蛋白质组学技术在术后谵妄中的研究进展

术后谵妄的病因病理非常复杂,其诊断主要依赖于主观的神经量表,因此对它们的诊断和治疗缺乏有效的方法。蛋白质组学研究主要是对生理与病理状态下的体液、组织或细胞中的蛋白质进行大通量的综合分析,并识别蛋白质表达的动态特征,这不仅可从蛋白质水平上揭示疾病的本质,还有助于全面探讨其病理机制,建立诊断标准,发现药物治疗靶点。蛋白质组学为术后谵妄的研究提供了有效的方法和手段。特别是针对术后谵妄的外泌体蛋白质组学研究极少,本文简要介绍了蛋白质组学在样品分离、定量、质谱检测及生物信息学等方面的技术发展,并对基于蛋白质组学在术后谵妄物标志物发现的研究进展进行综述。

Integrating proteomics and targeted metabolomics to reveal the material basis of liver-gallbladder damp-heat syndrome in chronic hepatitis B

Objective To elucidate the biological basis of liver-gallbladder damp-heat syndrome(LGDHS)within the framework of traditional Chinese medicine(TCM)as a complementary diagnostic and therapeutic approach in chronic hepatitis B(CHB).Methods CHB patients and healthy volunteers were enrolled from Shuguang Hospital Affili-ated to Shanghai University of Traditional Chinese Medicine between August 21,2018 and December 31,2020.They were divided into three groups:healthy group,LGDHS group,and latent syndrome(LP)group.Proteomic analysis using isobaric tags for relative and absolute quantitation(iTRAQ)was performed to identify differentially expressed proteins(DEPs).Metabolomic profiling via ultra-performance liquid chromatography-tandem mass spec-trometry(UPLC-MS/MS)was applied to serum samples to detect differentially regulated metabolites(DMs).Kyoto Encyclopedia of Genes and Genomes(KEGG)and Gene Ontology(GO)enrichment were employed to explore dysregulated pathways.Principal component analysis(PCA)and orthogonal partial least squares discriminant analysis(OPLS-DA)were utilized to visualize group separation and identify key metabolites and proteins contributing to LGDHS differentiation.Receiver operating characteristic(ROC)curve analysis evaluated the diagnostic performance of key biomarkers,while logistic regression models assessed their predictive accuracy.P values were corrected for multiple tests using the Benjamini-Hochberg method to control the false discovery rate(FDR).Validation of potential biomarkers was con-ducted using independent microarray data and real-time quantitative polymerase chain reac-tion(RT-qPCR).Results A total of 150 participants were enrolled,including healthy group(n=45),LGDHS group(n=60),and LP group(n=45).254 DEPs from proteomics data and 72 DMs from metabolomic profiling were identified by PCA and OPLS-DA.DEPs were mainly enriched in immune and complement pathways,while DMs involved in amino acid and energy metabolism.The integrated analysis identified seven key biomarkers:α1-acid glycoprotein(ORM1),asparagine synthetase(ASNS),solute carrier family 27 member 5(SLC27A5),glu-cosidase II alpha subunit(GANAB),hexokinase 2(HK2),5-methyltetrahydrofolate-homocys-teine methyltransferase(MTR),and maltase-glucoamylase(MGAM).Microarray validation confirmed the diagnostic potential of these genes,with area under the curve(AUC)values for ROC analysis ranging from 0.536 to 0.759.Among these,ORM1,ASNS,and SLC27A5 showed significant differential ability in differentiating LGDHS patients(P=0.016,P=0.035,and P<0.001,respectively),with corresponding AUC of 0.749,0.743,and 0.759,respectively.A logis-tic regression model incorporating these three genes demonstrated an AUC of 0.939,indicat-ing a high discriminatory power for LGDHS.RT-qPCR further validated the differential ex-pression of ORM1 and SLC27A5 between LGDHS and LP groups(P=0.011 and P=0.034,re-spectively),with ASNS showing a consistent trend in expression(P=0.928).Conclusion This study integrates multi-omics approaches to uncover the molecular mecha-nisms underlying LGDHS in CHB.The identification of biomarkers ORM1,ASNS,and SLC27A5 offers a solid basis for the objective diagnosis of LGDHS,contributing to the stan-dardization and modernization of TCM diagnostic practices.

Plant Proteomics in the Post-genomic Era

Proteomics is one of the most active research fields in the post-genomic era. Here we briefly introduce the scientific background of the origination of proteomics and its content, research method. The new developments of proteomics at the levels of individual plants, tissues, organs and organells, as well as its applications in the area of plant genetic diversity, mutant characterization, and plant physiology, etc are reviewed. At last, the challenge and prospect of proteomics are discussed.

Multi-Omics and Its Clinical Application in Hepatocellular Carcinoma:Current Progress and Future Opportunities

Hepatocellular carcinoma(HCC)is the sixth most common malignancy and the fourth leading cause of cancer related death worldwide.China covers over half of cases,leading HCC to be a vital threaten to public health.Despite advances in diagnosis and treatments,high recurrence rate remains a major obstacle in HCC management.Multi-omics currently facilitates surveillance,precise diagnosis,and personalized treatment decision making in clinical setting.Non-invasive radiomics utilizes preoperative radiological imaging to reflect subtle pixel-level pattern changes that correlate to specific clinical outcomes.Radiomics has been widely used in histopathological diagnosis prediction,treatment response evaluation,and prognosis prediction.High-throughput sequencing and gene expression profiling enabled genomics and proteomics to identify distinct transcriptomic subclasses and recurrent genetic alterations in HCC,which would reveal the complex multistep process of the pathophysiology.The accumulation of big medical data and the development of artificial intelligence techniques are providing new insights for our better understanding of the mechanism of HCC via multi-omics,and show potential to convert surgical/intervention treatment into an antitumorigenic one,which would greatly advance precision medicine in HCC management.

Comparative genomics of Helicobacter pylori

Genomic sequences have been determined for a number of strains of Helicobacter pylori （H pylori） and related bacteria. With the development of microarray analysis and the wide use of subtractive hybridization techniques, comparative studies have been carried out with respect to the interstrain differences between H pylori and inter-species differences in the genome of related bacteria. It was found that the core genome of H pylori constitutes 1111 genes that are determinants of the species properties. A great pool of auxiliary genes are mainly from the categories of cag pathogenicity islands, outer membrane proteins, restriction-modification system and hypothetical proteins of unknown function. Persistence of H pylori in the human stomach leads to the diversification of the genome. Comparative genomics suggest that a host jump has occurs from humans to felines. Candidate genes specific for the development of the gastric diseases were identified. With the aid of proteomics, population genetics and other molecular methods, future comparative genomic studies would dramatically promote our understanding of the evolution, pathogenesis and microbiology of Hpylori.

Comparative proteomic study of colorectal carcinoma with different clinical stages

Objective： Colorectal carcinoma clinical stage associated proteins would be found by comparing differential expressed proteins from colorectal carcinoma tissues with different clinical stages. Methods： Total protein from colorectal carcinoma tissues were extracted; differential proteome profiles were established and analyzed by means of immobilized pH gradient-based two-dimensional polyacrylamide gel electrophoresis （2-DE） and matrix-assisted laser desorption/ionization time of flight mass spectrometry （MALDI-TOF-MS）. Results： Well-resolved, reproducible 2-DE profiles of human colorectal carcinoma tissues were obtained. Average protein spots were 970 ± 41,980 ± 32, 1010 ± 43, 1240 ±34 in stage Ⅰ, stage Ⅱ, stage Ⅲ, stage Ⅳ respectively; Compared to stage Ⅰ, differential expressed protein spots was 52.00 ± 12 in stage Ⅱ, 42.00 ± 11 in stage Ⅲ, 72.00 ± 15 in stage Ⅳ; Part of differential expressing proteins were analyzed by mass spectrometry and bioinformation, 19 of them were well characterized. Three proteins were overexpressed in stage Ⅰ, stage Ⅲ, stage Ⅳ, and one protein were overexpressed in stage Ⅳ exclusively. Conclusion： Differential expressed proteins exist in clinical stage of colorectal carcinoma, which would be biomarkers for diagnosis and prediction of prognosis.

Chemometrics of differentially expressed proteins from colorectal cancer patients

AIM:To evaluate the usefulness of differentially expressed proteins from colorectal cancer (CRC) tissues for differentiating cancer and normal tissues.METHODS:A Proteomic approach was used to identify the differentially expressed proteins between CRC and normal tissues.The proteins were extracted using Tris buffer and thiourea lysis buffer (TLB) for extraction of aqueous soluble and membrane-associated proteins,respectively.Chemometrics,namely principal component analysis (PCA) and linear discriminant analysis (LDA),were used to assess the usefulness of these proteins for identifying the cancerous state of tissues.RESULTS:Differentially expressed proteins identified were 37 aqueous soluble proteins in Tris extracts and 24 membrane-associated proteins in TLB extracts.Based on the protein spots intensity on 2D-gel images,PCA by applying an eigenvalue > 1 was successfully used to reduce the number of principal components (PCs) into 12 and seven PCs for Tris and TLB extracts,respectively,and subsequently six PCs,respectively from both the extracts were used for LDA.The LDA classification for Tris extract showed 82.7% of original samples were correctly classified,whereas 82.7% were correctly classified for the cross-validated samples.The LDA for TLB extract showed that 78.8% of original samples and 71.2% of the cross-validated samples were correctly classified.CONCLUSION:The classification of CRC tissues by PCA and LDA provided a promising distinction between normal and cancer types.These methods can possibly be used for identification of potential biomarkers among the differentially expressed proteins identified.

Development of Bioinfo-Portal Tool for the Analysis of Genomic and Proteomic Data

The recent explosion of biological data and the concomitant proliferation of distributed databases make it challenging for biologists and bioinformaticians to discover the best data resources for their needs, and the most efficient way to access and use them For the biologist, running bioinformatics analyses involve a time-consuming management of data and tools. Users need support to organize their work, retrieve parameters and reproduce their analyses. They also need to be able to combine their analytic tools using a safe data flow software mechanism. Finally we have designed a system, Bioinfo-Portal, to provide a flexible and usable web environment for defining and running bioinformatics analyses. It embeds simple yet powerful data management features that allow the user to reproduce analyses and to combine tools using an adobe flex tool. Bioinfo-Portal can also act as a front end to provide a unified view of already-existing collections of bioinformatics resources. Users can analyze genomic and proteomic data by using the tools that has been integrated in the portal （tools for alignments, dotplots, motif detection, domain analysis, profile searching and tertiary structure prediction）. The sequences that user obtained from portal＇s nucleotide and protein databases are easily analyzed by the portal tools on the same interface in no time. User can also take benefit from the animations.

Psychrotolerant methanogenic archaea:Diversity and cold adaptation mechanisms

Because of their diversity and abundance in a wide range of environments, particularly in cold regions, cold-adaptive archaea are expected to play a pivotal role in material recycling in cold environments. Methanogenic archaea are ubiquitous on earth and produce a large amount of methane （CH4） as their main carbon metabolite. Methanogens are the most laboratory amenda- ble archaea. The few psychrophilic archaea that have been cultured to date are mainly affiliated with methanogens, thus make them a good model for investigating mechanisms of archaeal cold adaptation. Studies of psychrotolerant methanogens have been ongoing since the 1990s. Using Methanocoecoides burtonii, a methanogen isolated from Ace Lake in Antarctica, exten- sive studies on the genomic characteristics associated with cold adaptation have been carried out by the Cavicchioli laboratory. We recently analyzed the genome of another psychrophilic methanogen and identified the gene repertoire associated with cold adaptation. This review summarizes recent studies of psychroactive methanogens, particularly their diversity, the genomics and proteomics associated with their cold adaptation, and the cellular components and proteins likely involved in their cold protec- tion.

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.

Lifeomics leads the age of grand discoveries

When our knowledge of a field accumulates to a certain level,we are bound to see the rise of one or more great scientists.They will make a series of grand discoveries/breakthroughs and push the discipline into an 'age of grand discoveries'.Mathematics,geography,physics and chemistry have all experienced their ages of grand discoveries;and in life sciences,the age of grand discoveries has appeared countless times since the 16th century.Thanks to the ever-changing development of molecular biology over the past 50 years,contemporary life science is once again approaching its breaking point and the trigger for this is most likely to be 'lifeomics'.At the end of the 20th century,genomics wrote out the 'script of life';proteomics decoded the script;and RNAomics,glycomics and metabolomics came into bloom.These 'omics',with their unique epistemology and methodology,quickly became the thrust of life sciences,pushing the discipline to new high.Lifeomics,which encompasses all omics,has taken shape and is now signalling the dawn of a new era,the age of grand discoveries.

Review:Global nutrient profiling by Phenotype MicroArrays:a tool complementing genomic and proteomic studies in conidial fungi

Conidial fungi or molds and mildews are widely used in modern biotechnology as producers of antibiotics and other secondary metabolites,industrially important enzymes,chemicals and food.They are also important pathogens of animals including humans and agricultural crops.These various applications and extremely versatile natural phenotypes have led to the constantly growing list of complete genomes which are now available.Functional genomics and proteomics widely exploit the genomic information to study the cell-wide impact of altered genes on the phenotype of an organism and its function.This allows for global analysis of the information flow from DNA to RNA to protein,but it is usually not sufficient for the description of the global phenotype of an organism.More recently,Phenotype MicroArray (PM) technology has been introduced as a tool to characterize the metabolism of a (wild) fungal strain or a mutant.In this article,we review the background of PM applications for fungi and the methodic requirements to obtain reliable results.We also report examples of the versatility of this tool.

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.

Cancer:A proteomic disease

The development of cancer is a pathological process involving multiple environmental carcinogenic factors and genetic alterations.For decades,cancer researchers have focused on genomic and transcriptomic analyses.The completion of the Human Genome Project has opened the door to the post-genome era and oncoproteomics.Proteins play a critical role in tumorigenesis and influence the differences between normal cells and malignant cells.This report proposes the concept that cancer is a proteomic disease.This concept is based on examining protein expression profiles,post-translational modifications,and protein-protein interactions in carcinogenesis using recent advances in comparative,functional and structural proteomics.This approach provides a new way of viewing carcinogenesis,presents new clues in biomarker discovery for cancer diagnosis and therapy,and reveals important scientific findings and their significance to clinical applications.