AIM:To assess BGC823 gastric cancer(GC) cell metastasis after knockdown of liver-intestine cadherin(CDH17) and the therapeutic value of CDH17-RNAilentivirus in vivo.METHODS:We evaluated primary tumor growth and assess...AIM:To assess BGC823 gastric cancer(GC) cell metastasis after knockdown of liver-intestine cadherin(CDH17) and the therapeutic value of CDH17-RNAilentivirus in vivo.METHODS:We evaluated primary tumor growth and assessed local infiltration and systemic tumor dissemination using an orthotopic implantation technique.The therapeutic value of CDH17 knockdown was examined by intratumoral administration of CDH17-RNA interference(RNAi)-lentivirus in an established GC tumor xenograft mouse model.Furthermore,a comparative proteomic approach was utilized to identify differentially expressed proteins in BGC823 and lenti-CDH17-miRneg cells following CDH17 knockdown.RESULTS:Metastases in the liver and lung appeared earlier and more frequently in animals with tumors derived from BGC823 or lenti-CDH17-miR-neg cells than in tumors derived from lenti-CDH17-miR-B cells.Average tumor weight and volume in the CDH17-RNAi-lentivirus-treated group were significantly lower than those in the control group(tumor volume:0.89 ± 0.04 cm 3 vs 1.16 ± 0.06 cm 3,P < 0.05;tumor weight:1.15 ± 0.58 g vs 2.09 ± 0.08 g,P < 0.05).Fifteen differentially expressed proteins were identified after CDH17 silencing in BGC823 cells,including a variety of cytoskeletal and chaperone proteins as well as proteins involved in metabolism,immunity/defense,cell proliferation and differentiation,cell cycle,and signal transduction.CONCLUSION:Our data establish a foundation for future studies of the comprehensive protein expression patterns and effects of CDH17 in GC.展开更多
[Objective]To elucidate the role of ethylene(ET),a latex yield stimulant of the rubber tree,on the sieve tube(ST)transport efficiency of materials(especially sucrose)needed for natural rubber biosynthesis.[Method]Rubb...[Objective]To elucidate the role of ethylene(ET),a latex yield stimulant of the rubber tree,on the sieve tube(ST)transport efficiency of materials(especially sucrose)needed for natural rubber biosynthesis.[Method]Rubber tree seedlings were treated with ET solution or water which was used as a control on the bark,and latex samples and ST tissue samples were collected for proteomic analyses and latex sucrose content determination respectively.[Results]After ET treatment,the sucrose content of the latex was found significantly decreased.A total of 66 ethylene-responsive proteins(ERPs)were distinguished by two-dimensional gel electrophoresis(2-DE),and 54 were successfully identified by MALDI-TOF/TOF and database searching.The majority of these ERPs were involved in carbohydrate transport and metabolic processes in the ST.[Conclusion]Our findings suggest that the application of ET may increase the transport efficiency of the ST and that the application of ET promotes the consumption of energy and sucrose in the ST.展开更多
AIM:To explore the method for early diagnosis of gastric cancer by screening the expression spectrum of saliva protein in gastric cancer patients using mass spectrometry for proteomics.METHODS:Proportional peptide mas...AIM:To explore the method for early diagnosis of gastric cancer by screening the expression spectrum of saliva protein in gastric cancer patients using mass spectrometry for proteomics.METHODS:Proportional peptide mass fingerprints were obtained by analysis based on proteomics matrix-assisted laser desorption ionization time-of-flight/mass spectrometry.A diagnosis model was established using weak cation exchange magnetic beads to test saliva specimens from gastric cancer patients and healthy subjects.RESULTS:Significant differences were observed in the mass to charge ratio(m/z) peaks of four proteins(1472.78 Da,2936.49 Da,6556.81 Da and 7081.17 Da) between gastric cancer patients and healthy subjects.CONCLUSION:The finger print mass spectrum of saliva protein in patients with gastric cancer can be established using gastric cancer proteomics.A diagnostic model for distinguishing protein expression mass spectra of gastric cancer from non-gastric-cancer saliva can be established according to the different expression of proteins 1472.78 Da,2936.49 Da,6556.81 Da and 7081.17 Da.The method for early diagnosis of gastric cancer is of certain value for screening special biological markers.展开更多
Proteomics focuses on the systematic identification and quantification of entire proteomes and interpretation of proteins’biological functions.During the last decade,proteomics in China has grown much faster than oth...Proteomics focuses on the systematic identification and quantification of entire proteomes and interpretation of proteins’biological functions.During the last decade,proteomics in China has grown much faster than other research fields in life sciences.At the beginning of the second decade of the 21st century,the rapid development of high-resolution and high-speed mass spectrometry makes proteomics a powerful tool to study the mechanisms underlying physiological/pathological processes in organisms.This article provides a brief overview of proteomics technology development and representative scientific progress of the Human Liver Proteome Project in China over the past three years.展开更多
Urine is an important source of biomarkers. This article reviews current advances, major challenges, and future prospects in the field of urinary proteorrfics. Because the practical clinical problem is to distinguish ...Urine is an important source of biomarkers. This article reviews current advances, major challenges, and future prospects in the field of urinary proteorrfics. Because the practical clinical problem is to distinguish diseases with similar symptoms, merely comparing samples from patients of a particular disease to those of healthy individuals is inadequate for finding biomarkers with sufficient diagnostic power. In addition, the variation of expression levels of urinary proteins among healthy individuals and individuals under different physiological conditions adds to the difficulty in identifying biomarkers. We propose that es- tablishing the natural variation in urinary protein expression among a healthy population can serve as a reference to help iden- tify protein abundance changes that are caused by disease, not by individual variations or physiological changes. We also dis- cuss that comparing protein expression levels between urine and plasma may reveal the physiological function of the kidney and that may facilitate biomarker discovery. Finally, we propose that establishing a data-sharing platform for data collection and integrating results from all urinary biomarker studies will help promote the development of urinary proteomics.展开更多
Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased orga...Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs.In recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery.In addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease.Here,we present a comprehensive review of the major human protein bioinformatics databases.We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.展开更多
Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for ...Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics ofArabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins (H/PRPs) is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins (CWPs) were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.展开更多
In proteomics, attention has focused on various immobilized enzyme reactors (IMERs) for the realization of high throughput digestion. In this report, a novel organic-inorganic hybrid monolith based IMER was prepared i...In proteomics, attention has focused on various immobilized enzyme reactors (IMERs) for the realization of high throughput digestion. In this report, a novel organic-inorganic hybrid monolith based IMER was prepared in a 100 μm i.d. capillary with 3-glycidoxypropyltrimethoxysilane (GLYMO) as the monomer and tetraethoxysilane (TEOS) as the crosslinker. Trypsin immobilization was achieved via the reaction between vicinal diol groups, which were obtained from hydrolysis of epoxy groups, and the amino groups of trypsin. Bovine serum albumin was digested thoroughly by this IMER in 47 s. After micro-reverse phase liquid chromatography-tandem mass spectrometry (μRPLC-MS/MS) analysis and database searching, beyond 35% sequence coverage was obtained, and the result was comparable to that of 12 h in solution digestion. The present IMER has potential for high throughput digestion.展开更多
Apoptosis,or programmed cell death,is a complex,genetically-determined process involved in the development and maintenance of homeostasis in multicellular organisms.Dysregulation of apoptosis has been implicated in a ...Apoptosis,or programmed cell death,is a complex,genetically-determined process involved in the development and maintenance of homeostasis in multicellular organisms.Dysregulation of apoptosis has been implicated in a number of diseases,including cancer and autoimmune disease.Thus,the investigation of apoptotic regulation has evoked considerable interest.Many apoptotic proteins have been shown to be post-translationally modulated,such as by protein cleavage,translocation,protein-protein interaction,and various post-translational modifications,which fall precisely within the range of proteomic analysis.Recently,contemporary proteomic technologies have achieved significant advances and have accelerated research in functional and chemical proteomics,which have been applied to the field of apoptosis research and have the potential to be a driving force for the field.This review highlights some of the major achievements in the application of proteomics in apoptosis research and discusses new directions and challenges for the near future.展开更多
Mitochondrion plays the key functions in mammalian cells. It is believed that mitochondrion exerts the common biologic functions in many tissues, but also performs some specific functions correspondent with tissues wh...Mitochondrion plays the key functions in mammalian cells. It is believed that mitochondrion exerts the common biologic functions in many tissues, but also performs some specific functions correspondent with tissues where it is localized. To identify the tissue-specific mitochondrial proteins, we carried out a systematic survey towards mitochondrial proteins in the tissues of C57BL/6J mouse, such as liver, kidney and heart. The mitochondrial proteins were separated by 2DE and identified by MALDI-TOF/TOF MS. Total of 87 unique proteins were identified as the tissue-specific ones, and some representatives were further verified through ICPL quantification and Western blot. Because these issue-specific proteins are coded from nuclear genes, real-time PCR was employed to examine the mRNA status of six typical genes found in the tissues.With combining of the expression data and the co-localization images obtained from confocal microscope, we came to the conclusion that the tissue-specifically mitochondrial proteins were widely distributed among the mouse tissues. Our investigation, therefore, indeed provides a solid base to further explore the biological significance of the mitochondrial proteins with tissue-orientation.展开更多
Secreted proteins are important sources for early detection and diagnosis of disease, and as such have received considerable attention. The extraction of low concentration proteins from large volumes of culture media,...Secreted proteins are important sources for early detection and diagnosis of disease, and as such have received considerable attention. The extraction of low concentration proteins from large volumes of culture media, which are rich in salts and other compounds that interfere with most proteomics techniques, presents a problem for secretome studies. Ultrafiltration, precipitation, and dialysis are three major extraction methods that can be used to overcome this problem. The present study for the first time, compared the merits and shortcomings of these three methods, without bias. Centrifugal ultrafiltration provided the best extraction efficiency, and precipitation provided the highest number of identifiable proteins. The three methods yielded closely related, but different, information on the secretome; thus, they should be considered complementary or, at least, supplementary methods. Three hundred and sixty unique proteins were identified, including 211 potential secreted proteins. Compared with previous studies, this study also identified 42 new secreted proteins. The present study not only offers a reference for the selection of secretome extraction methods, but also expands the secretome database for the investigation of hepatocellular carcinoma.展开更多
Recently, there has been an overwhelming demand for studies on protein post-translational modification (PTM) to understand the increasing complexity from the level of the genome to the proteome. The covalent modific...Recently, there has been an overwhelming demand for studies on protein post-translational modification (PTM) to understand the increasing complexity from the level of the genome to the proteome. The covalent modifications of proteins with phosphates, lipids, sugars or other residues confer on these proteins additional structural and functional diversity. For instance, protein phosphorylation is involved in a wide range of cellular processes including signal transduction. Protein glycosylation is one of the most abundant PTMs and more than 50% of all human proteins are glycosylated. Glycoproteins are involved in many biological events, such as cell-cell adhesion, communication, immune response and development.展开更多
基金Supported by The National Natural Science Foundation of China,No.30871147
文摘AIM:To assess BGC823 gastric cancer(GC) cell metastasis after knockdown of liver-intestine cadherin(CDH17) and the therapeutic value of CDH17-RNAilentivirus in vivo.METHODS:We evaluated primary tumor growth and assessed local infiltration and systemic tumor dissemination using an orthotopic implantation technique.The therapeutic value of CDH17 knockdown was examined by intratumoral administration of CDH17-RNA interference(RNAi)-lentivirus in an established GC tumor xenograft mouse model.Furthermore,a comparative proteomic approach was utilized to identify differentially expressed proteins in BGC823 and lenti-CDH17-miRneg cells following CDH17 knockdown.RESULTS:Metastases in the liver and lung appeared earlier and more frequently in animals with tumors derived from BGC823 or lenti-CDH17-miR-neg cells than in tumors derived from lenti-CDH17-miR-B cells.Average tumor weight and volume in the CDH17-RNAi-lentivirus-treated group were significantly lower than those in the control group(tumor volume:0.89 ± 0.04 cm 3 vs 1.16 ± 0.06 cm 3,P < 0.05;tumor weight:1.15 ± 0.58 g vs 2.09 ± 0.08 g,P < 0.05).Fifteen differentially expressed proteins were identified after CDH17 silencing in BGC823 cells,including a variety of cytoskeletal and chaperone proteins as well as proteins involved in metabolism,immunity/defense,cell proliferation and differentiation,cell cycle,and signal transduction.CONCLUSION:Our data establish a foundation for future studies of the comprehensive protein expression patterns and effects of CDH17 in GC.
基金Supported by the Central Public-interest Scientific Institution Basal Research Fund(1630022015003)the National Natural Science Foundation of China(31270651,31570684)~~
文摘[Objective]To elucidate the role of ethylene(ET),a latex yield stimulant of the rubber tree,on the sieve tube(ST)transport efficiency of materials(especially sucrose)needed for natural rubber biosynthesis.[Method]Rubber tree seedlings were treated with ET solution or water which was used as a control on the bark,and latex samples and ST tissue samples were collected for proteomic analyses and latex sucrose content determination respectively.[Results]After ET treatment,the sucrose content of the latex was found significantly decreased.A total of 66 ethylene-responsive proteins(ERPs)were distinguished by two-dimensional gel electrophoresis(2-DE),and 54 were successfully identified by MALDI-TOF/TOF and database searching.The majority of these ERPs were involved in carbohydrate transport and metabolic processes in the ST.[Conclusion]Our findings suggest that the application of ET may increase the transport efficiency of the ST and that the application of ET promotes the consumption of energy and sucrose in the ST.
基金Supported by The National Natural Science Foundation of China,No. 30640071
文摘AIM:To explore the method for early diagnosis of gastric cancer by screening the expression spectrum of saliva protein in gastric cancer patients using mass spectrometry for proteomics.METHODS:Proportional peptide mass fingerprints were obtained by analysis based on proteomics matrix-assisted laser desorption ionization time-of-flight/mass spectrometry.A diagnosis model was established using weak cation exchange magnetic beads to test saliva specimens from gastric cancer patients and healthy subjects.RESULTS:Significant differences were observed in the mass to charge ratio(m/z) peaks of four proteins(1472.78 Da,2936.49 Da,6556.81 Da and 7081.17 Da) between gastric cancer patients and healthy subjects.CONCLUSION:The finger print mass spectrum of saliva protein in patients with gastric cancer can be established using gastric cancer proteomics.A diagnostic model for distinguishing protein expression mass spectra of gastric cancer from non-gastric-cancer saliva can be established according to the different expression of proteins 1472.78 Da,2936.49 Da,6556.81 Da and 7081.17 Da.The method for early diagnosis of gastric cancer is of certain value for screening special biological markers.
基金funded by the Chinese National Basic Research Program grants(2011CB910600,2013CB911201)to Xu Ping and Li Ning respectivelythe grants of National Natural Science Foundation of China(31070673,31170780)to Xu Ping
文摘Proteomics focuses on the systematic identification and quantification of entire proteomes and interpretation of proteins’biological functions.During the last decade,proteomics in China has grown much faster than other research fields in life sciences.At the beginning of the second decade of the 21st century,the rapid development of high-resolution and high-speed mass spectrometry makes proteomics a powerful tool to study the mechanisms underlying physiological/pathological processes in organisms.This article provides a brief overview of proteomics technology development and representative scientific progress of the Human Liver Proteome Project in China over the past three years.
文摘Urine is an important source of biomarkers. This article reviews current advances, major challenges, and future prospects in the field of urinary proteorrfics. Because the practical clinical problem is to distinguish diseases with similar symptoms, merely comparing samples from patients of a particular disease to those of healthy individuals is inadequate for finding biomarkers with sufficient diagnostic power. In addition, the variation of expression levels of urinary proteins among healthy individuals and individuals under different physiological conditions adds to the difficulty in identifying biomarkers. We propose that es- tablishing the natural variation in urinary protein expression among a healthy population can serve as a reference to help iden- tify protein abundance changes that are caused by disease, not by individual variations or physiological changes. We also dis- cuss that comparing protein expression levels between urine and plasma may reveal the physiological function of the kidney and that may facilitate biomarker discovery. Finally, we propose that establishing a data-sharing platform for data collection and integrating results from all urinary biomarker studies will help promote the development of urinary proteomics.
基金supported by the National Basic Research Program of China (Grant Nos. 2010CB912700 and 2011CB910601)
文摘Functional proteomics can be defined as a strategy to couple proteomic information with biochemical and physiological analyses with the aim of understanding better the functions of proteins in normal and diseased organs.In recent years,a variety of publicly available bioinformatics databases have been developed to support protein-related information management and biological knowledge discovery.In addition to being used to annotate the proteome,these resources also offer the opportunity to develop global approaches to the study of the functional role of proteins both in health and disease.Here,we present a comprehensive review of the major human protein bioinformatics databases.We conclude this review by discussing a few examples that illustrate the importance of these databases in functional proteomics research.
文摘Proteomics allows the large-scale study of protein expression either in whole organisms or in purified organelles. In particular, mass spectrometry (MS) analysis of gel-separated proteins produces data not only for protein identification, but for protein structure, location, and processing as well. An in-depth analysis was performed on MS data from etiolated hypocotyl cell wall proteomics ofArabidopsis thaliana. These analyses show that highly homologous members of multigene families can be differentiated. Two lectins presenting 93% amino acid identity were identified using peptide mass fingerprinting. Although the identification of structural proteins such as extensins or hydroxyproline/proline-rich proteins (H/PRPs) is arduous, different types of MS spectra were exploited to identify and characterize an H/PRP. Maturation events in a couple of cell wall proteins (CWPs) were analyzed using site mapping. N-glycosylation of CWPs as well as the hydroxylation or oxidation of amino acids were also explored, adding information to improve our understanding of CWP structure/function relationships. A bioinformatic tool was developed to locate by means of MS the N-terminus of mature secreted proteins and N-glycosylation.
基金supported by the National Natural Science Foundation of China (Grant Nos. 20935004 and 20775080)National Basic Research Program of China (Grant No. 2007CB914100)Knowledge Innovation Program of Chinese Academy of Sciences (Grant No. KJCX2YW.H09)
文摘In proteomics, attention has focused on various immobilized enzyme reactors (IMERs) for the realization of high throughput digestion. In this report, a novel organic-inorganic hybrid monolith based IMER was prepared in a 100 μm i.d. capillary with 3-glycidoxypropyltrimethoxysilane (GLYMO) as the monomer and tetraethoxysilane (TEOS) as the crosslinker. Trypsin immobilization was achieved via the reaction between vicinal diol groups, which were obtained from hydrolysis of epoxy groups, and the amino groups of trypsin. Bovine serum albumin was digested thoroughly by this IMER in 47 s. After micro-reverse phase liquid chromatography-tandem mass spectrometry (μRPLC-MS/MS) analysis and database searching, beyond 35% sequence coverage was obtained, and the result was comparable to that of 12 h in solution digestion. The present IMER has potential for high throughput digestion.
基金supported in part by the Ministry of Science and Technology of China(Grant Nos. 2006CB910104,2006AAZ105 and 2009CB918404)the National Natural Science Foundation of China(Grant Nos. 30630034,90813034 and 81071668)+1 种基金the Shanghai Science and Technology Commission(Grant Nos. 08JC1413700 and 07QA14041)the Shanghai Municipal Education Commission(Grant No. E09013)
文摘Apoptosis,or programmed cell death,is a complex,genetically-determined process involved in the development and maintenance of homeostasis in multicellular organisms.Dysregulation of apoptosis has been implicated in a number of diseases,including cancer and autoimmune disease.Thus,the investigation of apoptotic regulation has evoked considerable interest.Many apoptotic proteins have been shown to be post-translationally modulated,such as by protein cleavage,translocation,protein-protein interaction,and various post-translational modifications,which fall precisely within the range of proteomic analysis.Recently,contemporary proteomic technologies have achieved significant advances and have accelerated research in functional and chemical proteomics,which have been applied to the field of apoptosis research and have the potential to be a driving force for the field.This review highlights some of the major achievements in the application of proteomics in apoptosis research and discusses new directions and challenges for the near future.
基金supported by the National Natural Science Foundation of China (Grant No. 30700378)National High Technology Research and Development Program of China (Grant No. 2006AA02A308)
文摘Mitochondrion plays the key functions in mammalian cells. It is believed that mitochondrion exerts the common biologic functions in many tissues, but also performs some specific functions correspondent with tissues where it is localized. To identify the tissue-specific mitochondrial proteins, we carried out a systematic survey towards mitochondrial proteins in the tissues of C57BL/6J mouse, such as liver, kidney and heart. The mitochondrial proteins were separated by 2DE and identified by MALDI-TOF/TOF MS. Total of 87 unique proteins were identified as the tissue-specific ones, and some representatives were further verified through ICPL quantification and Western blot. Because these issue-specific proteins are coded from nuclear genes, real-time PCR was employed to examine the mRNA status of six typical genes found in the tissues.With combining of the expression data and the co-localization images obtained from confocal microscope, we came to the conclusion that the tissue-specifically mitochondrial proteins were widely distributed among the mouse tissues. Our investigation, therefore, indeed provides a solid base to further explore the biological significance of the mitochondrial proteins with tissue-orientation.
基金supported by the National Natural Science Foundation of China (Grant No. 209750240)the National Basic Research Program of China (Grant No. 2010CB912700)
文摘Secreted proteins are important sources for early detection and diagnosis of disease, and as such have received considerable attention. The extraction of low concentration proteins from large volumes of culture media, which are rich in salts and other compounds that interfere with most proteomics techniques, presents a problem for secretome studies. Ultrafiltration, precipitation, and dialysis are three major extraction methods that can be used to overcome this problem. The present study for the first time, compared the merits and shortcomings of these three methods, without bias. Centrifugal ultrafiltration provided the best extraction efficiency, and precipitation provided the highest number of identifiable proteins. The three methods yielded closely related, but different, information on the secretome; thus, they should be considered complementary or, at least, supplementary methods. Three hundred and sixty unique proteins were identified, including 211 potential secreted proteins. Compared with previous studies, this study also identified 42 new secreted proteins. The present study not only offers a reference for the selection of secretome extraction methods, but also expands the secretome database for the investigation of hepatocellular carcinoma.
文摘Recently, there has been an overwhelming demand for studies on protein post-translational modification (PTM) to understand the increasing complexity from the level of the genome to the proteome. The covalent modifications of proteins with phosphates, lipids, sugars or other residues confer on these proteins additional structural and functional diversity. For instance, protein phosphorylation is involved in a wide range of cellular processes including signal transduction. Protein glycosylation is one of the most abundant PTMs and more than 50% of all human proteins are glycosylated. Glycoproteins are involved in many biological events, such as cell-cell adhesion, communication, immune response and development.