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proteomics of adjacent-to-tumor samples uncovers clinically relevant biological events in hepatocellular carcinoma

National Science Review 2023年第8期10卷 88-104页

作者： Hongwen Zhu Youpei Lin Dayun Lu Shisheng Wang Yuejia Liu Liangqing Dong Qian Meng Jing Gao Yuqiu Wang Nixue Song Yuying Suo Li Ding Pei Wang Bing Zhang Daming Gao Jia Fan Qiang Gao Hu Zhou Department of Analytical Chemistry State Key Laboratory of Drug Research and CAS Key Laboratory of Receptor ResearchShanghai Institute of Materia Medica Chinese Academy of Sciences 2. Department of Liver Surgery and TransplantationLiver Cancer InstituteZhongshan Hospital and Key Laboratory of Carcinogenesis and Cancer Invasion of Ministry of Education Fudan University School of Chinese Materia Medica Nanjing University of Chinese Medicine Institutes for Systems Genetics and NHC Key Lab of Transplant Engineering and Immunology Sichuan Provincial Engineering Laboratory of Pathology in Clinical Application West China Hospital Sichuan University University of Chinese Academy of Sciences Department of Medicine McDonnell Genome Institute Siteman Cancer Center Washington University Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai Lester and Sue Smith Breast Center Department of Molecular and Human Genetics Baylor College of Medicine State Key Laboratory of Cell Biology CAS Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences

Normal adjacent tissues(NATs) of hepatocellular carcinoma(HCC) differ from healthy liver tissues and their heterogeneity may contain biological information associated with disease occurrence and clinical outcome that has yet to be fully evaluated at the proteomic level. This study provides a detailed description of the heterogeneity of NATs and the differences between NATs and healthy livers and revealed that molecular features of tumor subgroups in HCC were partially reflected in their respective NATs. Proteomic data classified HCC NATs into two subtypes(Subtypes 1 and 2), and Subtype 2 was associated with poor prognosis and high-risk recurrence. The pathway and immune features of these two subtypes were characterized. Proteomic differences between the two NAT subtypes and healthy liver tissues were further investigated using data-independent acquisition mass spectrometry, revealing the early molecular alterations associated with the progression from healthy livers to NATs. This study provides a high-quality resource for HCC researchers and clinicians and may significantly expand the knowledge of tumor NATs to eventually benefit clinical practice.

关键词： proteomics hepatocellular carcinoma normal tissue adjacent to tumor heterogeneity

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proteomics Study of Benzene Metabolite Hydroquinone Induced Hematotoxicity in K562 Cells

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Biomedical and Environmental Sciences 2024年第4期37卷 341-353页

作者： JIN Yi Shan YI Zong Chun ZHANG Yu Jing RONG Long YU Chun Hong School of Biological Science and Medical Engineering Beihang UniversityBeijing 100191China School of Engineering Medicine Beihang UniversityBeijing 100191China

Objective Hydroquinone(HQ),one of the phenolic metabolites of benzene,is widely recognized as an important participant in benzene-induced hematotoxicity.However,there are few relevant proteomics in HQ-induced hematotoxicity and the mechanism hasn’t been fully understood yet.Methods In this study,we treated K562 cells with 40μmol/L HQ for 72 h,examined and validated protein expression changes by Label-free proteomic analysis and Parallel reaction monitoring(PRM),and performed bioinformatics analysis to identify interaction networks.Results One hundred and eighty-seven upregulated differentially expressed proteins(DEPs)and 279 downregulated DEPs were identified in HQ-exposed K562 cells,which were involved in neutrophilmediated immunity,blood microparticle,and other GO terms,as well as the lysosome,metabolic,cell cycle,and cellular senescence-related pathways.Focusing on the 23 DEGs and 5 DEPs in erythroid differentiation-related pathways,we constructed the network of protein interactions and determined 6 DEPs(STAT1,STAT3,CASP3,KIT,STAT5B,and VEGFA)as main hub proteins with the most interactions,among which STATs made a central impact and may be potential biomarkers of HQ-induced hematotoxicity.Conclusion Our work reinforced the use of proteomics and bioinformatic approaches to advance knowledge on molecular mechanisms of HQ-induced hematotoxicity at the protein level and provide a valuable basis for further clarification.

关键词： Hydroquinone proteomics Hematotoxicity K562 cells

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proteomics study of Mycoplasma pneumoniae pneumonia reveals the Fc fragment of the IgG-binding protein as a serum biomarker and implicates potential therapeutic targets

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Frontiers of Medicine 2022年第3期16卷 378-388页

作者： Jinrong Liu Rongfang Shen Lin Feng Shujun Cheng Jun Chen Ting Xiao Shunying Zhao Department of Respiratory Medicine Beijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijing 100045China State Key Laboratory of Molecular Oncology Department of Etiology and CarcinogenesisNational Cancer Center/National Clinical Research Center for Cancer/Cancer HospitalChinese Academy of Medical Sciences and Peking Union Medical CollegeBeijing 100021China Beijing Engineering Research Center of Pediatric Surgery Engineering and Transformation CenterBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthBeijing 100045China

Macrolide and corticosteroid resistance has been reported in patients with Mycoplasma pneumoniae(MP)pneumonia(MPP).MP clearance is difficult to achieve through antibiotic treatment in sensitive patients with severe MPP(SMPP).SMPP in children might progress to airway remodeling and even bronchiolitis/bronchitis obliterans.Therefore,identifying serum biomarkers that indicate MPP progression and exploring new targeted drugs for SMPP treatment require urgency.In this study,serum samples were collected from patients with general MPP(GMPP)and SMPP to conduct proteomics profiling.The Fc fragment of the IgG-binding protein(FCGBP)was identified as the most promising indicator of SMPP.Biological enrichment analysis indicated uncontrolled inflammation in SMPP.ELISA results proved that the FCGBP level in patients with SMPP was substantially higher than that in patients with GMPP.Furthermore,the FCGBP levels showed a decreasing trend in patients with GMPP but the opposite trend in patients with SMPP during disease progression.Connectivity map analyses identified 25 possible targeted drugs for SMPP treatment.Among them,a mechanistic target of rapamycin kinase(mTOR)inhibitor,which is a macrolide compound and a cell proliferation inhibitor,was the most promising candidate for targeting SMPP.To our knowledge,this study was the first proteomics-based characterization of patients with SMPP and GMPP.

关键词： severe Mycoplasma pneumoniae pneumonia children proteomics Fc fragment of the IgG-binding protein mechanistic target of rapamycin kinase inhibitor

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proteomics as a tool to gain next level insights into photo-crosslinkable biopolymer modifications

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Bioactive Materials 2022年第11期7卷 204-220页

作者： Nele Pien Fabrice Bray Tom Gheysens Liesbeth Tytgat Christian Rolando Diego Mantovani Peter Dubruel Sandra Van Vlierberghe Ghent University Polymer Chemistry and Biomaterials Research GroupCentre of Macromolecular Chemistry(CMaC)Krijgslaan 281 S4bis9000 GentBelgium Laval University Laboratory for Biomaterials and BioengineeringCRC-IPavillon PouliotQuebec G1V 0A6Canada Univ.Lille CNRSUSR 3290MSAPMiniaturisation pour la Synthese l’Analyse et la ProteomiqueF-59000LilleFrance

The distribution of photo-crosslinkable moieties onto a protein backbone can affect a biomaterial’s crosslinking behavior, and therefore also its mechanical and biological properties. A profound insight in this respect is essential for biomaterials exploited in tissue engineering and regenerative medicine. In the present work, photo-crosslinkable moieties have been introduced on the primary amine groups of: (i) a recombinant collagen peptide (RCPhC1) with a known amino acid (AA) sequence, and (ii) bovine skin collagen (COL BS) with an unknown AA sequence. The degree of substitution (DS) was quantified with two conventional techniques: an ortho-phthalic dialdehyde (OPA) assay and ^(1)H NMR spectroscopy. However, neither of both provides information on the exact type and location of the modified AAs. Therefore, for the first time, proteomic analysis was evaluated herein as a tool to identify functionalized AAs as well as the exact position of photo-crosslinkable moieties along the AA sequence, thereby enabling an in-depth, unprecedented characterization of functionalized photo-crosslinkable biopolymers. Moreover, our strategy enabled to visualize the spatial distribution of the modifications within the overall structure of the protein. proteomics has proven to provide unprecedented insight in the distribution of photo-crosslinkable moieties along the protein backbone, undoubtedly contributing to superior functional biomaterial design to serve regenerative medicine.

关键词： (Photo-crosslinkable)biomaterials Chemical modifications Biomaterial characterization proteomics Localization of functionalizations

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proteomics techniques in protein biomarker discove

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Quantitative Biology 2024年第1期12卷 53-69页

作者： Mahsa Babaei Soheila Kashanian Huang-Teck Lee Frances Harding Department of Biology Faculty of ScienceRazi UniversityKermanshahIran Faculty of Chemistry Sensor and Biosensor Research Center(SBRC)Razi UniversityKermanshahIran Nanobiotechnology Department Faculty of Innovative Science and TechnologyRazi UniversityKermanshahIran Centre for Marine Bioproducts Development Flinders UniversityAdelaideSouth AustraliaAustralia Monash Institute of Pharmaceutical Sciences Monash UniversityMelbourneNew South WalesAustralia

Protein biomarkers represent specific biological activities and processes, so they have had a critical role in cancer diagnosis and medical care for more than 50 years. With the recent improvement in proteomics technologies, thousands of protein biomarker candidates have been developed for diverse disease states. Studies have used different types of samples for proteomics diagnosis. Samples were pretreated with appropriate techniques to increase the selectivity and sensitivity of the downstream analysis and purified to remove the contaminants. The purified samples were analyzed by several principal proteomics techniques to identify the specific protein. In this study, recent improvements in protein biomarker discovery, verification, and validation are investigated. Furthermore, the advantages, and disadvantages of conventional techniques, are discussed. Studies have used mass spectroscopy (MS) as a critical technique in the identification and quantification of candidate biomarkers. Nevertheless, after protein biomarker discovery, verification and validation have been required to reduce the false-positive rate where there have been higher number of samples. Multiple reaction monitoring (MRM), parallel reaction monitoring (PRM), and selected reaction monitoring (SRM), in combination with stable isotope-labeled internal standards, have been examined as options for biomarker verification, and enzyme-linked immunosorbent assay (ELISA) for validation.

关键词： biomarker discovery cancer biomarker gel-based methods gel-free methods mass spectroscopy proteomics

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proteomics Analysis of Soybean Seedlings under Short-Term Water Deficit

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Phyton-International Journal of Experimental Botany 2022年第7期91卷 1381-1401页

作者： Xiyue Wang Zihao Wu Chao Yan Chunmei Ma Shoukun Dong College of Agriculture Northeast Agricultural UniversityHarbin150030China

Soybeans are one of the most important grain crops worldwide.Water deficit,which seriously affects the yield and quality of soybeans,is the main abiotic stress factor in soybean production.As a follow-up study,the droughttolerant soybean variant Heinong 44 was analyzed via proteome analysis.Soybean was exposed to water deficit for 0,8,and 24 h,and protein samples were extracted for detection of differentially expressed proteins.Protein sequencing of leaf tissues under water stress yielded a total of 549 differentially expressed proteins:75 and 320 upregulated proteins as well as 70 and 84 downregulated proteins were obtained after 8 and 24 h of water deficit,respectively.Gene Ontology analysis revealed that most of the differentially expressed proteins(DEPs)were involved in catalytic activity,molecular function,and metabolic processes,whereas some of them were involved in photosynthesis,carbon metabolism,and energy metabolism.We also identified some differentially expressed proteins that may be involved in the regulation of water deficit response.Our study provides a theoretical basis for the breeding of drought-resistant soybean varieties.

关键词： Soybean water deficit proteomics stress time

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proteomics Study on the Differentially Expressed Proteins in c-fos-silenced Cells Exposed to PM2.5

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Biomedical and Environmental Sciences 2020年第9期33卷 680-689页

作者： CAI Ying ZHENG Kai LI Run Bing YU Shu Yuan LIU Ning JI Jia Jia YANG Chen WU De Sheng QIN Shuang Jian LI Bo Ru ZHANG Zhao Hui XU Xin Yun School of Public Health University'of South ChinaHengyang 421001HunanChina Institute of Environment and Health Shenzhen Center for Disease Control and PreventionShenzhen 518055GuangdongChina Xiangya School of Public Health Central South UniversityChangsha 410078HunanChina

Objective To investigate the effect of c-fos gene silencing on differentially expressed proteins(DEPs) in human bronchial epithelial(HBE) cells after exposure to fine particulate matter(PM2.5).Methods HBE cells and c-fos-silenced HBE cells were exposed to 50 μg/mL PM2.5, LC-MS/MS and tandem mass tag(TMT) labeling methods were combined with bioinformatics methods, and DEPs and interaction networks were identified.Results In the HBE group, 414 DEPs were screened, of which 227 were up-regulated and 187 downregulated. In the c-fos silenced HBE group, 480 DEPs were screened, including 240 up-regulated proteins and 240 down-regulated proteins. KEGG annotations showed that DEPs in the HBE group are mainly concentrated in the glycolysis/gluconeogenesis pathway and those in the c-fos silenced group are concentrated mainly in endoplasmic reticulum and the processing of proteins. Additionally, the abnormal expression of GPRC5 C, DKK4, and UBE2 C was identified in top 15 DEPs. After constructing the protein interaction network, 20 Hub proteins including HNRNPA2 B1, HNRNPL, RPS15 A, and RPS25 were screened from the HBE group and the c-fos silenced HBE group.Conclusion c-fos gene affected the expression of cancer-related proteins. Our results provided a scientific basis for further study of PM2.5-induced carcinogenesis mechanism.

关键词： PM2.5 Human bronchial epithelial cells Gene silence proteomics Bioinformatics

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Charcot-Marie-Tooth-1A and sciatic nerve crush rat models:insights from proteomics

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Neural Regeneration Research 2023年第6期18卷 1354-1363页

作者： Zeina Msheik Stephanie Durand Emilie Pinault Martial Caillaud Laetitia Vignaud Fabrice Billet Mohamed El Massry Alexis Desmoulière UR20218 NeurIT(NEURopathies périphériques et Innovation Thérapeutique) University of LimogesLimogesFrance BISCEm(Biologie Intégrative SantéChimie Environnement)Platform US 42 Inserm/UAR 2015 CNRSUniversity of LimogesLimogesFrance UMR 1308 Inserm/CHU–CAPTuR(Contrôle de l’Activation cellulaire Progression Tumorale et Résistance thérapeutique)University of LimogesLimogesFrance Inserm UMR1235–TENS(The Enteric Nervous System in Gut and Brain Diseases) University of NantesNantesFrance

The sensorimotor and histological aspects of peripheral neuropathies were already studied by our team in two rat models:the sciatic nerve crush and the Charcot-Marie-Tooth-1A disease.In this study,we sought to highlight and compare the protein signature of these two pathological situations.Indeed,the identification of protein profiles in diseases can play an important role in the development of pharmacological targets.In fact,Charcot-Marie-Tooth-1A rats develop motor impairments that are more severe in the hind limbs.Therefore,for the first time,protein expression in sciatic nerve of Charcot-Marie-Tooth-1A rats was examined.First,distal sciatic nerves were collected from Charcot-Marie-Tooth-1A and uninjured wild-type rats aged 3 months.After protein extraction,sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry was employed.445 proteins mapped to Swiss-Prot or trEMBL Uniprot databases were identified and quantified.Of these,153 proteins showed statistically significant differences between Charcot-Marie-Tooth-1A and wild-type groups.The majority of these proteins were overexpressed in Charcot-Marie-Tooth-1A.Hierarchical clustering and functional enrichment using Gene Ontology were used to group these proteins based on their biological effects concerning Charcot-Marie-Tooth-1A pathophysiology.Second,proteomic characterization of wild-type rats subjected to sciatic nerve crush was performed sequential window acquisition of all theoretical fragment ion spectra liquid chromatography and mass spectrometry.One month after injury,distal sciatic nerves were collected and analyzed as described above.Out of 459 identified proteins,92 showed significant differences between sciatic nerve crush and the uninjured wild-type rats used in the first study.The results suggest that young adult Charcot-Marie-Tooth-1A rats(3 months old)develop compensatory mechanisms at the level of redox balance,protein folding,myelination,and axonogenesis.These mechanisms seem insufficient

关键词： Charcot-Marie-Tooth-1A endoplasmic reticulum Gene Ontology neurogenesis oxidative stress proteomics rat repair sciatic nerve crush SWATH-MS

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proteomics Analysis of Lipid Droplets from the Oleaginous Alga Chromochloris zofingiensis Reveals Novel Proteins for Lipid Metabolism

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Genomics, proteomics & Bioinformatics 2019年第3期17卷 260-272页

作者： Xiaofei Wang Hehong Wei Xuemei Mao Jin Liu Laboratory for Algae Biotechnology & Innovation College of EngineeringPeking University

Chromochloris zofingiensis represents an industrially relevant and unique green alga,given its capability of synthesizing triacylglycerol(TAG)and astaxanthin simultaneously for storage in lipid droplets(LDs).To further decipher lipid metabolism,the nitrogen deprivation(ND)-induced LDs from C.zofingiensis were isolated,purified,and subjected to proteomic analysis.Intriguingly,many C.zofingiensis LD proteins had no orthologs present in LD proteome of the model alga Chlamydomonas reinhardtii.Seven novel LD proteins(i.e.,two functionally unknown proteins,two caleosins,two lipases,and one L-gulonolactone oxidase)and the major LD protein(MLDP),which were all transcriptionally up-regulated by ND,were selected for further investigation.Heterologous expression in yeast demonstrated that all tested LD proteins were localized to LDs and all except the two functionally unknown proteins enabled yeast to produce more TAG.MLDP could restore the phenotype of mldp mutant strain and enhance TAG synthesis in wildtype strain of C.reinhardtii.Although MLDP and caleosins had a comparable abundance in LDs,they responded distinctly to ND at the transcriptional level.The two lipases,instead of functioning as TAG lipases,likely recycled polar lipids to support TAG synthesis.For the first time,we reported that L-gulonolactone oxidase was abundant in LDs and facilitated TAG accumulation.Moreover,we also proposed a novel working model for C.zofingiensis LDs.Taken together,our work unravels the unique characteristics of C.zofingiensis LDs and provides insights into algal LD biogenesis and TAG synthesis,which would facilitate genetic engineering of this alga for TAG improvement.

关键词： Lipid droplet Caleosin proteomics Triacylglycerol Lipase

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Effects of electroacupuncture on rats with cognitive impairment:An iTRAQ-based proteomics analysis

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Journal of Integrative Medicine 2023年第1期21卷 89-98页

作者： Zhe-yan Sa Jin-sen Xu Xiao-hua Pan Shu-xia Zheng Qian-ru Huang Long Wan Xiao-xiang Zhu Cai-lian Lan Xiao-ran Ye Department of Meridian Research Fujian Academy of Chinese Medical SciencesFuzhou 350003Fujian ProvinceChina Key Laboratory of Propagated Sensation along Meridian of Fujian Province Fuzhou 350003Fujian ProvinceChina

Objective The study explores the effects of electroacupuncture(EA)at the governing vessel(GV)on proteomic changes in the hippocampus of rats with cognitive impairment.Methods Healthy male rats were randomly divided into 3 groups:sham,model and EA.Cognitive impairment was induced by left middle cerebral artery occlusion in the model and EA groups.Rats in the EA group were treated with EA at Shenting(GV24)and Baihui(GV20)for 7 d.Neurological deficit was scored using the Longa scale,the learning and memory ability was detected using the Morris water maze(MWM)test,and the proteomic profiling in the hippocampus was analyzed using protein-labeling technology based on the isobaric tag for relative and absolute quantitation(iTRAQ).The Western blot(WB)analysis was used to detect the proteins and validate the results of iTRAQ.Results Compared with the model group,the neurological deficit score was significantly reduced,and the escape latency in the MWM test was significantly shortened,while the number of platform crossings increased in the EA group.A total of 2872 proteins were identified by iTRAQ.Differentially expressed proteins(DEPs)were identified between different groups:92 proteins were upregulated and 103 were downregulated in the model group compared with the sham group,while 142 proteins were upregulated and 126 were downregulated in the EA group compared with the model group.Most of the DEPs were involved in oxidative phosphorylation,glycolipid metabolism and synaptic transmission.Furthermore,we also verified 4 DEPs using WB technology.Although the WB results were not exactly the same as the iTRAQ results,the expression trends of the DEPs were consistent.The upregulation of heat-shock proteinβ1(Hspb1)was the highest in the EA group compared to the model group.Conclusion EA can effect proteomic changes in the hippocampus of rats with cognitive impairment.Hspb1 may be involved in the molecular mechanism by which acupuncture improves cognitive impairment.

关键词： Cerebral ischemia Vascular cognitive impairment Electroacupuncture proteomics Isobaric tag for relative Absolute quantitation

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