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Jordaens S, Oeyen E, Willems H, Ameye F, De Wachter S, Pauwels P, Mertens I. Protein Biomarker Discovery Studies on Urinary sEV Fractions Separated with UF-SEC for the First Diagnosis and Detection of Recurrence in Bladder Cancer Patients. Biomolecules 2023; 13:932. [PMID: 37371512 DOI: 10.3390/biom13060932] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Revised: 05/26/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Urinary extracellular vesicles (EVs) are an attractive source of bladder cancer biomarkers. Here, a protein biomarker discovery study was performed on the protein content of small urinary EVs (sEVs) to identify possible biomarkers for the primary diagnosis and recurrence of non-muscle-invasive bladder cancer (NMIBC). The sEVs were isolated by ultrafiltration (UF) in combination with size-exclusion chromatography (SEC). The first part of the study compared healthy individuals with NMIBC patients with a primary diagnosis. The second part compared tumor-free patients with patients with a recurrent NMIBC diagnosis. The separated sEVs were in the size range of 40 to 200 nm. Based on manually curated high quality mass spectrometry (MS) data, the statistical analysis revealed 69 proteins that were differentially expressed in these sEV fractions of patients with a first bladder cancer tumor vs. an age- and gender-matched healthy control group. When the discriminating power between healthy individuals and first diagnosis patients is taken into account, the biomarkers with the most potential are MASP2, C3, A2M, CHMP2A and NHE-RF1. Additionally, two proteins (HBB and HBA1) were differentially expressed between bladder cancer patients with a recurrent diagnosis vs. tumor-free samples of bladder cancer patients, but their biological relevance is very limited.
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Affiliation(s)
- Stephanie Jordaens
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
| | - Eline Oeyen
- Health Unit, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
- Centre for Proteomics (CfP), University of Antwerp, 2020 Antwerp, Belgium
| | - Hanny Willems
- Health Unit, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
| | - Filip Ameye
- Department of Urology, AZ Maria Middelares, 9000 Ghent, Belgium
| | - Stefan De Wachter
- Department of Urology, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Patrick Pauwels
- Center for Oncological Research (CORE), Integrated Personalized & Precision Oncology Network (IPPON), University of Antwerp, 2610 Wilrijk, Belgium
- Laboratory of Pathological Anatomy, Antwerp University Hospital (UZA), 2650 Edegem, Belgium
| | - Inge Mertens
- Health Unit, Flemish Institute for Technological Research (VITO), 2400 Mol, Belgium
- Centre for Proteomics (CfP), University of Antwerp, 2020 Antwerp, Belgium
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Sala M, Ros M, Saltel F. A Complex and Evolutive Character: Two Face Aspects of ECM in Tumor Progression. Front Oncol 2020; 10:1620. [PMID: 32984031 PMCID: PMC7485352 DOI: 10.3389/fonc.2020.01620] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 07/27/2020] [Indexed: 12/24/2022] Open
Abstract
Tumor microenvironment, including extracellular matrix (ECM) and stromal cells, is a key player during tumor development, from initiation, growth and progression to metastasis. During all of these steps, remodeling of matrix components occurs, changing its biochemical and physical properties. The global and basic cancer ECM model is that tumors are surrounded by activated stromal cells, that remodel physiological ECM to evolve into a stiffer and more crosslinked ECM than in normal conditions, thereby increasing invasive capacities of cancer cells. In this review, we show that this too simple model does not consider the complexity, specificity and heterogeneity of each organ and tumor. First, we describe the general ECM in context of cancer. Then, we go through five invasive and most frequent cancers from different origins (breast, liver, pancreas, colon, and skin), and show that each cancer has its own specific matrix, with different stromal cells, ECM components, biochemical properties and activated signaling pathways. Furthermore, in these five cancers, we describe the dual role of tumor ECM: as a protective barrier against tumor cell proliferation and invasion, and as a major player in tumor progression. Indeed, crosstalk between tumor and stromal cells induce changes in matrix organization by remodeling ECM through invadosome formation in order to degrade it, promoting tumor progression and cell invasion. To sum up, in this review, we highlight the specificities of matrix composition in five cancers and the necessity not to consider the ECM as one general and simple entity, but one complex, dynamic and specific entity for each cancer type and subtype.
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Affiliation(s)
- Margaux Sala
- Univ. Bordeaux, INSERM, BaRITOn, U1053, Bordeaux, France
| | - Manon Ros
- Univ. Bordeaux, INSERM, BaRITOn, U1053, Bordeaux, France
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3
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Lee PY, Chin SF, Low TY, Jamal R. Probing the colorectal cancer proteome for biomarkers: Current status and perspectives. J Proteomics 2018; 187:93-105. [PMID: 29953962 DOI: 10.1016/j.jprot.2018.06.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Revised: 06/13/2018] [Accepted: 06/23/2018] [Indexed: 02/07/2023]
Abstract
Colorectal cancer (CRC) is one of the most prevalent malignancies worldwide. Biomarkers that can facilitate better clinical management of CRC are in high demand to improve patient outcome and to reduce mortality. In this regard, proteomic analysis holds a promising prospect in the hunt of novel biomarkers for CRC and in understanding the mechanisms underlying tumorigenesis. This review aims to provide an overview of the current progress of proteomic research, focusing on discovery and validation of diagnostic biomarkers for CRC. We will summarize the contributions of proteomic strategies to recent discoveries of protein biomarkers for CRC and also briefly discuss the potential and challenges of different proteomic approaches in biomarker discovery and translational applications.
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Affiliation(s)
- Pey Yee Lee
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia.
| | - Siok-Fong Chin
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Teck Yew Low
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
| | - Rahman Jamal
- UKM Medical Molecular Biology Institute (UMBI), Universiti Kebangsaan Malaysia, 56000 Kuala Lumpur, Malaysia
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4
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Bloch MB, Yavin E, Nissan A, Ariel I, Kenett R, Brass D, Rubinstein A. The effect of linker type and recognition peptide conjugation chemistry on tissue affinity and cytotoxicity of charged polyacrylamide. J Control Release 2017; 257:102-117. [DOI: 10.1016/j.jconrel.2016.06.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2016] [Revised: 05/27/2016] [Accepted: 06/26/2016] [Indexed: 12/16/2022]
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5
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Crotti S, Piccoli M, Rizzolio F, Giordano A, Nitti D, Agostini M. Extracellular Matrix and Colorectal Cancer: How Surrounding Microenvironment Affects Cancer Cell Behavior? J Cell Physiol 2016; 232:967-975. [PMID: 27775168 DOI: 10.1002/jcp.25658] [Citation(s) in RCA: 98] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 10/20/2016] [Indexed: 12/12/2022]
Abstract
Colorectal cancer (CRC) whit more than a million of new cases per year is one of the most common registered cancers worldwide with few treatment options especially for advanced and metastatic patients.The tumor microenvironment is composed by extracellular matrix (ECM), cells, and interstitial fluids. Among all these constituents, in the last years an increased interest around the ECM and its potential role in cancer tumorigenesis is arisen. During cancer progression the ECM structure and composition became disorganized, allowing cellular transformation and metastasis. Up to now, the focus has mainly been on the characterization of CRC microenvironment analyzing separately structural ECM components or cell secretome modifications. A more extensive view that interconnects these aspects should be addressed. In this review, biochemical (secretome) and biomechanical (structure and architecture) changes of tumor microenvironment will be discussed, giving suggestions on how these changes can affect cancer cell behavior. J. Cell. Physiol. 232: 967-975, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Sara Crotti
- Institute of Paediatric Research-Città della Speranza, Corso Stati Uniti 4, Padova, Italy
| | - Martina Piccoli
- Institute of Paediatric Research-Città della Speranza, Corso Stati Uniti 4, Padova, Italy
| | - Flavio Rizzolio
- Department of Translational Research, IRCCS-National Cancer Institute, Aviano, Italy
| | - Antonio Giordano
- Sbarro Institute for Cancer Research and Molecular Medicine, Center for Biotechnology, College of Science and Technology, Temple University, Philadelphia, Pennsylvania.,Department of Medicine, Surgery and Neuroscience, University of Siena, Siena, Italy
| | - Donato Nitti
- First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Via Nicolo Giustiniani 2, Padova, Italy
| | - Marco Agostini
- Institute of Paediatric Research-Città della Speranza, Corso Stati Uniti 4, Padova, Italy.,First Surgical Clinic Section, Department of Surgical, Oncological and Gastroenterological Sciences, University of Padua, Via Nicolo Giustiniani 2, Padova, Italy
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6
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Kim S, Ahn SH, Yang HY, Lee JS, Choi HG, Park YK, Lee TH. Modification of cysteine 457 in plakoglobin modulates the proliferation and migration of colorectal cancer cells by altering binding to E-cadherin/catenins. Redox Rep 2016; 22:272-281. [PMID: 27571934 DOI: 10.1080/13510002.2016.1215120] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
OBJECTIVES In tissue samples from patients with colorectal cancer (CRC), oxidation of C420 and C457 of plakoglobin (Pg) within tumor tissue was identified by proteomic analysis. The aim of this study was to identify the roles of Pg C420 and C457. METHODS Human CRC tissues, CRC and breast cancer cells, and normal mouse colon were prepared to validate Pg oxidation. MC38 cells were co-transfected with E-cadherin plus wild type (WT) or mutant (C420S or C457S) Pg to evaluate protein interactions and cellular localization, proliferation, and migration. RESULTS Pg was more oxidized in stage III CRC tumor tissue than in non-tumor tissue. Similar oxidation of Pg was elicited by H2O2 treatment in normal colon and cancer cells. C457S Pg exhibited diminished binding to E-cadherin and α-catenin, and reduced the assembly of E-cadherin-α-/β-catenin complexes. Correspondingly, immunofluorescent analysis of Pg cellular localization suggested impaired binding of C457S Pg to membranes. Cell migration and proliferation were also suppressed in C457S-expressing cells. DISCUSSION Pg appears to be redox-sensitive in cancer, and the C457 modification may impair cell migration and proliferation by affecting its interaction with the E-cadherin/catenin axis. Our findings suggest that redox-sensitive cysteines of Pg may be the targets for CRC therapy.
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Affiliation(s)
- Suhee Kim
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea.,b Department of Molecular Medicine (BK21plus) , Chonnam National University Graduate School , Gwangju , Republic of Korea
| | - Sun Hee Ahn
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea
| | - Hee-Young Yang
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea
| | - Jin-Sil Lee
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea
| | - Hyang-Gi Choi
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea.,b Department of Molecular Medicine (BK21plus) , Chonnam National University Graduate School , Gwangju , Republic of Korea
| | - Young-Kyu Park
- c Department of Surgery , Chonnam National University Hwasun Hospital , Hwasun , Republic of Korea
| | - Tae-Hoon Lee
- a Department of Oral Biochemistry , Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University , Gwangju , Republic of Korea.,b Department of Molecular Medicine (BK21plus) , Chonnam National University Graduate School , Gwangju , Republic of Korea
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7
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Chen Y, Li Y, Zhong J, Zhang J, Chen Z, Yang L, Cao X, He QY, Zhang G, Wang T. Identification of Missing Proteins Defined by Chromosome-Centric Proteome Project in the Cytoplasmic Detergent-Insoluble Proteins. J Proteome Res 2015; 14:3693-709. [DOI: 10.1021/pr501103r] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Yang Chen
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Yaxing Li
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jiayong Zhong
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Jing Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Zhipeng Chen
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Lijuan Yang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Xin Cao
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Qing-Yu He
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Gong Zhang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
| | - Tong Wang
- Key Laboratory of Functional
Protein Research of Guangdong Higher Education Institutes, Institute
of Life and Health Engineering, College of Life Science and Technology, Jinan University, Guangzhou 510632, China
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8
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Quantitative proteomic analysis of paired colorectal cancer and non-tumorigenic tissues reveals signature proteins and perturbed pathways involved in CRC progression and metastasis. J Proteomics 2015; 126:54-67. [PMID: 26054784 DOI: 10.1016/j.jprot.2015.05.037] [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: 02/25/2015] [Revised: 05/18/2015] [Accepted: 05/31/2015] [Indexed: 02/07/2023]
Abstract
Modern proteomics has proven instrumental in our understanding of the molecular deregulations associated with the development and progression of cancer. Herein, we profile membrane-enriched proteome of tumor and adjacent normal tissues from eight CRC patients using label-free nanoLC-MS/MS-based quantitative proteomics and advanced pathway analysis. Of the 948 identified proteins, 184 proteins were differentially expressed (P<0.05, fold change>1.5) between the tumor and non-tumor tissue (69 up-regulated and 115 down-regulated in tumor tissues). The CRC tumor and non-tumor tissues clustered tightly in separate groups using hierarchical cluster analysis of the differentially expressed proteins, indicating a strong CRC-association of this proteome subset. Specifically, cancer associated proteins such as FN1, TNC, DEFA1, ITGB2, MLEC, CDH17, EZR and pathways including actin cytoskeleton and RhoGDI signaling were deregulated. Stage-specific proteome signatures were identified including up-regulated ribosomal proteins and down-regulated annexin proteins in early stage CRC. Finally, EGFR(+) CRC tissues showed an EGFR-dependent down-regulation of cell adhesion molecules, relative to EGFR(-) tissues. Taken together, this study provides a detailed map of the altered proteome and associated protein pathways in CRC, which enhances our mechanistic understanding of CRC biology and opens avenues for a knowledge-driven search for candidate CRC protein markers.
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9
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French CL, Ye F, Revetta F, Zhang B, Coffey RJ, Washington MK, Deane NG, Beauchamp RD, Weaver AM. Linking patient outcome to high throughput protein expression data identifies novel regulators of colorectal adenocarcinoma aggressiveness. F1000Res 2015; 4:99. [PMID: 26097693 PMCID: PMC4457132 DOI: 10.12688/f1000research.6388.1] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 04/22/2015] [Indexed: 12/14/2022] Open
Abstract
A key question in cancer systems biology is how to use molecular data to predict the biological behavior of tumors from individual patients. While genomics data have been heavily used, protein signaling data are more directly connected to biological phenotype and might predict cancer phenotypes such as invasion, metastasis, and patient survival. In this study, we mined publicly available data for colorectal adenocarcinoma from the Cancer Genome Atlas and identified protein expression and signaling changes that are statistically associated with patient outcome. Our analysis identified a number of known and potentially new regulators of colorectal cancer. High levels of insulin growth factor binding protein 2 (IGFBP2) were associated with both recurrence and death, and this was validated by immunohistochemical staining of a tissue microarray for a secondary patient dataset. Interestingly, GATA binding protein 3 (GATA3) was the protein most frequently associated with death in our analysis, and GATA3 expression was significantly decreased in tumor samples from stage I-II deceased patients. Experimental studies using engineered colon cancer cell lines show that exogenous expression of GATA3 decreases three-dimensional colony growth and invasiveness of colon cancer cells but does not affect two-dimensional proliferation. These findings suggest that protein data are useful for biomarker discovery and identify GATA3 as a regulator of colorectal cancer aggressiveness.
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Affiliation(s)
- Christi L French
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA
| | - Fei Ye
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA ; Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Frank Revetta
- Department of Pathology,Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Bing Zhang
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA ; Center for Quantitative Sciences, Vanderbilt University, Nashville, TN, 37232, USA ; Department of Biomedical Informatics, Vanderbilt University Medical Center, Nashville, TN, 37232, USA ; Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
| | - Robert J Coffey
- Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA ; Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, 37232, USA ; Department of Veterans Affairs Medical Center, Nashville, TN, 37232, USA
| | - M Kay Washington
- Department of Pathology,Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | - Natasha G Deane
- Department of Surgery, Vanderbilt University Medical Center, Nashville, TN, 37232, USA
| | | | - Alissa M Weaver
- Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA ; Department of Pathology,Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, 37232, USA ; Department of Cell and Developmental Biology, Vanderbilt University School of Medicine, Nashville, TN, 37232, USA ; Vanderbilt Ingram Cancer Center, Nashville, TN, 37232, USA
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10
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Ahn SH, Yang HY, Tran GB, Kwon J, Son KY, Kim S, Dinh QT, Jung S, Lee HM, Cho KO, Lee TH. Interaction of peroxiredoxin V with dihydrolipoamide branched chain transacylase E2 (DBT) in mouse kidney under hypoxia. Proteome Sci 2015; 13:4. [PMID: 25670924 PMCID: PMC4323032 DOI: 10.1186/s12953-014-0061-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Accepted: 12/23/2014] [Indexed: 11/28/2022] Open
Abstract
Background Peroxiredoxin V (Prdx V) plays a major role in preventing oxidative damage as an effective antioxidant protein within a variety of cells through peroxidase activity. However, the function of Prdx V is not limited to peroxidase enzymatic activity per se. It appears to have unique function in regulating cellular response to external stimuli by directing interaction with signaling protein. In this study, we identified Prdx V interacting partners in mouse kidney under hypoxic stress using immunoprecipitation and shotgun proteomic analysis (LC-MS/MS). Results Immunoprecipitation coupled with nano-UPLC-MSE shotgun proteomics was employed to identify putative interacting partners of Prdx V in mouse kidney in the setting of hypoxia. A total of 17 proteins were identified as potential interacting partners of Prdx V by a comparative interactomics analysis in kidney under normoxia versus hypoxia. Dihydrolipoamide branched chain transacylase E2 (DBT) appeared to be a prominent candidate protein displaying enhanced interaction with Prdx V under hypoxic stress. Moreover, hypoxic kidney exhibited altered DBT enzymatic activity compared to normoxia. An enhanced colocalization of these two proteins under hypoxic stress was successfully observed in vitro. Furthermore, peroxidatic cysteine residue (Cys48) of Prdx V is likely to be responsible for interacting with DBT. Conclusions We identified several proteins interacting with Prdx V under hypoxic condition known to induce renal oxidative stress. In hypoxic condition, we observed an enhanced interaction of Prdx V and DBT protein as well as increased DBT enzymatic activity. The results from this study will contribute to enhance our understanding of Prdx V’s role in hypoxic stress and may suggest new directions for future research. Electronic supplementary material The online version of this article (doi:10.1186/s12953-014-0061-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sun Hee Ahn
- Department of Oral Biochemistry, Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, 300 Yongbong-Dong, Buk-Ku, Gwangju, 500-757 Republic of Korea
| | - Hee-Young Yang
- Department of Oral Biochemistry, Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, 300 Yongbong-Dong, Buk-Ku, Gwangju, 500-757 Republic of Korea
| | - Gia Buu Tran
- Department of Molecular Medicine, Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Joseph Kwon
- Korea Basic Science Institute, Daejeon, Republic of Korea
| | - Kyu-Yeol Son
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Suhee Kim
- Department of Oral Biochemistry, Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, 300 Yongbong-Dong, Buk-Ku, Gwangju, 500-757 Republic of Korea
| | - Quoc Thuong Dinh
- Department of Molecular Medicine, Graduate School, Chonnam National University, Gwangju, Republic of Korea
| | - Seunggon Jung
- Department of Oral and Maxillofacial Surgery, School of Dentistry, Chonnam National University, Gwangju, Republic of Korea
| | - Ha-Mi Lee
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Kyoung-Oh Cho
- Laboratory of Veterinary Pathology, College of Veterinary Medicine, Chonnam National University, Gwangju, Republic of Korea
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Dental Science Research Institute, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University, 300 Yongbong-Dong, Buk-Ku, Gwangju, 500-757 Republic of Korea.,Department of Molecular Medicine, Graduate School, Chonnam National University, Gwangju, Republic of Korea
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11
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UPLC–MSE application in disease biomarker discovery: The discoveries in proteomics to metabolomics. Chem Biol Interact 2014; 215:7-16. [DOI: 10.1016/j.cbi.2014.02.014] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2013] [Revised: 02/14/2014] [Accepted: 02/28/2014] [Indexed: 01/05/2023]
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12
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Álvarez-Chaver P, Otero-Estévez O, Páez de la Cadena M, Rodríguez-Berrocal FJ, Martínez-Zorzano VS. Proteomics for discovery of candidate colorectal cancer biomarkers. World J Gastroenterol 2014; 20:3804-3824. [PMID: 24744574 PMCID: PMC3983438 DOI: 10.3748/wjg.v20.i14.3804] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/25/2013] [Revised: 01/24/2014] [Accepted: 03/10/2014] [Indexed: 02/06/2023] Open
Abstract
Colorectal cancer (CRC) is the second most common cause of cancer-related deaths in Europe and other Western countries, mainly due to the lack of well-validated clinically useful biomarkers with enough sensitivity and specificity to detect this disease at early stages. Although it is well known that the pathogenesis of CRC is a progressive accumulation of mutations in multiple genes, much less is known at the proteome level. Therefore, in the last years many proteomic studies have been conducted to find new candidate protein biomarkers for diagnosis, prognosis and as therapeutic targets for this malignancy, as well as to elucidate the molecular mechanisms of colorectal carcinogenesis. An important advantage of the proteomic approaches is the capacity to look for multiple differentially expressed proteins in a single study. This review provides an overview of the recent reports describing the different proteomic tools used for the discovery of new protein markers for CRC such as two-dimensional electrophoresis methods, quantitative mass spectrometry-based techniques or protein microarrays. Additionally, we will also focus on the diverse biological samples used for CRC biomarker discovery such as tissue, serum and faeces, besides cell lines and murine models, discussing their advantages and disadvantages, and summarize the most frequently identified candidate CRC markers.
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13
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Luo Y, Wang L, Wang J. Developing proteomics-based biomarkers for colorectal neoplasms for clinical practice: opportunities and challenges. Proteomics Clin Appl 2014; 7:30-41. [PMID: 23255431 DOI: 10.1002/prca.201200071] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2012] [Revised: 10/30/2012] [Accepted: 11/20/2012] [Indexed: 12/17/2022]
Abstract
Colorectal cancer (CRC) arises from the normal colon epithelium through the accumulation of genetic mutations and epigenetic alterations that are associated with progression along the histological adenoma-adenocarcinoma sequence. Elucidating the molecular alterations underlying disease progression will not only provide insight into the behavior of the tumors, but also could lead to the discovery of useful biomarkers for diagnosis, monitoring treatment responsiveness, or predicting disease outcomes. In the past a few years, there have been several evaluating differentially expressed protein biomarkers by employing proteomics technologies coupled with mass spectrometry. In the current review, we will briefly summarize the results from selected recent studies using tissue or serum samples from CRC patients in the past 5 years and discuss the opportunities and challenges in translating these findings from the research setting to clinical practice.
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Affiliation(s)
- Yanxin Luo
- Department of Colorectal Surgery, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, PR China
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14
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Martínez-Aguilar J, Chik J, Nicholson J, Semaan C, McKay MJ, Molloy MP. Quantitative mass spectrometry for colorectal cancer proteomics. Proteomics Clin Appl 2014; 7:42-54. [PMID: 23027722 DOI: 10.1002/prca.201200080] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2012] [Revised: 09/05/2012] [Accepted: 09/12/2012] [Indexed: 12/15/2022]
Abstract
This review documents the uses of quantitative MS applied to colorectal cancer (CRC) proteomics for biomarker discovery and molecular pathway profiling. Investigators are adopting various labeling and label-free MS approaches to quantitate differential protein levels in cells, tumors, and plasma/serum. We comprehensively review recent uses of this technology to examine mouse models of CRC, CRC cell lines, their secretomes and subcellular fractions, CRC tumors, CRC patient plasma/serum, and stool samples. For biomarker discovery these approaches are uncovering proteins with potential diagnostic and prognostic utility, while in vitro cell culture experiments are characterizing proteomic and phosphoproteomic responses to disrupted signaling pathways due to mutations or to inhibition of drugable enzymes.
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Affiliation(s)
- Juan Martínez-Aguilar
- Australian Proteome Analysis Facility (APAF), Department of Chemistry & Biomolecular Sciences, Macquarie University, Sydney, Australia
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Megger DA, Bracht T, Meyer HE, Sitek B. Label-free quantification in clinical proteomics. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2013; 1834:1581-90. [DOI: 10.1016/j.bbapap.2013.04.001] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2012] [Revised: 03/26/2013] [Accepted: 04/01/2013] [Indexed: 12/31/2022]
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Yang HY, Chay KO, Kwon J, Kwon SO, Park YK, Lee TH. Comparative proteomic analysis of cysteine oxidation in colorectal cancer patients. Mol Cells 2013; 35:533-42. [PMID: 23677378 PMCID: PMC3887873 DOI: 10.1007/s10059-013-0058-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 04/09/2013] [Accepted: 04/10/2013] [Indexed: 12/30/2022] Open
Abstract
Oxidative stress promotes damage to cellular proteins, lipids, membranes and DNA, and plays a key role in the development of cancer. Reactive oxygen species disrupt redox homeostasis and promote tumor formation by initiating aberrant activation of signaling pathways that lead to tumorigenesis. We used shotgun proteomics to identify proteins containing oxidation-sensitive cysteines in tissue specimens from colorectal cancer patients. We then compared the patterns of cysteine oxidation in the membrane fractions between the tumor and non-tumor tissues. Using nano-UPLC-MS(E) proteomics, we identified 31 proteins containing 37 oxidation-sensitive cysteines. These proteins were observed with IAM-binding cysteines in non-tumoral region more than tumoral region of CRC patients. Then using the Ingenuity pathway program, we evaluated the cellular canonical networks connecting those proteins. Within the networks, proteins with multiple connections were related with organ morphology, cellular metabolism, and various disorders. We have thus identified networks of proteins whose redox status is altered by oxidative stress, perhaps leading to changes in cellular functionality that promotes tumorigenesis.
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Affiliation(s)
- Hee-Young Yang
- Department of Oral Biochemistry, Dental Science Research Institute and the Brain Korea 21 Project, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University
| | - Kee-Oh Chay
- Department of Biochemistry, Chonnam National University Medical School
| | - Joseph Kwon
- Korea Basic Science Institute, Gwangju 500-757,
Korea
| | - Sang-Oh Kwon
- Division of Life Science, Korea Basic Science Institute, Daejeon 305-806,
Korea
| | - Young-Kyu Park
- Department of Surgery, Chonnam National University Hwasun Hospital, Hwasun 519-763,
Korea
| | - Tae-Hoon Lee
- Department of Oral Biochemistry, Dental Science Research Institute and the Brain Korea 21 Project, Medical Research Center for Biomineralization Disorders, School of Dentistry, Chonnam National University
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de Wit M, Fijneman RJ, Verheul HM, Meijer GA, Jimenez CR. Proteomics in colorectal cancer translational research: Biomarker discovery for clinical applications. Clin Biochem 2013; 46:466-79. [DOI: 10.1016/j.clinbiochem.2012.10.039] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2012] [Revised: 10/30/2012] [Accepted: 10/31/2012] [Indexed: 12/22/2022]
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18
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