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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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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 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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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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Effect of riboflavin deficiency on intestinal morphology,jejunum mucosa Proteomics,and cecal microbiota of Pekin ducks

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Animal Nutrition 2023年第1期12卷 215-226页

作者： Yaxi Xu Bo Zhang Rui Zhao Kexin Gao Suyun Liang Yongbao Wu Yongsheng Hao Dapeng Liu Zhanbao Guo Jian Hu Zhengkui Zhou Ming Xie Jing Tang State Key Laboratory of Animal Nutrition Key Laboratory of Animal(Poultry)Genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsInstitute of Animal ScienceChinese Academy of Agricultural SciencesBeijing100193China

This study was to determine the effects of riboflavin deficiency(RD)on intestinal development,jejunum mucosa proteome,cecal short-chain fatty acids(SCFA)profiling,and cecal microbial diversity and community of starter Pekin ducks.Male white Pekin ducks(1 d old,n=240)were allocated into 2 groups,with 12 replicates and 10 birds per replicate in each group.For 21 d,all ducks had ad libitum access to either an RD or a riboflavin adequate(control,CON)diet,formulated by supplementing a basal diet with 0 or 10 mg riboflavin per kg of diet,respectively.Compared to the CON group,growth retardation,high mortality,and poor riboflavin status were observed in the RD group.Furthermore,RD reduced the villus height and the ratio of villus height to crypt depth of jejunum and ileum(PProteomics showed that 208 proteins were upregulated and 229 proteins were downregulated in the RD group compared to those in the CON group.Among these,RD mainly suppressed intestinal absorption and energy generation processes such as glycolysis and gluconeogenesis,fatty acid beta oxidation,tricarboxylic acid cycle,and oxidative phosphorylation,leading to impaired ATP generation.In addition,RD decreased the community richness and diversity of the bacterial community in the cecum of ducks.Specifically,RD reduced the abundance of butyrate-producing bacteria in the cecum(P<0.05),such as Eubacterium coprostanoligenes,Prevotella and Faecalibacterium.Dietary RD resulted in growth depression and intestinal hypofunction of Pekin ducks,which could be associated with impaired intestinal absorption and energy generation processes in intestinal mucosa,as well as gut microbiota dysbiosis.These findings contribute to our understanding of the mechanisms of intestinal hypofunction due to RD.

关键词： Riboflavin Deficiency Intestinal morphology Proteomics Cecal microbiota Short-chain fatty acids

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Tandem Mass Tag-based Proteomics analysis reveals the vital role of inflammation in traumatic brain injury in a mouse model

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Neural Regeneration Research 2023年第1期18卷 155-161页

作者： Jin-Qian Dong Qian-Qian Ge Sheng-Hua Lu Meng-Shi Yang Yuan Zhuang Bin Zhang Fei Niu Xiao-Jian Xu Bai-Yun Liu Department of Neurosurgery Beijing Tiantan HospitalCapital Medical UniversityBeijingChina Beijing Key Laboratory of Central Nervous System Injury Beijing Neurosurgical InstituteCapital Medical UniversityBeijingChina Center for Nerve Injury and Repair Beijing Institute of Brain DisordersBeijingChina China National Clinical Research Center for Neurological Diseases BeijingChina

Proteomics is a powerful tool that can be used to elucidate the underlying mechanisms of diseases and identify new biomarkers.Therefore,it may also be helpful for understanding the detailed pathological mechanism of traumatic brain injury(TBI).In this study,we performed Tandem Mass Tag-based quantitative analysis of cortical proteome profiles in a mouse model of TBI.Our results showed that there were 302 differentially expressed proteins in TBI mice compared with normal mice 7 days after injury.Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses showed that these differentially expressed proteins were predominantly involved in inflammatory responses,including complement and coagulation cascades,as well as chemokine signaling pathways.Subsequent transcription factor analysis revealed that the inflammation-related transcription factors NF-κB1,RelA,IRF1,STAT1,and Spi1 play pivotal roles in the secondary injury that occurs after TBI,which further corroborates the functional enrichment for inflammatory factors.Our results suggest that inflammation-related proteins and inflammatory responses are promising targets for the treatment of TBI.

关键词： bioinformatics complement cascade mass spectrometry neuroinflammation Proteomics secondary injury subacute phase tandem mass tag transcription factor traumatic brain injury

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Cell type-specific Proteomics uncovers a RAF15-SnRK2.6/OST1 kinase cascade in guard cells

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植物学报:英文版 2023年第9期65卷 2122-2137页

作者： Hongliang Wang Yubei Wang Tian Sang Zhen Lin Rongxia Li Weiwei Ren Xin Shen Bing Zhao Xiao Wang Xuebin Zhang Shaoqun Zhou Shaojun Dai Honghong Hu Chun-Peng Song Pengcheng Wang Shanghai Center for Plant Stress Biology CAS Center for Excellence in Molecular Plant SciencesChinese Academy of SciencesShanghai 200032China University of Chinese Academy of Sciences Beijing 100049China Institute of Advanced Biotechnology and School of Life Sciences Southern University of Science and TechnologyShenzhen 518055China Shanghai Bioprofile Technology Company Ltd Shanghai 200241China Center of Plant Germplasm Resources College of Life SciencesShanghai Normal UniversityShanghai 200234China National Key Laboratory of Crop Genetic Improvement College of Life Science and TechnologyHuazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Crop Stress Adaptation and Improvement College of Life SciencesCollege of AgricultureAcademy for Advanced Interdisciplinary StudiesHenan UniversityKaifeng 475004China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureKey Laboratory of Synthetic BiologyMinistry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Multicellular organisms such as plants contain various cell types with specialized functions.Analyzing the characteristics of each cell type reveals specific cell functions and enhances our understanding of organization and function at the organismal level.Guard cells(GCs)are specialized epidermal cells that regulate the movement of the stomata and gaseous exchange,and provide a model genetic system for analyzing cell fate,signaling,and function.Several Proteomics analyses of GC are available,but these are limited in depth.Here we used enzymatic isolation and flow cytometry to enrich GC and mesophyll cell protoplasts and perform in-depth Proteomics in these two major cell types in Arabidopsis leaves.We identified approximately 3,000 proteins not previously found in the GC proteome and more than600 proteins that may be specific to GC.The depth of our Proteomics enabled us to uncover a guard cell-specific kinase cascade whereby Raf15and Snf1-related kinase2.6(SnRK2.6)/OST1(open stomata 1)mediate abscisic acid(ABA)-induced stomatal closure.RAF15 directly phosphorylated SnRK2.6/OST1 at the conserved Ser175 residue in its activation loop and was sufficient to reactivate the inactive form of SnRK2.6/OST1.ABAtriggered SnRK2.6/OST1 activation and stomatal closure was impaired in raf15 mutants.We also showed enrichment of enzymes and flavone metabolism in GC,and consistent,dramatic accumulation of flavone metabolites.Our study answers the long-standing question of how ABA activates SnRK2.6/OST1 in GCs and represents a resource potentially providing further insights into the molecular basis of GC and mesophyll cell development,metabolism,structure,and function.

关键词： abscisic acid guard cell metabolomics phosphorylation Proteomics signaling

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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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Phospho-Proteomics identifies a critical role of ATF2 in pseudorabies virus replication

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Virologica Sinica 2022年第4期37卷 591-600页

作者： Fang-Fang Jiang Ren-Qi Wang Chao-Yue Guo Ke Zheng Hai-Long Liu Le Su Sheng-Song Xie Huan-Chun Chen Zheng-Fei Liu State Key Laboratory of Agricultural Microbiology Hongshan Laboratory and Key laboratory of Preventive Veterinary Medicine in Hubei ProvinceCollege of Veterinary MedicineHuazhong Agricultural UniversityWuhan430070China Key Lab of Agricultural Animal Genetics Breedingand Reproduction of Ministry of EducationHuazhong Agricultural UniversityWuhan430070China

Pseudorabies virus(PRV),an etiological agent of pseudorabies in livestock,has negatively affected the porcine industry all over the world.Epithelial cells are reported as the first site of PRV infection.However,the role of host proteins and its related signaling pathways in PRV replication is largely unclear.In this study,we performed a quantitative phosphoProteomics screening on PRV-infected porcine kidney(PK-15)epithelial cells.Totally 5723phosphopeptides,corresponding to 2180 proteins,were obtained,and the phosphorylated states of 810 proteins were significantly different in PRV-infected cells compared with mock-infected cells(P<0.05).GO and KEGG analysis revealed that these differentially expressed phosphorylated proteins were predominantly related to RNA transport and MAPK signaling pathways.Further functional studies of NF-κB,transcription activator factor-2(ATF2),MAX and SOS genes in MAPK signaling pathway were analyzed using RNA interference(RNAi)knockdown.It showed that only ATF2-knockdown reduces both PRV titer and viral genome copy number.JNK pathway inhibition and CRISPR/Cas9 gene knockout showed that ATF2 was required for the effective replication of PRV,especially during the biogenesis of viral genome DNA.Subsequently,by overexpression of the ATF2 gene and point mutation of the amino acid positions 69/71 of ATF2,it was further demonstrated that the phosphorylation of ATF2 promoted PRV replication.These findings suggest that ATF2 may provide potential therapeutic target for inhibiting PRV infection.

关键词： Pseudorabies virus(PRV) Transcription activator factor-2(ATF2) iTRAQ Proteomics Phosphorylation

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Integrated liver Proteomics and metabolomics identify metabolic pathways affected by pantothenic acid deficiency in Pekin ducks

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Animal Nutrition 2022年第4期11卷 1-14页

作者： Jing Tang Yongbao Wu Bo Zhang Suyun Liang Zhanbao Guo Jian Hu Zhengkui Zhou Ming Xie Shuisheng Hou State Key Laboratory of Animal Nutrition Key Laboratory of Animal(Poultry)Genetics Breeding and ReproductionMinistry of Agriculture and Rural AffairsInstitute of Animal SciencesChinese Academy of Agricultural Sciences100193BeijingChina

Pantothenic acid deficiency(PAD)in animals causes growth depression,fasting hypoglycemia and impaired lipid and glucose metabolism.However,a systematic multi-omics analysis of effects of PAD on hepatic function has apparently not been reported.We investigated liver proteome and metabolome changes induced by PAD to explain its effects on growth and liver metabolic disorders.Pekin ducks(1-dold,n=128)were allocated into 2 groups,with 8 replicates and 8 birds per replicate.For 16 d,all ducks had ad libitum access to either a PAD or a pantothenic acid adequate(control,CON)diet,formulated by supplementing a basal diet with 0 or 8 mg pantothenic acid/kg of diet,respectively.Liver enlargement,elevated liver glycogen concentrations and decreased liver concentrations of triglyceride and unsaturated fatty acids were present in the PAD group compared to the CON group.Based on integrated liver Proteomics and metabolomics,PAD mainly affected glycogen synthesis and degradation,glycolysis and gluconeogenesis,tricarboxylic acid(TCA)cycle,peroxisome proliferator-activated receptor(PPAR)signaling pathway,fatty acid beta oxidation,and oxidative phosphorylation.Selected proteins were confirmed by Western blotting.Downregulation of proteins and metabolites involved in glycogen synthesis and degradation,glycolysis and gluconeogenesis implied that these processes were impaired in PAD ducks,which could have contributed to fasting hypoglycemia,liver glycogen storage,insufficient ATP production,and growth retardation.In contrast,PAD also upregulated proteins and metabolites involved in fatty acid beta oxidation,the TCA cycle,and oxidative phosphorylation processes in the liver;presumably compensatory responses to produce ATP.We inferred that PAD decreased liver triglyceride and unsaturated fatty acids by activating fatty acid beta oxidation and impairing unsaturated fatty acid synthesis.These findings contributed to our understanding of the mechanisms of PAD-induced changes in hepatic metabolism.

关键词： Pantothenic acid Hepatic metabolism Proteomics Metabolomics Hypoglycemia

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