen Jimin Shao Shu Zheng tiannan guo Key Laboratory of Cancer Prevention and Intervention Ministry of EducationDepartment of Breast Surgery and OncologySecond Affiliated HospitalSchool of MedicineCancer InstituteZhejiang UniversityHangzhouZhejiang 310009P.R.China Zhejiang Provincial Laboratory of Life Sciences and Biomedicine Key Laboratory of Structural Biology of Zhejiang ProvinceSchool of Life SciencesWestlake University18 Shilongshan RoadHangzhouZhejiang 310024P.R.China Institute of Basic Medical Sciences Westlake Institute for Advanced Study18 Shilongshan RoadHangzhouZhejiang 310024P.R.China CAS Key Laboratory of Standardization and Measurement for Nanotechnology CAS Key Laboratory for Biomedical Effects of Nanomaterials and NanosafetyCAS Center for Excellence in NanoscienceNational Center for Nanoscience and Technology of ChinaBeijing 100190P.R.China Zhejiang Provincial Key Laboratory of Pancreatic Disease The First Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiangP.R.China Department of Colorectal Surgery the Second Affiliated Hospital of Zhejiang University School of MedicineHangzhouZhejiang 310009P.R.China Department of Pathology The Second Affiliated HospitalZhejiang University School of MedicineHangzhouZhejiang 310009P.R.China School of Nanoscience and Technology Sino-Danish CollegeUniversity of Chinese Academy of SciencesBeijing 100049P.R.China Fujian Provincial Key Laboratory of Brain Aging and Neurodegenerative Diseases School of Basic Medical SciencesFujian Medical UniversityFuzhouFujian 350108P.R.China Department of Pathology and Pathophysiology Key Laboratory of Disease Proteomics of Zhejiang ProvinceZhejiang University School of MedicineHangzhouZhejiang 310058P.R.China

Dear editors,Colorectal cancer(CRC)is the second leading cause of cancer deaths in developed countries[1].The malignant transformation from small clumps to cancer takes about 10 years[2].This study aimed to characterize proteomic dynamics associated with CRC development and progres-sion,and identify novel therapeutic targets for intercepting the underlying oncogenic *** have optimized pressure cycling technology(PCT)coupled with data-independent acquisition mass spectrometry(DIA-MS)for robust and reproducible proteomic analysis of biopsy-level formalin-fixed paraffin-embedded(FFPE)tissues[3].

关键词： therapeutic cancer colorectal

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