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Future of non-invasive graft evaluation:A systematic review of proteomics in kidney transplantation

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World Journal of Transplantation 2025年第1期15卷 135-149页

作者： Eleni Avramidou Konstantina Psatha Kallisti St John Georgios Tsoulfas Michalis Aivaliotis Department of Transplantation Surgery Center for Research and Innovation in Solid Organ TransplantationAristotle University of ThessalonikiSchool of MedicineThessaloniki 54642Greece Laboratory of Medical Biology-Genetics School of MedicineAristotle University of ThessalonikiThessaloniki 54124Greece Functional proteomics and Systems Biology(FunPATh) Center for Interdisciplinary Research and Innovation(CIRI-AUTH)Thessaloniki GR-57001Greece Laboratory of Biological Chemistry School of MedicineAristotle University of ThessalonikiThessaloniki 54124Greece

BACKGROUND Despite the developments in the field of kidney transplantation,the already existing diagnostic techniques for patient monitoring are considered *** biomarkers that can be derived from modern approaches of proteomic analysis of liquid biopsies(serum,urine)represent a promising innovation in the monitoring of kidney transplant *** To investigate the diagnostic utility of protein biomarkers derived from proteomics approaches in renal allograft *** A systematic review was conducted in accordance with PRISMA guidelines,based on research results from the PubMed and Scopus *** primary focus was on evaluating the role of biomarkers in the non-invasive diagnosis of transplant-related *** criteria included protein biomarkers and urine and blood samples,while exclusion criteria were language other than English and the use of low resolution and sensitivity *** selected research articles,were categorized based on the biological sample,condition and methodology and the significantly and reproducibly differentiated proteins were manually selected and *** and network analysis of the selected proteins was *** In 17 included studies,58 proteins were studied,with the cytokine CXCL10 being the most *** pathways related to immune response and fibrosis have shown to be *** of biomarkers for the assessment of renal damage as well as the prediction of short-term and long-term function of the graft were ***,all studies have shown satisfactory diagnostic accuracy of proteins alone or in combination with conventional methods,as far as renal graft assessment is *** Our review suggests that protein biomarkers,evaluated in specific biological fluids,can make a significant contribution to the timely,valid and non-invasive assessment of kidney graft.

关键词： proteomics Kidney transplantation Graft evaluation Non-invasive diagnosis Kidney graft function

Clinical proteomics identifies potential biomarkers in Helicobacter pylori for gastrointestinal diseases

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World Journal of Gastroenterology 2014年第6期20卷 1529-1536页

作者： Chun-Hao Huang Shyh-Horng Chiou Quantitative proteomics Center and Graduate Institute of Medicine Kaohsiung Medical University Institute of Biological Chemistry Academia Sinica

The development of gastrointestinal diseases has been found to be associated with Helicobacter pylori (H. pylori) infection and various biochemical stresses in stomach and intestine. These stresses, such as oxidative, osmotic and acid stresses, may bring about bi-directional effects on both hosts and H. pylori, leading to changes of protein expression in their proteomes. Therefore, proteins differentially expressed in H. pylori under various stresses not only reflect gastrointestinal environment but also provide useful biomarkers for disease diagnosis and prognosis. In this regard, proteomic technology is an ideal tool to identify potential biomarkers as it can systematically monitor proteins and protein variation on a large scale of cell’s translational landscape, permitting in-depth analyses of host and pathogen interactions. By performing two-dimensional polyacrylamide gel electrophoresis (2-DE) followed by liquid chromatography-nanoESI-mass spectrometry (nanoLC-MS/MS), we have successfully pinpointed alkylhydroperoxide reductase (AhpC), neutrophil-activating protein and non-heme iron-binding ferritin as three prospective biomarkers showing up-regulation in H. pylori under oxidative, osmotic and acid stresses, respectively. Further biochemical characterization reveals that various environmental stresses can induce protein structure change and functional conversion in the identified biomarkers. Especially salient is the antioxidant enzyme AhpC, an abundant antioxidant protein present in H. pylori. It switches from a peroxide reductase of low-molecular-weight (LMW) oligomers to a molecular chaperone of high-molecular-weight (HMW) complexes under oxidative stress. Different seropositivy responses against LMW or HMW AhpC in H. pylori-infected patients faithfully match the disease progression from disease-free healthy persons to patients with gastric ulcer and cancer. These results has established AhpC of H. pylori as a promising diagnostic marker for gastroin

关键词： proteomics Biomarker Helicobacter pylori Gastritis Gastric ulcer Gastric cancer Alkylhydroperoxide reductase Neutrophil-activating protein Non-heme iron-binding ferritin

Alendronate and FTI-277 combination as a possible therapeutic approach for hepatocellular carcinoma:An in vitro study

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Hepatobiliary & Pancreatic Diseases international 2018年第3期17卷 241-250页

作者： Amber Ilyas Zehra Hashim Iffat Saeed Channa Shamshad Zarina National Center for proteomics University of Karachi

Background： An important product of mevalonate pathway is downstream synthesis of isoprenoid unitsthat has long been implicated in development and progression of tumor. It has been speculated thatinhibition of protein prenylation might be therapeutically beneficial. The objective of current study wasto evaluate antitumor potential of a novel therapeutic combination of mevalonate pathway inhibitors, FTI-277 and alendronate. We also examined differentially expressed proteins in response to treatment usingproteomics approach.

关键词： Chemotherapy Hepatocellular carcinoma Gene expression proteomics Therapeutic

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A Putative NES Mediates Cytoplasmic Localization of Apoptin in Normal Cells

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Acta Biochimica et Biophysica Sinica 2004年第12期36卷 817-823页

作者： Qing-Ming WANG*, Guo-Cai FAN, Ji-Zhong CHEN, Hui-Peng CHEN, and Fu-Chu HE* Department of Genomics and proteomics, Beijing Institute of Radiation Medicine, Beijing 100850, China Department of Genomics and proteomics Beijing Institute of Radiation MedicineBeijing 100850 China

Apoptin, a protein expressed by chicken anemia virus, is found predominantly in the cytoplasm in normal cells, whereas it localizes in the nucleus in transformed and malignant cells. However, the mecha- nisms that regulate the different subcellular localization of Apoptin in normal and tumor cells have not been fully clarified. In this work, a putative nuclear export signal (NES) in Apoptin was predicted. It was testified that the putative NES (pNES) of Apoptin was not a functional NES, but actually acted as a cytoplasmic retention signal. Deletion of the pNES led to the nuclear accumulation of Apoptin in normal cells. In addition, when a strong nuclear localization signal was introduced into Apoptin, it exclusively translocated to the nucleus in normal cells. These observations indicated that the cytoplasmic localization of Apoptin in normal cells results from the balance between cytoplasmic retention and nuclear import. On the other hand, the pNES was also proved to be necessary for Apoptin multimerization. Mutants lacking the pNES did not form obviously visible globular aggregates in normal or tumor cells.

关键词： Apoptin nuclear localization signal cytoplasmic retention signal nuclear export signal

At a glance:proteomics in China

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Science China(Life Sciences) 2011年第1期54卷 1-2页

作者： HE FuChu State Key Laboratory of proteomics Beijing Proteome Research Center Beijing Institute of Radiation Medicine Beijing 102206 China

proteomics is a new science that focuses on the comprehensive analysis of proteins in intact organisms or in molecule machineries, organelles, cells, tissues, or organs. It has become an important area of interests in... 详细信息

关键词：蛋白质组学中国生物科技生命科学细胞器新科学有机体

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S-Adenosyl-L-methionine towards hepatitis C virus expression: Need to consider S-Adenosyl-L-methionine's chemistry, physiology and pharmacokinetics

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World Journal of Gastroenterology 2017年第40期23卷 7343-7346页

作者： Dimitrios Tsikas Erik Hanff Alexander Bollenbach Core Unit proteomics Hannover Medical School

S-Adenosyl-L-methionine(SAM) is a cofactor serving as a methyl donor in numerous enzymatic reactions. It has been reported that SAM has the potential to modify antioxidant-enzymes, glutathione-biosynthesis and methionine adenosyltransferases-1/2 in hepatitis C virus-expressing cells at millimolar concentrations. The efficacy of SAM at micromolar concentrations and the underlying mechanisms remain to be demonstrated.

关键词： S-Adenosyl-L-methionine Bioavailability Concentration Liver

Making topological protein links using enzymatic reactions

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National Science Review 2024年第3期11卷 50-51页

作者： Roger Castells-Graells Todd O.Yeates Department of Chemistry and Biochemistry University of California UCLA-DOE Institute for Genomics and proteomics

Proteins are exceedingly complex molecules though, at their heart, they are essentially linear polymers. Pull at their ends and one obtains an extended backbone. While that is true in most cases, some natural proteins...

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RegVar:Tissue-specific Prioritization of Non-coding Regulatory Variants

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Genomics, proteomics & Bioinformatics 2023年第2期21卷 385-395页

作者： Hao Lu Luyu Ma Cheng Quan Lei Li Yiming Lu Gangqiao Zhou Chenggang Zhang Beijing Institute of Radiation Medicine State Key Laboratory of ProteomicsBeijing 100850China

Non-coding genomic variants constitute the majority of trait-associated genome variations;however,the identification of functional non-coding variants is still a challenge in human genetics,and a method for systematically assessing the impact of regulatory variants on gene expression and linking these regulatory variants to potential target genes is still ***,we introduce a deep neural network(DNN)-based computational framework,RegVar,which can accurately predict the tissue-specific impact of non-coding regulatory variants on target *** show that by robustly learning the genomic characteristics of massive variant-gene expression associations in a variety of human tissues,RegVar vastly surpasses all current non-coding variant prioritization methods in predicting regulatory variants under different *** unique features of RegVar make it an excellent framework for assessing the regulatory impact of any variant on its putative target genes in a variety of tissues.

关键词： Non-coding variant Variantprioritization Expressionregulation Expressionquantitative trait locus Deep neural network

Bile proteomics for differentiation of malignant from benign biliary strictures:a pilot study

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Gastroenterology Report 2015年第2期3卷 136-143页

作者： Udayakumar Navaneethan Vennisvasanth Lourdusamy Preethi GK Venkatesh Belinda Willard Madhusudhan R Sanaka Mansour A Parsi Department of Gastroenterology and Hepatology Digestive Disease InstituteCleveland ClinicClevelandOHUSA proteomics Core Laboratory Lerner Research InstituteCleveland ClinicClevelandOHUSA

Background:Determining the etiology of biliary strictures is challenging,and the sensitivities of the current tests to diagnose them are *** biomarkers in bile,in combination with other tests,may improve sensitivity in diagnosing biliary ***:To analyse the differential abundance of proteins in benign and malignant biliary strictures through proteomic analysis of ***:In this prospective,cross-sectional study,bile was aspirated in 24 patients undergoing endoscopic retrograde cholangiopancreatography(ERCP)including six patients with primary sclerosing cholangitis(PSC),three with cholangiocarcinoma(CCA),ten with pancreatic cancer,and five with benign biliary *** chromatography/mass spectrometry was used to examine the bile for differential abundance of protein *** relative abundance of various proteins was compared in the malignant *** groups and in CCA ***:The majority of the proteins identified in bile were similar to those of the plasma(plasma proteins)and certain proteins were differentially expressed among the different groups(CCA,pancreatic cancer,PSC or benign).A total of 18 proteins were identified as being more abundant in the malignant group(CCA and pancreatic cancer)than in the benign strictures group,including myeloperoxidase,complement C3,inter-alpha-trypsin inhibitor heavy chain H4,apolipoprotein B-100,and kininogen-1 isoform 2.A total of 30 proteins were identified to be less abundant in the malignant group than in the benign group,including trefoil factor 2,superoxide dismutase[Cu-Zn],kallikrein-1,carboxypeptidase B and trefoil factor ***:Protein biomarkers in bile may differentiate malignant from benign biliary *** studies are warranted to validate these observations.

关键词： pancreatic cancer proteomics bile cholangiocarcinoma