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Duan Y, Yu J, Chen M, Lu Q, Ning F, Gan X, Liu H, Ye Y, Lu S, Lash GE. Knockdown of heat shock protein family D member 1 (HSPD1) promotes proliferation and migration of ovarian cancer cells via disrupting the stability of mitochondrial 3-oxoacyl-ACP synthase (OXSM). J Ovarian Res 2023; 16:81. [PMID: 37087461 PMCID: PMC10122320 DOI: 10.1186/s13048-023-01156-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 04/06/2023] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Heat shock protein 60 (HSP60) is essential for the folding and assembly of newly imported proteins to the mitochondria. HSP60 is overexpressed in most types of cancer, but its association with ovarian cancer is still in dispute. SKOV3 and OVCAR3 were used as experimental models after comparing the expression level of mitochondrial HSP60 in a normal human ovarian epithelial cell line and four ovarian cancer cell lines. RESULTS Low HSPD1 (Heat Shock Protein Family D (HSP60) Member 1) expression was associated with unfavorable prognosis in ovarian cancer patients. Knockdown of HSPD1 significantly promoted the proliferation and migration of ovarian cancer cells. The differentially expressed proteins after HSPD1 knockdown were enriched in the lipoic acid (LA) biosynthesis and metabolism pathway, in which mitochondrial 3-oxoacyl-ACP synthase (OXSM) was the most downregulated protein and responsible for lipoic acid synthesis. HSP60 interacted with OXSM and overexpression of OXSM or LA treatment could reverse proliferation promotion mediated by HSPD1 knockdown. CONCLUSIONS HSP60 interacted with OXSM and maintained its stability. Knockdown of HSPD1 could promote the proliferation and migration of SKOV3 and OVCAR3 via lowering the protein level of OXSM and LA synthesis.
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Affiliation(s)
- Yaoyun Duan
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Juan Yu
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Miaojuan Chen
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Qinsheng Lu
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Fen Ning
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Xiaowen Gan
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Hanbo Liu
- School of Medicine, South China University of Technology, Guangzhou, China
| | - Yixin Ye
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Shenjiao Lu
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China
| | - Gendie E Lash
- Division of Uterine Vascular Biology, Guangdong Provincial Clinical Research Center for Child Health, Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, 510623, Guangzhou, China.
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Dressler FF, Brägelmann J, Reischl M, Perner S. Normics: Proteomic Normalization by Variance and Data-Inherent Correlation Structure. Mol Cell Proteomics 2022; 21:100269. [PMID: 35853575 PMCID: PMC9450154 DOI: 10.1016/j.mcpro.2022.100269] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2021] [Revised: 06/16/2022] [Accepted: 07/13/2022] [Indexed: 11/17/2022] Open
Abstract
Several algorithms for the normalization of proteomic data are currently available, each based on a priori assumptions. Among these is the extent to which differential expression (DE) can be present in the dataset. This factor is usually unknown in explorative biomarker screens. Simultaneously, the increasing depth of proteomic analyses often requires the selection of subsets with a high probability of being DE to obtain meaningful results in downstream bioinformatical analyses. Based on the relationship of technical variation and (true) biological DE of an unknown share of proteins, we propose the “Normics” algorithm: Proteins are ranked based on their expression level–corrected variance and the mean correlation with all other proteins. The latter serves as a novel indicator of the non-DE likelihood of a protein in a given dataset. Subsequent normalization is based on a subset of non-DE proteins only. No a priori information such as batch, clinical, or replicate group is necessary. Simulation data demonstrated robust and superior performance across a wide range of stochastically chosen parameters. Five publicly available spike-in and biologically variant datasets were reliably and quantitively accurately normalized by Normics with improved performance compared to standard variance stabilization as well as median, quantile, and LOESS normalizations. In complex biological datasets Normics correctly determined proteins as being DE that had been cross-validated by an independent transcriptome analysis of the same samples. In both complex datasets Normics identified the most DE proteins. We demonstrate that combining variance analysis and data-inherent correlation structure to identify non-DE proteins improves data normalization. Standard normalization algorithms can be consolidated against high shares of (one-sided) biological regulation. The statistical power of downstream analyses can be increased by focusing on Normics-selected subsets of high DE likelihood. Normics is a tool for the normalization of proteomic data based on existing algorithms. Specifically addresses data with high shares of differential expression. Combines variance and data-inherent correlation structure. Provides a ranking of differential expression likelihood. Enables normalization based on the most stable proteins.
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Affiliation(s)
- Franz F Dressler
- Institute of Pathology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany; Institute of Pathology, University Medical Center Schleswig-Holstein, Luebeck Site, Luebeck, Germany.
| | - Johannes Brägelmann
- Mildred Scheel School of Oncology, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Department of Translational Genomics, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany; Center for Molecular Medicine Cologne, University of Cologne, Faculty of Medicine and University Hospital Cologne, Cologne, Germany
| | - Markus Reischl
- Institute for Automation and Applied Informatics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Sven Perner
- Institute of Pathology, University Medical Center Schleswig-Holstein, Luebeck Site, Luebeck, Germany; Institute of Pathology, Research Center Borstel, Leibniz Lung Center, Borstel, Germany
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Schöttl T, Pachl F, Giesbertz P, Daniel H, Kuster B, Fromme T, Klingenspor M. Proteomic and Metabolite Profiling Reveals Profound Structural and Metabolic Reorganization of Adipocyte Mitochondria in Obesity. Obesity (Silver Spring) 2020; 28:590-600. [PMID: 32034895 DOI: 10.1002/oby.22737] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2019] [Accepted: 11/26/2019] [Indexed: 01/08/2023]
Abstract
OBJECTIVE Previous studies have revealed decreased mitochondrial respiration in adipocytes of obese mice. This study aimed to identify the molecular underpinnings of altered mitochondrial metabolism in adipocytes. METHODS Untargeted proteomics of mitochondria isolated from adipocytes and metabolite profiling of adipose tissues were conducted in diet-induced obese (DIO) and lean mice. Subcutaneous and intra-abdominal adipose tissues were studied to depict depot-specific alterations. RESULTS In subcutaneous adipocytes of DIO mice, changes in proteins related to mitochondrial structure and function were observed. Mitochondrial proteins of the inner and outer membrane were strongly reduced, whereas proteins of key matrix metabolic pathways were increased in the obese versus lean state, as further substantiated by metabolite profiling. A pronounced decrease in the oxidative phosphorylation (OXPHOS) enzymatic equipment and cristae density of the inner membrane was identified. In intra-abdominal adipocytes, similar systematic downregulation of the OXPHOS machinery in obesity occurred, but there was no regulation of outer membrane or matrix proteins. CONCLUSIONS Protein components of the OXPHOS machinery are systematically downregulated in adipose tissues of DIO mice compared with lean mice. Loss of the mitochondrial OXPHOS capacity in adipocytes may aggravate the development of metabolic disease.
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Affiliation(s)
- Theresa Schöttl
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- EKFZ-Else Kröner Fresenius Zentrum for Nutritional Medicine, Technical Universtiy of Munich, Freising, Germany
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Fiona Pachl
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Pieter Giesbertz
- Chair of Nutritional Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Hannelore Daniel
- Chair of Nutritional Physiology, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Bernhard Kuster
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
- Chair of Proteomics and Bioanalytics, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
| | - Tobias Fromme
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- EKFZ-Else Kröner Fresenius Zentrum for Nutritional Medicine, Technical Universtiy of Munich, Freising, Germany
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Martin Klingenspor
- Chair of Molecular Nutritional Medicine, TUM School of Life Sciences Weihenstephan, Technical University of Munich, Freising, Germany
- EKFZ-Else Kröner Fresenius Zentrum for Nutritional Medicine, Technical Universtiy of Munich, Freising, Germany
- ZIEL-Institute for Food & Health, Technical University of Munich, Freising, Germany
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Huang YH, Lin KH, Yu JS, Wu TJ, Lee WC, Chao CCK, Pan TL, Yeh CT. Targeting HSP60 by subcutaneous injections of jetPEI/HSP60-shRNA destabilizes cytoplasmic survivin and inhibits hepatocellular carcinoma growth. Mol Carcinog 2018; 57:1087-1101. [PMID: 29672920 DOI: 10.1002/mc.22827] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Revised: 03/28/2018] [Accepted: 04/17/2018] [Indexed: 01/14/2023]
Abstract
Heat shock protein 60 (HSP60) overexpresses in various types of cancer, but its expression levels and functions in hepatocellular carcinoma (HCC) are still in dispute. We aim to clarify this issue and examine whether HSP60 could be a therapeutic target for HCC. We found drastically enhanced cell apoptosis and suppressed cell proliferation in two HCC cell lines with HSP60-silencing, and also indicated survivin was involved in this regulatory process in vitro and in vivo. However, HSP60-silencing in normal human hepatocytes only resulted in a minimal reduction of cell proliferation but without effects on cell apoptosis. We also showed HSP60 interacted with cytosolic but not mitochondrial survivin by immunoprecipitation assay. A rigorous method was used to standardize quantification from immunoblot assay to obtain more precise expression levels of HSP60 and survivin. The expression of HSP60 and survivin positively correlated in both cancerous and non-cancerous liver tissues (P < 0.001) after analyzing 145 surgically removed HCC tissues. A total of 56.6% of HCC patients overexpressed HSP60 in cancerous tissues, and 40.0% under-expressed HSP60. Higher expression of HSP60 and survivin in non-cancerous tissues both correlated with shorter overall survival (P = 0.029 and P < 0.001, respectively). Finally, we evaluated the therapeutic potential of HSP60 using extraneous delivery of jetPEI/shHSP60 complexes. The treatment results showed significant reduction of tumor weight by 44.3% (P < 0.05), accompanied by under-expression of survivin. These studies suggested that HSP60 not only served as a prognostic marker but also served as a novel therapeutic target for HCC.
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Affiliation(s)
- Ya-Hui Huang
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan
| | - Kwang-Huei Lin
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Jau-Song Yu
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang-Gung University, Taoyuan, Taiwan
| | - Ting-Jung Wu
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Division of Liver and Transplantation Surgery, Department of General Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Wei-Chen Lee
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Division of Liver and Transplantation Surgery, Department of General Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Chuck C-K Chao
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan
| | - Tai-Long Pan
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,School of Traditional Chinese Medicine, Chang-Gung University, Taoyuan, Taiwan.,Research Center of Industry of Human Ecology, Chang-Gung University of Science and Technology, Taoyuan, Taiwan
| | - Chau-Ting Yeh
- Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan, Taiwan.,Department of Biochemistry, College of Medicine, Chang-Gung University, Taoyuan, Taiwan.,Molecular Medicine Research Center, Chang-Gung University, Taoyuan, Taiwan
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5
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Moritz CP. Tubulin or Not Tubulin: Heading Toward Total Protein Staining as Loading Control in Western Blots. Proteomics 2018; 17. [PMID: 28941183 DOI: 10.1002/pmic.201600189] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 09/13/2017] [Indexed: 12/30/2022]
Abstract
Western blotting is an analytical method widely used for detecting and (semi-)quantifying specific proteins in given samples. Western blots are continuously applied and developed by the protein community. This review article focuses on a significant, but not yet well-established, improvement concerning the internal loading control as a prerequisite to accurately quantifying Western blots. Currently, housekeeping proteins (HKPs) like actin, tubulin, or GAPDH are often used to check for equal loading or to compensate potential loading differences. However, this loading control has multiple drawbacks. Staining of the total protein on the blotting membrane has emerged as a better loading control. Total protein staining (TPS) represents the actual loading amount more accurately than HKPs due to minor technical and biological variation. Further, the broad dynamic range of TPS solves the issue of HKPs that commonly fail to show loading differences above small loading amounts of 0.5-10 μg. Although these and further significant advantages have been demonstrated over the past 10 years, only a small percentage of laboratories take advantage of it. The objective of this review article is to collect and compare information about TPS options and to invite users to reconsider their applied loading control. Nine benefits of TPS are discussed and seven different variants are critically evaluated by comparing technical details. Consequently, this review article offers an orientation in selecting the appropriate staining type. I conclude that TPS should be the preferred loading control in future Western blot approaches.
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Affiliation(s)
- Christian P Moritz
- Synaptopathies and Autoantibodies, Faculty of Medicine, University Jean Monnet, Saint-Étienne, France.,Institut NeuroMyoGène, Team Synaptopathies and Autoantibodies, Lyon/Saint-Étienne, France
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6
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Lee W, Lazar IM. Endogenous Protein “Barcode” for Data Validation and Normalization in Quantitative MS Analysis. Anal Chem 2014; 86:6379-86. [DOI: 10.1021/ac500855q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wooram Lee
- Department of Biological
Sciences, Virginia Polytechnic Institute and State University, 1981 Kraft Drive, Blacksburg, Virginia 24061, United States
| | - Iulia M. Lazar
- Department of Biological
Sciences, Virginia Polytechnic Institute and State University, 1981 Kraft Drive, Blacksburg, Virginia 24061, United States
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Wang T, Lee H, Hwang J, Oh J, Lim J, Kang H, Joo J, Lee K. Myoglobin: A promising exogenous reference marker using in proteomics analysis. Food Sci Biotechnol 2013. [DOI: 10.1007/s10068-013-0092-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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8
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Lanoix D, St-Pierre J, Lacasse AA, Viau M, Lafond J, Vaillancourt C. Stability of reference proteins in human placenta: General protein stains are the benchmark. Placenta 2012; 33:151-6. [DOI: 10.1016/j.placenta.2011.12.008] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2011] [Revised: 12/08/2011] [Accepted: 12/09/2011] [Indexed: 11/16/2022]
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Pérez-Pérez R, López JA, García-Santos E, Camafeita E, Gómez-Serrano M, Ortega-Delgado FJ, Ricart W, Fernández-Real JM, Peral B. Uncovering suitable reference proteins for expression studies in human adipose tissue with relevance to obesity. PLoS One 2012; 7:e30326. [PMID: 22272336 PMCID: PMC3260266 DOI: 10.1371/journal.pone.0030326] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 12/19/2011] [Indexed: 12/29/2022] Open
Abstract
Background Protein expression studies based on the two major intra-abdominal human fat depots, the subcutaneous and the omental fat, can shed light into the mechanisms involved in obesity and its co-morbidities. Here we address, for the first time, the identification and validation of reference proteins for data standardization, which are essential for accurate comparison of protein levels in expression studies based on fat from obese and non-obese individuals. Methodology and Findings To uncover adipose tissue proteins equally expressed either in omental and subcutaneous fat depots (study 1) or in omental fat from non-obese and obese individuals (study 2), we have reanalyzed our previously published data based on two-dimensional fluorescence difference gel electrophoresis. Twenty-four proteins (12 in study 1 and 12 in study 2) with similar expression levels in all conditions tested were selected and identified by mass spectrometry. Immunoblotting analysis was used to confirm in adipose tissue the expression pattern of the potential reference proteins and three proteins were validated: PARK7, ENOA and FAA. Western Blot analysis was also used to test customary loading control proteins. ENOA, PARK7 and the customary loading control protein Beta-actin showed steady expression profiles in fat from non-obese and obese individuals, whilst FAA maintained steady expression levels across paired omental and subcutaneous fat samples. Conclusions ENOA, PARK7 and Beta-actin are proper reference standards in obesity studies based on omental fat, whilst FAA is the best loading control for the comparative analysis of omental and subcutaneous adipose tissues either in obese and non-obese subjects. Neither customary loading control proteins GAPDH and TBB5 nor CALX are adequate standards in differential expression studies on adipose tissue. The use of the proposed reference proteins will facilitate the adequate analysis of proteins differentially expressed in the context of obesity, an aim difficult to achieve before this study.
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Affiliation(s)
- Rafael Pérez-Pérez
- Instituto de Investigaciones Biomédicas, Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
| | - Juan A. López
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Eva García-Santos
- Instituto de Investigaciones Biomédicas, Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
| | - Emilio Camafeita
- Unidad de Proteómica, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - María Gómez-Serrano
- Instituto de Investigaciones Biomédicas, Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
| | - Francisco J. Ortega-Delgado
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
- Department of Diabetes, Endocrinology and Nutrition, Hospital Dr. Josep Trueta, Girona, Spain
| | - Wifredo Ricart
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
- Department of Diabetes, Endocrinology and Nutrition, Hospital Dr. Josep Trueta, Girona, Spain
| | - José M. Fernández-Real
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
- Department of Diabetes, Endocrinology and Nutrition, Hospital Dr. Josep Trueta, Girona, Spain
| | - Belén Peral
- Instituto de Investigaciones Biomédicas, Alberto Sols, Consejo Superior de Investigaciones Científicas (CSIC) & Universidad Autónoma de Madrid (UAM), Madrid, Spain
- CIBER Fisiopatología de la Obesidad y Nutrición (CIBERobn), ISCIII, Madrid, Spain
- * E-mail:
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Wong KF, Luk JM. Discovery of lamin B1 and vimentin as circulating biomarkers for early hepatocellular carcinoma. Methods Mol Biol 2012; 909:295-310. [PMID: 22903723 DOI: 10.1007/978-1-61779-959-4_19] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The recent advancements in proteomic technologies have reconstituted our research strategies over different type of liver diseases including hepatocellular carcinoma (HCC). Combined analyses on HCC proteome and clinicopathological data of patients have allowed identification of many promising biomarkers that can be further developed into noninvasive diagnostic assays for cancer surveillance. Capitalizing our established proteomic platform primarily based on two-dimensional polyacrylamide gel electrophoresis (2DE) and MALDI-TOF/TOF mass spectrometry, our groups have identified lamin B1 (LMNB1) and vimentin (VIM) as promising biomarkers for detection of early HCC. Protein levels of both biomarkers were significantly elevated in cancerous tissues when compared to the controls in disease-free and cirrhotic liver subjects. Further investigation of the circulating LMNB1 mRNA level in patients' blood samples by standard PCR showed 76% sensitivity and 82% specificity for detection of early HCC. In parallel, an ELISA assay for measuring circulating vimentin level in patients' serum samples could detect small HCC at 40.91% sensitivity and 87.5% specificity. The candidate biomarkers were evaluated with the diagnostic performance of α-fetoprotein (AFP) for HCC. In this article, we address the current protocols for HCC biomarker discovery, ranging from clinical sample preparation, 2DE proteomic profiling and informatics analysis, and assay development and clinical validation study. Focus is emphasized on the methods for sample preservation and low-abundance protein enrichment.
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Affiliation(s)
- Kwong-Fai Wong
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore
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Li X, Bai H, Wang X, Li L, Cao Y, Wei J, Liu Y, Liu L, Gong X, Wu L, Liu S, Liu G. Identification and validation of rice reference proteins for western blotting. JOURNAL OF EXPERIMENTAL BOTANY 2011; 62:4763-72. [PMID: 21705388 PMCID: PMC3192993 DOI: 10.1093/jxb/err084] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Studies of rice protein expression have increased considerably with the development of rice functional genomics. In order to obtain reliable expression results in western blotting, information on appropriate reference proteins is necessary for data normalization. To date, no published study has identified and systematically validated reference proteins suitable for the investigation of rice protein expression. In this study, nine candidate proteins were selected and their specific antibodies were obtained through immunization of rabbits with either recombinant proteins expressed in Escherichia coli or synthesized peptides. Western blotting was carried out to detect the expression of target proteins in a set of 10 rice samples representing different rice tissues/organs at different developmental stages. The expression stability of the proteins was analysed using geNorm and Microcal Origin 6.0 software. The results indicated that heat shock protein (HSP) and elongation factor 1-α (eEF-1α) were the most constantly expressed among all rice proteins tested throughout all developmental stages, while the proteins encoded by conventional internal reference genes fluctuated in amount. Comparison among the profiling of translation and transcription [expressed sequence tags (EST) and massively parallel signature sequencing (MPSS)] revealed that a correlation existed. Based on the standard curves derived from the antigen-antibody reaction, the concentrations of HSP and eEF-1α proteins in rice leaves were ∼0.12%. Under the present experimental conditions, the lower limits of detection for HSP and eEF-1α proteins in rice were 0.24 ng and 0.06 ng, respectively. In conclusion, the reference proteins selected in this study, and the corresponding antibodies, can be used in qualitative and quantitative analysis of rice proteins.
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Affiliation(s)
- Xiaoming Li
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Hui Bai
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101318, China
| | - Xianyun Wang
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Liyun Li
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Yinghao Cao
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Jian Wei
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Yumeng Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Lijuan Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Xiaodong Gong
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
| | - Lin Wu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101318, China
| | - Siqi Liu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, 101318, China
| | - Guozhen Liu
- College of Life Sciences, Agricultural University of Hebei, Baoding, 071001, China
- To whom correspondence should be addressed. E-mail:
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Albrethsen J, Miller LM, Novikoff PM, Angeletti RH. Gel-based proteomics of liver cancer progression in rat. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:1367-76. [DOI: 10.1016/j.bbapap.2011.05.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2011] [Revised: 05/26/2011] [Accepted: 05/26/2011] [Indexed: 02/08/2023]
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Giusti L, Cetani F, Ciregia F, Da Valle Y, Donadio E, Giannaccini G, Banti C, Pardi E, Saponaro F, Basolo F, Berti P, Miccoli P, Pinchera A, Marcocci C, Lucacchini A. A proteomic approach to study parathyroid glands. MOLECULAR BIOSYSTEMS 2010; 7:687-99. [PMID: 21180715 DOI: 10.1039/c0mb00191k] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Parathyroid tumours are heterogeneous and in some cases the diagnosis may be difficult using histological features. In this study we used a two-dimensional electrophoresis (2D)/mass spectrometry (MS)-based approach to examine the global changes of parathyroid adenoma tissues protein profile compared to the parathyroid normal tissues. Validation of protein expression was performed by immunoblotting using specific antibodies. Ingenuity software was used to identify the biological processes to which these proteins belong and to construct a potential network. A total of 30 proteins were found to be differentially expressed, of which 22 resulted in being over-expressed. Proteins identified by 2D/MS/MS proteomics were classified into functional categories and a major change (≥ 2-fold) in terms of expression was found in proteins involved in response to biotic stimuli, cell organization and signal transduction. After Ingenuity analysis, 14-3-3 ζ/δ appears to be a key protein in the network of parathyroid adenoma, where it is linked to other proteins such as annexin A2, B box and SPRY domain-containing protein (BSPRY), p53 and epidermal growth factor receptor (EGFR). Our results suggest that the proteomic approach was able to differentiate the protein profiles of normal parathyroid and parathyroid adenoma and identify a panel of proteins which are differentially expressed. The functional role of these proteins in the network of intracellular pathways is discussed.
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Affiliation(s)
- Laura Giusti
- Department of Psychiatry, Neurobiology, Pharmacology and Biotechnology, Via, Bonanno 6, 56126 Pisa, Italy
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14
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Sun S, Poon RTP, Lee NP, Yeung C, Chan KL, Ng IOL, Day PJR, Luk JM. Proteomics of hepatocellular carcinoma: serum vimentin as a surrogate marker for small tumors (<or=2 cm). J Proteome Res 2010; 9:1923-30. [PMID: 20121168 DOI: 10.1021/pr901085z] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Small hepatocellular carcinomas (HCCs) can be effectively cured by surgery with good clinical outcomes. However, the conventional AFP marker is ineffective in detecting small tumors. Here we employed a proteomic profiling approach to identify a candidate marker for HCC (<or=2 cm) in tumor tissues and then evaluate its clinical feasibility in patients' sera. The study was divided into 2 phases. (i) Biomarker discovery: we collected 76 frozen liver tissues (40 HCC and 36 controls) for proteomics profiling. Candidate protein markers were identified by MALDI-TOF/TOF and confirmed by immunoblot and qPCR. (ii) Clinical evaluation: Selected biomarker was tested by ELISA for sensitivity and specificity using serum samples from a separate cohort of 152 subjects (88 HCC and 64 controls). Vimentin was found significantly overexpressed in HCC, in particular the small-size subgroup (<or=2 cm) with p < 0.01. When tested in the serum samples, vimentin level was significantly higher in small tumors than the non-neoplastic controls (AUC = 0.69 and p < 0.01). Further analysis suggested that elevated circulating vimentin level could detect small HCC at 40.91% sensitivity and 87.50% specificity. Moreover, vimentin was found to be superior to serum AFP assayed at different cut-offs in detecting small tumors. When combined with AFP, the detection sensitivity and specificity could be further enhanced to 58.77 and 98.15%, respectively. In conclusion, serum vimentin is a potential surrogate marker, either alone or in combination with AFP, for detection of small HCCs.
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Affiliation(s)
- Stella Sun
- Department of Surgery, University of Hong Kong, Hong Kong, China
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15
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Zhao Y, Ben H, Qu S, Zhou X, Yan L, Xu B, Zhou S, Lou Q, Ye R, Zhou T, Yang P, Qu D. Proteomic analysis of primary duck hepatocytes infected with duck hepatitis B virus. Proteome Sci 2010; 8:28. [PMID: 20529248 PMCID: PMC2904733 DOI: 10.1186/1477-5956-8-28] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Accepted: 06/07/2010] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) is a major cause of liver infection in human. Because of the lack of an appropriate cell culture system for supporting HBV infection efficiently, the cellular and molecular mechanisms of hepadnavirus infection remain incompletely understood. Duck heptatitis B virus (DHBV) can naturally infect primary duck hepatocytes (PDHs) that provide valuable model systems for studying hepadnavirus infection in vitro. In this report, we explored global changes in cellular protein expression in DHBV infected PDHs by two-dimension gel electrophoresis (2-DE) combined with MALDI-TOF/TOF tandem mass spectrometry (MS/MS). RESULTS The effects of hepadnavirus infection on hepatocytes were investigated in DHBV infected PDHs by the 2-DE analysis. Proteomic profile of PDHs infected with DHBV were analyzed at 24, 72 and 120 h post-infection by comparing with uninfected PDHs, and 75 differentially expressed protein spots were revealed by 2-DE analysis. Among the selected protein spots, 51 spots were identified corresponding to 42 proteins by MS/MS analysis; most of them were matched to orthologous proteins of Gallus gallus, Anas platyrhynchos or other avian species, including alpha-enolase, lamin A, aconitase 2, cofilin-2 and annexin A2, etc. The down-regulated expression of beta-actin and annexin A2 was confirmed by Western blot analysis, and potential roles of some differentially expressed proteins in the virus-infected cells have been discussed. CONCLUSIONS Differentially expressed proteins of DHBV infected PDHs revealed by 2-DE, are involved in carbohydrate metabolism, amino acid metabolism, stress responses and cytoskeleton processes etc, providing the insight to understanding of interactions between hepadnavirus and hepatocytes and molecular mechanisms of hepadnavirus pathogenesis.
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Affiliation(s)
- Yanfeng Zhao
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Haijing Ben
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Su Qu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Xinwen Zhou
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Liang Yan
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Bin Xu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Shuangcheng Zhou
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Qiang Lou
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Rong Ye
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Tianlun Zhou
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
| | - Pengyuan Yang
- Department of Chemistry, Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Di Qu
- Key Laboratory of Medical Molecular Virology of Ministries of Education and Health, Institute of Medical Microbiology and Institutes of Biomedical Sciences, Shanghai Medical College of Fudan University, Shanghai, China
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