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Steiner C, Lescuyer P, Cutler P, Tille JC, Ducret A. Relative Quantification of Proteins in Formalin-Fixed Paraffin-Embedded Breast Cancer Tissue Using Multiplexed Mass Spectrometry Assays. Mol Cell Proteomics 2022; 21:100416. [PMID: 36152753 PMCID: PMC9638817 DOI: 10.1016/j.mcpro.2022.100416] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 09/15/2022] [Accepted: 09/17/2022] [Indexed: 01/18/2023] Open
Abstract
The identification of clinically relevant biomarkers represents an important challenge in oncology. This problem can be addressed with biomarker discovery and verification studies performed directly in tumor samples using formalin-fixed paraffin-embedded (FFPE) tissues. However, reliably measuring proteins in FFPE samples remains challenging. Here, we demonstrate the use of liquid chromatography coupled to multiple reaction monitoring mass spectrometry (LC-MRM/MS) as an effective technique for such applications. An LC-MRM/MS method was developed to simultaneously quantify hundreds of peptides extracted from FFPE samples and was applied to the targeted measurement of 200 proteins in 48 triple-negative, 19 HER2-overexpressing, and 20 luminal A breast tumors. Quantitative information was obtained for 185 proteins, including known markers of breast cancer such as HER2, hormone receptors, Ki-67, or inflammation-related proteins. LC-MRM/MS results for these proteins matched immunohistochemistry or chromogenic in situ hybridization data. In addition, comparison of our results with data from the literature showed that several proteins representing potential biomarkers were identified as differentially expressed in triple-negative breast cancer samples. These results indicate that LC-MRM/MS assays can reliably measure large sets of proteins using the analysis of surrogate peptides extracted from FFPE samples. This approach allows to simultaneously quantify the expression of target proteins from various pathways in tumor samples. LC-MRM/MS is thus a powerful tool for the relative quantification of proteins in FFPE tissues and for biomarker discovery.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland,BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland,For correspondence: Carine Steiner
| | - Pierre Lescuyer
- Division of Laboratory Medicine, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland,Department of Medical Specialties, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Paul Cutler
- BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland
| | - Jean-Christophe Tille
- Division of Clinical Pathology, Diagnostic Department, Geneva University Hospitals, Geneva, Switzerland
| | - Axel Ducret
- BiOmics and Pathology, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, Switzerland
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2
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García-Vence M, Chantada-Vazquez MDP, Sosa-Fajardo A, Agra R, Barcia de la Iglesia A, Otero-Glez A, García-González M, Cameselle-Teijeiro JM, Nuñez C, Bravo JJ, Bravo SB. Protein Extraction From FFPE Kidney Tissue Samples: A Review of the Literature and Characterization of Techniques. Front Med (Lausanne) 2021; 8:657313. [PMID: 34055835 PMCID: PMC8158658 DOI: 10.3389/fmed.2021.657313] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 04/01/2021] [Indexed: 12/15/2022] Open
Abstract
Most tissue biopsies from patients in hospital environments are formalin-fixed and paraffin-embedded (FFPE) for long-term storage. This fixation process produces a modification in the proteins called “crosslinks”, which improves protein stability necessary for their conservation. Currently, these samples are mainly used in clinical practice for performing immunohistochemical analysis, since these modifications do not suppose a drawback for this technique; however, crosslinks difficult the protein extraction process. Accordingly, these modifications make the development of a good protein extraction protocol necessary. Due to the specific characteristics of each tissue, the same extraction buffers or deparaffinization protocols are not equally effective in all cases. Therefore, it is necessary to obtain a specific protocol for each tissue. The present work aims to establish a deparaffinization and protein extraction protocol from FFPE kidney samples to obtain protein enough of high quality for the subsequent proteomic analysis. Different deparaffination, protocols and protein extraction buffers will be tested in FFPE kidney samples. The optimized conditions will be applied in the identification by LC-MS/MS analysis of proteins extracted from 5, 10, and 15 glomeruli obtained through the microdissection of FFPE renal samples.
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Affiliation(s)
- Maria García-Vence
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Maria Del Pilar Chantada-Vazquez
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain.,Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain
| | - Ana Sosa-Fajardo
- Research Group of Industrial Microbiology and Food Biotechnology (IMDO), Vrije Universiteit, Brussels, Belgium
| | - Rebeca Agra
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Ana Barcia de la Iglesia
- Nephrology Laboratory, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - Alfonso Otero-Glez
- Nephrology Service, University Clinical Hospital of Ourense (CHOU), Orense, Spain
| | - Miguel García-González
- Nephrology Laboratory, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
| | - José M Cameselle-Teijeiro
- Department of Pathology, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Santiago, Spain
| | - Cristina Nuñez
- Research Unit, Lucus Augusti University Hospital (HULA), Servizo Galego de Saúde (SERGAS), Lugo, Spain
| | - Juan J Bravo
- Nephrology Service, University Clinical Hospital of Vigo (Alvaro Cunqueiro-CHUVI), Vigo, Spain
| | - Susana B Bravo
- Proteomic Unit, Health Research Institute of Santiago de Compostela (IDIS), University Clinical Hospital of Santiago de Compostela (CHUS), Santiago de Compostela, Spain
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3
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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4
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Steiner C, Lescuyer P, Tille JC, Cutler P, Ducret A. Development of a Highly Multiplexed SRM Assay for Biomarker Discovery in Formalin-Fixed Paraffin-Embedded Tissues. Methods Mol Biol 2019; 1959:185-203. [PMID: 30852824 DOI: 10.1007/978-1-4939-9164-8_13] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The search for novel and clinically relevant biomarkers still represents a major clinical challenge and mass-spectrometry-based technologies are essential tools to help in this process. In this application, we demonstrate how selected reaction monitoring (SRM) can be applied in a highly multiplexed way to analyze formalin-fixed paraffin-embedded (FFPE) tissues. Such an assay can be used to analyze numerous samples for narrowing down a list of potential biomarkers to the most relevant candidates. The use of FFPE tissues is of high relevance in this context as large sample collections linked with valuable clinical information are available in hospitals around the world. Here we describe in detail how we proceeded to develop such an assay for 200 proteins in breast tumor FFPE tissues. We cover the selection of suitable peptides, which are different in FFPE compared to fresh frozen tissues and show how we deliberately biased our assay toward proteins with a high probability of being measurable in human clinical samples.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland.
- Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland.
- Late Stage Analytical Development, Small Molecules Technical Development, Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland.
| | - Pierre Lescuyer
- Division of Laboratory Medicine, Geneva University Hospitals, Geneva, Switzerland
- Clinical Proteomics and Chemistry Group, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | | | - Paul Cutler
- Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
- Translational Biomarkers and Bioanalysis, Development Sciences, UCB Pharma, Slough, UK
| | - Axel Ducret
- Biomarkers, Bioinformatics and Omics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Basel, Switzerland
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5
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Ongay S, Langelaar-Makkinje M, Stoop MP, Liu N, Overkleeft H, Luider TM, Groothuis GMM, Bischoff R. Cleavable Crosslinkers as Tissue Fixation Reagents for Proteomic Analysis. Chembiochem 2018; 19:736-743. [PMID: 29356267 DOI: 10.1002/cbic.201700625] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Indexed: 12/17/2022]
Abstract
Formaldehyde fixation is widely used for long-term maintenance of tissue. However, due to formaldehyde-induced crosslinks, fixed tissue proteins are difficult to extract, which hampers mass spectrometry (MS) proteomic analyses. Recent years have seen the use of different combinations of high temperature and solubilizing agents (usually derived from antigen retrieval techniques) to unravel formaldehyde-fixed paraffin-embedded tissue proteomes. However, to achieve protein extraction yields similar to those of fresh-frozen tissue, high-temperature heating is necessary. Such harsh extraction conditions can affect sensitive amino acids and post-translational modifications, resulting in the loss of important information, while still not resulting in protein yields comparable to those of fresh-frozen tissue. Herein, the objective is to evaluate cleavable protein crosslinkers as fixatives that allow tissue preservation and efficient protein extraction from fixed tissue for MS proteomics under mild conditions. With this goal in mind, disuccinimidyl tartrate (DST) and dithiobis(succinimidylpropionate) (DSP) are investigated as cleavable fixating reagents. These compounds crosslink proteins by reacting with amino groups, leading to amide bond formation, and can be cleaved with sodium metaperiodate (cis-diols, DST) or reducing agents (disulfide bonds, DSP), respectively. Results show that cleavable protein crosslinking with DST and DSP allows tissue fixation with morphology preservation comparable to that of formaldehyde. In addition, cleavage of DSP improves protein recovery from fixed tissue by a factor of 18 and increases the number of identified proteins by approximately 20 % under mild extraction conditions compared with those of formaldehyde-fixed paraffin-embedded tissue. A major advantage of DSP is the introduction of well-defined protein modifications that can be taken into account during database searching. In contrast to DSP fixation, DST fixation followed by cleavage with sodium metaperiodate, although effective, results in side reactions that prevent effective protein extraction and interfere with protein identification. Protein crosslinkers that can be cleaved under mild conditions and result in defined modifications, such as DSP, are thus viable alternatives to formaldehyde as tissue fixatives to facilitate protein analysis from paraffin-embedded, fixed tissue.
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Affiliation(s)
- Sara Ongay
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Miriam Langelaar-Makkinje
- Department Pharmacokinetics, Toxicology and Targeting, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Marcel P Stoop
- Department of Neurology, Erasmus University Medical Center, P. O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Nora Liu
- Department of Bio-Organic Synthesis, Leiden University, P. O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Hermen Overkleeft
- Department of Bio-Organic Synthesis, Leiden University, P. O. Box 9502, 2300 RA, Leiden, The Netherlands
| | - Theo M Luider
- Department of Neurology, Erasmus University Medical Center, P. O. Box 1738, 3000 DR, Rotterdam, The Netherlands
| | - Geny M M Groothuis
- Department Pharmacokinetics, Toxicology and Targeting, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
| | - Rainer Bischoff
- Department of Analytical Biochemistry, University of Groningen, Antonius Deusinglaan 1, 9713, AV, Groningen, The Netherlands
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Miyagawa-Hayashino A, Yoshifuji H, Kitagori K, Ito S, Oku T, Hirayama Y, Salah A, Nakajima T, Kiso K, Yamada N, Haga H, Tsuruyama T. Increase of MZB1 in B cells in systemic lupus erythematosus: proteomic analysis of biopsied lymph nodes. Arthritis Res Ther 2018; 20:13. [PMID: 29382365 PMCID: PMC5791339 DOI: 10.1186/s13075-018-1511-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2017] [Accepted: 01/02/2018] [Indexed: 12/20/2022] Open
Abstract
Background Systemic lupus erythematosus (SLE) is a prototypical autoimmune disease in which dysregulation of B cells has been recognized. Here, we searched for potential biomarkers of SLE using liquid chromatography-tandem mass spectrometry (LC-MS). Methods Lymph nodes from SLE patients and controls were analyzed by LC-MS. To validate the identified molecules, immunoblotting and immunohistochemistry were performed and B cells from SLE patients were analyzed by quantitative RT-PCR. B-cell subsets from NZB/W F1 mice, which exhibit autoimmune disease resembling human SLE, were analyzed by flow cytometry. Endoplasmic reticulum (ER) stress was induced by tunicamycin and the serum concentration of anti-dsDNA antibodies was determined by ELISA. TUNEL methods and immunoblotting were used to assess the effect of tunicamycin. Results MZB1, which comprises part of a B-cell-specific ER chaperone complex and is a key player in antibody secretion, was one of the differentially expressed proteins identified by LC-MS and confirmed by immunoblotting. Immunohistochemically, larger numbers of MZB1+ cells were located mainly in interfollicular areas and scattered in germinal centers in specimens from SLE patients compared with those from controls. MZB1 colocalized with CD138+ plasma cells and IRTA1+ marginal zone B cells. MZB1 mRNA was increased by 2.1-fold in B cells of SLE patients with active disease (SLE Disease Activity Index 2000 ≥ 6) compared with controls. In aged NZB/W F1 mice, splenic marginal zone B cells and plasma cells showed elevated MZB1 levels. Tunicamycin induced apoptosis of MZB1+ cells in target organs, resulting in decreased serum anti-dsDNA antibody levels. Additionally, MZB1+ cells were increased in synovial tissue specimens from patients with rheumatoid arthritis. Conclusions MZB1 may be a potential therapeutic target in excessive antibody-secreting cells in SLE. Electronic supplementary material The online version of this article (10.1186/s13075-018-1511-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Aya Miyagawa-Hayashino
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan. .,Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan. .,Present address: Department of Clinical Pathology, Kansai Medical University, Osaka, Japan.
| | - Hajime Yoshifuji
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Koji Kitagori
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Shinji Ito
- Bio Frontier Platform, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Takuma Oku
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Research Portfolio & Science, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Japan
| | - Yoshitaka Hirayama
- Center for Innovation in Immunoregulative Technology and Therapeutics, Graduate School of Medicine, Kyoto University, Yoshida-konoe-cho, Sakyo-ku, Kyoto, 606-8501, Japan.,Research Portfolio & Science, Drug Discovery Research, Astellas Pharma Inc., Tsukuba, Japan
| | - Adeeb Salah
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Toshiki Nakajima
- Department of Rheumatology and Clinical Immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Kaori Kiso
- Center for Anatomical, Pathological and Forensic Medical Research, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Norishige Yamada
- Center for Anatomical, Pathological and Forensic Medical Research, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Hironori Haga
- Department of Diagnostic Pathology, Kyoto University Hospital, Kyoto, Japan
| | - Tatsuaki Tsuruyama
- Center for Anatomical, Pathological and Forensic Medical Research, Graduate School of Medicine, Kyoto University, Kyoto, Japan
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7
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Alnabulsi A, Murray GI. Proteomics for early detection of colorectal cancer: recent updates. Expert Rev Proteomics 2017; 15:55-63. [PMID: 29064727 DOI: 10.1080/14789450.2018.1396893] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION Colorectal cancer (CRC) is a common type of cancer with a relatively poor survival rate. The survival rate of patients could be improved if CRC is detected early. Biomarkers associated with early stages of tumor development might provide useful tools for the early diagnosis of colorectal cancer. Areas covered: Online searches using PubMed and Google Scholar were performed using keywords and with a focus on recent proteomic studies. The aim of this review is to highlight the need for biomarkers to improve the detection rate of early CRC and provide an overview of proteomic technologies used for biomarker discovery and validation. This review will also discuss recent proteomic studies which focus on identifying biomarkers associated with the early stages of CRC development. Expert commentary: A large number of CRC biomarkers are increasingly being identified by proteomics using diverse approaches. However, the clinical relevance and introduction of these markers into clinical practice cannot be determined without a robust validation process. The size of validation cohorts remains a major limitation in many biomarker studies.
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Affiliation(s)
- Abdo Alnabulsi
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
| | - Graeme I Murray
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
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8
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High Expression of Galectin-3 in Patients with IgG4-Related Disease: A Proteomic Approach. PATHOLOGY RESEARCH INTERNATIONAL 2017; 2017:9312142. [PMID: 28593065 PMCID: PMC5448067 DOI: 10.1155/2017/9312142] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Revised: 04/24/2017] [Accepted: 04/26/2017] [Indexed: 12/24/2022]
Abstract
Objectives Immunoglobulin G4-related disease (IgG4-RD) is a multiorgan condition manifesting itself in different forms. This study aimed to investigate protein expression profiles and to find the possible biomarker for IgG4-RD by liquid chromatography mass spectrometry (LC-MS) using tissue sections in IgG4-RD patients. Methods Protein expression profiles in five IgG4-related pancreatitis and three normal pancreatic samples were compared using LC-MS and were validated by quantitative real-time PCR (qRT-PCR), immunoblotting, and immunohistochemistry. ELISA was employed in the serum of 20 patients with systemic IgG4-RD before and during steroid treatment. Results LC-MS indicated that the levels of 17 proteins were significantly higher and 12 others were significantly lower in IgG4-related pancreatitis patients compared to controls. Among these proteins, galectin-3 levels were 13-fold higher in IgG4-related pancreatitis (P < 0.01). These results were confirmed by immunoblotting and qRT-PCR. The average number of galectin-3 + cells in various organs of IgG4-RD patients, including salivary glands, lungs, and lymph nodes, was higher than in controls. Galectin-3 was detectable in macrophages, dendritic cells, and stromal myofibroblast-like cells, but not in lymphocytes by immunofluorescence staining. Serum galectin-3 levels were higher in patients with IgG4-RD compared with healthy donors and remained high during steroid therapy. Conclusion Galectin-3 was overexpressed in IgG4-RD and the levels were indirectly related to clinical activity.
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9
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Alnabulsi A, Murray GI. Integrative analysis of the colorectal cancer proteome: potential clinical impact. Expert Rev Proteomics 2016; 13:917-927. [PMID: 27598033 DOI: 10.1080/14789450.2016.1233062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
INTRODUCTION Colorectal cancer (CRC) is one of the common types of cancer that affects a significant proportion of the population and is a major contributor to cancer related mortality. The relatively poor survival rate of CRC could be improved through the identification of clinically useful biomarkers. Areas covered: This review highlights the need for biomarkers and discusses recent proteomics discoveries in the aspects of CRC clinical practice including diagnosis, prognosis, therapy, screening and molecular pathological epidemiology (MPE). Studies have been evaluated in relation to biomarker target, methodology, sample selection, limitations, and potential impact. Finally, the progress in proteomic approaches is briefly discussed and the main difficulties facing the translation of proteomics biomarkers into the clinical practice are highlighted. Expert commentary: The establishment of specific guidelines, best practice recommendations and the improvement in proteomic strategies will significantly improve the prospects for developing clinically useful biomarkers.
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Affiliation(s)
- Abdo Alnabulsi
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK.,b Zoology Building , Vertebrate Antibodies , Aberdeen , UK
| | - Graeme I Murray
- a Pathology, School of Medicine, Medical Sciences and Nutrition , University of Aberdeen , Aberdeen , UK
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10
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Miura K, Egawa Y, Moriki T, Mineta H, Harada H, Baba S, Yamamoto S. Microscopic observation of chemical modification in sections using scanning acoustic microscopy. Pathol Int 2015; 65:355-66. [PMID: 25824722 DOI: 10.1111/pin.12288] [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] [Received: 10/03/2014] [Accepted: 02/27/2015] [Indexed: 12/01/2022]
Abstract
A scanning acoustic microscope (SAM) calculates the speed of sound (SOS) through tissues and plots the data on the screen to form images. Hard tissues result in greater SOS; based on these differences in tissue properties regarding SOS, SAM can provide data on tissue elasticity. The present study evaluated whether tissue modifications, such as formalin fixation, periodic acid-Schiff (PAS) reactions and protein degradation, changed the acoustic properties of the tissues and whether SAM could be a useful tool for following chemical changes in sections. The fixation process was observable by the increased SOS. During the PAS reaction, the glycosylation of tissues was characterized by an increased SOS. Mucous or glycogen distribution was visualized and was found to be statistically comparable among lesions and states. Protease digestion by pepsin led to a decreased SOS. Tissue sensitivity to proteases varied due to the stage, cause and duration of inflammation or ageing. Changes in acoustic properties were more sensitive than those in optical histology. SAM facilitates the visualisation of the time course or distribution of chemical modifications in tissue sections, thus aiding their comparison among tissues. SAM may be an effective tool for studying changes such as protein cross-linkage, tissue repair and ageing.
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Affiliation(s)
- Katsutoshi Miura
- Department of Health Science, Pathology and Anatomy, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Yuki Egawa
- Department of Diagnostic Pathology, Shizuoka City Shizuoka Hospital, Shizuoka, Japan
| | - Toshiaki Moriki
- Department of Diagnostic Pathology, Shizuoka City Shizuoka Hospital, Shizuoka, Japan
| | - Hiroyuki Mineta
- Department of Otorhinolaryngology, Hamamatsu University School of Medicine, Hamamatsu, Japan
| | - Hidekazu Harada
- Division of Pathology, Hamamatsu University Hospital, Hamamatsu, Japan
| | - Satoshi Baba
- Division of Pathology, Hamamatsu University Hospital, Hamamatsu, Japan
| | - Seiji Yamamoto
- Medical Photonics Research Center, Hamamatsu University School of Medicine, Hamamatsu, Japan
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11
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Becker KF. Using tissue samples for proteomic studies-Critical considerations. Proteomics Clin Appl 2015; 9:257-67. [DOI: 10.1002/prca.201400106] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Revised: 12/08/2014] [Accepted: 01/07/2015] [Indexed: 01/09/2023]
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12
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Shah P, Zhang B, Choi C, Yang S, Zhou J, Harlan R, Tian Y, Zhang Z, Chan DW, Zhang H. Tissue proteomics using chemical immobilization and mass spectrometry. Anal Biochem 2014; 469:27-33. [PMID: 25283129 DOI: 10.1016/j.ab.2014.09.017] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2014] [Revised: 09/23/2014] [Accepted: 09/25/2014] [Indexed: 01/04/2023]
Abstract
Proteomics analysis is important for characterizing tissues to gain biological and pathological insights, which could lead to the identification of disease-associated proteins for disease diagnostics or targeted therapy. However, tissues are commonly embedded in optimal cutting temperature medium (OCT) or are formalin-fixed and paraffin-embedded (FFPE) in order to maintain tissue morphology for histology evaluation. Although several tissue proteomic analyses have been performed on FFPE tissues using advanced mass spectrometry (MS) technologies, high-throughput proteomic analysis of OCT-embedded tissues has been difficult due to the interference of OCT in the MS analysis. In addition, molecules other than proteins present in tissues further complicate tissue proteomic analysis. Here, we report the development of a method using chemical immobilization of proteins for peptide extraction (CIPPE). In this method, proteins are chemically immobilized onto a solid support; interferences from tissues and OCT embedding are removed by extensive washing of proteins conjugated on the solid support. Peptides are then released from the solid phase by proteolysis, enabling MS analysis. This method was first validated by eliminating OCT interference from a standard protein, human serum albumin, where all of the unique peaks contributed by OCT contamination were eradicated. Finally, this method was applied for the proteomic analysis of frozen and OCT-embedded tissues using iTRAQ (isobaric tag for relative and absolute quantitation) labeling and two-dimensional liquid chromatography tandem mass spectrometry. The data showed reproducible extraction and quantitation of 10,284 proteins from 3996 protein groups and a minimal impact of OCT embedding on the analysis of the global proteome of the stored tissue samples.
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Affiliation(s)
- Punit Shah
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Bai Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Caitlin Choi
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Shuang Yang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Jianying Zhou
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Robert Harlan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Yuan Tian
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Zhen Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Daniel W Chan
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA
| | - Hui Zhang
- Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
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13
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Tanca A, Abbondio M, Pisanu S, Pagnozzi D, Uzzau S, Addis MF. Critical comparison of sample preparation strategies for shotgun proteomic analysis of formalin-fixed, paraffin-embedded samples: insights from liver tissue. Clin Proteomics 2014; 11:28. [PMID: 25097466 PMCID: PMC4115481 DOI: 10.1186/1559-0275-11-28] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 07/03/2014] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND The growing field of formalin-fixed paraffin-embedded (FFPE) tissue proteomics holds promise for improving translational research. Direct tissue trypsinization (DT) and protein extraction followed by in solution digestion (ISD) or filter-aided sample preparation (FASP) are the most common workflows for shotgun analysis of FFPE samples, but a critical comparison of the different methods is currently lacking. EXPERIMENTAL DESIGN DT, FASP and ISD workflows were compared by subjecting to the same label-free quantitative approach three independent technical replicates of each method applied to FFPE liver tissue. Data were evaluated in terms of method reproducibility and protein/peptide distribution according to localization, MW, pI and hydrophobicity. RESULTS DT showed lower reproducibility, good preservation of high-MW proteins, a general bias towards hydrophilic and acidic proteins, much lower keratin contamination, as well as higher abundance of non-tryptic peptides. Conversely, FASP and ISD proteomes were depleted in high-MW proteins and enriched in hydrophobic and membrane proteins; FASP provided higher identification yields, while ISD exhibited higher reproducibility. CONCLUSIONS These results highlight that diverse sample preparation strategies provide significantly different proteomic information, and present typical biases that should be taken into account when dealing with FFPE samples. When a sufficient amount of tissue is available, the complementary use of different methods is suggested to increase proteome coverage and depth.
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Affiliation(s)
- Alessandro Tanca
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Marcello Abbondio
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Salvatore Pisanu
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Daniela Pagnozzi
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
| | - Sergio Uzzau
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy ; Dipartimento di Scienze Biomediche, Università di Sassari, Viale San Pietro 43/B, 07100, Sassari, Italy
| | - Maria Filippa Addis
- Porto Conte Ricerche, S.P. 55 Porto Conte/Capo Caccia Km 8.400, Tramariglio, 07041 Alghero, Italy
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14
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Current applications of chromatographic methods for diagnosis and identification of potential biomarkers in cancer. Trends Analyt Chem 2014. [DOI: 10.1016/j.trac.2013.12.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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15
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Abstract
Advancement in electrophoresis and mass spectrometry techniques along with the recent progresses in genomics, culminating in bovine and pig genome sequencing, widened the potential application of proteomics in the field of veterinary medicine. The aim of the present review is to provide an in-depth perspective about the application of proteomics to animal disease pathogenesis, as well as its utilization in veterinary diagnostics. After an overview on the various proteomic techniques that are currently applied to veterinary sciences, the article focuses on proteomic approaches to animal disease pathogenesis. Included as well are recent achievements in immunoproteomics (ie, the identifications through proteomic techniques of antigen involved in immune response) and histoproteomics (ie, the application of proteomics in tissue processed for immunohistochemistry). Finally, the article focuses on clinical proteomics (ie, the application of proteomics to the identification of new biomarkers of animal diseases).
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16
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Orton DJ, Doucette AA. Proteomic Workflows for Biomarker Identification Using Mass Spectrometry - Technical and Statistical Considerations during Initial Discovery. Proteomes 2013; 1:109-127. [PMID: 28250400 PMCID: PMC5302744 DOI: 10.3390/proteomes1020109] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Revised: 08/22/2013] [Accepted: 08/22/2013] [Indexed: 01/13/2023] Open
Abstract
Identification of biomarkers capable of differentiating between pathophysiological states of an individual is a laudable goal in the field of proteomics. Protein biomarker discovery generally employs high throughput sample characterization by mass spectrometry (MS), being capable of identifying and quantifying thousands of proteins per sample. While MS-based technologies have rapidly matured, the identification of truly informative biomarkers remains elusive, with only a handful of clinically applicable tests stemming from proteomic workflows. This underlying lack of progress is attributed in large part to erroneous experimental design, biased sample handling, as well as improper statistical analysis of the resulting data. This review will discuss in detail the importance of experimental design and provide some insight into the overall workflow required for biomarker identification experiments. Proper balance between the degree of biological vs. technical replication is required for confident biomarker identification.
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Affiliation(s)
- Dennis J Orton
- Department of Pathology, 11th Floor Tupper Medical Building, Room 11B, Dalhousie University, Halifax, NS B3H 4R2, Canada.
| | - Alan A Doucette
- Department of Chemistry, Room 212, Chemistry Building, Dalhousie University, Halifax, NS B3H 4R2, Canada.
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