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Burton JB, Carruthers NJ, Stemmer PM. Enriching extracellular vesicles for mass spectrometry. MASS SPECTROMETRY REVIEWS 2023; 42:779-795. [PMID: 34632607 DOI: 10.1002/mas.21738] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/19/2021] [Accepted: 09/24/2021] [Indexed: 06/13/2023]
Abstract
Extracellular vesicles from plasma, other body fluids and cell culture media hold great promise in the search for biomarkers. Exosomes in particular, the vesicle type that is secreted after being produced in the endocytic pathway and having a diameter of 30-150 nm, are considered to be a conveyance for signaling molecules and, therefore, to hold valuable information regarding the health and activity status of the cells from which they are released. The vesicular nature of exosomes is central to all methods used to separate them from the highly abundant proteins in plasma and other fluids. The enrichment of the vesicles is essential for mass spectrometry-based analysis as they represent only a very small component of all plasma proteins. The progression of isolation techniques for exosomes from ultracentrifugation through chromatographic separation using hydrophobic packing materials shows that effective enrichment is possible and that high throughput approaches to exosome enrichment are achievable.
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Affiliation(s)
- Jordan B Burton
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
| | | | - Paul M Stemmer
- Institute of Environmental Health Sciences, Wayne State University, Detroit, Michigan, USA
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2
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He B, Huang Z, Huang C, Nice EC. Clinical applications of plasma proteomics and peptidomics: Towards precision medicine. Proteomics Clin Appl 2022; 16:e2100097. [PMID: 35490333 DOI: 10.1002/prca.202100097] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 04/16/2022] [Accepted: 04/28/2022] [Indexed: 02/05/2023]
Abstract
In the context of precision medicine, disease treatment requires individualized strategies based on the underlying molecular characteristics to overcome therapeutic challenges posed by heterogeneity. For this purpose, it is essential to develop new biomarkers to diagnose, stratify, or possibly prevent diseases. Plasma is an available source of biomarkers that greatly reflects the physiological and pathological conditions of the body. An increasing number of studies are focusing on proteins and peptides, including many involving the Human Proteome Project (HPP) of the Human Proteome Organization (HUPO), and proteomics and peptidomics techniques are emerging as critical tools for developing novel precision medicine preventative measures. Excitingly, the emerging plasma proteomics and peptidomics toolbox exhibits a huge potential for studying pathogenesis of diseases (e.g., COVID-19 and cancer), identifying valuable biomarkers and improving clinical management. However, the enormous complexity and wide dynamic range of plasma proteins makes plasma proteome profiling challenging. Herein, we summarize the recent advances in plasma proteomics and peptidomics with a focus on their emerging roles in COVID-19 and cancer research, aiming to emphasize the significance of plasma proteomics and peptidomics in clinical applications and precision medicine.
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Affiliation(s)
- Bo He
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Zhao Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, P. R. China.,Department of Pharmacology, and Provincial Key Laboratory of Pathophysiology in Ningbo University School of Medicine, Ningbo, Zhejiang, China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
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Comparative Proteomic Analyses of Poorly Motile Swamp Buffalo Spermatozoa Reveal Low Energy Metabolism and Deficiencies in Motility-Related Proteins. Animals (Basel) 2022; 12:ani12131706. [PMID: 35804605 PMCID: PMC9264820 DOI: 10.3390/ani12131706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 11/17/2022] Open
Abstract
The acquisition of mammalian sperm motility is a main indicator of epididymal sperm maturation and helps ensure fertilization. Poor sperm motility will prevent sperm cells from reaching the fertilization site, resulting in fertilization failure. To investigate the proteomic profiling of normal and poorly motile buffalo spermatozoa, a strategy applying liquid chromatography tandem mass spectrometry combined with tandem mass targeting was used. As a result, 145 differentially expressed proteins (DEPs) were identified in poorly motile spermatozoa (fold change > 1.5), including 52 upregulated and 93 downregulated proteins. The upregulated DEPs were mainly involved in morphogenesis and regulation of cell differentiation. The downregulated DEPs were involved with transport, oxidation-reduction, sperm motility, regulation of cAMP metabolism and regulation of DNA methylation. The mRNA and protein levels of PRM1 and AKAP3 were lower in poorly motile spermatozoa, while the expressions of SDC2, TEKT3 and IDH1 were not correlated with motility, indicating that their protein changes were affected by transcription or translation. Such changes in the expression of these proteins suggest that the formation of poorly motile buffalo spermatozoa reflects a low efficiency of energy metabolism, decreases in sperm protamine proteins, deficiencies in motility-related proteins, and variations in tail structural proteins. Such proteins could be biomarkers of poorly motile spermatozoa. These results illustrate some of the molecular mechanisms associated with poorly motile spermatozoa and provide clues for finding molecular markers of these pathways.
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KOBAYASHI H, WADA H, KUBO T, OTSUKA K. Development and Evaluation of a Silica-monolithic Micro-trap Column for LC/MS Analysis of Intact Proteins. BUNSEKI KAGAKU 2022. [DOI: 10.2116/bunsekikagaku.71.341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Affiliation(s)
| | | | - Takuya KUBO
- Graduate School of Engineering, Kyoto University
| | - Koji OTSUKA
- Graduate School of Engineering, Kyoto University
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Su M, Zhang Z, Zhou L, Han C, Huang C, Nice EC. Proteomics, Personalized Medicine and Cancer. Cancers (Basel) 2021; 13:2512. [PMID: 34063807 PMCID: PMC8196570 DOI: 10.3390/cancers13112512] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2021] [Revised: 05/12/2021] [Accepted: 05/17/2021] [Indexed: 02/05/2023] Open
Abstract
As of 2020 the human genome and proteome are both at >90% completion based on high stringency analyses. This has been largely achieved by major technological advances over the last 20 years and has enlarged our understanding of human health and disease, including cancer, and is supporting the current trend towards personalized/precision medicine. This is due to improved screening, novel therapeutic approaches and an increased understanding of underlying cancer biology. However, cancer is a complex, heterogeneous disease modulated by genetic, molecular, cellular, tissue, population, environmental and socioeconomic factors, which evolve with time. In spite of recent advances in treatment that have resulted in improved patient outcomes, prognosis is still poor for many patients with certain cancers (e.g., mesothelioma, pancreatic and brain cancer) with a high death rate associated with late diagnosis. In this review we overview key hallmarks of cancer (e.g., autophagy, the role of redox signaling), current unmet clinical needs, the requirement for sensitive and specific biomarkers for early detection, surveillance, prognosis and drug monitoring, the role of the microbiome and the goals of personalized/precision medicine, discussing how emerging omics technologies can further inform on these areas. Exemplars from recent onco-proteogenomic-related publications will be given. Finally, we will address future perspectives, not only from the standpoint of perceived advances in treatment, but also from the hurdles that have to be overcome.
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Affiliation(s)
- Miao Su
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Zhe Zhang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Chao Han
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, and West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, and Collaborative Innovation Center for Biotherapy, Chengdu 610041, China; (M.S.); (Z.Z.); (L.Z.); (C.H.)
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
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Ahn SB, Kamath KS, Mohamedali A, Noor Z, Wu JX, Pascovici D, Adhikari S, Cheruku HR, Guillemin GJ, McKay MJ, Nice EC, Baker MS. Use of a Recombinant Biomarker Protein DDA Library Increases DIA Coverage of Low Abundance Plasma Proteins. J Proteome Res 2021; 20:2374-2389. [PMID: 33752330 DOI: 10.1021/acs.jproteome.0c00898] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Credible detection and quantification of low abundance proteins from human blood plasma is a major challenge in precision medicine biomarker discovery when using mass spectrometry (MS). In this proof-of-concept study, we employed a mixture of selected recombinant proteins in DDA libraries to subsequently identify (not quantify) cancer-associated low abundance plasma proteins using SWATH/DIA. The exemplar DDA recombinant protein spectral library (rPSL) was derived from tryptic digestion of 36 recombinant human proteins that had been previously implicated as possible cancer biomarkers from both our own and other studies. The rPSL was then used to identify proteins from nondepleted colorectal cancer (CRC) EDTA plasmas by SWATH-MS. Most (32/36) of the proteins used in the rPSL were reliably identified from CRC plasma samples, including 8 proteins (i.e., BTC, CXCL10, IL1B, IL6, ITGB6, TGFα, TNF, TP53) not previously detected using high-stringency protein inference MS according to PeptideAtlas. The rPSL SWATH-MS protocol was compared to DDA-MS using MARS-depleted and postdigestion peptide fractionated plasmas (here referred to as a human plasma DDA library). Of the 32 proteins identified using rPSL SWATH, only 12 could be identified using DDA-MS. The 20 additional proteins exclusively identified using the rPSL SWATH approach were almost exclusively lower abundance (i.e., <10 ng/mL) proteins. To mitigate justified FDR concerns, and to replicate a more typical library creation approach, the DDA rPSL library was merged with a human plasma DDA library and SWATH identification repeated using such a merged library. The majority (33/36) of the low abundance plasma proteins added from the rPSL were still able to be identified using such a merged library when high-stringency HPP Guidelines v3.0 protein inference criteria were applied to our data set. The MS data set has been deposited to ProteomeXchange Consortium via the PRIDE partner repository (PXD022361).
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Affiliation(s)
- Seong Beom Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Karthik S Kamath
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Zainab Noor
- ProCan, Children's Medical Research Institute, The University of Sydney, Westmead, Newtown, NSW 2042, Australia
| | - Jemma X Wu
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Dana Pascovici
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Subash Adhikari
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Harish R Cheruku
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Gilles J Guillemin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Matthew J McKay
- Australian Proteome Analysis Facility (APAF), Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, Macquarie Park, NSW 2109, Australia
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Faculty of Medicine, Nursing and Health Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, Macquarie Park, NSW 2109, Australia
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Kobayashi H, Wada H, Imai K. Phenyl-bonded monolithic silica capillary column liquid chromatographic separation and detection of fluorogenic derivatized intact proteins. Biomed Chromatogr 2021; 35:e5078. [PMID: 33491229 DOI: 10.1002/bmc.5078] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 01/18/2021] [Accepted: 01/21/2021] [Indexed: 12/31/2022]
Abstract
Prior to the identification of proteins for proteomics analysis in human cells, separation of fluorogenic derivatized proteins with a fluorogenic reagent, 7-chloro-N-[2-(dimethylamino)ethyl]-2,1,3-benzoxadiazole-4-sulfonamide, has typically been performed by using a conventional reversed-phase HPLC column. However, the number of proteins in human cells (HepaRG) that are separated by this conventional approach is limited to approximately 500. In this study, a nanoflow liquid chromatography system with an evaluated phenyl-bonded monolithic silica capillary column (0.1 mm i.d., 700 mm length) was used to increase the number of separated fluorogenic derivatized proteins. This system was used to separate derivatized human cell proteins (K562) and yeast (Saccharomyces cerevisiae) proteins as model cell proteomes. More than 1,300 protein peaks were separated/detected from both cell proteomes. We present a straightforward comparison of multiple separation profiles using a novel chromatogram display approach, termed the "spiderweb" chromatogram. In addition, to validate that the detected peaks are derived from proteins, a mass spectrometer was connected to the capillary column and deconvolution of the obtained mass spectra was performed. Furthermore, different molecular weight distribution profiles of the expressed proteins were observed between the two cell proteomes.
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Affiliation(s)
- Hiroshi Kobayashi
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan.,R&D group, Shinwa Chemical Industries Ltd, Kyoto, Japan
| | - Hiroo Wada
- R&D group, Shinwa Chemical Industries Ltd, Kyoto, Japan
| | - Kazuhiro Imai
- Laboratory of Proteomics Analysis, Research Institute of Pharmaceutical Sciences, Musashino University, Tokyo, Japan
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Wu X, Luo L, Kong R, Song Y, Li Q, Nice EC, Wang K. Recent advances in autophagic machinery: a proteomic perspective. Expert Rev Proteomics 2020; 17:561-579. [PMID: 32772586 DOI: 10.1080/14789450.2020.1808464] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
INTRODUCTION Autophagy is an evolutionarily conserved cellular clearance process, by which cytosolic components are delivered to autolysosomes for breakdown and recycling to maintain cellular homeostasis. During the past decades, autophagy has been found to be tightly implicated in various physiological and pathological progresses. Unraveling the regulatory mechanisms of the autophagy process will contribute to the development of emerging autophagy-targeting strategies for the treatment of various diseases. Recently, the rapid development of proteomics approaches has enabled the use of large-scale unbiased strategies to unravel autophagy machinery. AREAS COVERED In this review, we will highlight the recent contributions of proteomics strategies in clarifying the autophagy machinery, with an emphasis on the three different types of autophagy (namely macroautophagy, microautophagy, and chaperone-mediated autophagy). We will also discuss the emerging role of proteomics approaches in investigating the mechanism of the autophagy-based unconventional secretory pathway (secretory autophagy). EXPERT OPINION Proteomics has provided an effective strategy for the comprehensive analysis of the autophagy process, which will broaden our understanding of autophagy machinery, and holds great promise for developing clinical therapies targeting autophagy.
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Affiliation(s)
- Xingyun Wu
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Li Luo
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China.,Key Laboratory of Birth Defects and Related Diseases of Women and Children, Sichuan University, Ministry of Education , Chengdu, P.R. China
| | - Ruxin Kong
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Yabing Song
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
| | - Qifu Li
- Department of Neurology, the First Affiliated Hospital of Hainan Medical University, and Key Laboratory of Brain Science Research & Transformation in Tropical Environment of Hainan Province, Hainan Medical University , Haikou, P.R. China
| | - Edouard C Nice
- Department of Biochemistry and Molecular Biology, Monash University , Clayton, Australia
| | - Kui Wang
- West China School of Basic Medical Sciences & Forensic Medicine, Center of Reproductive Medicine, West China Second University Hospital, and State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, and Collaborative Innovation Center for Biotherapy , Chengdu, P.R. China
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He Y, Mohamedali A, Huang C, Baker MS, Nice EC. Oncoproteomics: Current status and future opportunities. Clin Chim Acta 2019; 495:611-624. [PMID: 31176645 DOI: 10.1016/j.cca.2019.06.006] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 06/05/2019] [Accepted: 06/05/2019] [Indexed: 02/07/2023]
Abstract
Oncoproteomics is the systematic study of cancer samples using omics technologies to detect changes implicated in tumorigenesis. Recent progress in oncoproteomics is already opening new avenues for the identification of novel biomarkers for early clinical stage cancer detection, targeted molecular therapies, disease monitoring, and drug development. Such information will lead to new understandings of cancer biology and impact dramatically on the future care of cancer patients. In this review, we will summarize the advantages and limitations of the key technologies used in (onco)proteogenomics, (the Omics Pipeline), explain how they can assist us in understanding the biology behind the overarching "Hallmarks of Cancer", discuss how they can advance the development of precision/personalised medicine and the future directions in the field.
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Affiliation(s)
- Yujia He
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Abidali Mohamedali
- Department of Molecular Sciences, Faculty of Science and Engineering, Macquarie University, New South Wales 2109, Australia
| | - Canhua Huang
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China
| | - Mark S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia.
| | - Edouard C Nice
- West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu 610041, PR China; Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, New South Wales 2109, Australia; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Australia.
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Lin H, He QY, Shi L, Sleeman M, Baker MS, Nice EC. Proteomics and the microbiome: pitfalls and potential. Expert Rev Proteomics 2018; 16:501-511. [PMID: 30223687 DOI: 10.1080/14789450.2018.1523724] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Introduction: Human symbiotic microbiota are now known to play important roles in human health and disease. Significant progress in our understanding of the human microbiome has been driven by recent technological advances in the fields of genomics, transcriptomics, and proteomics. As a complementary method to metagenomics, proteomics is enabling detailed protein profiling of the microbiome to decipher its structure and function and to analyze its relationship with the human body. Fecal proteomics is being increasingly applied to discover and validate potential health and disease biomarkers, and Therapeutic Goods Administration (TGA)-approved instrumentation and a range of clinical assays are being developed that will collectively play key roles in advancing personalized medicine. Areas covered: This review will introduce the complexity of the microbiome and its role in health and disease (in particular the gastrointestinal tract or gut microbiome), discuss current genomic and proteomic methods for studying this system, including the discovery of potential biomarkers, and outline the development of clinically accepted protocols leading to personalized medicine. Expert commentary: Recognition of the important role the microbiome plays in both health and disease is driving current research in this key area. A proteogenomics approach will be essential to unravel the biologies underlying this complex network.
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Affiliation(s)
- Huafeng Lin
- a Department of Biotechnology , College of Life Science and Technology, Jinan University , Guangzhou , Guangdong , China.,b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Qing-Yu He
- c Institute of Life and Health Engineering, College of Life Science and Technology , Jinan University , Guangzhou , China
| | - Lei Shi
- b Institute of Food Safety and Nutrition Research , Jinan University , Guangzhou , China
| | - Mark Sleeman
- d Biomedicine Discovery Institute , Monash University , Melbourne , Australia
| | - Mark S Baker
- e Department of Biomedical Sciences, Faculty of Medicine and Health Sciences , Macquarie University , Sydney , Australia
| | - Edouard C Nice
- f Department of Biochemistry and Molecular Biology , Monash University , Melbourne , Victoria , Australia
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Juling S, Niedzwiecka A, Böhmert L, Lichtenstein D, Selve S, Braeuning A, Thünemann AF, Krause E, Lampen A. Protein Corona Analysis of Silver Nanoparticles Links to Their Cellular Effects. J Proteome Res 2017; 16:4020-4034. [PMID: 28929768 DOI: 10.1021/acs.jproteome.7b00412] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The breadth of applications of nanoparticles and the access to food-associated consumer products containing nanosized materials lead to oral human exposure to such particles. In biological fluids nanoparticles dynamically interact with biomolecules and form a protein corona. Knowledge about the protein corona is of great interest for understanding the molecular effects of particles as well as their fate inside the human body. We used a mass spectrometry-based toxicoproteomics approach to elucidate mechanisms of toxicity of silver nanoparticles and to comprehensively characterize the protein corona formed around silver nanoparticles in Caco-2 human intestinal epithelial cells. Results were compared with respect to the cellular function of proteins either affected by exposure to nanoparticles or present in the protein corona. A transcriptomic data set was included in the analyses in order to obtain a combined multiomics view of nanoparticle-affected cellular processes. A relationship between corona proteins and the proteomic or transcriptomic responses was revealed, showing that differentially regulated proteins or transcripts were engaged in the same cellular signaling pathways. Protein corona analyses of nanoparticles in cells might therefore help in obtaining information about the molecular consequences of nanoparticle treatment.
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Affiliation(s)
- Sabine Juling
- BfR, German Federal Institute for Risk Assessment , Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Alicia Niedzwiecka
- BfR, German Federal Institute for Risk Assessment , Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Linda Böhmert
- BfR, German Federal Institute for Risk Assessment , Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Dajana Lichtenstein
- BfR, German Federal Institute for Risk Assessment , Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Sören Selve
- Technical University Berlin, ZE Electronmicroscopy , Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Albert Braeuning
- BfR, German Federal Institute for Risk Assessment , Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Andreas F Thünemann
- BAM, German Federal Institute for Materials Research and Testing , Unter den Eichen 87, 12205 Berlin, Germany
| | - Eberhard Krause
- Leibniz Institute for Molecular Pharmacology , Robert-Roessle Str. 10, 13125 Berlin, Germany
| | - Alfonso Lampen
- BfR, German Federal Institute for Risk Assessment , Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
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12
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Ang CS, Baker MS, Nice EC. Mass Spectrometry-Based Analysis for the Discovery and Validation of Potential Colorectal Cancer Stool Biomarkers. Methods Enzymol 2016; 586:247-274. [PMID: 28137566 DOI: 10.1016/bs.mie.2016.10.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Colorectal cancer (CRC) is the third leading cause of cancer mortality for both men and women, and the second leading cause of cancer death for men and women combined. If detected early, before metastasis has occurred, survival following surgical resection of the tumor is >90%. Early detection is therefore critical for effective disease surveillance. Unfortunately, current biomarker assays lack the necessary sensitivity and specificity for reliable early disease detection. Development of new robust, non- or minimally invasive specific and sensitive biomarkers or panels with improved compliance and performance is therefore urgently required. The use of fecal samples offers several advantages over other clinical biospecimens (e.g., plasma or serum) as a source of CRC biomarkers, including: collection is noninvasive, the test can be performed at home, one is not sample limited, and the stool effectively samples the entire length of the inner bowel wall contents (including tumor) as it passes down the gastrointestinal tract. Recent advances in mass spectrometry now facilitate both the targeted discovery and validation of potential CRC biomarkers. We describe, herein, detailed protocols that can be used to mine deeply into the fecal proteome to reveal candidate proteins, identify proteotypic/unitypic peptides (i.e., peptides found in only a single known human protein that serve to identify that protein) suitable for sensitive and specific quantitative multiplexed analysis, and undertake high-throughput analysis of clinical samples. Finally, we discuss future directions that may further position this technology to support the current switch in translation research toward personalized medicine.
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Affiliation(s)
- C S Ang
- Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, VIC, Australia
| | - M S Baker
- Faculty of Medicine and Health Sciences, Macquarie University, North Ryde, NSW, Australia
| | - E C Nice
- Monash University, Clayton, VIC, Australia.
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13
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Huang Z, Ma L, Huang C, Li Q, Nice EC. Proteomic profiling of human plasma for cancer biomarker discovery. Proteomics 2016; 17. [PMID: 27550791 DOI: 10.1002/pmic.201600240] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/03/2016] [Accepted: 08/18/2016] [Indexed: 02/05/2023]
Affiliation(s)
- Zhao Huang
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou P. R. China
- Criminal police detachment of Guang'an City Public Security Bureau; P. R. China
| | - Linguang Ma
- Criminal police detachment of Guang'an City Public Security Bureau; P. R. China
| | - Canhua Huang
- State Key Laboratory for Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center of Biotherapy; Chengdu P. R. China
| | - Qifu Li
- Key Laboratory of Tropical Diseases and Translational Medicine of Ministry of Education & Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou P. R. China
| | - Edouard C. Nice
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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14
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Zhou L, Li Q, Wang J, Huang C, Nice EC. Oncoproteomics: Trials and tribulations. Proteomics Clin Appl 2015; 10:516-31. [PMID: 26518147 DOI: 10.1002/prca.201500081] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 09/19/2015] [Accepted: 10/27/2015] [Indexed: 02/05/2023]
Affiliation(s)
- Li Zhou
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Qifu Li
- Department of Neurology; The Affiliated Hospital of Hainan Medical College; Haikou Hainan P. R. China
| | - Jiandong Wang
- Department of Biomedical; Chengdu Medical College; Chengdu Sichuan Province P. R. China
| | - Canhua Huang
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
| | - Edouard C. Nice
- State Key Laboratory of Biotherapy and Cancer Center; West China Hospital; Sichuan University, and Collaborative Innovation Center for Biotherapy; Chengdu P. R. China
- Department of Biochemistry and Molecular Biology; Monash University; Clayton Australia
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15
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Schadock-Hewitt AJ, Bruce TF, Marcus RK. Evidence for the Intercalation of Lipid Acyl Chains into Polypropylene Fiber Matrices. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2015; 31:10418-10425. [PMID: 26381380 DOI: 10.1021/acs.langmuir.5b01964] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Headgroup-functionalized lipids are being developed as ligand tethers for high selectivity separations on polypropylene capillary-channeled polymer fiber stationary phases. Surface modification is affected under ambient conditions from aqueous solution. This basic methodology has promise in many areas where robust modifications are desired on hydrophobic surfaces. In order to understand the mode of adsorption of the lipid tail to the polypropylene surface, lipids labeled with the environmentally sensitive 7-nitro-2-1,3-benzoxadiazol-4-yl (NBD) fluorophore were used, with NBD covalently attached to the headgroup (NBD-PE) or the acyl chain (acyl NBD-PE) of the lipid. When modified with the acyl NBD-PE, fluorescence imaging of the fiber at excitation wavelengths increasing from 470 to 510 nm caused a 32 nm shift in emission toward the red edge of the absorption band, indicating that the NBD molecule (and thus the lipid tail) is motionally restricted. Fluorescence imaging on fibers modified with NBD-PE or the free NBD-Cl dye molecule yields no change in the emission response. The results of these imaging studies provide evidence that the acyl chain portions of the lipids intercalate into free volume of the polypropylene fiber structure, yielding a robust means of surface modification and the potential for high ligand densities.
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Affiliation(s)
- Abby J Schadock-Hewitt
- Department of Chemistry, Biosystems Research Complex, and ‡Clemson Light Imaging Facility, Life Sciences Building, Clemson University , Clemson, South Carolina 29634, United States
| | - Terri F Bruce
- Department of Chemistry, Biosystems Research Complex, and ‡Clemson Light Imaging Facility, Life Sciences Building, Clemson University , Clemson, South Carolina 29634, United States
| | - R Kenneth Marcus
- Department of Chemistry, Biosystems Research Complex, and ‡Clemson Light Imaging Facility, Life Sciences Building, Clemson University , Clemson, South Carolina 29634, United States
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16
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Mahboob S, Mohamedali A, Ahn SB, Schulz-Knappe P, Nice E, Baker MS. Is isolation of comprehensive human plasma peptidomes an achievable quest? J Proteomics 2015; 127:300-9. [PMID: 25979773 DOI: 10.1016/j.jprot.2015.05.010] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Revised: 05/06/2015] [Accepted: 05/09/2015] [Indexed: 01/12/2023]
Abstract
The low molecular weight (LMW; <10kDa)* plasma peptidome has been considered a source of useful diagnostic biomarkers and potentially therapeutic molecules, as it contains many cytokines, peptide hormones, endogenous peptide products and potentially bioactive fragments derived from the parent proteome. The small size of the peptides allows them almost unrestricted vascular and interstitial access, and hence distribution across blood-brain barriers, tumour and other vascular permeability barriers. Therefore, the peptidome may carry specific signatures or fingerprints of an individual's health, wellbeing or disease status. This occurs primarily because of the advantage the peptidome has in being readily accessible in human blood and/or other biofluids. However, the co-expression of highly abundant proteins (>10kDa) and other factors present inherently in human plasma make direct analysis of the blood peptidome one of the most challenging tasks faced in contemporary analytical biochemistry. A comprehensive compendium of extraction and fractionation tools has been collected concerning the isolation and micromanipulation of peptides. However, the search for a reliable, accurate and reproducible single or combinatorial separation process for capturing and analysing the plasma peptidome remains a challenge. This review outlines current techniques used for the separation and detection of plasma peptides and suggests potential avenues for future investigation. This article is part of a Special Issue entitled: HUPO 2014.
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Affiliation(s)
- S Mahboob
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | - A Mohamedali
- Department of Chemistry and Biomolecular Sciences, Faculty of Science, Macquarie University, NSW 2109, Australia
| | - S B Ahn
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia
| | | | - E Nice
- Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria 3800, Australia
| | - M S Baker
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Macquarie University, NSW 2109, Australia.
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17
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Golizeh M, Schneider C, Ohlund LB, Sleno L. Multidimensional LC–MS/MS analysis of liver proteins in rat, mouse and human microsomal and S9 fractions. EUPA OPEN PROTEOMICS 2015. [DOI: 10.1016/j.euprot.2015.01.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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18
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Wang K, Huang C, Nice E. Recent advances in proteomics: towards the human proteome. Biomed Chromatogr 2015; 28:848-57. [PMID: 24861753 DOI: 10.1002/bmc.3157] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
After the successful completion of the Human Genome project in 2003, the next major challenge was to understand when and where the encoded proteins were expressed, and to generate a map of the complex, interconnected pathways, networks and molecular systems (the human proteome) that, taken together, control the workings of all cells, tissues, organs and organisms. Proteomics will be fundamental for such studies. This review summarizes the key discoveries that laid down the foundations for proteomics as we now know it, and describes key recent technological advances that will undoubtedly contribute to achieving the initial goal of the Human Proteome Organization of identifying and characterizing at least one protein product and representative post-translational modifications, single amino acid polymorphisms and splice variant isoforms from the 20,300 human protein-coding genes within the next 10 years. Successful unraveling of the human proteome will undoubtedly improve our understanding of human biology at the cellular level and lay the foundations for improved diagnostic, prognostic, therapeutic and preventive medical outcomes as we enter the era of personalized medicine.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, Chengdu, 610041, People's Republic of China; Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, 3800, Australia
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19
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Wang H, Sun S, Zhang Y, Chen S, Liu P, Liu B. An off-line high pH reversed-phase fractionation and nano-liquid chromatography–mass spectrometry method for global proteomic profiling of cell lines. J Chromatogr B Analyt Technol Biomed Life Sci 2015; 974:90-5. [DOI: 10.1016/j.jchromb.2014.10.031] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 10/23/2014] [Accepted: 10/26/2014] [Indexed: 12/30/2022]
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20
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Combined docking, molecular dynamics simulations and spectroscopic studies for the rational design of a dipeptide ligand for affinity chromatography separation of human serum albumin. J Mol Model 2014; 20:2446. [DOI: 10.1007/s00894-014-2446-7] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2014] [Accepted: 08/26/2014] [Indexed: 01/07/2023]
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21
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Gao M, Qi D, Zhang P, Deng C, Zhang X. Development of multidimensional liquid chromatography and application in proteomic analysis. Expert Rev Proteomics 2014; 7:665-78. [DOI: 10.1586/epr.10.49] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
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22
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Zhai L, Chang C, Li N, Duong DM, Chen H, Deng Z, Yang J, Hong X, Zhu Y, Xu P. Systematic research on the pretreatment of peptides for quantitative proteomics using a C18
microcolumn. Proteomics 2013; 13:2229-37. [DOI: 10.1002/pmic.201200591] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2012] [Revised: 04/16/2013] [Accepted: 04/29/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Linhui Zhai
- State Key Laboratory of Proteomics, Beijing Proteome Research Center; National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine; Beijing P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education, and Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Cheng Chang
- State Key Laboratory of Proteomics, Beijing Proteome Research Center; National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Ning Li
- State Key Laboratory of Proteomics, Beijing Proteome Research Center; National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Duc M. Duong
- State Key Laboratory of Proteomics, Beijing Proteome Research Center; National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Hao Chen
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education, and Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Zixin Deng
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education, and Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Jian Yang
- Tianjin Institute of Medical Equipment; Tianjin P. R. China
| | - Xuechuan Hong
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education, and Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
| | - Yunping Zhu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center; National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine; Beijing P. R. China
| | - Ping Xu
- State Key Laboratory of Proteomics, Beijing Proteome Research Center; National Engineering Research Center for Protein Drugs, National Center for Protein Sciences, Beijing Institute of Radiation Medicine; Beijing P. R. China
- Key Laboratory of Combinatorial Biosynthesis and Drug Discovery (Wuhan University); Ministry of Education, and Wuhan University School of Pharmaceutical Sciences; Wuhan P. R. China
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23
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Catimel B, Kapp E, Yin MX, Gregory M, Wong LSM, Condron M, Church N, Kershaw N, Holmes AB, Burgess AW. The PI(3)P interactome from a colon cancer cell. J Proteomics 2013; 82:35-51. [DOI: 10.1016/j.jprot.2013.01.031] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2012] [Revised: 12/21/2012] [Accepted: 01/24/2013] [Indexed: 02/07/2023]
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24
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Abstract
Protein glycosylation represents the most abundant extracellular posttranslational modification in multicellular organisms. These glycoproteins unequivocally comprise the major biomolecules involved in extracellular processes, such as growth factors, signaling proteins for cellular communication, enzymes, and proteases for on- and off-site processing. It is now known that altered protein glycosylation is a hallmark event in many different pathologies. Glycoproteins are found mostly in the so-called secretome, which comprises classically and nonclassically secreted proteins and protein fragments that are released from the cell surface through ectodomain shedding. Due to biological complexity and technical difficulty, comparably few studies have taken an in-depth investigation of cellular secretomes using system-wide approaches. The cellular secretomes are considered to be a valuable source of therapeutic targets and novel biomarkers. It is not surprising that many existing biomarkers, including biomarkers for breast, ovarian, prostate, and colorectal cancers are glycoproteins. Focused analysis of secreted glycoproteins could thus provide valuable information for early disease diagnosis, and surveillance. Furthermore, since most secreted proteins are glycosylated and glycosylation predominantly targets secreted proteins, the glycan/sugar moiety itself can be used as a chemical "handle" for the targeted analysis of cellular secretomes, thereby reducing sample complexity and allowing detection of low abundance proteins in proteomic workflows. This review will focus on various glycoprotein enrichment strategies that facilitate proteomics-based technologies for the quantitative analysis of cell secretomes and cell surface proteomes.
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Affiliation(s)
- Zon W Lai
- Institute for Molecular Medicine and Cell Research, University of Freiburg, Stefan-Meier-Strasse 17, Freiburg, Germany
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25
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Wang K, Yang T, Wu Q, Zhao X, Nice EC, Huang C. Chemistry-based functional proteomics for drug target deconvolution. Expert Rev Proteomics 2013; 9:293-310. [PMID: 22809208 DOI: 10.1586/epr.12.19] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Drug target deconvolution, a process that identifies targets to small molecules in complex biological samples, which underlie the biological responses that are observed when a drug is administered, plays an important role in current drug discovery. Despite the fact that genomics and proteomics have provided a flood of information that contributes to the progress of drug target identification and validation, the current approach to drug target deconvolution still poses dilemmas. Chemistry-based functional proteomics, a multidisciplinary strategy, has become the preferred method of choice to deconvolute drug target pools, based on direct interactions between small molecules and their protein targets. This approach has already identified a broad panel of previously undefined enzymes with potential as drug targets and defined targets that can rationalize side effects and toxicity for new drug candidates and existing therapeutics. Herein, the authors discuss both activity-based protein profiling and compound-centric chemical proteomics approaches used in chemistry-based functional proteomics and their applications for the identification and characterization of small molecular targets.
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Affiliation(s)
- Kui Wang
- The State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, 610041, PR China
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26
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Lai ZW, Yan Y, Caruso F, Nice EC. Emerging techniques in proteomics for probing nano-bio interactions. ACS NANO 2012; 6:10438-10448. [PMID: 23214939 DOI: 10.1021/nn3052499] [Citation(s) in RCA: 80] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Nanoengineered particles that can facilitate drug formulation and improve specificity of delivery afford exciting opportunities for improved lesion-specific therapy. Understanding and controlling the nano-bio interactions of these materials is central to future developments in this area. Mass-spectrometry-based proteomics techniques, in conjunction with other emerging technologies, are enabling novel insights into the modulation of particle surfaces by biological fluids (formation of the protein corona) and subsequent particle-induced cellular responses. In this Perspective, we summarize important recent developments using proteomics-based techniques to understand nano-bio interactions and discuss the impact of such knowledge on improving particle design.
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Affiliation(s)
- Zon W Lai
- Department of Biochemistry and Molecular Biology, Monash University, Victoria 3800, Australia
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27
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Gajdosik MS, Clifton J, Josic D. Sample displacement chromatography as a method for purification of proteins and peptides from complex mixtures. J Chromatogr A 2012; 1239:1-9. [PMID: 22520159 PMCID: PMC3340482 DOI: 10.1016/j.chroma.2012.03.046] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 03/13/2012] [Accepted: 03/14/2012] [Indexed: 01/06/2023]
Abstract
Sample displacement chromatography (SDC) in reversed-phase and ion-exchange modes was introduced approximately twenty years ago. This method takes advantage of relative binding affinities of components in a sample mixture. During loading, there is a competition among different sample components for the sorption on the surface of the stationary phase. SDC was first used for the preparative purification of proteins. Later, it was demonstrated that this kind of chromatography can also be performed in ion-exchange, affinity and hydrophobic-interaction mode. It has also been shown that SDC can be performed on monoliths and membrane-based supports in both analytical and preparative scale. Recently, SDC in ion-exchange and hydrophobic interaction mode was also employed successfully for the removal of trace proteins from monoclonal antibody preparations and for the enrichment of low abundance proteins from human plasma. In this review, the principals of SDC are introduced, and the potential for separation of proteins and peptides in micro-analytical, analytical and preparative scale is discussed.
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Affiliation(s)
| | - James Clifton
- Department of Molecular Pharmacology, Physiology and Biotechnology, Brown University, Providence, RI, USA
| | - Djuro Josic
- COBRE Center for Cancer Research Development, Rhode Island Hospital and Brown University, Providence, RI, USA
- Department of Biotechnology, University of Rijeka, 51000 Rijeka, Croatia
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28
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Delobel J, Prudent M, Rubin O, Crettaz D, Tissot JD, Lion N. Subcellular fractionation of stored red blood cells reveals a compartment-based protein carbonylation evolution. J Proteomics 2012; 76 Spec No.:181-93. [PMID: 22580360 DOI: 10.1016/j.jprot.2012.05.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2012] [Revised: 04/28/2012] [Accepted: 05/02/2012] [Indexed: 12/13/2022]
Abstract
During blood banking, erythrocytes undergo storage lesions, altering or degrading their metabolism, rheological properties, and protein content. Carbonylation is a hallmark of protein oxidative lesions, thus of red blood cell oxidative stress. In order to improve global erythrocyte protein carbonylation assessment, subcellular fractionation has been established, allowing us to work on four different protein populations, namely soluble hemoglobin, hemoglobin-depleted soluble fraction, integral membrane and cytoskeleton membrane protein fractions. Carbonylation in erythrocyte-derived microparticles has also been investigated. Carbonylated proteins were derivatized with 2,4-dinitrophenylhydrazine (2,4-DNPH) and quantified by western blot analyses. In particular, carbonylation in the cytoskeletal membrane fraction increased remarkably between day 29 and day 43 (P<0.01). Moreover, protein carbonylation within microparticles released during storage showed a two-fold increase along the storage period (P<0.01). As a result, carbonylation of cytoplasmic and membrane protein fractions differs along storage, and the present study allows explaining two distinct steps in global erythrocyte protein carbonylation evolution during blood banking. This article is part of a Special Issue entitled: Integrated omics.
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Affiliation(s)
- Julien Delobel
- Service Régional Vaudois de Transfusion Sanguine, route de Corniche 2, CH-1066 Epalinges, Switzerland
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29
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Guerrier L, Fortis F, Boschetti E. Solid-phase fractionation strategies applied to proteomics investigations. Methods Mol Biol 2012; 818:11-33. [PMID: 22083813 DOI: 10.1007/978-1-61779-418-6_2] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Methods for protein fractionation in the proteomics investigation field are relatively numerous. They apply to the prefractionation of the sample to obtain less complex protein mixtures for an easier analysis; they are also used as a means to evidence specific proteins or protein classes otherwise impossible to detect. They involve depletion of high-abundance proteins suppressing the signal of dilute species; they are also capable to enhance the detectability of low-abundance species while concomitantly decreasing the concentration of abundant proteins such as albumin in serum and hemoglobin in red blood cell lysates. Fractionation of proteomes is also used for the isolation of targeted species that are selected for their different expression under certain pathological conditions and that are detected by mass spectrometry. Two unconventional methods of large interest in proteomics due to the low level of protein redundancy between fractions are also reported.All these methods are reviewed and detailed method given to allow specialists of proteomics investigation to access selected separation methods generally dispersed on different technical reviews or books.
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Affiliation(s)
- Luc Guerrier
- Bio-Rad Laboratories, Marnes la Coquette, France
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30
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Wright P, Noirel J, Ow SY, Fazeli A. A review of current proteomics technologies with a survey on their widespread use in reproductive biology investigations. Theriogenology 2012; 77:738-765.e52. [DOI: 10.1016/j.theriogenology.2011.11.012] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 11/08/2011] [Accepted: 11/11/2011] [Indexed: 12/27/2022]
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31
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Rucevic M, Hixson D, Josic D. Mammalian plasma membrane proteins as potential biomarkers and drug targets. Electrophoresis 2011; 32:1549-64. [PMID: 21706493 DOI: 10.1002/elps.201100212] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Defining the plasma membrane proteome is crucial to understand the role of plasma membrane in fundamental biological processes. Change in membrane proteins is one of the first events that take place under pathological conditions, making plasma membrane proteins a likely source of potential disease biomarkers with prognostic or diagnostic potential. Membrane proteins are also potential targets for monoclonal antibodies and other drugs that block receptors or inhibit enzymes essential to the disease progress. Despite several advanced methods recently developed for the analysis of hydrophobic proteins and proteins with posttranslational modifications, integral membrane proteins are still under-represented in plasma membrane proteome. Recent advances in proteomic investigation of plasma membrane proteins, defining their roles as diagnostic and prognostic disease biomarkers and as target molecules in disease treatment, are presented.
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Affiliation(s)
- Marijana Rucevic
- COBRE Center for Cancer Research Development, Rhode Island Hospital, Providence, RI, USA
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32
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Hu H, Deng C, Yang T, Dong Q, Chen Y, Nice EC, Huang C, Wei Y. Proteomics revisits the cancer metabolome. Expert Rev Proteomics 2011; 8:505-533. [DOI: 10.1586/epr.11.31] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/30/2023]
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33
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Capriotti AL, Cavaliere C, Foglia P, Samperi R, Laganà A. Intact protein separation by chromatographic and/or electrophoretic techniques for top-down proteomics. J Chromatogr A 2011; 1218:8760-76. [PMID: 21689823 DOI: 10.1016/j.chroma.2011.05.094] [Citation(s) in RCA: 68] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Revised: 04/13/2011] [Accepted: 05/28/2011] [Indexed: 12/26/2022]
Abstract
Mass spectrometry used in combination with a wide variety of separation methods is the principal methodology for proteomics. In bottom-up approach, proteins are cleaved with a specific proteolytic enzyme, followed by peptide separation and MS identification. In top-down approach intact proteins are introduced into the mass spectrometer. The ions generated by electrospray ionization are then subjected to gas-phase separation, fragmentation, fragment separation, and automated interpretation of mass spectrometric and chromatographic data yielding both the molecular weight of the intact protein and the protein fragmentation pattern. This approach requires high accuracy mass measurement analysers capable of separating the multi-charged isotopic cluster of proteins, such as hybrid ion trap-Fourier transform instruments (LTQ-FTICR, LTQ-Orbitrap). Front-end separation technologies tailored for proteins are of primary importance to implement top-down proteomics. This review intends to provide the state of art of protein chromatographic and electrophoretic separation methods suitable for MS coupling, and to illustrate both monodimensional and multidimensional approaches used for LC-MS top-down proteomics. In addition, some recent progresses in protein chromatography that may provide an alternative to those currently employed are also discussed.
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Affiliation(s)
- Anna Laura Capriotti
- Department of Chemistry, Sapienza Università di Roma, Piazzale Aldo Moro 5, 00185 Rome, Italy
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34
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Evans ST, Holstein M, Cramer SM. Detection of trace proteins in multicomponent mixtures using displacement chromatography. Anal Chem 2011; 83:4184-92. [PMID: 21524131 DOI: 10.1021/ac200486e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Model protein feed mixtures containing three abundant and seven trace proteins at various concentrations were identified and employed in a series of displacement experiments. Reversed-phase liquid chromatography (RPLC) and matrix assisted laser desorption ionization-time-of-flight (MALDI-TOF) mass spectrometry were used to evaluate the compositions of both the feed mixtures and effluent fractions from the displacement experiments. The results demonstrated that trace proteins were focused at the boundaries between the abundant solutes where they were enriched and concentrated. For many of the multicomponent feed mixtures, mass spectrometry analyses of the displacement column effluent fractions resulted in the identification of trace proteins that were not detectable in the feed. In addition, the use of minimal or no salt in the carrier solutions enabled the analysis of displacement fractions by direct infusion mass spectrometry. These results are significant in that they indicate that while the presence of abundant proteins can often be problematic for the detection of trace components, displacement chromatography may be able to employ these abundant proteins to focus trace proteins in the displacement train, thus facilitating detection.
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Affiliation(s)
- Steven T Evans
- Department of Chemical and Biological Engineering, Center for Biotechnology and Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York 12180, USA
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35
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Ang CS, Rothacker J, Patsiouras H, Gibbs P, Burgess AW, Nice EC. Use of multiple reaction monitoring for multiplex analysis of colorectal cancer-associated proteins in human feces. Electrophoresis 2011; 32:1926-38. [PMID: 21538981 DOI: 10.1002/elps.201000502] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Revised: 11/25/2010] [Accepted: 12/17/2010] [Indexed: 12/14/2022]
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related deaths worldwide with an annual incidence of almost a million cases and an annual mortality around 500,000. The fecal occult blood test is currently the first line method for CRC screening, but has unacceptably low sensitivity and specificity. Improved screening tests are therefore urgently required for early-stage CRC screening when therapy is most likely to be effective. We describe a discovery-based proteomics hypothesis using orthogonal multi-dimensional fractionation (1-D SDS-PAGE, RP-HPLC, size exclusion chromatography) to mine deep into the fecal proteome for the initial discovery process, which generated a library containing 108 human fecal proteins with the associated peptide and MS/MS data. These data were then used to develop and optimize a multiplex multiple reaction monitoring assay for 40 non-redundant human proteins present in the feces. To show proof of principal for clinical analysis, multiplex screening of these 40 proteins was carried out on fecal samples from eight CRC patient and seven normal volunteers. We identified 24 proteins consistently found in all samples and nine proteins found only in the CRC patients, showing the potential of this approach for the analysis of potential CRC biomarkers. Absolute quantitation using C-terminal isotopically labeled synthetic peptides corresponding to hemoglobin and carcinoembryonic antigen 5 was also performed.
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Affiliation(s)
- Ching-Seng Ang
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Melbourne, Victoria, Australia
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36
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Brgles M, Clifton J, Walsh R, Huang F, Rucevic M, Cao L, Hixson D, Müller E, Josic D. Selectivity of monolithic supports under overloading conditions and their use for separation of human plasma and isolation of low abundance proteins. J Chromatogr A 2010; 1218:2389-95. [PMID: 21186030 DOI: 10.1016/j.chroma.2010.11.059] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2010] [Revised: 10/19/2010] [Accepted: 11/25/2010] [Indexed: 01/06/2023]
Abstract
Human serum albumin (HSA) and immunoglobulin G (IgG) represent over 75% of all proteins present in human plasma. These two proteins frequently interfere with detection, determination and purification of low abundance proteins that can be potential biomarkers and biomarker candidates for various diseases. Some low abundance plasma proteins such as clotting factors and inhibitors are also important therapeutic agents. In this paper, the characterization of ion-exchange monolithic supports under overloading conditions was performed by use of sample displacement chromatography (SDC). If these supports were used for separation of human plasma, the composition of bound and eluted proteins in both anion- and cation-exchange mode is dependent on column loading. Under overloading conditions, the weakly bound proteins such as HSA in anion-exchange and IgG in cation-exchange mode are displaced by stronger binding proteins, and this phenomenon was not dependent on column size. Consequently, small monolithic columns with a column volume of 100 and 200 μL are ideal supports for high-throughput screening in order to develop new methods for separation of complex mixtures, and for sample preparation in proteomic technology.
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37
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Bareither R, Pollard D. A review of advanced small-scale parallel bioreactor technology for accelerated process development: current state and future need. Biotechnol Prog 2010; 27:2-14. [PMID: 21312350 DOI: 10.1002/btpr.522] [Citation(s) in RCA: 144] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2010] [Revised: 06/13/2010] [Indexed: 11/10/2022]
Abstract
The pharmaceutical and biotech industries face continued pressure to reduce development costs and accelerate process development. This challenge occurs alongside the need for increased upstream experimentation to support quality by design initiatives and the pursuit of predictive models from systems biology. A small scale system enabling multiple reactions in parallel (n ≥ 20), with automated sampling and integrated to purification, would provide significant improvement (four to fivefold) to development timelines. State of the art attempts to pursue high throughput process development include shake flasks, microfluidic reactors, microtiter plates and small-scale stirred reactors. The limitations of these systems are compared to desired criteria to mimic large scale commercial processes. The comparison shows that significant technological improvement is still required to provide automated solutions that can speed upstream process development.
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Affiliation(s)
- Rachel Bareither
- Biologics New & Enabling Technologies, Biologics Development, Merck Research Laboratories, Merck & Co. Inc., Rahway, NJ 07065, USA
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38
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Ang CS, Phung J, Nice EC. The discovery and validation of colorectal cancer biomarkers. Biomed Chromatogr 2010; 25:82-99. [PMID: 21058408 DOI: 10.1002/bmc.1528] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2010] [Accepted: 08/23/2010] [Indexed: 12/27/2022]
Abstract
Colorectal cancer is currently the third most common malignancy in the world. Patients have excellent prognosis following surgical resection if their tumour is still localized at diagnosis. By contrast, once the tumour has started to metastasize, prognosis is much poorer. Accurate early detection can therefore significantly reduce the mortality from this disease. However, current tests either lack the required sensitivity and selectivity or are costly and invasive. Improved biomarkers, or panels of biomarkers, are therefore urgently required. We have addressed current screening strategies and potential protein biomarkers that have been proposed. The role of both discovery and hypothesis-driven proteomics approaches for biomarker discovery and validation is discussed. Using such approaches we show how multiple reaction monitoring (MRM) can be successfully developed and used for quantitative multiplexed analysis of potential faecal biomarkers.
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Affiliation(s)
- Ching-Seng Ang
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Melbourne, Australia
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39
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Zhang X, Liu B, Zhang L, Zou H, Cao J, Gao M, Tang J, Liu Y, Yang P, Zhang Y. Recent advances in proteolysis and peptide/protein separation by chromatographic strategies. Sci China Chem 2010; 53:685-694. [PMID: 32214996 PMCID: PMC7089403 DOI: 10.1007/s11426-010-0135-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2010] [Accepted: 01/28/2010] [Indexed: 11/05/2022]
Abstract
This review gives a broad glance on the progress of recent advances on proteolysis and peptide/protein separation by chromatographic strategies in the past ten years, covering the main research in these areas especially in China. The reviewed research focused on enzymatic micro-reactors and peptide separation in bottom-up approaches, and protein and peptide separation in top-down approaches. The new enzymatic micro-reactor is able to accelerate proteolytic reaction rate from conventionally a couple of hours to a few seconds, and the multiple dimensional chromatographic-separation with various models or arrays could sufficiently separate the proteomic mixture. These advances have significantly promoted the research of protein/peptide separation and identification in proteomics.
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Affiliation(s)
- XiangMin Zhang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - BaoHong Liu
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - LiHua Zhang
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - HanFa Zou
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
| | - Jing Cao
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - MingXia Gao
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - Jia Tang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - Yun Liu
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - PengYuan Yang
- 1Department of Chemistry and Institutes of Biomedical Sciences, Fudan University, Shanghai, 200433 China
| | - YuKui Zhang
- 2Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023 China
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40
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Ikonomou G, Samiotaki M, Panayotou G. Proteomic methodologies and their application in colorectal cancer research. Crit Rev Clin Lab Sci 2009; 46:319-42. [DOI: 10.3109/10408360903375277] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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41
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Chomicki A, Ślązak P, Dzido TH. Preliminary results for 2-D separation with high-performance thin-layer chromatography and pressurized planar electrochromatography. Electrophoresis 2009; 30:3718-25. [DOI: 10.1002/elps.200900471] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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42
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Ahmed FE. Sample preparation and fractionation for proteome analysis and cancer biomarker discovery by mass spectrometry. J Sep Sci 2009; 32:771-98. [PMID: 19219839 DOI: 10.1002/jssc.200800622] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Sample preparation and fractionation technologies are one of the most crucial processes in proteomic analysis and biomarker discovery in solubilized samples. Chromatographic or electrophoretic proteomic technologies are also available for separation of cellular protein components. There are, however, considerable limitations in currently available proteomic technologies as none of them allows for the analysis of the entire proteome in a simple step because of the large number of peptides, and because of the wide concentration dynamic range of the proteome in clinical blood samples. The results of any undertaken experiment depend on the condition of the starting material. Therefore, proper experimental design and pertinent sample preparation is essential to obtain meaningful results, particularly in comparative clinical proteomics in which one is looking for minor differences between experimental (diseased) and control (nondiseased) samples. This review discusses problems associated with general and specialized strategies of sample preparation and fractionation, dealing with samples that are solution or suspension, in a frozen tissue state, or formalin-preserved tissue archival samples, and illustrates how sample processing might influence detection with mass spectrometric techniques. Strategies that dramatically improve the potential for cancer biomarker discovery in minimally invasive, blood-collected human samples are also presented.
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Affiliation(s)
- Farid E Ahmed
- Department of Radiation Oncology, Leo W. Jenkins Cancer Center, The Brody School of Medicine at East Carolina University, Greenville, NC, USA.
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43
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Catimel B, Schieber C, Condron M, Patsiouras H, Connolly L, Catimel J, Nice EC, Burgess AW, Holmes AB. The PI(3,5)P2 and PI(4,5)P2 Interactomes. J Proteome Res 2008; 7:5295-313. [DOI: 10.1021/pr800540h] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Bruno Catimel
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christine Schieber
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Melanie Condron
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Heather Patsiouras
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Lisa Connolly
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jenny Catimel
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Edouard C. Nice
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Antony W. Burgess
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andrew B. Holmes
- Ludwig Institute for Cancer Research, Melbourne Tumour Biology Branch, Royal Melbourne Hospital, Parkville Victoria 3052, Australia, and School of Chemistry, Bio21 Institute, University of Melbourne, Parkville, Victoria 3010, Australia
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44
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Rich RL, Myszka DG. Survey of the year 2007 commercial optical biosensor literature. J Mol Recognit 2008; 21:355-400. [DOI: 10.1002/jmr.928] [Citation(s) in RCA: 144] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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45
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Dormeyer W, van Hoof D, Mummery CL, Krijgsveld J, Heck AJR. A practical guide for the identification of membrane and plasma membrane proteins in human embryonic stem cells and human embryonal carcinoma cells. Proteomics 2008; 8:4036-53. [DOI: 10.1002/pmic.200800143] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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46
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Kruse U, Bantscheff M, Drewes G, Hopf C. Chemical and pathway proteomics: powerful tools for oncology drug discovery and personalized health care. Mol Cell Proteomics 2008; 7:1887-901. [PMID: 18676365 DOI: 10.1074/mcp.r800006-mcp200] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
In recent years mass spectrometry-based proteomics has moved beyond a mere quantitative description of protein expression levels and their possible correlation with disease or drug action. Impressive progress in LC-MS instrumentation together with the availability of new enabling tools and methods for quantitative proteome analysis and for identification of posttranslational modifications has triggered a surge of chemical and functional proteomics studies dissecting mechanisms of action of cancer drugs and molecular mechanisms that modulate signal transduction pathways. Despite the tremendous progress that has been made in the field, major challenges, relating to sensitivity, dynamic range, and throughput of the described methods, remain. In this review we summarize recent advances in LC-MS-based approaches and their application to cancer drug discovery and to studies of cancer-related pathways in cell culture models with particular emphasis on mechanistic studies of drug action in these systems. Moreover we highlight the emerging utility of pathway and chemical proteomics techniques for translational research in patient tissue.
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Affiliation(s)
- Ulrich Kruse
- Deptartment of Discovery Technology, Cellzome AG, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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47
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Jandera P. Stationary phases for hydrophilic interaction chromatography, their characterization and implementation into multidimensional chromatography concepts. J Sep Sci 2008; 31:1421-37. [PMID: 18428181 DOI: 10.1002/jssc.200800051] [Citation(s) in RCA: 185] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Hydrophilic interaction chromatography (HILIC) is becoming increasingly popular for separation of polar samples on polar columns in aqueous-organic mobile phases rich in organic solvents (usually ACN). Silica gel with decreased surface concentration of silanol groups, or with chemically bonded amino-, amido-, cyano-, carbamate-, diol-, polyol-, or zwitterionic sulfobetaine ligands are used as the stationary phases for HILIC separations, in addition to the original poly(2-sulphoethyl aspartamide) strong cation-exchange HILIC material. The type of the stationary and the composition of the mobile phase play important roles in the mixed-mode HILIC retention mechanism and can be flexibly tuned to suit specific separation problems. Because of excellent mobile phase compatibility and complementary selectivity to RP chromatography, HILIC is ideally suited for highly orthogonal 2-D LC-LC separations of complex samples containing polar compounds, such as peptides, proteins, oligosaccharides, drugs, metabolites and natural compounds. This review attempts to present an overview of the HILIC separation systems, possibilities for their characterization and emerging HILIC applications in 2-D off-line and on-line LC-LC separations of various samples, in combination with RP and other separation modes.
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Affiliation(s)
- Pavel Jandera
- Department of Analytical Chemistry, Faculty of Chemical Technology, University of Pardubice, Pardubice, Czech Republic.
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48
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Recent development of multi-dimensional chromatography strategies in proteome research. J Chromatogr B Analyt Technol Biomed Life Sci 2008; 866:123-32. [PMID: 18289947 PMCID: PMC7185551 DOI: 10.1016/j.jchromb.2008.01.029] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2007] [Revised: 01/15/2008] [Accepted: 01/18/2008] [Indexed: 11/23/2022]
Abstract
As a complementary approach to two-dimensional polyacrylamide gel electrophoresis (2D-PAGE), multi-dimensional chromatography separation methods have been widely applied in all kinds of biological sample investigations. Multi-dimensional liquid chromatography (MDLC) coupled with bio-mass spectrometry (MS) is playing important roles in proteome research due to its high speed, high resolution and high sensitivity. Proteome analysis strategies mainly include bottom-up and top-down approaches which carry out biological sample separation based on peptide and protein levels, respectively. Electrophoretic methods combined with liquid chromatography like IEF-HPLC and HPLC-SDS-PAGE have been successful applied for protein separations. As for MDLC strategy, ion-exchange chromatography (IEX) together with reversed phase liquid chromatography (RPLC) is still a most widely used chromatography in proteome analysis, other chromatographic methods are also frequently used in protein pre-fractionations, while affinity chromatography is usually adopted for specific functional protein analysis. Recent MDLC technologies and applications to variety of proteome analysis have been achieved great development. A digest peptide-based approach as so-called “bottom-up” and intact protein-based approach “top-down” analysis of proteome samples were briefly reviewed in this paper. The diversity of combinations of different chromatography modes to set up MDLC systems was demonstrated and discussed. Novel developments of MDLC techniques such as high-abundance protein depletion and chromatography array were also included in this review.
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