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Panthong W, Pientong C, Nukpook T, Roytrakul S, Yingchutrakul Y, Teeramatwanich W, Aromseree S, Ekalaksananan T. Integrated Proteomics and Machine Learning Approach Reveals PYCR1 as a Novel Biomarker to Predict Prognosis of Sinonasal Squamous Cell Carcinoma. Int J Mol Sci 2024; 25:13234. [PMID: 39768999 PMCID: PMC11675701 DOI: 10.3390/ijms252413234] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2024] [Revised: 12/06/2024] [Accepted: 12/08/2024] [Indexed: 01/11/2025] Open
Abstract
Sinonasal squamous cell carcinoma (SNSCC) is a rare tumor with a high 5-year mortality rate. However, proteomic technologies have not yet been utilized to identify SNSCC-associated proteins, which could be used as biomarkers. In this study, we aimed to discover a biomarker to predict SNSCC patients using proteomic analysis integrated with machine learning models. Support vector machine (SVM), logistic regression (LR), random forest (RF), and gradient boost (GB) classifiers were developed to predict SNSCC based on proteomic profiles of SNSCC compared with nasal polyps (NP) as control. Seventeen feature proteins were found in all models, indicating possible biomarkers for SNSCC. Analysis of gene expression across multiple cancer types and their associations with cancer stage and patient survival in the TCGA-HNSC dataset identified a PYCR1 and MYO1B gene that could be a potential tumor-associated marker. The expression of PYCR1 was confirmed by RT-qPCR in SNSCC tissues, and its high expression was associated with poor overall survival, indicating PYCR1 as a potential tumor-associated biomarker to predict the prognosis of SNSCC.
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Affiliation(s)
- Watcharapong Panthong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand; (W.P.); (T.N.); (S.A.)
- HPV&EBV and Carcinogenesis (HEC) Research Group, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand
| | - Chamsai Pientong
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand; (W.P.); (T.N.); (S.A.)
- HPV&EBV and Carcinogenesis (HEC) Research Group, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand
| | - Thawaree Nukpook
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand; (W.P.); (T.N.); (S.A.)
- HPV&EBV and Carcinogenesis (HEC) Research Group, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand
| | - Sittiruk Roytrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand; (S.R.); (Y.Y.)
| | - Yodying Yingchutrakul
- Functional Ingredients and Food Innovation Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency, Khlong Luang, Pathum Thani 12120, Thailand; (S.R.); (Y.Y.)
| | - Watchareporn Teeramatwanich
- Department of Otorhinolaryngology, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand;
| | - Sirinart Aromseree
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand; (W.P.); (T.N.); (S.A.)
- HPV&EBV and Carcinogenesis (HEC) Research Group, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand
| | - Tipaya Ekalaksananan
- Department of Microbiology, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand; (W.P.); (T.N.); (S.A.)
- HPV&EBV and Carcinogenesis (HEC) Research Group, Faculty of Medicine, Khon Kaen University, Mueang Khon Kaen, Khon Kaen 40002, Thailand
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2
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G Jagadeeshaprasad M, Zeng J, Zheng N. LC-MS bioanalysis of protein biomarkers and protein therapeutics in formalin-fixed paraffin-embedded tissue specimens. Bioanalysis 2024; 16:245-258. [PMID: 38226835 DOI: 10.4155/bio-2023-0210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024] Open
Abstract
Formalin-fixed paraffin-embedded (FFPE) is a form of preservation and preparation for biopsy specimens. FFPE tissue specimens are readily available as part of oncology studies because they are often collected for disease diagnosis or confirmation. FFPE tissue specimens could be extremely useful for retrospective studies on protein biomarkers because the samples preserved in FFPE blocks could be stable for decades. However, LC-MS bioanalysis of FFPE tissues poses significant challenges. In this Perspective, we review the benefits and recent developments in LC-MS approach for targeted protein biomarker and protein therapeutic analysis using FFPE tissues and their clinical and translational applications. We believe that LC-MS bioanalysis of protein biomarkers in FFPE tissue specimens represents a great potential for its clinical applications.
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Affiliation(s)
| | - Jianing Zeng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
| | - Naiyu Zheng
- Department of Protein Sciences & Mass Spectrometry, Translational Medicine, Bristol Myers Squibb, Princeton, NJ 08543, USA
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3
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Darville LNF, Lockhart JH, Putty Reddy S, Fang B, Izumi V, Boyle TA, Haura EB, Flores ER, Koomen JM. A Fast-Tracking Sample Preparation Protocol for Proteomics of Formalin-Fixed Paraffin-Embedded Tumor Tissues. Methods Mol Biol 2024; 2823:193-223. [PMID: 39052222 PMCID: PMC11648944 DOI: 10.1007/978-1-0716-3922-1_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/27/2024]
Abstract
Archived tumor specimens are routinely preserved by formalin fixation and paraffin embedding. Despite the conventional wisdom that proteomics might be ineffective due to the cross-linking and pre-analytical variables, these samples have utility for both discovery and targeted proteomics. Building on this capability, proteomics approaches can be used to maximize our understanding of cancer biology and clinical relevance by studying preserved tumor tissues annotated with the patients' medical histories. Proteomics of formalin-fixed paraffin-embedded (FFPE) tissues also integrates with histological evaluation and molecular pathology strategies, so that additional collection of research biopsies or resected tumor aliquots is not needed. The acquisition of data from the same tumor sample also overcomes concerns about biological variation between samples due to intratumoral heterogeneity. However, the protein extraction and proteomics sample preparation from FFPE samples can be onerous, particularly for small (i.e., limited or precious) samples. Therefore, we provide a protocol for a recently introduced kit-based EasyPep method with benchmarking against a modified version of the well-established filter-aided sample preparation strategy using laser-capture microdissected lung adenocarcinoma tissues from a genetically engineered mouse model. This model system allows control over the tumor preparation and pre-analytical variables while also supporting the development of methods for spatial proteomics to examine intratumoral heterogeneity. Data are posted in ProteomeXchange (PXD045879).
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Affiliation(s)
| | | | | | - Bin Fang
- H. Lee Moffitt Cancer Center, Tampa, FL, USA
| | | | | | | | | | - John M Koomen
- H. Lee Moffitt Cancer Center, Tampa, FL, USA.
- Molecular Oncology/Pathology, Moffitt Cancer Center, Tampa, FL, USA.
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4
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Cho A, Ahn J, Kim A, Lee JH, Ryu HS, Kim KM, Yi EC. Proteomics analysis of an individual formalin-fixed paraffin-embedded tissue section using isobaric-tag amplification. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2023; 37:e9616. [PMID: 37817342 DOI: 10.1002/rcm.9616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Revised: 07/13/2023] [Accepted: 07/14/2023] [Indexed: 10/12/2023]
Abstract
RATIONALE The comprehensive analysis of formalin-fixed paraffin-embedded (FFPE) tissues is essential for retrospective clinical studies. However, detecting low-abundance proteins and obtaining proteome-scale data from FFPE samples pose analytical challenges in mass spectrometry-based proteomics. To overcome this challenge, our study focuses on implementing an isobaric labeling approach to improve the detection of low-abundance target proteins in FFPE tissues, thereby enhancing the qualitative and quantitative analysis. METHODS We employed an isobaric labeling approach utilizing synthetic peptides or proteins to enable the qualitative and quantitative measurement of target proteins in FFPE tissue samples. To achieve this, we incorporated tandem mass tag (TMT)-labeled recombinant proteins or synthetic peptides into TMT-labeled metastatic breast cancer FFPE tissues. Through this strategy, we successfully detect coexisting CD276 (B7-H3) and CD147 proteins while identifying over 6000 proteins using targeted analysis of individual FFPE tissue sections. RESULTS Our findings provide compelling evidence that the incorporation of isobaric labeling, along with the inclusion of TMT-labeled peptides or proteins, greatly enhances the detection of target proteins in FFPE tissue samples. By employing this approach, we were able to obtain robust qualitative measurements of CD276 and CD147 proteins, showcasing its effectiveness in identifying more than 6000 proteins in FFPE samples. CONCLUSIONS The integration of an isobaric labeling approach, in conjunction with synthetic peptides or proteins, presents a valuable strategy for enhancing the detection and validation of target proteins in FFPE tissue analysis. This technique holds immense potential in retrospective clinical studies, as it enables comprehensive analysis of low-abundance proteins and facilitating proteome-scale investigations in FFPE samples. By leveraging this methodology, researchers can unlock new insights into disease mechanisms and advance our understanding of complex biological processes.
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Affiliation(s)
- Ara Cho
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jinsung Ahn
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Andrew Kim
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
| | - Jeong Hyun Lee
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
| | - Han Suk Ryu
- Department of Pathology, Seoul National University Hospital, Seoul, Republic of Korea
| | - Kristine M Kim
- Division of Biomedical Convergence, College of Biomedical Science, Kangwon National University, Chuncheon, Republic of Korea
- Department of Bio-Health Convergence, Kangwon National University, Chuncheon, Republic of Korea
| | - Eugene C Yi
- Department of Molecular Medicine and Biopharmaceutical Sciences, Graduate School of Convergence Science and Technology, and College of Medicine, Seoul National University, Seoul, Republic of Korea
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Brožová K, Hantusch B, Kenner L, Kratochwill K. Spatial Proteomics for the Molecular Characterization of Breast Cancer. Proteomes 2023; 11:17. [PMID: 37218922 PMCID: PMC10204503 DOI: 10.3390/proteomes11020017] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2023] [Revised: 03/30/2023] [Accepted: 04/23/2023] [Indexed: 05/24/2023] Open
Abstract
Breast cancer (BC) is a major global health issue, affecting a significant proportion of the female population and contributing to high rates of mortality. One of the primary challenges in the treatment of BC is the disease's heterogeneity, which can lead to ineffective therapies and poor patient outcomes. Spatial proteomics, which involves the study of protein localization within cells, offers a promising approach for understanding the biological processes that contribute to cellular heterogeneity within BC tissue. To fully leverage the potential of spatial proteomics, it is critical to identify early diagnostic biomarkers and therapeutic targets, and to understand protein expression levels and modifications. The subcellular localization of proteins is a key factor in their physiological function, making the study of subcellular localization a major challenge in cell biology. Achieving high resolution at the cellular and subcellular level is essential for obtaining an accurate spatial distribution of proteins, which in turn can enable the application of proteomics in clinical research. In this review, we present a comparison of current methods of spatial proteomics in BC, including untargeted and targeted strategies. Untargeted strategies enable the detection and analysis of proteins and peptides without a predetermined molecular focus, whereas targeted strategies allow the investigation of a predefined set of proteins or peptides of interest, overcoming the limitations associated with the stochastic nature of untargeted proteomics. By directly comparing these methods, we aim to provide insights into their strengths and limitations and their potential applications in BC research.
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Affiliation(s)
- Klára Brožová
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Division of Molecular and Structural Preclinical Imaging, Department of Biomedical Imaging and Image-Guided Therapy, Medical University of Vienna, 1210 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
| | - Brigitte Hantusch
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Lukas Kenner
- Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
- Unit of Laboratory Animal Pathology, University of Veterinary Medicine, 1090 Vienna, Austria
- CBmed GmbH—Center for Biomarker Research in Medicine, 8010 Graz, Austria
- Christian Doppler Laboratory for Applied Metabolomics, Medical University of Vienna, 1090 Vienna, Austria
| | - Klaus Kratochwill
- Core Facility Proteomics, Medical University of Vienna, 1090 Vienna, Austria
- Christian Doppler Laboratory for Molecular Stress Research in Peritoneal Dialysis, Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, 1090 Vienna, Austria
- Division of Pediatric Nephrology and Gastroenterology, Department of Pediatrics and Adolescent Medicine, Comprehensive Center for Pediatrics, Medical University of Vienna, 1090 Vienna, Austria
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6
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Thorsen ASF, Riber LPS, Rasmussen LM, Overgaard M. A targeted multiplex mass spectrometry method for quantitation of abundant matrix and cellular proteins in formalin-fixed paraffin embedded arterial tissue. J Proteomics 2023; 272:104775. [PMID: 36414230 DOI: 10.1016/j.jprot.2022.104775] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 08/30/2022] [Accepted: 11/17/2022] [Indexed: 11/20/2022]
Abstract
Assessment of proteins in formalin-fixed paraffin-embedded (FFPE) tissue traditionally hinges on immunohistochemistry and immunoblotting. These methods are far from optimal for quantitative studies and not suitable for large-scale testing of multiple protein panels. In this study, we developed and optimised a novel targeted isotope dilution mass spectrometry (MS)-based method for FFPE samples, designed to quantitate 17 matrix and cytosolic proteins abundantly present in arterial tissue. Our new method was developed on FFPE human tissue samples of the internal thoracic artery obtained from coronary artery bypass graft (CABG) operations. The workflow has a limit of 60 samples per day. Assay precision improved by normalisation to both beta-actin and smooth muscle actin with inter-assay coefficients of variation (CV) ranging from 5.3% to 31.9%. To demonstrate clinical utility of the assay we analysed 40 FFPE artery specimens from two groups of patients with or without type 2 diabetes. We observed increased levels of collagen type IV α1 and α2 in patients with diabetes. The assay is scalable for larger cohorts and advantageous for pathophysiological studies in diabetes and the method is easily convertible to analysis of other proteins in FFPE artery samples. SIGNIFICANCE: This article presents a novel robust and precise targeted mass spectrometry assay for relative quantitation of a panel of abundant matrix and cellular arterial proteins in archived formalin-fixed paraffin-embedded arterial samples. We demonstrate its utility in pathophysiological studies of cardiovascular disease in diabetes.
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Affiliation(s)
- Anne-Sofie Faarvang Thorsen
- Department of Clinical Biochemistry and Center for Individualised Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Steno Diabetes Center Odense (SDCO), Odense, Denmark
| | - Lars Peter Schødt Riber
- Department of Clinical Research, University of Southern Denmark, Odense, Denmark; Department of Cardiac, Thoracic and Vascular Surgery, Odense University Hospital, Odense, Denmark
| | - Lars Melholt Rasmussen
- Department of Clinical Biochemistry and Center for Individualised Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark
| | - Martin Overgaard
- Department of Clinical Biochemistry and Center for Individualised Medicine in Arterial Diseases (CIMA), Odense University Hospital, Odense, Denmark; Department of Clinical Research, University of Southern Denmark, Odense, Denmark.
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7
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Van Haver D, Dendooven A, Impens F. Proteomics-Based Analysis and Diagnosis of Formalin-Fixed Paraffin-Embedded Amyloidosis Samples. Methods Mol Biol 2023; 2718:213-233. [PMID: 37665462 DOI: 10.1007/978-1-0716-3457-8_12] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Amyloidosis is a group of rare pathologies characterized by abnormal folding and deposition of susceptible proteins in tissues and organs. Diagnosis of amyloidosis often relies on immunohistochemistry of formalin-fixed paraffin-embedded (FFPE) patient samples; however, dependency on antibodies for protein staining is one of the major pitfalls of this approach, especially for the detection of rare amyloidosis types. In recent years, mass spectrometry-based proteomics has emerged as a promising alternative for adequate detection and amyloid typing, despite the fact that preparing FFPE samples for proteomics remains a challenging task. Major hurdles are removal of formalin-induced protein cross-links and water-insoluble paraffin prior to mass spectrometry analysis. With the recent development of the suspension trapping protocol, enabling the use of high concentrations of SDS, these obstacles can be overcome. In this chapter, we describe the implementation of suspension trapping for FFPE sample processing and its application to analyze human amyloidosis samples, comparing a standard procedure with probe sonication with a more advanced workflow based on ultrasonication.
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Affiliation(s)
- Delphi Van Haver
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
- VIB Proteomics Core, Ghent, Belgium
| | - Amélie Dendooven
- Department of Pathology, Ghent University Hospital, Ghent, Belgium
- Laboratory for Experimental Medicine and Pediatrics, Antwerp University, Edegem, Belgium
| | - Francis Impens
- VIB-UGent Center for Medical Biotechnology, Ghent, Belgium.
- Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
- VIB Proteomics Core, Ghent, Belgium.
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8
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Ni J, Tian S, Bai L, Lv Q, Liu J, Liu J, Fang Y, Zhai Y, Shen Q, Rao J, Ding C, Xu H. Comparative proteomic analysis of children FSGS FFPE tissues. BMC Pediatr 2022; 22:707. [PMID: 36503536 PMCID: PMC9743561 DOI: 10.1186/s12887-022-03764-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/28/2022] [Accepted: 11/21/2022] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND In children, focal segmental glomerulosclerosis (FSGS) is the main cause of steroid resistant nephrotic syndrome (SRNS). To identify specific candidates and the mechanism of steroid resistance, we examined the formalin-fixed paraffin embedded (FFPE) renal tissue protein profiles via liquid chromatography tandem mass spectrometry (LC-MS/MS). METHODS Renal biopsies from seven steroid-sensitive (SS) and eleven steroid-resistant (SR) children FSGS patients were obtained. We examined the formalin-fixed paraffin embedded (FFPE) renal tissue protein profiles via liquid chromatography tandem mass spectrometry (LC-MS/MS). Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment and Gene Ontology (GO) analysis, as well as the construction of protein-protein interaction (PPI) network were performed. Two proteins were further valiadated by immunohistochemistry staining in FSGS patients and mice models. RESULTS In total, we quantified more than 4000 proteins, of which 325 were found to be differentially expressed proteins (DEPs) between the SS and SR group (foldchange ≥2, P<0.05). The results of GO revealed that the most significant up-regulated proteins were primarily related to protein transportation, regulation of the complement activation process and cytolysis. Moreover, clustering analysis showed differences in the pathways (lysosome, terminal pathway of complement) between the two groups. Among these potential candidates, validation analyses for LAMP1 and ACSL4 were conducted. LAMP1 was observed to have a higher expression in glomerulus, while ACSL4 was expressed more in tubular epithelial cells. CONCLUSIONS In this study, the potential mechanism and candidates related to steroid resistance in children FSGS patients were identified. It could be helpful in identifying potential therapeutic targets and predicting outcomes with these proteomic changes for children FSGS patients.
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Affiliation(s)
- Jiajia Ni
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Sha Tian
- grid.413087.90000 0004 1755 3939State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Lin Bai
- grid.413087.90000 0004 1755 3939State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Qianying Lv
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jialu Liu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jiaojiao Liu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Ye Fang
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Yihui Zhai
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Qian Shen
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Jia Rao
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
| | - Chen Ding
- grid.413087.90000 0004 1755 3939State Key Laboratory of Genetic Engineering and Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Institute of Biomedical Sciences, Human Phenome Institute, Zhongshan Hospital, Fudan University, Shanghai, 200433 China
| | - Hong Xu
- grid.411333.70000 0004 0407 2968Department of Nephrology, Children’s Hospital of Fudan University, National Pediatric Medical Center of China, Shanghai, China ,Kidney Development and Pediatric Kidney Disease Research Center, Shanghai, China
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9
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Schoffman H, Levin Y, Itzhaki-Alfia A, Tselekovits L, Gonen L, Vainer GW, Hout-Siloni G, Barshack I, Cohen ZR, Margalit N, Shahar T. Comparison of matched formalin-fixed paraffin embedded and fresh frozen meningioma tissue reveals bias in proteomic profiles. Proteomics 2022; 22:e2200085. [PMID: 36098096 DOI: 10.1002/pmic.202200085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 12/29/2022]
Abstract
Tissue biopsies are most commonly archived in a paraffin block following tissue fixation with formaldehyde (FFPE) or as fresh frozen tissue (FFT). While both methods preserve biological samples, little is known about how they affect the quantifiable proteome. We performed a 'bottom-up' proteomic analysis (N = 20) of short and long-term archived FFPE surgical samples of human meningiomas and compared them to matched FFT specimens. FFT facilitated a similar number of proteins assigned by MetaMorpheus compared with matched FFPE specimens (5378 vs. 5338 proteins, respectively (p = 0.053), regardless of archival time. However, marked differences in the proteome composition were apparent between FFPE and FFT specimens. Twenty-three percent of FFPE-derived peptides and 8% of FFT-derived peptides contained at least one chemical modification. Methylation and formylation were most prominent in FFPE-derived peptides (36% and 17% of modified FFPE peptides, respectively) while, most of phosphorylation and iron modifications appeared in FFT-derived peptides (p < 0.001). A mean 14% (± 2.9) of peptides identified in FFPE contained at least one modified Lysine residue. Importantly, larger proteins were significantly overrepresented in FFT specimens, while FFPE specimens were enriched with smaller proteins.
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Affiliation(s)
- Hanan Schoffman
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Yishai Levin
- de Botton Institute for Protein Profiling, The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel
| | | | - Lea Tselekovits
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel
| | - Lior Gonen
- Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
| | - Gilad Wolf Vainer
- Department of Pathology, Hadassah Hebrew University Medical School, Jerusalem, Israel
| | - Goni Hout-Siloni
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel
| | - Iris Barshack
- Department of Pathology, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Zvi R Cohen
- Department of Neurosurgery, Sheba Medical Center, Ramat Gan, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nevo Margalit
- Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
| | - Tal Shahar
- Laboratory of Molecular Neuro Oncology, Neurosurgery Department, Shaare Zedek Medical Center, Jerusalem, Israel.,Neurosurgery Department, Shaare Zedek Medical Center, Hebrew University Medical School, Jerusalem, Israel
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10
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Shidham VB. Cell-blocks and other ancillary studies (including molecular genetic tests and proteomics). Cytojournal 2021; 18:4. [PMID: 33880127 PMCID: PMC8053490 DOI: 10.25259/cytojournal_3_2021] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/18/2021] [Indexed: 01/28/2023] Open
Abstract
Many types of elective ancillary tests may be required to support the cytopathologic interpretations. Most of these tests can be performed on cell-blocks of different cytology specimens. The cell-block sections can be used for almost any special stains including various histochemistry stains and for special stains for different microorganisms including fungi, Pneumocystis jirovecii (carinii), and various organisms including acid-fast organisms similar to the surgical biopsy specimens. Similarly, in addition to immunochemistry, different molecular tests can be performed on cell-blocks. Molecular tests broadly can be divided into two main types Molecular genetic tests and Proteomics.
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Affiliation(s)
- Vinod B Shidham
- Department of Pathology, Wayne State University School of Medicine, Karmanos Cancer Center, and Detroit Medical Center, Detroit, Michigan, United States
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11
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Herrera JA, Mallikarjun V, Rosini S, Montero MA, Lawless C, Warwood S, O’Cualain R, Knight D, Schwartz MA, Swift J. Laser capture microdissection coupled mass spectrometry (LCM-MS) for spatially resolved analysis of formalin-fixed and stained human lung tissues. Clin Proteomics 2020; 17:24. [PMID: 32565759 PMCID: PMC7302139 DOI: 10.1186/s12014-020-09287-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2019] [Accepted: 06/11/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Haematoxylin and eosin (H&E)-which respectively stain nuclei blue and other cellular and stromal material pink-are routinely used for clinical diagnosis based on the identification of morphological features. A richer characterization can be achieved by laser capture microdissection coupled to mass spectrometry (LCM-MS), giving an unbiased assay of the proteins that make up the tissue. However, the process of fixing and H&E staining of tissues provides challenges with standard sample preparation methods for mass spectrometry, resulting in low protein yield. Here we describe a microproteomics technique to analyse H&E-stained, formalin-fixed paraffin-embedded (FFPE) tissues. METHODS Herein, we utilize heat extraction, physical disruption, and in column digestion for the analysis of H&E stained FFPE tissues. Micro-dissected morphologically normal human lung alveoli (0.082 mm3) and human lung blood vessels (0.094 mm3) from FFPE-fixed H&E-stained sections from Idiopathic Pulmonary Fibrosis (IPF) specimens (n = 3 IPF specimens) were then subject to a qualitative and then quantitative proteomics approach using BayesENproteomics. In addition, we tested the sensitivity of this method by processing and analysing a range of micro-dissected human lung blood vessel tissue volumes. RESULTS This approach yields 1252 uniquely expressed proteins (at a protein identification threshold of 3 unique peptides) with 892 differentially expressed proteins between these regions. In accord with prior knowledge, our methodology approach confirms that human lung blood vessels are enriched with smoothelin, CNN1, ITGA7, MYH11, TAGLN, and PTGIS; whereas morphologically normal human lung alveoli are enriched with cytokeratin-7, -8, -18, -19, 14, and -17. In addition, we identify a total of 137 extracellular matrix (ECM) proteins and immunohistologically validate that laminin subunit beta-1 localizes to morphologically normal human lung alveoli and tenascin localizes to human lung blood vessels. Lastly, we show that this micro-proteomics technique can be applied to tissue volumes as low as 0.0125 mm3. CONCLUSION Herein we show that our multistep sample preparation methodology of LCM-MS can identify distinct, characteristic proteomic compositions of anatomical features within complex fixed and stained tissues.
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Affiliation(s)
- Jeremy A. Herrera
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Venkatesh Mallikarjun
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Silvia Rosini
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Maria Angeles Montero
- Histopathology Department, Manchester University NHS Foundation Trust, Southmoor Road, Wythenshawe, Manchester, M23 9LT UK
| | - Craig Lawless
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Stacey Warwood
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Ronan O’Cualain
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - David Knight
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Martin A. Schwartz
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
| | - Joe Swift
- The Wellcome Centre for Cell-Matrix Research, University of Manchester, Manchester, M13 9PT UK
- Division of Cell Matrix Biology and Regenerative Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, University of Manchester, Manchester Academic Health Science Centre, Manchester, M13 9PL UK
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Wagner R, Ayoub L, Kahnamoui S, Li H, Patel D, Liu D, Del Bigio MR, Stefanovici C, Lacher M, Keijzer R. Establishment of a biobank for human lung tissues of congenital diaphragmatic hernia and congenital pulmonary airway malformation. J Pediatr Surg 2019; 54:2439-2442. [PMID: 31130348 DOI: 10.1016/j.jpedsurg.2019.05.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/02/2019] [Accepted: 05/06/2019] [Indexed: 12/20/2022]
Abstract
BACKGROUND Human tissue samples are an invaluable and little available source of information for translational studies of congenital lung diseases such as Congenital Diaphragmatic Hernia (CDH) or Congenital Pulmonary Airway Malformation (CPAM). PURPOSE We aimed to establish a human lung tissue biobank of CDH and CPAM patients together with age-matched controls, coupled with a clinical database. METHODS Pathology records from autopsies or surgical specimens for CDH and CPAM cases between 1980 and 2017 were reviewed. For surviving individuals, clinical patient data was obtained from corresponding pediatric surgery reports. Formalin-fixed, paraffin-embedded tissues of patients and age-matched controls were systematically stored for further translational studies. RNA integrity was determined on selected CDH blocks. RESULTS A total of 16 CDH and 18 CPAM and age-matched control lung tissue blocks were included in our biobank. Ages ranged from 22 to 41 weeks of gestation (GA) in CDH (33.9 ± 6.35 weeks) and 26 weeks (GA) and 12 years in CPAM (2.3 ± 3.7 y). RNA isolation from CDH and control blocks yielded good RNA quality (OD 260/280 ratio: 2.01-2.09, OD 260/230 ratio: 2.04-2.09). CONCLUSION We established a unique human biobank for CDH and CPAM tissues. The combination with clinical patient data will allow us to design future translational studies to improve our understanding of the disease pathogenesis of these congenital malformations.
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Affiliation(s)
- Richard Wagner
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatric Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Lojine Ayoub
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada
| | - Shana Kahnamoui
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada
| | - Henry Li
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada
| | - Daywin Patel
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada
| | - Daisy Liu
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada
| | - Marc R Del Bigio
- Department of Pathology, University of Manitoba, and Shared Services Manitoba, Winnipeg, MB, Canada
| | - Camelia Stefanovici
- Department of Pathology, University of Manitoba, and Shared Services Manitoba, Winnipeg, MB, Canada
| | - Martin Lacher
- Department of Pediatric Surgery, University Hospital Leipzig, Leipzig, Germany
| | - Richard Keijzer
- Department of Surgery, Division of Pediatric Surgery, University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada; Department of Pediatrics & Child Health and Physiology & Pathophysiology (Adjunct), University of Manitoba and Children's Hospital Research Institute of Manitoba, Biology of Breathing Theme, Winnipeg, Manitoba, Canada.
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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: 4.5] [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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Giusti L, Angeloni C, Lucacchini A. Update on proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2019; 16:513-520. [DOI: 10.1080/14789450.2019.1615452] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Laura Giusti
- School of Pharmacy, University of Camerino, Camerino, Italy
| | | | - Antonio Lucacchini
- Department of Clinical and Experimental Medicine, University of Pisa, Pisa, Italy
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15
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Zhou Q, Andersson R, Hu D, Bauden M, Kristl T, Sasor A, Pawłowski K, Pla I, Hilmersson KS, Zhou M, Lu F, Marko-Varga G, Ansari D. Quantitative proteomics identifies brain acid soluble protein 1 (BASP1) as a prognostic biomarker candidate in pancreatic cancer tissue. EBioMedicine 2019; 43:282-294. [PMID: 30982764 PMCID: PMC6557784 DOI: 10.1016/j.ebiom.2019.04.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 03/27/2019] [Accepted: 04/03/2019] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Pancreatic cancer is a heterogenous disease with a poor prognosis. This study aimed to discover and validate prognostic tissue biomarkers in pancreatic cancer using a mass spectrometry (MS) based proteomics approach. METHODS Global protein sequencing of fresh frozen pancreatic cancer and healthy pancreas tissue samples was conducted by MS to discover potential protein biomarkers. Selected candidate proteins were further verified by targeted proteomics using parallel reaction monitoring (PRM). The expression of biomarker candidates was validated by immunohistochemistry in a large tissue microarray (TMA) cohort of 141 patients with resectable pancreatic cancer. Kaplan-Meier and Cox proportional hazard modelling was used to investigate the prognostic utility of candidate protein markers. FINDINGS In the initial MS-discovery phase, 165 proteins were identified as potential biomarkers. In the subsequent MS-verification phase, a panel of 45 candidate proteins was verified by the development of a PRM assay. Brain acid soluble protein 1 (BASP1) was identified as a new biomarker candidate for pancreatic cancer possessing largely unknown biological and clinical functions and was selected for further analysis. Importantly, bioinformatic analysis indicated that BASP1 interacts with Wilms tumour protein (WT1) in pancreatic cancer. TMA-based immunohistochemistry analysis showed that BASP1 was an independent predictor of prolonged survival (HR 0.468, 95% CI 0.257-0.852, p = .013) and predicted favourable response to adjuvant chemotherapy, whereas WT1 indicated a worsened survival (HR 1.636, 95% CI 1.083-2.473, p = .019) and resistance to chemotherapy. Interaction analysis showed that patients with negative BASP1 and high WT1 expression had the poorest outcome (HR 3.536, 95% CI 1.336-9.362, p = .011). INTERPRETATION We here describe an MS-based proteomics platform for developing biomarkers for pancreatic cancer. Bioinformatic analysis and clinical data from our study suggest that BASP1 and its putative interaction partner WT1 can be used as biomarkers for predicting outcomes in pancreatic cancer patients.
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Affiliation(s)
- Qimin Zhou
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden; The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China; Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Roland Andersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Dingyuan Hu
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Monika Bauden
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Theresa Kristl
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Agata Sasor
- Department of Pathology, Skåne University Hospital, Lund, Sweden
| | - Krzysztof Pawłowski
- Department of Experimental Design and Bioinformatics, Warsaw University of Life Sciences, Warsaw, Poland; Department of Translational Medicine, Lund University, Malmö, Sweden
| | - Indira Pla
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Katarzyna Said Hilmersson
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden
| | - Mengtao Zhou
- Key Laboratory of Diagnosis and Treatment of Severe Hepato-Pancreatic Diseases of Zhejiang Province, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Fan Lu
- The Eye Hospital, School of Ophthalmology and Optometry, Wenzhou Medical University, Wenzhou, Zhejiang, China
| | - György Marko-Varga
- Department of Biomedical Engineering, Clinical Protein Science and Imaging, Lund University, Lund, Sweden
| | - Daniel Ansari
- Department of Surgery, Clinical Sciences Lund, Lund University and Skåne University Hospital, Lund, Sweden.
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16
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Rolland DC, Lim MS, Elenitoba-Johnson KS. Mass spectrometry and proteomics in hematology. Semin Hematol 2019; 56:52-57. [DOI: 10.1053/j.seminhematol.2018.05.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2018] [Accepted: 05/07/2018] [Indexed: 01/02/2023]
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Hayama T, Ohyama K. Recent development and trends in sample extraction and preparation for mass spectrometric analysis of nucleotides, nucleosides, and proteins. J Pharm Biomed Anal 2018; 161:51-60. [PMID: 30145449 DOI: 10.1016/j.jpba.2018.08.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2018] [Revised: 08/02/2018] [Accepted: 08/16/2018] [Indexed: 12/20/2022]
Abstract
This review describes the recent developments in sample extraction and preparation techniques for mass spectrometric analysis of nucleotides, nucleosides, and proteins. Unique materials and techniques have been developed for highly selective extraction of nucleotides and nucleosides by solid-phase extraction strategies using various affinities. However, for proteins, the analysis of small-scale sections of diseased tissues (formalin-fixed, paraffin-embedded tissues) and the direct analysis of an exact lesion on the surface of diseased tissues (liquid extraction surface analysis) have become important advances in this field. In this review, we focus on the latest developments of these techniques and strategies.
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Affiliation(s)
- Tadashi Hayama
- Faculty of Pharmaceutical Sciences, Fukuoka University, 8-19-1 Nanakuma, Johnan, Fukuoka 814-0180, Japan
| | - Kaname Ohyama
- Graduate School of Biomedical Sciences, Nagasaki University, 1-7-1 Sakamoto-machi, Nagasaki 852-8588, Japan.
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Ozgyin L, Horvath A, Balint BL. Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing. Oncotarget 2018; 9:31312-31329. [PMID: 30140372 PMCID: PMC6101130 DOI: 10.18632/oncotarget.25764] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2017] [Accepted: 06/22/2018] [Indexed: 11/25/2022] Open
Abstract
Biobanks operating at ambient temperatures would dramatically reduce the costs associated with standard cryogenic storage. In the present study, we used lyophilization to stabilize unfractionated human cells in a dried state at room temperature and tested the yield and integrity of the isolated RNA by microfluidic electrophoresis, RT-qPCR and RNA sequencing. RNA yields and integrity measures were not reduced for lyophilized cells (unstored, stored for two weeks or stored for two months) compared to their paired controls. The abundance of the selected mRNAs with various expression levels, as well as enhancer-associated RNAs and cancer biomarker long non-coding RNAs (MALAT1, GAS5 and TUG1), were not significantly different between the two groups as assessed by RT-qPCR. RNA sequencing data of three lyophilized samples stored for two weeks at room temperature revealed a high degree of similarity with their paired controls in terms of the RNA biotype distribution, cumulative gene diversity, gene body read coverage and per base mismatch rate. Among the 28 differentially expressed genes transcriptional regulators, as well as certain transcript properties suggestive of a residual active decay mechanism were enriched. Our study suggests that freeze-drying of human cells is a suitable alternative for the long-term stabilization of total RNA in whole human cells for routine diagnostics and high-throughput biomedical research.
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Affiliation(s)
- Lilla Ozgyin
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen H-4012, Hungary
| | - Attila Horvath
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen H-4012, Hungary.,Department of Biochemistry and Molecular Biology, Nuclear Hormone Receptor Research Laboratory, University of Debrecen, Debrecen H-4012, Hungary
| | - Balint Laszlo Balint
- Department of Biochemistry and Molecular Biology, Genomic Medicine and Bioinformatic Core Facility, University of Debrecen, Debrecen H-4012, Hungary
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Keam SP, Gulati T, Gamell C, Caramia F, Huang C, Schittenhelm RB, Kleifeld O, Neeson PJ, Haupt Y, Williams SG. Exploring the oncoproteomic response of human prostate cancer to therapeutic radiation using data-independent acquisition (DIA) mass spectrometry. Prostate 2018. [PMID: 29520850 DOI: 10.1002/pros.23500] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
INTRODUCTION The development of radioresistance in prostate cancer (PCa) is an important clinical issue and is still largely uninformed by personalized molecular characteristics. The aim of this study was to establish a platform that describes the early oncoproteomic response of human prostate tissue to radiation therapy (RT) using a prospective human tissue cohort. METHODS Fresh and fixed transperineal biopsies from eight men with clinically localized tumors were taken prior to and 14 days following a single fraction of high-dose-rate brachytherapy. Quantitative protein analysis was achieved using an optimized protein extraction pipeline and subsequent data-independent acquisition mass spectroscopy (DIA-MS). Ontology analyses were used to identify enriched functional pathways, with the candidates further interrogated in formalin-fixed paraffin-embedded tissue biopsies from five additional patients. RESULTS We obtained a mean coverage of 5660 proteins from fresh tissue biopsies; with the principal post-radiation change observed being an increase in levels amongst a total of 49 proteins exhibiting abundance changes. Many of these changes in abundance varied between patients and, typically to prostate cancer tissue, exhibited a high level of heterogeneity. Ontological analysis revealed the enrichment of the protein activation cascades of three immunological pathways: humoral immune response, leukocyte mediated immunity and complement activation. These were predominantly associated with the extracellular space. We validated significant expression differences in between 20% and 61% of these candidates using the separate fixed-tissue cohort and established their feasibility as an experimental tissue resource by acquiring quantitative data for a mean of 5152 proteins per patient. DISCUSSION In this prospective study, we have established a sensitive and reliable oncoproteomic pipeline for the analysis of both fresh and formalin-fixed human PCa tissue. We identified multiple pathways known to be radiation-responsive and have established a powerful database of candidates and pathways with no current association with RT. This information may be beneficial in the advancement of personalized therapies and potentially, predictive biomarkers.
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Affiliation(s)
- Simon P Keam
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Twishi Gulati
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Cristina Gamell
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Franco Caramia
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Cheng Huang
- Monash Biomedical Proteomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Ralf B Schittenhelm
- Monash Biomedical Proteomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
| | - Oded Kleifeld
- The Smoler Proteomics Center Technion, Israel Institute of Technology, Haifa, Israel
| | - Paul J Neeson
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Cancer Immunology Research, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Ygal Haupt
- Tumor Suppression Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
- The Sir Peter MacCallum Department of Oncology, The University of Melbourne, Melbourne, Victoria, Australia
- Monash Biomedical Proteomics Facility, Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, Victoria, Australia
- Department of Pathology, The University of Melbourne, Melbourne, Victoria, Australia
| | - Scott G Williams
- Division of Radiation Oncology and Cancer Imaging, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
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Biomedical analysis of formalin-fixed, paraffin-embedded tissue samples: The Holy Grail for molecular diagnostics. J Pharm Biomed Anal 2018; 155:125-134. [PMID: 29627729 DOI: 10.1016/j.jpba.2018.03.065] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Revised: 03/30/2018] [Accepted: 03/31/2018] [Indexed: 02/07/2023]
Abstract
More than a century ago in 1893, a revolutionary idea about fixing biological tissue specimens was introduced by Ferdinand Blum, a German physician. Since then, a plethora of fixation methods have been investigated and used. Formalin fixation with paraffin embedment became the most widely used types of fixation and preservation method, due to its proper architectural conservation of tissue structures and cellular shape. The huge collection of formalin-fixed, paraffin-embedded (FFPE) sample archives worldwide holds a large amount of unearthed information about diseases that could be the Holy Grail in contemporary biomarker research utilizing analytical omics based molecular diagnostics. The aim of this review is to critically evaluate the omics options for FFPE tissue sample analysis in the molecular diagnostics field.
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21
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Sadick JS, Darling EM. Processing fixed and stored adipose-derived stem cells for quantitative protein array assays. Biotechniques 2017; 63:275-280. [PMID: 29235974 DOI: 10.2144/000114620] [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] [Received: 09/21/2017] [Accepted: 11/06/2017] [Indexed: 01/05/2023] Open
Abstract
Accurately characterizing cellular subpopulations is essential for elucidating the mechanisms underlying normal and pathological biology. Isolation of specific cell types can be accomplished by labeling unique cell-associated proteins with fluorescent antibodies. Cell fixation is commonly used to prepare these samples and allow for long-term storage, but this poses challenges for subsequent protein analysis. We previously established the FITSAR (formaldehyde-fixed intracellular target-sorted antigen retrieval) method, in which protein can be isolated and characterized from fixed, enriched cell subpopulations. Here, we improve on this method by allowing compatibility with highly sensitive multiplex protein arrays and demonstrating applicability to long-term stored samples. Feasibility experiments demonstrated parallel detection of cell adhesion molecules (CAMs) using an enzyme-linked immunosorbent assay (ELISA) panel with human adipose-derived stem cells (ASCs) stored for up to 1 month.
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Affiliation(s)
- Jessica S Sadick
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI
| | - Eric M Darling
- Department of Molecular Pharmacology, Physiology, and Biotechnology, Brown University, Providence, RI.,Center for Biomedical Engineering, Brown University, Providence, RI.,School of Engineering, Brown University, Providence, RI.,Department of Orthopaedics, Brown University, Providence, RI
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Zhao X, Huffman KE, Fujimoto J, Canales JR, Girard L, Nie G, Heymach JV, Wistuba II, Minna JD, Yu Y. Quantitative Proteomic Analysis of Optimal Cutting Temperature (OCT) Embedded Core-Needle Biopsy of Lung Cancer. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2017; 28:2078-2089. [PMID: 28752479 PMCID: PMC5693617 DOI: 10.1007/s13361-017-1706-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/30/2017] [Revised: 05/03/2017] [Accepted: 05/04/2017] [Indexed: 06/07/2023]
Abstract
With recent advances in understanding the genomic underpinnings and oncogenic drivers of pathogenesis in different subtypes, it is increasingly clear that proper pretreatment diagnostics are essential for the choice of appropriate treatment options for non-small cell lung cancer (NSCLC). Tumor tissue preservation in optimal cutting temperature (OCT) compound is commonly used in the surgical suite. However, proteins recovered from OCT-embedded specimens pose a challenge for LC-MS/MS experiments, due to the large amounts of polymers present in OCT. Here we present a simple workflow for whole proteome analysis of OCT-embedded NSCLC tissue samples, which involves a simple trichloroacetic acid precipitation step. Comparisons of protein recovery between frozen versus OCT-embedded tissue showed excellent consistency with more than 9200 proteins identified. Using an isobaric labeling strategy, we quantified more than 5400 proteins in tumor versus normal OCT-embedded core needle biopsy samples. Gene ontology analysis indicated that a number of proliferative as well as squamous cell carcinoma (SqCC) marker proteins were overexpressed in the tumor, consistent with the patient's pathology based diagnosis of "poorly differentiated SqCC". Among the most downregulated proteins in the tumor sample, we noted a number of proteins with potential immunomodulatory functions. Finally, interrogation of the aberrantly expressed proteins using a candidate approach and cross-referencing with publicly available databases led to the identification of potential druggable targets in DNA replication and DNA damage repair pathways. We conclude that our approach allows LC-MS/MS proteomic analyses on OCT-embedded lung cancer specimens, opening the way to bring powerful proteomics into the clinic. Graphical Abstract ᅟ.
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Affiliation(s)
- Xiaozheng Zhao
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, People's Republic of China
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kenneth E Huffman
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Pharmacology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Junya Fujimoto
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jamie Rodriguez Canales
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Luc Girard
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Pharmacology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Guangjun Nie
- CAS Center for Excellence in Nanoscience, National Center for Nanoscience and Technology, Beijing, 100190, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
| | - John V Heymach
- Department of Head and Neck and Thoracic Oncology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Igacio I Wistuba
- Department of Translational Molecular Pathology, University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - John D Minna
- Hamon Center for Therapeutic Oncology Research, Simmons Comprehensive Cancer Center, Pharmacology and Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yonghao Yu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX, USA.
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Ostasiewicz P, Wiśniewski J. A Protocol for Large-Scale Proteomic Analysis of Microdissected Formalin Fixed and Paraffin Embedded Tissue. Methods Enzymol 2017; 585:159-176. [DOI: 10.1016/bs.mie.2016.09.017] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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24
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Kim E, Wright MJ, Sioson L, Novos T, Gill AJ, Benn DE, White C, Dwight T, Clifton-Bligh RJ. Utility of the succinate: Fumarate ratio for assessing SDH dysfunction in different tumor types. Mol Genet Metab Rep 2016; 10:45-49. [PMID: 28070496 PMCID: PMC5219629 DOI: 10.1016/j.ymgmr.2016.12.006] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 12/17/2016] [Indexed: 12/14/2022] Open
Abstract
Objective Mutations of genes encoding the four subunits of succinate dehydrogenase (SDH) have been associated with pheochromocytoma and paraganglioma (PPGLs), gastrointestinal stromal tumors (GISTs) and renal cell carcinomas (RCCs). These tumors have not been characterized in a way that reflects severity of SDH dysfunction. Mass spectrometric analysis now allows measurement of metabolites extracted from formalin fixed paraffin embedded (FFPE) specimens. We assess whether SDH deficiency in various tumor types characterized by loss of SDHB protein expression correlates with SDH dysfunction as assessed by the ratio of succinate:fumarate in FFPE specimens. Patients and methods Sections of FFPE tumor specimens from 18 PPGL, 10 GIST and 11 RCC patients with known SDHx mutation status for SDH deficiency were collected for mass spectrometric analysis of succinate and fumarate. Results FFPE samples showed higher succinate:fumarate ratios in SDH-deficient PPGLs compared to SDH-sufficient PPGLs. Similarly, a higher succinate:fumarate ratio was able to distinguish SDH-deficient GISTs and RCCs from their SDH-sufficient counterparts with great selectivity. Interestingly, the cut-off value of the succinate:fumarate ratio was two-folds greater in RCCs than GISTs. Conclusion Analyzing biochemical imbalances preserved in FFPE specimens with mass spectrometry expands the method and sample type repertoire available for characterisation of multiple neoplasias associated with SDH deficiency.
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Affiliation(s)
- Edward Kim
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia; University of Sydney, Sydney, Australia
| | - Michael Jp Wright
- Clinical Chemistry, South Eastern Area Laboratory Services Pathology, Prince of Wales Private Hospital, Sydney, Australia
| | - Loretta Sioson
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia
| | - Talia Novos
- Clinical Chemistry, South Eastern Area Laboratory Services Pathology, Prince of Wales Private Hospital, Sydney, Australia
| | - Anthony J Gill
- Cancer Diagnosis and Pathology Group, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia; University of Sydney, Sydney, Australia
| | - Diana E Benn
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia; University of Sydney, Sydney, Australia
| | - Christopher White
- Clinical Chemistry, South Eastern Area Laboratory Services Pathology, Prince of Wales Private Hospital, Sydney, Australia; Department of Endocrinology and Diabetes, Prince of Wales Hospital, Sydney, Australia
| | - Trisha Dwight
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia; University of Sydney, Sydney, Australia
| | - Roderick J Clifton-Bligh
- Cancer Genetics, Kolling Institute of Medical Research, Royal North Shore Hospital, Sydney, Australia; University of Sydney, Sydney, Australia
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25
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Broeckx V, Boonen K, Pringels L, Sagaert X, Prenen H, Landuyt B, Schoofs L, Maes E. Comparison of multiple protein extraction buffers for GeLC-MS/MS proteomic analysis of liver and colon formalin-fixed, paraffin-embedded tissues. MOLECULAR BIOSYSTEMS 2016; 12:553-65. [PMID: 26676081 DOI: 10.1039/c5mb00670h] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a potential valuable source of samples for clinical research. Since these specimens are banked in hospital archives, large cohorts of samples can be collected in short periods of time which can all be linked with a patients' clinical history. Therefore, the use of FFPE tissue in protein biomarker discovery studies gains interest. However, despite the growing number of FFPE proteome studies in the literature, there is a lack of a FFPE proteomics standard operating procedure (SOP). One of the challenging steps in the development of such a SOP is the ability to obtain an efficient and repeatable extraction of full length FFPE proteins. In this study, the protein extraction efficiency of eight protein extraction buffers is critically compared with GeLC-MS/MS (1D gel electrophoresis followed by in-gel digestion and LC-MS/MS). The data variation caused by using these extraction buffers was investigated since the variation is a very important aspect when using FFPE tissue as a source for biomarker detection. In addition, a qualitative comparison was made between the protein extraction efficiency and repeatability for FFPE tissue and fresh frozen tissue.
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Affiliation(s)
- Valérie Broeckx
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Kurt Boonen
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Lentel Pringels
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Xavier Sagaert
- Centre for Translational Cell and Tissue Research, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Hans Prenen
- Department of Gastro-Enterology, Digestive Oncology Unit, University Hospital of Leuven, Herestraat 49, 3000 Leuven, Belgium
| | - Bart Landuyt
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Liliane Schoofs
- Research Group of Functional Genomics and Proteomics, Department of Biology, University of Leuven, Zoological Institute, Naamsestraat 59, 3000 Leuven, Belgium.
| | - Evelyne Maes
- Flemish Institute for Technological Research (VITO), Boeretang 200, 2400 Mol, Belgium and Centre for Proteomics, University of Antwerp/Flemish Institute for Technological Research (VITO), Groenenborgerlaan 171, 2020 Antwerp, Belgium
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26
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Kennedy JJ, Whiteaker JR, Schoenherr RM, Yan P, Allison K, Shipley M, Lerch M, Hoofnagle AN, Baird GS, Paulovich AG. Optimized Protocol for Quantitative Multiple Reaction Monitoring-Based Proteomic Analysis of Formalin-Fixed, Paraffin-Embedded Tissues. J Proteome Res 2016; 15:2717-28. [PMID: 27462933 DOI: 10.1021/acs.jproteome.6b00245] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Despite a clinical, economic, and regulatory imperative to develop companion diagnostics, precious few new biomarkers have been successfully translated into clinical use, due in part to inadequate protein assay technologies to support large-scale testing of hundreds of candidate biomarkers in formalin-fixed paraffin-embedded (FFPE) tissues. Although the feasibility of using targeted, multiple reaction monitoring mass spectrometry (MRM-MS) for quantitative analyses of FFPE tissues has been demonstrated, protocols have not been systematically optimized for robust quantification across a large number of analytes, nor has the performance of peptide immuno-MRM been evaluated. To address this gap, we used a test battery approach coupled to MRM-MS with the addition of stable isotope-labeled standard peptides (targeting 512 analytes) to quantitatively evaluate the performance of three extraction protocols in combination with three trypsin digestion protocols (i.e., nine processes). A process based on RapiGest buffer extraction and urea-based digestion was identified to enable similar quantitation results from FFPE and frozen tissues. Using the optimized protocols for MRM-based analysis of FFPE tissues, median precision was 11.4% (across 249 analytes). There was excellent correlation between measurements made on matched FFPE and frozen tissues, both for direct MRM analysis (R(2) = 0.94) and immuno-MRM (R(2) = 0.89). The optimized process enables highly reproducible, multiplex, standardizable, quantitative MRM in archival tissue specimens.
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Affiliation(s)
- Jacob J Kennedy
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Jeffrey R Whiteaker
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Regine M Schoenherr
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Ping Yan
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
| | - Kimberly Allison
- Department of Pathology, Stanford University , Stanford, California 94305 United States
| | - Melissa Shipley
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Melissa Lerch
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Andrew N Hoofnagle
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Geoffrey Stuart Baird
- Department of Laboratory Medicine, University of Washington , Seattle, Washington 98195 United States
| | - Amanda G Paulovich
- Clinical Research Division, Fred Hutchinson Cancer Research Center , Seattle, Washington 98109, United States
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27
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Analysis of formalin-fixed, paraffin-embedded (FFPE) tissue via proteomic techniques and misconceptions of antigen retrieval. Biotechniques 2016; 60:229-38. [DOI: 10.2144/000114414] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2015] [Accepted: 02/20/2016] [Indexed: 11/23/2022] Open
Abstract
Since emerging in the late 19th century, formaldehyde fixation has become a standard method for preservation of tissues from clinical samples. The advantage of formaldehyde fixation is that fixed tissues can be stored at room temperature for decades without concern for degradation. This has led to the generation of huge tissue banks containing thousands of clinically significant samples. Here we review techniques for proteomic analysis of formalin-fixed, paraffin-embedded (FFPE) tissue samples with a specific focus on the methods used to extract and break formaldehyde crosslinks. We also discuss an error-of-interpretation associated with the technique known as “antigen retrieval.” We have discovered that this term has been mistakenly applied to two disparate molecular techniques; therefore, we argue that a terminology change is needed to ensure accurate reporting of experimental results. Finally, we suggest that more investigation is required to fully understand the process of formaldehyde fixation and its subsequent reversal.
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28
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Bennike TB, Kastaniegaard K, Padurariu S, Gaihede M, Birkelund S, Andersen V, Stensballe A. Comparing the proteome of snap frozen, RNAlater preserved, and formalin-fixed paraffin-embedded human tissue samples. EUPA OPEN PROTEOMICS 2016; 10:9-18. [PMID: 29900094 PMCID: PMC5988570 DOI: 10.1016/j.euprot.2015.10.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 08/19/2015] [Accepted: 10/25/2015] [Indexed: 01/14/2023]
Abstract
Large biobanks exist worldwide containing formalin-fixed, paraffin-embedded samples and samples stored in RNAlater. However, the impact of tissue preservation on the result of a quantative proteome analysis remains poorly described. Human colon mucosal biopsies were extracted from the sigmoideum and either immediately frozen, stabilized in RNAlater, or stabilized by formalin-fixation. In one set of biopsies, formalin stabilization was delayed for 30 min. The protein content of the samples was characterized by high throughput quantitative proteomics. We were able to identify a similar high number of proteins in the samples regardless of preservation method, with only minor differences in protein quantitation.
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Key Words
- CAN, acetonitrile
- DF, directly-frozen
- FA, formic acid
- FASP, filter-aided sample preparation
- FDR, false discovery rate
- FFPE, formalin-fixed
- Formalin-fixed
- HLA-A class I, histocompatibility antigen A-23 alpha chain
- HLA-DRB1 class II, histocompatibility antigen DRB1-4 beta chain
- Human colon mucosa
- LFQ, label-free quantification
- Mass spectrometry
- PCA, principle component analysis
- PSM, peptide spectral match
- PTM, post-translational modification
- Paraffin-embedded
- Preservation
- Proteomics
- RNAlater
- SDC, sodium deoxycholate
- SDS, sodium dodecyl sulfate
- TEAB, triethylammonium bicarbonate
- iFFPE, immediately formalin-fixed
- s, standard deviation
- sFFPE, stored for 30 min prior to formalin-fixed
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Affiliation(s)
- Tue Bjerg Bennike
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | | | - Simona Padurariu
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
| | - Michael Gaihede
- Department of Otolaryngology, Head and Neck Surgery, Aalborg University Hospital, Aalborg, Denmark
- Department of Clinical Medicine, Aalborg University, Aalborg, Denmark
| | - Svend Birkelund
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
| | - Vibeke Andersen
- Research Unit for Molecular Diagnostic and Clinical Research, Hospital of Southern Jutland, Aabenraa, Denmark
- Institute of Regional Health Research-Center Soenderjylland, University of Southern Denmark, Odense, Denmark
| | - Allan Stensballe
- Department of Health Science and Technology, Aalborg University, Aalborg, Denmark
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29
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Shen K, Sun J, Cao X, Zhou D, Li J. Comparison of Different Buffers for Protein Extraction from Formalin-Fixed and Paraffin-Embedded Tissue Specimens. PLoS One 2015; 10:e0142650. [PMID: 26580073 PMCID: PMC4651363 DOI: 10.1371/journal.pone.0142650] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2015] [Accepted: 10/26/2015] [Indexed: 01/26/2023] Open
Abstract
We determined the best extraction buffer for proteomic investigation using formalin-fixation and paraffin-embedded (FFPE) specimens. A Zwittergent 3–16 based buffer, sodium dodecyl sulfate (SDS)-containing buffer with/without polyethylene glycol 20000 (PEG20000), urea-containing buffer, and FFPE-FASP protein preparation kit were compared for protein extraction from different types of rat FFPE tissues, including the heart, brain, liver, lung, and kidney. All of the samples were divided into two groups of laser microdissected (LMD) and non-LMD specimens. For both kinds of specimens, Zwittergent was the most efficient buffer for identifying peptides and proteins, was broadly applicable to different tissues without impairing the enzymatic digestion, and was well compatible with mass spectrometry analysis. As a high molecular weight carrier substance, PEG20000 improved the identification of peptides and proteins; however, such an advantage is limited to tissues containing submicrograms to micrograms of protein. Considering its low lytic strength, urea-containing buffer would not be the first alternative for protein recovery. In conclusion, Zwittergent 3–16 is an effective buffer for extracting proteins from FFPE specimens for downstream proteomics analysis.
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Affiliation(s)
- Kaini Shen
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jian Sun
- Department of Pathology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Xinxin Cao
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Daobin Zhou
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jian Li
- Department of Hematology, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
- * E-mail:
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30
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O'Rourke MB, Djordjevic SP, Padula MP. A non-instrument-based method for the analysis of formalin-fixed paraffin-embedded human spinal cord via matrix-assisted laser desorption/ionisation imaging mass spectrometry. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2015; 29:1836-1840. [PMID: 26331935 DOI: 10.1002/rcm.7283] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/03/2015] [Revised: 07/15/2015] [Accepted: 07/16/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE This paper, in conjunction with a work published earlier this year by O'Rourke et al., aims to provide a comprehensive set of protocols for the analysis of formalin-fixed paraffin-embedded (FFPE) tissue via matrix-assisted laser desorption/ionisation imaging mass spectrometry (MALDI IMS) in a low-cost and highly repeatable and robust way, thereby allowing other research teams to begin their own IMS-centered avenues of research. METHODS Samples of FFPE tissue were sectioned at 5 µm, water float mounted to specially prepared ITO glass slides and then dilipidated in a graded alcohol series. Tissue sections were then antigen retrieved under pressure in 20 mmol Tris-HCl (pH 8.8), coated with trypsin and digested O/N at 37°C. Samples were then sublimated with matrix to a final coverage of 0.2 mg/cm(2), recrystallised at 37°C with 50:50 acetonitrile (ACN)/0.1% trifluoroacetic acid (TFA) for 1 h and analysed with a MALDI TOF/TOF mass spectrometer. RESULTS Serial sections were imaged, revealing little to no variation with regards to image quality and corresponding spectra. We have also attempted to describe the processes that govern the various aspects of this protocol with respect to each step necessary to ensure reproducibility. CONCLUSIONS We are confident that this protocol in conjunction with the work published earlier by O'Rourke et al. provides the basis for a repeatable and robust protocol for the analysis of tissues from various sources via MALDI-IMS. The descriptions of key steps within allows for easy adoption of the protocol while allowing for desired modifications to be performed with minimal yet intuitive adjustment.
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Affiliation(s)
- Matthew B O'Rourke
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia
| | - Steven P Djordjevic
- The iThree Institute, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia
| | - Matthew P Padula
- Proteomics Core Facility, University of Technology Sydney, Cnr Harris and Thomas St, Ultimo, NSW, 2007, Australia
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31
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Steiner C, Tille JC, Lamerz J, Kux van Geijtenbeek S, McKee TA, Venturi M, Rubbia-Brandt L, Hochstrasser D, Cutler P, Lescuyer P, Ducret A. Quantification of HER2 by Targeted Mass Spectrometry in Formalin-Fixed Paraffin-Embedded (FFPE) Breast Cancer Tissues. Mol Cell Proteomics 2015; 14:2786-99. [PMID: 26149442 DOI: 10.1074/mcp.o115.049049] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Indexed: 11/06/2022] Open
Abstract
The ability to accurately quantify proteins in formalin-fixed paraffin-embedded tissues using targeted mass spectrometry opens exciting perspectives for biomarker discovery. We have developed and evaluated a selectedreaction monitoring assay for the human receptor tyrosine-protein kinase erbB-2 (HER2) in formalin-fixed paraffin-embedded breast tumors. Peptide candidates were identified using an untargeted mass spectrometry approach in relevant cell lines. A multiplexed assay was developed for the six best candidate peptides and evaluated for linearity, precision and lower limit of quantification. Results showed a linear response over a calibration range of 0.012 to 100 fmol on column (R(2): 0.99-1.00).The lower limit of quantification was 0.155 fmol on column for all peptides evaluated. The six HER2 peptides were quantified by selected reaction monitoring in a cohort of 40 archival formalin-fixed paraffin-embedded tumor tissues from women with invasive breast carcinomas, which showed different levels of HER2 gene amplification as assessed by standard methods used in clinical pathology. The amounts of the six HER2 peptides were highly and significantly correlated with each other, indicating that peptide levels can be used as surrogates of protein amounts in formalin-fixed paraffin-embedded tissues. After normalization for sample size, selected reaction monitoring peptide measurements were able to correctly predict 90% of cases based on HER2 amplification as defined by the American Society of Clinical Oncology and College of American Pathologists. In conclusion, the developed assay showed good analytical performance and a high agreement with immunohistochemistry and fluorescence in situ hybridization data. This study demonstrated that selected reaction monitoring allows to accurately quantify protein expression in formalin-fixed paraffin-embedded tissues and represents therefore a powerful approach for biomarker discovery studies. The untargeted mass spectrometry data is available via ProteomeXchange whereas the quantification data by selected reaction monitoring is available on the Panorama Public website.
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Affiliation(s)
- Carine Steiner
- From the ‡Division of Laboratory Medicine, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva, Switzerland; §Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland;
| | - Jean-Christophe Tille
- ¶Division of Clinical Pathology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva, Switzerland
| | - Jens Lamerz
- §Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Sabine Kux van Geijtenbeek
- §Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Thomas A McKee
- ¶Division of Clinical Pathology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva, Switzerland
| | - Miro Venturi
- ‖Oncology Division, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Penzberg, Roche Diagnostics GmbH, Nonnenwald 2, D-82377 Penzberg, Germany
| | - Laura Rubbia-Brandt
- ¶Division of Clinical Pathology, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva, Switzerland
| | - Denis Hochstrasser
- From the ‡Division of Laboratory Medicine, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva, Switzerland
| | - Paul Cutler
- §Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
| | - Pierre Lescuyer
- From the ‡Division of Laboratory Medicine, Geneva University Hospitals, Rue Gabrielle-Perret-Gentil 4, CH-1211 Geneva, Switzerland
| | - Axel Ducret
- §Translational Technologies and Bioinformatics, Pharmaceutical Sciences, Roche Pharma Research & Early Development (pRED), Roche Innovation Center Basel, F. Hoffmann-La Roche AG, Grenzacherstrasse 124, CH-4070 Basel, Switzerland
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32
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Bader S, Zajac M, Friess T, Ruge E, Rieder N, Gierke B, Heubach Y, Thomas M, Pawlak M. Evaluation of Protein Profiles From Treated Xenograft Tumor Models Identifies an Antibody Panel for Formalin-fixed and Paraffin-embedded (FFPE) Tissue Analysis by Reverse Phase Protein Arrays (RPPA). Mol Cell Proteomics 2015; 14:2775-85. [PMID: 26106084 DOI: 10.1074/mcp.o114.045542] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2014] [Indexed: 12/31/2022] Open
Abstract
Reverse phase protein arrays (RPPA) are an established tool for measuring the expression and activation status of multiple proteins in parallel using only very small amounts of tissue. Several studies have demonstrated the value of this technique for signaling pathway analysis using proteins extracted from fresh frozen (FF) tissue in line with validated antibodies for this tissue type; however, formalin fixation and paraffin embedding (FFPE) is the standard method for tissue preservation in the clinical setting. Hence, we performed RPPA to measure profiles for a set of 300 protein markers using matched FF and FFPE tissue specimens to identify which markers performed similarly using the RPPA technique in fixed and unfixed tissues. Protein lysates were prepared from matched FF and FFPE tissue specimens of individual tumors taken from three different xenograft models of human cancer. Materials from both untreated mice and mice treated with either anti-HER3 or bispecific anti-IGF-1R/EGFR monoclonal antibodies were analyzed. Correlations between signals from FF and FFPE tissue samples were investigated. Overall, 60 markers were identified that produced comparable profiles between FF and FFPE tissues, demonstrating significant correlation between the two sample types. The top 25 markers also showed significance after correction for multiple testing. The panel of markers covered several clinically relevant tumor signaling pathways and both phosphorylated and nonphosphorylated proteins were represented. Biologically relevant changes in marker expression were noted when RPPA profiles from treated and untreated xenografts were compared. These data demonstrate that, using appropriately selected antibodies, RPPA analysis from FFPE tissue is well feasible and generates biologically meaningful information. The identified panel of markers that generate similar profiles in matched fixed and unfixed tissue samples may be clinically useful for pharmacodynamic studies of drug effect using FFPE tissues.
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Affiliation(s)
- Sabine Bader
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Magdalena Zajac
- §Pharma Research & Early Development, Roche Innovation Centre Welwyn, 6 Falcon Way, Shire Park, Welwyn Garden City, Herts, AL7 1TW, United Kingdom
| | - Thomas Friess
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Elisabeth Ruge
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Natascha Rieder
- From the ‡Pharma Research & Early Development, Roche Innovation Center Penzberg, Nonnenwald 2, 82377, Penzberg, Germany
| | - Berthold Gierke
- ¶Department Biochemistry & Protein Profiling, NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Yvonne Heubach
- ¶Department Biochemistry & Protein Profiling, NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany
| | - Marlene Thomas
- ‖Roche Pharma AG, Emil-Barell-Str. 1, 79639, Grenzach-Wyhlen, Germany
| | - Michael Pawlak
- ¶Department Biochemistry & Protein Profiling, NMI Natural and Medical Sciences Institute at the University of Tuebingen, Markwiesenstrasse 55, 72770, Reutlingen, Germany;
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Zhang Y, Muller M, Xu B, Yoshida Y, Horlacher O, Nikitin F, Garessus S, Magdeldin S, Kinoshita N, Fujinaka H, Yaoita E, Hasegawa M, Lisacek F, Yamamoto T. Unrestricted modification search reveals lysine methylation as major modification induced by tissue formalin fixation and paraffin embedding. Proteomics 2015; 15:2568-79. [PMID: 25825003 DOI: 10.1002/pmic.201400454] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Revised: 01/22/2015] [Accepted: 03/25/2015] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue is considered as an appropriate alternative to frozen/fresh tissue for proteomic analysis. Here we study formalin-induced alternations on a proteome-wide level. We compared LC-MS/MS data of FFPE and frozen human kidney tissues by two methods. First, clustering analysis revealed that the biological variation is higher than the variation introduced by the two sample processing techniques and clusters formed in accordance with the biological tissue origin and not with the sample preservation method. Second, we combined open modification search and spectral counting to find modifications that are more abundant in FFPE samples compared to frozen samples. This analysis revealed lysine methylation (+14 Da) as the most frequent modification induced by FFPE preservation. We also detected a slight increase in methylene (+12 Da) and methylol (+30 Da) adducts as well as a putative modification of +58 Da, but they contribute less to the overall modification count. Subsequent SEQUEST analysis and X!Tandem searches of different datasets confirmed these trends. However, the modifications due to FFPE sample processing are a minor disturbance affecting 2-6% of all peptide-spectrum matches and the peptides lists identified in FFPE and frozen tissues are still highly similar.
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Affiliation(s)
- Ying Zhang
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland.,Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
| | - Markus Muller
- SIB-Swiss Institute of Bioinformatics, Geneva, Switzerland
| | - Bo Xu
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Yutaka Yoshida
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | | | | | | | - Sameh Magdeldin
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Egypt
| | - Naohiko Kinoshita
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Hidehiko Fujinaka
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Institute of Clinical Research, Niigata National Hospital, Kashiwazaki, Japan
| | - Eishin Yaoita
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan
| | - Miki Hasegawa
- Division of Digestive & General Surgery, Niigata University, Niigata, Japan
| | | | - Tadashi Yamamoto
- Department of Structural Pathology, Institute of Nephrology, Graduate School of Medical and Dental Sciences, Niigata University, Niigata, Japan.,Biofluid Biomarker Center (BB-C), Institute for Research Collaboration and Promotion, Niigata University, Niigata, Japan
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Matsuda Y, Ishiwata T. Fixation methods for the preservation of morphology, RNAs, and proteins in paraffin-embedded human cervical cancer cell xenografts in mice. Methods Mol Biol 2015; 1249:253-263. [PMID: 25348312 DOI: 10.1007/978-1-4939-2013-6_19] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
After various types of fixation, paraffin-embedded tissues are commonly used for histological analysis and pathological diagnosis; they are also suitable for long-term storage. Neutral buffered formalin, paraformaldehyde, and ethanol are common fixatives for histopathological analysis. For molecular biological analysis, fixed paraffin-embedded tissues are valuable resources; suitable fixative solutions and methods are needed to quantify and perform molecular biological analyses including immunohistochemistry, in situ hybridization, and quantitative polymerase chain reaction. Currently, 4 % paraformaldehyde is the recommended fixative for the preservation of RNAs and proteins, as well as for morphological study in paraffin-embedded human cervical cancer tissues that were xenografted in immunodeficient mice. Here, we describe the method for the fixation and preparation of paraffin-embedded tissue specimens for analysis of RNAs, proteins, and morphology.
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Affiliation(s)
- Yoko Matsuda
- Department of Pathology, Tokyo Metropolitan Geriatric Hospital and Institute of Gerontology, 35-2 Sakae-cho, Itabashi-ku, Tokyo, 173-0015, Japan
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35
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Kriegsmann J, Kriegsmann M, Casadonte R. MALDI TOF imaging mass spectrometry in clinical pathology: a valuable tool for cancer diagnostics (review). Int J Oncol 2014; 46:893-906. [PMID: 25482502 DOI: 10.3892/ijo.2014.2788] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 11/04/2014] [Indexed: 11/06/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) time-of-flight (TOF) imaging mass spectrometry (IMS) is an evolving technique in cancer diagnostics and combines the advantages of mass spectrometry (proteomics), detection of numerous molecules, and spatial resolution in histological tissue sections and cytological preparations. This method allows the detection of proteins, peptides, lipids, carbohydrates or glycoconjugates and small molecules.Formalin-fixed paraffin-embedded tissue can also be investigated by IMS, thus, this method seems to be an ideal tool for cancer diagnostics and biomarker discovery. It may add information to the identification of tumor margins and tumor heterogeneity. The technique allows tumor typing, especially identification of the tumor of origin in metastatic tissue, as well as grading and may provide prognostic information. IMS is a valuable method for the identification of biomarkers and can complement histology, immunohistology and molecular pathology in various fields of histopathological diagnostics, especially with regard to identification and grading of tumors.
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Affiliation(s)
- Jörg Kriegsmann
- MVZ for Histology, Cytology and Molecular Diagnostics, Trier, Germany
| | - Mark Kriegsmann
- Institute for Pathology, University of Heidelberg, Heidelberg, Germany
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36
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Gustafsson OJR, Briggs MT, Condina MR, Winderbaum LJ, Pelzing M, McColl SR, Everest-Dass AV, Packer NH, Hoffmann P. MALDI imaging mass spectrometry of N-linked glycans on formalin-fixed paraffin-embedded murine kidney. Anal Bioanal Chem 2014; 407:2127-39. [PMID: 25434632 PMCID: PMC4357650 DOI: 10.1007/s00216-014-8293-7] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Revised: 10/20/2014] [Accepted: 10/21/2014] [Indexed: 11/28/2022]
Abstract
Recent developments in spatial proteomics have paved the way for retrospective in situ mass spectrometry (MS) analyses of formalin-fixed paraffin-embedded clinical tissue samples. This type of analysis is commonly referred to as matrix-assisted laser desorption/ionization (MALDI) imaging. Recently, formalin-fixed paraffin-embedded MALDI imaging analyses were augmented to allow in situ analyses of tissue-specific N-glycosylation profiles. In the present study, we outline an improved automated sample preparation method for N-glycan MALDI imaging, which uses in situ PNGase F-mediated release and measurement of N-linked glycans from sections of formalin-fixed murine kidney. The sum of the presented data indicated that N-glycans can be cleaved from proteins within formalin-fixed tissue and characterized using three strategies: (i) extraction and composition analysis through on-target MALDI MS and liquid chromatography coupled to electrospray ionization ion trap MS; (ii) MALDI profiling, where N-glycans are released and measured from large droplet arrays in situ; and (iii) MALDI imaging, which maps the tissue specificity of N-glycans at a higher resolution. Thus, we present a complete, straightforward method that combines MALDI imaging and characterization of tissue-specific N-glycans and complements existing strategies. MALDI imaging MS of N-linked glycans released from formalin-fixed paraffin-embedded murine kidney sections. Ion intensity maps for (Hex)2(HexNAc)3(Deoxyhexose)3+(Man)3(GlcNAc)2 (m/z 2304.932, red), (Hex)6+(Man)3(GlcNAc)2 (m/z 1905.742, green) and (Hex)2(HexNAc)2+(Man)3(GlcNAc)2 (m/z 1663.756, blue) ![]()
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Affiliation(s)
- Ove J R Gustafsson
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, University of Adelaide, Adelaide, South Australia, 5005, Australia
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Steiner C, Ducret A, Tille JC, Thomas M, McKee TA, Rubbia-Brandt L, Scherl A, Lescuyer P, Cutler P. Applications of mass spectrometry for quantitative protein analysis in formalin-fixed paraffin-embedded tissues. Proteomics 2014; 14:441-51. [PMID: 24339433 PMCID: PMC4265304 DOI: 10.1002/pmic.201300311] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2013] [Revised: 11/04/2013] [Accepted: 11/11/2013] [Indexed: 12/12/2022]
Abstract
Proteomic analysis of tissues has advanced in recent years as instruments and methodologies have evolved. The ability to retrieve peptides from formalin-fixed paraffin-embedded tissues followed by shotgun or targeted proteomic analysis is offering new opportunities in biomedical research. In particular, access to large collections of clinically annotated samples should enable the detailed analysis of pathologically relevant tissues in a manner previously considered unfeasible. In this paper, we review the current status of proteomic analysis of formalin-fixed paraffin-embedded tissues with a particular focus on targeted approaches and the potential for this technique to be used in clinical research and clinical diagnosis. We also discuss the limitations and perspectives of the technique, particularly with regard to application in clinical diagnosis and drug discovery.
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Affiliation(s)
- Carine Steiner
- Division of Laboratory Medicine, Geneva University Hospital, Geneva, Switzerland; Human Protein Sciences Department, University of Geneva, Geneva, Switzerland; Translational Technologies and Bioinformatics, Pharma Research and Early Development, F. Hoffmann-La Roche AG, Basel, Switzerland
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Gustafsson OJR, Arentz G, Hoffmann P. Proteomic developments in the analysis of formalin-fixed tissue. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2014; 1854:559-80. [PMID: 25315853 DOI: 10.1016/j.bbapap.2014.10.003] [Citation(s) in RCA: 82] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Revised: 09/22/2014] [Accepted: 10/06/2014] [Indexed: 02/07/2023]
Abstract
Retrospective proteomic studies, including those which aim to elucidate the molecular mechanisms driving cancer, require the assembly and characterization of substantial patient tissue cohorts. The difficulty of maintaining and accessing native tissue archives has prompted the development of methods to access archives of formalin-fixed tissue. Formalin-fixed tissue archives, complete with patient meta data, have accumulated for decades, presenting an invaluable resource for these retrospective studies. This review presents the current knowledge concerning formalin-fixed tissue, with descriptions of the mechanisms of formalin fixation, protein extraction, top-down proteomics, bottom-up proteomics, quantitative proteomics, phospho- and glycoproteomics as well as imaging mass spectrometry. Particular attention has been given to the inclusion of proteomic investigations of archived tumour tissue. This article is part of a Special Issue entitled: Medical Proteomics.
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Affiliation(s)
- Ove J R Gustafsson
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005
| | - Georgia Arentz
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005
| | - Peter Hoffmann
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia 5005.
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Longuespée R, Fléron M, Pottier C, Quesada-Calvo F, Meuwis MA, Baiwir D, Smargiasso N, Mazzucchelli G, De Pauw-Gillet MC, Delvenne P, De Pauw E. Tissue Proteomics for the Next Decade? Towards a Molecular Dimension in Histology. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2014; 18:539-52. [DOI: 10.1089/omi.2014.0033] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Rémi Longuespée
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Maximilien Fléron
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Charles Pottier
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Florence Quesada-Calvo
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Marie-Alice Meuwis
- Hepato-Gastroenterology and Digestive Oncology Department, Liège University Hospital, University of Liège, Liège, Belgium
| | - Dominique Baiwir
- GIGA-R, GIGA Proteomic Facilities, University of Liège, Liège, Belgium
| | - Nicolas Smargiasso
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Gabriel Mazzucchelli
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
| | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, GIGA-Research, Department of Biomedical and Preclinical Sciences, University of Liège, Liège, Belgium
| | - Philippe Delvenne
- Laboratory of Experimental Pathology, GIGA-Cancer, Department of Pathology, University of Liège, Liège, Belgium
| | - Edwin De Pauw
- Mass Spectrometry Laboratory, GIGA-Research, Department of Chemistry, University of Liège, Liège, Belgium
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Finne K, Vethe H, Skogstrand T, Leh S, Dahl TD, Tenstad O, Berven FS, Reed RK, Vikse BE. Proteomic analysis of formalin-fixed paraffin-embedded glomeruli suggests depletion of glomerular filtration barrier proteins in two-kidney, one-clip hypertensive rats. Nephrol Dial Transplant 2014; 29:2217-27. [PMID: 25129444 PMCID: PMC4240179 DOI: 10.1093/ndt/gfu268] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background It is well known that hypertension may cause glomerular damage, but the molecular mechanisms involved are still incompletely understood. Methods In the present study, we used formalin-fixed paraffin-embedded (FFPE) tissue to investigate changes in the glomerular proteome in the non-clipped kidney of two-kidney one-clip (2K1C) hypertensive rats, with special emphasis on the glomerular filtration barrier. 2K1C hypertension was induced in 6-week-old Wistar Hannover rats (n = 6) that were sacrificed 23 weeks later and compared with age-matched sham-operated controls (n = 6). Tissue was stored in FFPE tissue blocks and later prepared on tissue slides for laser microdissection. Glomeruli without severe morphological damage were isolated, and the proteomes were analysed using liquid chromatography–tandem mass spectrometry. Results 2K1C glomeruli showed reduced abundance of proteins important for slit diaphragm complex, such as nephrin, podocin and neph1. The podocyte foot process had a pattern of reduced abundance of transmembrane proteins but unchanged abundances of the podocyte cytoskeletal proteins synaptopodin and α-actinin-4. Lower abundance of important glomerular basement membrane proteins was seen. Possible glomerular markers of damage with increased abundance in 2K1C were transgelin, desmin and acyl-coenzyme A thioesterase 1. Conclusions Microdissection and tandem mass spectrometry could be used to investigate the proteome of isolated glomeruli from FFPE tissue. Glomerular filtration barrier proteins had reduced abundance in the non-clipped kidney of 2K1C hypertensive rats.
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Affiliation(s)
- Kenneth Finne
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Heidrun Vethe
- Department of Clinical Medicine, University of Bergen, Bergen, Norway
| | - Trude Skogstrand
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Sabine Leh
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Pathology, Haukeland University Hospital, Bergen, Norway
| | - Tone D Dahl
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Olav Tenstad
- Department of Biomedicine, University of Bergen, Bergen, Norway
| | - Frode S Berven
- Department of Biomedicine, University of Bergen, Bergen, Norway The Norwegian Multiple Sclerosis National Competence Centre, Department of Neurology, Haukeland University Hospital, Bergen, Norway
| | - Rolf K Reed
- Department of Biomedicine, University of Bergen, Bergen, Norway Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - Bjørn Egil Vikse
- Department of Clinical Medicine, University of Bergen, Bergen, Norway Department of Medicine, Haukeland University Hospital, Bergen, Norway Department of Medicine, Haugesund Hospital, Haugesund, Norway
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Hammer E, Ernst FD, Thiele A, Karanam NK, Kujath C, Evert M, Völker U, Barthlen W. Kidney protein profiling of Wilms' tumor patients by analysis of formalin-fixed paraffin-embedded tissue samples. Clin Chim Acta 2014; 433:235-41. [PMID: 24680863 DOI: 10.1016/j.cca.2014.03.020] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2013] [Revised: 03/02/2014] [Accepted: 03/19/2014] [Indexed: 01/31/2023]
Abstract
UNLABELLED Wilms' tumor (nephroblastoma, WT) is the most frequent renal cancer in children. However, molecular details leading to WT have not been characterized sufficiently yet. Proteomic studies might provide new insights but are hampered by limited availability of fresh frozen tissue specimen. Therefore, we tested formalin-fixed paraffin-embedded (FFPE) tissue sections routinely collected for pathological inspection for their use in in-depth-proteomic analyses of WT samples in comparison to fresh frozen specimen. The overlap of the proteins identified was over 65%. Thus we used FFPE material from 7 patients for tandem mass spectrometry based comparison of the proteomes of WT and healthy renal tissues. We detected 262 proteins, which were differentially expressed in tumor compared to healthy renal tissue. The majority of these proteins displayed lower levels in the tumor tissue and only 30% higher levels. For selected candidates data were confirmed by immunohistochemical staining. Correlation analysis of blastemal proportions in WT and protein intensities revealed candidates for tumor stratification. CONCLUSION This proof of principle proteomic study of FFPE tissue sections from WT patients demonstrates that these archived tissues constitute a valuable resource for larger in-depth proteomic studies to identify markers to follow chemotherapy efficiency or for stratification of tumor subtypes.
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Affiliation(s)
- Elke Hammer
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, D-17475 Greifswald, Germany.
| | - Florian D Ernst
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, D-17475 Greifswald, Germany; Clinic for Pediatric Surgery, University Medicine Greifswald, Sauerbruchstr. 1, D-17475 Greifswald, Germany.
| | - Andrea Thiele
- Institute for Pathology, University Medicine Greifswald, Friedrich-Loeffler-Str. 23e, D-17489 Greifswald, Germany.
| | - Narasimha Kumar Karanam
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, D-17475 Greifswald, Germany.
| | - Christina Kujath
- Clinic for Pediatric Surgery, University Medicine Greifswald, Sauerbruchstr. 1, D-17475 Greifswald, Germany.
| | - Matthias Evert
- Institute for Pathology, University Medicine Greifswald, Friedrich-Loeffler-Str. 23e, D-17489 Greifswald, Germany.
| | - Uwe Völker
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, University Medicine Greifswald, Friedrich-Ludwig-Jahn-Str. 15a, D-17475 Greifswald, Germany.
| | - Winfried Barthlen
- Clinic for Pediatric Surgery, University Medicine Greifswald, Sauerbruchstr. 1, D-17475 Greifswald, Germany.
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Minerva L, Ceulemans A, Baggerman G, Arckens L. MALDI MS imaging as a tool for biomarker discovery: methodological challenges in a clinical setting. Proteomics Clin Appl 2014; 6:581-95. [PMID: 23090913 DOI: 10.1002/prca.201200033] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2012] [Revised: 10/01/2012] [Accepted: 10/05/2012] [Indexed: 12/12/2022]
Abstract
MALDI MS imaging (MSI) is an analytical tool capable of providing spatial distribution and relative abundance of biomolecules directly in tissue. After 15 years of intense efforts to improve the acquisition and quality of molecular images, MSI has matured into an asset of the proteomic toolbox. The power of MSI lies in the ability to differentiate tissue regions that are not histologically distinct but are characterized by different MS profiles. Recently, MSI has been gaining momentum in biomedical research and has found applications in disease diagnosis and prognosis, biomarker discovery, and drug therapy. Although the technology holds great promise, MSI is still faced with a set of methodological challenges presented by the clinical setting. There is a growing awareness regarding this topic and efforts are being taken to develop clear and practical standards to overcome these challenges. This review presents an overview of MALDI MSI as a biomarker discovery tool and recent methodological progress in the field.
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Affiliation(s)
- Laurens Minerva
- Laboratory of Neuroplasticity and Neuroproteomics, Katholieke Universiteit Leuven, Leuven, Belgium
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Extraction of tamoxifen and its metabolites from formalin-fixed, paraffin-embedded tissues: an innovative quantitation method using liquid chromatography and tandem mass spectrometry. Cancer Chemother Pharmacol 2014; 73:475-84. [PMID: 24414550 PMCID: PMC3931943 DOI: 10.1007/s00280-013-2346-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2013] [Accepted: 10/31/2013] [Indexed: 12/29/2022]
Abstract
PURPOSE Tamoxifen is a key therapeutic option for breast cancer treatment. Understanding its complex metabolism and pharmacokinetics is important for dose optimization. We examined the possibility of utilizing archival formalin-fixed paraffin-embedded (FFPE) tissue as an alternative sample source for quantification since well-annotated retrospective samples were always limited. METHODS Six 15 μm sections of FFPE tissues were deparaffinized with xylene and purified using solid-phase extraction. Tamoxifen and its metabolites were separated and detected by liquid chromatography-tandem mass spectrometry using multiple-reaction monitoring. RESULTS This method was linear between 0.4 and 200 ng/g for 4-hydroxy-tamoxifen and endoxifen, and 4-2,000 ng/g for tamoxifen and N-desmethyl-tamoxifen. Inter- and intra-assay precisions were <9 %, and mean accuracies ranged from 81 to 106 %. Extraction recoveries were between 83 and 88 %. The validated method was applied to FFPE tissues from two groups of patients, who received 20 mg/day of tamoxifen for >6 months, and were classified into breast tumor recurrence and non-recurrence. Our preliminary data show that levels of tamoxifen metabolites were significantly lower in patients with recurrent cancer, suggesting that inter-individual variability in tamoxifen metabolism might partly account for the development of cancer recurrence. Nevertheless, other causes such as non-compliance or stopping therapy of tamoxifen could possibly lead to the concentration differences. CONCLUSIONS The ability to successfully study tamoxifen metabolism in such tissue samples will rapidly increase our knowledge of how tamoxifen's action, metabolism and tissue distribution contribute to breast cancer control. However, larger population studies are required to understand the underlying mechanism of tamoxifen metabolism for optimization of its treatment.
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Abstract
Proteomics was initially viewed as a promising new scientific discipline to study complex disorders such as polygenic, infectious and environment-related diseases. However, the first attempts to understand a monogenic disease such as cystic fibrosis (CF) by proteomics-based approaches have proved quite rewarding. In CF, the impairment of a unique protein, the CF transmembrane conductance regulator, does not completely explain the complex and variable CF clinical phenotype. The great advances in our knowledge about the molecular and cellular consequences of such impairment have not been sufficient to be translated into effective treatments, and CF patients are still dying due to chronic progressive lung dysfunction. The progression of proteomics application in CF will certainly unravel new proteins that could be useful as biomarkers either to elucidate CF basic mechanisms and to better monitor the disease progression, or to promote the development of novel therapeutic strategies against CF. This review will summarize the recent technological advances in proteomics and the first results of its application to address the most important issues in the CF field.
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Affiliation(s)
- Deborah Penque
- Instituto Nacional de Saúde Dr Ricardo Jorge, Laboratório de Proteómica, Centro de Genética Humana, Lisboa, Portugal.
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Guo S, Zou J, Wang G. Advances in the proteomic discovery of novel therapeutic targets in cancer. DRUG DESIGN DEVELOPMENT AND THERAPY 2013; 7:1259-71. [PMID: 24187485 PMCID: PMC3810204 DOI: 10.2147/dddt.s52216] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Proteomic approaches are continuing to make headways in cancer research by helping to elucidate complex signaling networks that underlie tumorigenesis and disease progression. This review describes recent advances made in the proteomic discovery of drug targets for therapeutic development. A variety of technical and methodological advances are overviewed with a critical assessment of challenges and potentials. A number of potential drug targets, such as baculoviral inhibitor of apoptosis protein repeat-containing protein 6, macrophage inhibitory cytokine 1, phosphoglycerate mutase 1, prohibitin 1, fascin, and pyruvate kinase isozyme 2 were identified in the proteomic analysis of drug-resistant cancer cells, drug action, and differential disease state tissues. Future directions for proteomics-based target identification and validation to be more translation efficient are also discussed.
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Affiliation(s)
- Shanchun Guo
- Department of Microbiology, Biochemistry, and Immunology, Morehouse School of Medicine, Clark Atlanta University, Atlanta, GA, USA
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Giusti L, Lucacchini A. Proteomic studies of formalin-fixed paraffin-embedded tissues. Expert Rev Proteomics 2013; 10:165-77. [PMID: 23573783 DOI: 10.1586/epr.13.3] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue specimens represent a valuable informational resource of histologically characterized specimens for proteomic studies. In this article, the authors review the advancement performed in the field of FFPE proteomics focusing on formaldehyde treatment and on strategies addressed to obtain the best recovery in the protein/peptide extraction. A variety of approaches have been used to characterize protein tissue extracts, and many efforts have been performed demonstrating the comparability between fresh/frozen and FFPE proteomes. Finally, the authors report and discuss the large numbers of works aimed at developing new strategies and sophisticated platforms in the analysis of FFPE samples to validate known potential biomarkers and to discover new ones.
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Affiliation(s)
- Laura Giusti
- Department of Pharmacy, University of Pisa, Via Bonanno 6, 56126 Pisa, Italy
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47
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Analysis of the formalin-fixed paraffin-embedded tissue proteome: pitfalls, challenges, and future prospectives. Amino Acids 2013; 45:205-18. [PMID: 23592010 DOI: 10.1007/s00726-013-1494-0] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2013] [Accepted: 04/02/2013] [Indexed: 10/26/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissues are a real treasure for retrospective analysis considering the amount of samples present in hospital archives, combined with pathological, clinical, and outcome information available for every sample. Although unlocking the proteome of these tissues is still a challenge, new approaches are being developed. In this review, we summarize the different mass spectrometry platforms that are used in human clinical studies to unravel the FFPE proteome. The different ways of extracting crosslinked proteins and the analytical strategies are pointed out. Also, the pitfalls and challenges concerning the quality of FFPE proteomic approaches are depicted. We also evaluated the potential of these analytical methods for future clinical FFPE proteomics applications.
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48
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Thompson SM, Craven RA, Nirmalan NJ, Harnden P, Selby PJ, Banks RE. Impact of pre-analytical factors on the proteomic analysis of formalin-fixed paraffin-embedded tissue. Proteomics Clin Appl 2013; 7:241-51. [PMID: 23027712 DOI: 10.1002/prca.201200086] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2012] [Accepted: 08/15/2012] [Indexed: 12/14/2022]
Abstract
Formalin-fixed paraffin-embedded (FFPE) tissue samples represent a tremendous potential resource for biomarker discovery, with large numbers of samples in hospital pathology departments and links to clinical information. However, the cross-linking of proteins and nucleic acids by formalin fixation has hampered analysis and proteomic studies have been restricted to using frozen tissue, which is more limited in availability as it needs to be collected specifically for research. This means that rare disease subtypes cannot be studied easily. Recently, improved extraction techniques have enabled analysis of FFPE tissue by a number of proteomic techniques. As with all clinical samples, pre-analytical factors are likely to impact on the results obtained, although overlooked in many studies. The aim of this review is to discuss the various pre-analytical factors, which include warm and cold ischaemic time, size of sample, fixation duration and temperature, tissue processing conditions, length of storage of archival tissue and storage conditions, and to review the studies that have considered these factors in more detail. In those areas where investigations are few or non-existent, illustrative examples of the possible importance of specific factors have been drawn from studies using frozen tissue or from immunohistochemical studies of FFPE tissue.
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Affiliation(s)
- Seonaid M Thompson
- Clinical and Biomedical Proteomics Group, Leeds Institute of Molecular Medicine, St. James's University Hospital, United Kingdom
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49
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Abstract
Reverse phase protein array (RPPA) is a very suitable technique to analyze large numbers of proteins in small samples like for example tumor biopsies. Beside their small size another major hindrance for the analysis of proteins from biopsies is the extraction of proteins from formalin-fixed and paraffin-embedded (FFPE) tissues. Here we describe a protocol, allowing quantitative extraction of large numbers of proteins from FFPE tissues and their subsequent analysis by RPPA. To elucidate the role of epidermal growth factor receptor (EGFR) signalling in ovarian cancer, we analyzed 23 primary tumors and corresponding metastases for the expression of 25 proteins involved in EGFR signalling with special emphasis on epithelial-mesenchymal transition (EMT). We found a significant correlation of Snail with EGFR((Tyr1086)) and p38 MAPK((Thr180/Tyr182)) in primary ovarian carcinoma and with EGFR((Tyr1086)) in their corresponding metastases. Additionally, we showed that high expression levels of the E-cadherin repressor Snail in primary tumors combined with high expression levels of the pp38 MAPK((Thr180/Tyr182)) in metastasis lead to an increased risk for death in ovarian carcinoma patients.
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50
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Meding S, Martin K, Gustafsson OJR, Eddes JS, Hack S, Oehler MK, Hoffmann P. Tryptic peptide reference data sets for MALDI imaging mass spectrometry on formalin-fixed ovarian cancer tissues. J Proteome Res 2012; 12:308-15. [PMID: 23214983 DOI: 10.1021/pr300996x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
MALDI imaging mass spectrometry is a powerful tool for morphology-based proteomic tissue analysis. However, peptide identification is still a major challenge due to low S/N ratios, low mass accuracy and difficulties in correlating observed m/z species with peptide identities. To address this, we have analyzed tryptic digests of formalin-fixed paraffin-embedded tissue microarray cores, from 31 ovarian cancer patients, by LC-MS/MS. The sample preparation closely resembled the MALDI imaging workflow in order to create representative reference data sets containing peptides also observable in MALDI imaging experiments. This resulted in 3844 distinct peptide sequences, at a false discovery rate of 1%, for the entire cohort and an average of 982 distinct peptide sequences per sample. From this, a total of 840 proteins and, on average, 297 proteins per sample could be inferred. To support the efforts of the Chromosome-centric Human Proteome Project Consortium, we have annotated these proteins with their respective chromosome location. In the presented work, the benefit of using a large cohort of data sets was exemplified by correct identification of several m/z species observed in a MALDI imaging experiment. The tryptic peptide data sets generated will facilitate peptide identification in future MALDI imaging studies on ovarian cancer.
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Affiliation(s)
- Stephan Meding
- Adelaide Proteomics Centre, School of Molecular and Biomedical Science, The University of Adelaide, SA 5005, Adelaide, Australia
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