结直肠癌中潜在的S-棕榈酰化蛋白质组学分析

目的 通过质谱鉴定分析结直肠癌中S-棕榈酰化蛋白,为寻找临床治疗结直肠癌的新靶点提供依据.方法 选取2022年12月至2023年3月吉林大学第二医院获取的11例患者的结直肠癌组织(其中男7例,女4例),同时与结直肠癌细胞系进行酰基-生物素基交换(ABE)后进行质谱鉴定,分析潜在S-棕榈酰化蛋白并进行蛋白质印迹法(Western blot)验证.两组间比较采用配对样本t检验.结果 在人结直肠癌组织和SW480、SW620细胞系中共同含有潜在的S-棕榈酰化位点的蛋白有21个,这些蛋白经基因本体(GO)和通路Pathway分析与免疫调节密切相关;Western blot验证了磷脂爬行酶1(PLSCR1)和细胞骨架相关蛋白4(CKAP4)是S-棕榈酰化修饰的;在人结直肠癌组织 CKAP4(0.693±0.092、1.162±0.003、0.771±0.012、1.683±0.085、1.144±0.266)CKAP4 总蛋白水平低于癌旁组织(2.306±0.231、1.471±0.055、1.201±0.01、1.978±0.031、2.107±0.035),差异有统计学意义(t=11.260、9.744、15.260、5.398、6.221,P<0.05);而 PLSCR1(3.185±0.047、1.305±0.153、2.131±0.0752、2.542±0.106)总蛋白水平高于癌旁组织(0.833±0.0529、1.038±0.057、1.477±0.095、2.108±0.034),差异有统计学意义(t=21.372、28.770、13.559、11.460,P<0.05).结论 结直肠癌中含有潜在的S-棕榈酰化修饰蛋白,这些蛋白可能通过调节免疫功能而影响结直肠癌的增殖.

Mass Spectrometry-based Deep Coverage Proteome:Evaluation of Cellular Protein Extraction Methods

The current study comprehensively evaluates four different protein extraction methods based on urea,sodium dodecyl sulfate(SDS),anionic surfactants(BT),and total RNA extractor(Trizol),aiming to optimize the sample preparation workflow for mass spectrometry-based proteomics.Using HeLa cells as an example,we found that the method employing the mass spectrometry-compatible surfactant BT reagent significantly reduces the total time consumed for protein extraction and minimizes protein losses during the sample preparation process.Further integrating the four protein extraction methods,we identified over 7000 proteins from HeLa cells without relying on pre-fractionation techniques,and 2990 of them were quantified using label-free quantification.It is worth noting that the BT and SDS methods demonstrate higher efficiency in extracting membrane proteins,while the Urea and Trizol methods are more effective in extracting proteins from nuclear and cytoplasmic fractions.In summary,this study provides a novel solution for deep proteome coverage,particularly in the context of cellular protein extraction,by integrating mass spectrometry-compatible surfactants with traditional extraction methods to effectively enhance protein identification numbers.

Knockdown of liver-intestine cadherin decreases BGC823 cell invasiveness and metastasis in vivo

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.

Comparative Proteomics Analysis of the Sieve Tube from Rubber Tree(Hevea brasiliensis) Seedlings under Contrasting Ethylene Treatments

[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.

Diagnostic model of saliva protein finger print analysis of patients with gastric cancer

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.

Rapid development of proteomics in China: from the perspective of the Human Liver Proteome Project and technology development

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.

Applications of urinary proteomics in biomarker discovery

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.

An overview of human protein databases and their application to functional proteomics in health and disease

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.

Plant Cell Wall Proteomics： Mass Spectrometry Data, a Trove for Research on Protein Structure/Function Relationships

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.

A novel organic-inorganic hybrid monolith for trypsin immobilization

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.

Current advances in the application of proteomics in apoptosis research

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.

Proteomic survey towards the tissue-specific proteins of mouse mitochondria

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.

Comparison of alternative extraction methods for secretome profiling in human hepatocellular carcinoma cells

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.

Chemical synthesis of glycoproteins

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.