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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 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] [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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2
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Pu J, Xue C, Huo S, Shen Q, Qu Y, Yang X, An B, Angel TE, Chen Z, Mehl JT, Tang H, Yang E, Sikorski TW, Qu J. Highly Accurate and Robust Absolute Quantification of Target Proteins in Formalin-Fixed Paraffin-Embedded (FFPE) Tissues by LC-MS. Anal Chem 2023; 95:924-934. [PMID: 36534410 PMCID: PMC10581745 DOI: 10.1021/acs.analchem.2c03473] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Accurate, absolute liquid chromatography-mass spectrometry (LC-MS)-based quantification of target proteins in formalin-fixed paraffin-embedded (FFPE) tissues would greatly expand sample availability for pharmaceutical/clinical investigations but remains challenging owing to the following issues: (i) efficient/quantitative recovery of target signature peptides from FFPE tissues is essential but an optimal procedure for targeted, absolute quantification is lacking; (ii) most FFPE samples are long-term-stored; severe immunohistochemistry (IHC) signal losses of target proteins during storage were widely reported, while the effect of storage on LC-MS-based methods was unknown; and (iii) the proper strategy to prepare calibration/quality-control samples to ensure accurate targeted protein analysis in FFPE tissues remained elusive. Using targeted quantification of monoclonal antibody (mAb), antigen, and 40 tissue markers in FFPE tissues as a model system, we extensively investigate those issues and develope an LC-MS-based strategy enabling accurate and precise targeted protein quantification in FFPE samples. First, we demonstrated a surfactant cocktail-based procedure (f-SEPOD), providing high/reproducible recovery of target signature peptides from FFPE tissues. Second, a heat-accelerated degradation study within a roughly estimated 5 year storage period recapitulated the loss of protein IHC signals while LC-MS signals of all targets remained constant. This indicates that the storage of FFPE tissues mainly causes decreased immunoreactivity but unlikely chemical degradation of proteins, which strongly suggests that the storage of FFPE tissues does not cause significant quantitative bias for LC-MS-based methods. Third, while a conventional spike-and-extract approach for calibration caused substantial negative biases, a novel approach, using FFPE-treated calibration standards, enabled accurate and precise quantification. With the pipeline, we conducted the first-ever pharmacokinetics measurement of mAb and its target in FFPE tissues, where time courses by FFPE vs fresh tissues showed excellent correlation.
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Affiliation(s)
- Jie Pu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Chao Xue
- Department of Chemical and Biological Engineering, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Shihan Huo
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Qingqing Shen
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Yang Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
| | - Xinxin Yang
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States
| | - Bo An
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Thomas E. Angel
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Zhuo Chen
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - John T. Mehl
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Huaping Tang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Eric Yang
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States
| | - Timothy W. Sikorski
- Bioanalysis, Immunogenicity & Biomarkers, In-Vitro/In-Vivo Translation, R&D Research, GlaxoSmithKline, Collegeville, Pennsylvania 19426, United States; Phone: (610) 270-4978
| | - Jun Qu
- Department of Pharmaceutical Sciences, University at Buffalo, State University of New York, Buffalo, New York 14214, United States; New York State Center of Excellence in Bioinformatics and Life Sciences, Buffalo, New York 14203, United States
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Skoworonska M, Blank A, Centeno I, Hammer C, Perren A, Zlobec I, Rau TT. Real-life data from standardized preanalytical coding (SPREC) in tissue biobanking and its dual use for sample characterization and process optimization. J Pathol Clin Res 2022; 9:137-148. [PMID: 36484086 PMCID: PMC9896154 DOI: 10.1002/cjp2.305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Revised: 11/07/2022] [Accepted: 11/17/2022] [Indexed: 12/13/2022]
Abstract
The standardized preanalytical code (SPREC) aggregates warm ischemia (WIT), cold ischemia (CIT), and fixation times (FIT) in a precise format. Despite its growing importance underpinned by the European in vitro diagnostics regulation or broad preanalytical programs by the National Institutes of Health, little is known about its empirical occurrence in biobanked surgical specimen. In several steps, the Tissue Bank Bern achieved a fully informative SPREC code with insights from 10,555 CIT, 4,740 WIT, and 3,121 FIT values. During process optimization according to LEAN six sigma principles, we identified a dual role of the SPREC code as a sample characteristic and a traceable process parameter. With this preanalytical study, we outlined real-life data in a variety of organs with specific differences in WIT, CIT, and FIT values. Furthermore, our FIT data indicate the potential to adapt the SPREC fixation toward concrete paraffin-embedding time points and to extend its categories beyond 72 h due to weekend delays. Additionally, we identified dependencies of preanalytical variables from workload, daytime, and clinics that were actionable with LEAN process management. Thus, streamlined biobanking workflows during the day were significantly resilient to workload peaks, diminishing the turnaround times of native tissue processing (i.e. CIT) from 74.6 to 46.1 min under heavily stressed conditions. In conclusion, there are surgery-specific preanalytics that are surgico-pathologically limited even under process optimization, which might affect biomarker transfer from one entity to another. Beyond sample characteristics, SPREC coding is highly beneficial for tissue banks and Institutes of Pathology to track WIT, CIT, and FIT for process optimization and monitoring measurements.
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Affiliation(s)
| | - Annika Blank
- Institute of PathologyUniversity of BernBern,Institute of PathologyTriemli HospitalZurichSwitzerland
| | | | | | | | - Inti Zlobec
- Institute of PathologyUniversity of BernBern
| | - Tilman T Rau
- Institute of PathologyUniversity of BernBern,Institute of PathologyUniversity Hospital and Heinrich‐Heine‐University DüsseldorfDüsseldorfGermany
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Systematic evaluation and optimization of protein extraction parameters in diagnostic FFPE specimens. Clin Proteomics 2022; 19:10. [PMID: 35501693 PMCID: PMC9063121 DOI: 10.1186/s12014-022-09346-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 04/04/2022] [Indexed: 11/10/2022] Open
Abstract
Objectives Formalin-fixed paraffin-embedded (FFPE) tissue is the standard material for diagnostic pathology but poses relevant hurdles to accurate protein extraction due to cross-linking and chemical alterations. While numerous extraction protocols and chemicals have been described, systematic comparative analyses are limited. Various parameters were thus investigated in their qualitative and quantitative effects on protein extraction (PE) efficacy. Special emphasis was put on preservation of membrane proteins (MP) as key subgroup of functionally relevant proteins. Methods Using the example of urothelial carcinoma, FFPE tissue sections were subjected to various deparaffinization, protein extraction and antigen retrieval protocols and buffers as well as different extraction techniques. Performance was measured by protein concentration and western blot analysis of cellular compartment markers as well as liquid chromatography-coupled mass spectrometry (LC–MS). Results Commercially available extraction buffers showed reduced extraction of MPs and came at considerably increased costs. On-slide extraction did not improve PE whereas several other preanalytical steps could be simplified. Systematic variation of temperature and exposure duration demonstrated a quantitatively relevant corridor of optimal antigen retrieval. Conclusions Preanalytical protein extraction can be optimized at various levels to improve unbiased protein extraction and to reduce time and costs. Supplementary Information The online version contains supplementary material available at 10.1186/s12014-022-09346-0.
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Evaluation of Fast and Sensitive Proteome Profiling of FF and FFPE Kidney Patient Tissues. Molecules 2022; 27:molecules27031137. [PMID: 35164409 PMCID: PMC8838561 DOI: 10.3390/molecules27031137] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 01/27/2022] [Accepted: 02/01/2022] [Indexed: 12/14/2022] Open
Abstract
The application of proteomics to fresh frozen (FF) and formalin-fixed paraffin-embedded (FFPE) human tissues is an important development spurred on by requests from stakeholder groups in clinical fields. One objective is to complement current diagnostic methods with new specific molecular information. An important goal is to achieve adequate and consistent protein recovery across and within large-scale studies. Here, we describe development of several protocols incorporating mass spectrometry compatible detergents, including Rapigest, PPS, and ProteaseMax. Methods were applied on 4 and 15 μm thick FF tissues, and 4 μm thick FFPE tissues. We evaluated sensitivity and repeatability of the methods and found that the protocol containing Rapigest enabled detection of 630 proteins from FF tissue of 1 mm2 and 15 μm thick, whereas 498 and 297 proteins were detected with the protocols containing ProteaseMax and PPS, respectively. Surprisingly, PPS-containing buffer showed good extraction of the proteins from 4 μm thick FFPE tissue with the average of 270 protein identifications (1 mm2), similar to the results on 4 μm thick FF. Moreover, we found that temperature increases during incubation with urea on 4 μm thick FF tissue revealed a decrease in the number of identified proteins and increase in the number of the carbamylated peptides.
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Pirog A, Faktor J, Urban-Wojciuk Z, Kote S, Chruściel E, Arcimowicz Ł, Marek-Trzonkowska N, Vojtesek B, Hupp TR, Al Shboul S, Brennan PM, Smoleński RT, Goodlett DR, Dapic I. Comparison of different digestion methods for proteomic analysis of isolated cells and FFPE tissue samples. Talanta 2021; 233:122568. [PMID: 34215064 DOI: 10.1016/j.talanta.2021.122568] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Revised: 05/22/2021] [Accepted: 05/26/2021] [Indexed: 12/14/2022]
Abstract
Proteomics of human tissues and isolated cellular subpopulations create new opportunities for therapy and monitoring of a patients' treatment in the clinic. Important considerations in such analysis include recovery of adequate amounts of protein for analysis and reproducibility in sample collection. In this study we compared several protocols for proteomic sample preparation: i) filter-aided sample preparation (FASP), ii) in-solution digestion (ISD) and iii) a pressure-assisted digestion (PCT) method. PCT method is known for already a decade [1], however it is not widely used in proteomic research. We assessed protocols for proteome profiling of isolated immune cell subsets and formalin-fixed paraffin embedded (FFPE) tissue samples. Our results show that the ISD method has very good efficiency of protein and peptide identification from the whole proteome, while the FASP method is particularly effective in identification of membrane proteins. Pressure-assisted digestion methods generally provide lower numbers of protein/peptide identifications, but have gained in popularity due to their shorter digestion time making them considerably faster than for ISD or FASP. Furthermore, PCT does not result in substantial sample loss when applied to samples of 50 000 cells. Analysis of FFPE tissues shows comparable results. ISD method similarly yields the highest number of identifications. Furthermore, proteins isolated from FFPE samples show a significant reduction of cleavages at lysine sites due to chemical modifications with formaldehyde-such as methylation (+14 Da) being among the most common. The data we present will be helpful for making decisions about the robust preparation of clinical samples for biomarker discovery and studies on pathomechanisms of various diseases.
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Affiliation(s)
- Artur Pirog
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland
| | - Jakub Faktor
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland
| | - Zuzanna Urban-Wojciuk
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland
| | - Sachin Kote
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland
| | - Elżbieta Chruściel
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland
| | - Łukasz Arcimowicz
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland
| | - Natalia Marek-Trzonkowska
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland; Laboratory of Immunoregulation and Cellular Therapies, Department of Family Medicine, Medical University of Gdańsk, Dębinki 2, 80-210, Gdańsk, Poland
| | - Borek Vojtesek
- Research Centre for Applied Molecular Oncology (RECAMO), Masaryk Memorial Cancer Institute, 656 53, Brno, Czech Republic
| | - Ted R Hupp
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland; Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, EH4 2XR, United Kingdom
| | - Sofian Al Shboul
- Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, Scotland, EH4 2XR, United Kingdom; Department of Basic Medical Sciences, Faculty of Medicine, The Hashemite University, Zarqa, Jordan
| | - Paul M Brennan
- Translational Neurosurgery, Centre for Clinical Brain Sciences, Bioquarter, University of Edinburgh, Edinburgh, UK
| | | | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland; Department of Biochemistry and Microbiology, University of Victoria, Victoria, British Columbia, V8P 5C2, Canada
| | - Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Kładki 24, 80-822, Gdańsk, Poland.
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7
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Chapman J, Dogan A. Fibrinogen alpha amyloidosis: insights from proteomics. Expert Rev Proteomics 2019; 16:783-793. [PMID: 31443619 PMCID: PMC6788741 DOI: 10.1080/14789450.2019.1659137] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 08/20/2019] [Indexed: 12/17/2022]
Abstract
Introduction: Systemic amyloidosis is a diverse group of diseases that, although rare, pose a serious health issue and can lead to organ failure and death. Amyloid typing is essential in determining the causative protein and initiating proper treatment. Mass spectrometry-based proteomics is currently the most sensitive and accurate means of typing amyloid. Areas covered: Amyloidosis can be systemic or localized, acquired or hereditary, and can affect any organ or tissue. Diagnosis requires biopsy, histological analysis, and typing of the causative protein to determine treatment. The kidneys are the most commonly affected organ in systemic disease. Fibrinogen alpha chain amyloidosis (AFib) is the most prevalent form of hereditary renal amyloidosis. Select mutations in the fibrinogen Aα (FGA) gene lead to AFib. Expert commentary: Mass spectrometry is currently the most specific and sensitive method for amyloid typing. Identification of the mutated fibrinogen alpha chain can be difficult in the case of 'private' frameshift mutations, which dramatically change the sequences of the expressed fibrinogen alpha chain. A combination of expert pathologist review, mass spectrometry, and gene sequencing can allow for confident diagnosis and determination of the fibrinogen alpha chain mutated sequence.
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Affiliation(s)
- Jessica Chapman
- Hematopathology Service, Memorial Sloan Kettering Cancer Center , New York , NY , USA
| | - Ahmet Dogan
- Hematopathology Service, Memorial Sloan Kettering Cancer Center , New York , NY , USA
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8
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Dapic I, Baljeu-Neuman L, Uwugiaren N, Kers J, Goodlett DR, Corthals GL. Proteome analysis of tissues by mass spectrometry. MASS SPECTROMETRY REVIEWS 2019; 38:403-441. [PMID: 31390493 DOI: 10.1002/mas.21598] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2019] [Accepted: 06/17/2019] [Indexed: 06/10/2023]
Abstract
Tissues and biofluids are important sources of information used for the detection of diseases and decisions on patient therapies. There are several accepted methods for preservation of tissues, among which the most popular are fresh-frozen and formalin-fixed paraffin embedded methods. Depending on the preservation method and the amount of sample available, various specific protocols are available for tissue processing for subsequent proteomic analysis. Protocols are tailored to answer various biological questions, and as such vary in lysis and digestion conditions, as well as duration. The existence of diverse tissue-sample protocols has led to confusion in how to choose the best protocol for a given tissue and made it difficult to compare results across sample types. Here, we summarize procedures used for tissue processing for subsequent bottom-up proteomic analysis. Furthermore, we compare protocols for their variations in the composition of lysis buffers, digestion procedures, and purification steps. For example, reports have shown that lysis buffer composition plays an important role in the profile of extracted proteins: the most common are tris(hydroxymethyl)aminomethane, radioimmunoprecipitation assay, and ammonium bicarbonate buffers. Although, trypsin is the most commonly used enzyme for proteolysis, in some protocols it is supplemented with Lys-C and/or chymotrypsin, which will often lead to an increase in proteome coverage. Data show that the selection of the lysis procedure might need to be tissue-specific to produce distinct protocols for individual tissue types. Finally, selection of the procedures is also influenced by the amount of sample available, which range from biopsies or the size of a few dozen of mm2 obtained with laser capture microdissection to much larger amounts that weight several milligrams.
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Affiliation(s)
- Irena Dapic
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | | | - Naomi Uwugiaren
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
| | - Jesper Kers
- Department of Pathology, Amsterdam Infection & Immunity Institute (AI&II), Amsterdam Cardiovascular Sciences (ACS), Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
- Ragon Institute of Massachusetts General Hospital, Massachusetts Institute of Technology and Harvard University, Cambridge, MA
| | - David R Goodlett
- International Centre for Cancer Vaccine Science, University of Gdansk, Gdansk, Poland
- University of Maryland, 20N. Pine Street, Baltimore, MD 21201
| | - Garry L Corthals
- van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, The Netherlands
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Mass spectrometric imaging of cysteine rich proteins in human skin. Int J Biol Macromol 2018; 125:270-277. [PMID: 30517841 DOI: 10.1016/j.ijbiomac.2018.11.272] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Revised: 11/18/2018] [Accepted: 11/29/2018] [Indexed: 12/18/2022]
Abstract
Looking insight pathological processes, metallothioneins (MTs) are considered to be potential biomarkers for monitoring of a development of various types of diseases, such as cancer. The early identification of the MTs in biological tissues could be important tool for the estimation of appropriate clinical therapy. Therefore, here we investigated the application of matrix assisted laser desorption/ionization mass spectrometry imaging (MALDI MSI) together with immunohistochemical analyses (IHC) using MT-1/2 antibody for MT detection in formalin-fixed paraffin-embedded (FFPE) biopsy specimens of human skin. Principal component analyses revealed differences in the peptide/protein profiles separating healthy skin from the carcinoma specimens. Statistically significant ion peaks at m/z 6038, 6300, 6676, and 7026 were more frequently detected in squamous cell carcinoma (SCC), basal cell carcinoma (BCC) and melanoma. Using IHC, we found that MT-1/2 was significantly higher in SCC and melanoma compared to healthy skin. Surprisingly, significantly low levels of MT-1/2 were found in BCC. On one side, the results indicate important role of MTs in melanoma occurrence and progression, as on the second side, there are hidden processes associated with MTs based on differences of the occurrence of the MS peaks, which could be associated with cycling of MTs isoforms.
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10
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Holfeld A, Valdés A, Malmström PU, Segersten U, Lind SB. Parallel Proteomic Workflow for Mass Spectrometric Analysis of Tissue Samples Preserved by Different Methods. Anal Chem 2018; 90:5841-5849. [PMID: 29624047 DOI: 10.1021/acs.analchem.8b00379] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Formalin-fixed and paraffin-embedded (FFPE) and optimal cutting temperature (OCT)-embedded and frozen tissue specimens in biobanks are highly valuable in clinical studies but proteomic and post-translational modification (PTM) studies using mass spectrometry (MS) have been limited due to structural arrangement of proteins and contaminations from embedding material. This study aims to develop a parallel proteomic workflow for FFPE and OCT/frozen samples that allows for large-scale, quick, reproducible, qualitative, and quantitative high-resolution MS analysis. The optimized protocol gives details on removal of embedding material, protein extraction, and multienzyme digestion using filter-aided sample preparation method. The method was evaluated by investigating the protein expression levels in nonmuscle-invasive and muscle-invasive bladder cancer samples in two cohorts and MS spectra were carefully reviewed for contaminations. More than 2000 and 3000 proteins in FFPE and OCT/frozen samples, respectively, were identified, and samples could be clustered in different tumor stages based on their protein expression. Furthermore, more than 250 and 400 phosphopeptides could be identified from specific patient samples of FFPE and OCT/frozen, respectively, using titanium dioxide enrichment. The paper presents unique data describing the similarities and differences observed in FFPE and OCT/frozen samples and shows the feasibility to detect proteins and site-specific phosphorylation even after long-term storage of clinical samples.
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11
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Dapic I, Uwugiaren N, Jansen PJ, Corthals GL. Fast and Simple Protocols for Mass Spectrometry-Based Proteomics of Small Fresh Frozen Uterine Tissue Sections. Anal Chem 2017; 89:10769-10775. [PMID: 28910098 PMCID: PMC5647562 DOI: 10.1021/acs.analchem.7b01937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
![]()
Human
tissues are an important link between organ-specific spatial
molecular information, patient pathology, and patient treatment options.
However, patient tissues are uniquely obtained by time and location,
and limited in their availability and size. Currently, little knowledge
exists about appropriate and simplified protocols for routine MS-based
analysis of the various types and sizes of tissues. Following standard
procedures used in pathology, we selected small fresh frozen uterine
tissue samples to investigate how the tissue preparation protocol
affected the subsequent proteomics analysis. First, we observed that
protein extraction with 0.1% SDS followed by extraction with a 30%
ACN/urea resulted in a decrease in the number of identified proteins,
when compared to extraction with 30% ACN/urea only. The decrease in
the number of proteins was approximately 55% and 20%, for 10 and 16
μm thick tissue, respectively. Interestingly, the relative abundance
of the proteins shared between the two methods was higher when SDS/ACN/urea
was used, compared to the 30% ACN/urea extraction, indicating the
role of SDS to be beneficial for protein solubility. Second, the influence
of tissue thickness was investigated by comparing the results obtained
for 10, 16, and 20 μm thick (1 mm2) tissue using
urea/30% ACN. We observed an increase in the number of identified
proteins and corresponding quantity with an increase in the tissue
thickness. Finally, by analyzing very small amounts of tissues (∼0.2
mm2) of 10, 16, and 20 μm thickness, we observed
that the increase in tissue thickness resulted in a higher number
of protein identifications and corresponding quantitative values.
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Affiliation(s)
- Irena Dapic
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Naomi Uwugiaren
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Petra J Jansen
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
| | - Garry L Corthals
- University of Amsterdam, Van 't Hoff Institute for Molecular Sciences (HIMS) , Science Park 904, 1098 XH Amsterdam, The Netherlands
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12
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Sebire NJ. Implications of placental pathology for disease mechanisms; methods, issues and future approaches. Placenta 2017; 52:122-126. [DOI: 10.1016/j.placenta.2016.05.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2016] [Accepted: 05/10/2016] [Indexed: 12/12/2022]
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13
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Quesada-Calvo F, Massot C, Bertrand V, Longuespée R, Blétard N, Somja J, Mazzucchelli G, Smargiasso N, Baiwir D, De Pauw-Gillet MC, Delvenne P, Malaise M, Coimbra Marques C, Polus M, De Pauw E, Meuwis MA, Louis E. OLFM4, KNG1 and Sec24C identified by proteomics and immunohistochemistry as potential markers of early colorectal cancer stages. Clin Proteomics 2017; 14:9. [PMID: 28344541 PMCID: PMC5364649 DOI: 10.1186/s12014-017-9143-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 02/21/2017] [Indexed: 12/17/2022] Open
Abstract
Background Despite recent advances in colorectal cancer (CRC) diagnosis and population screening programs, the identification of patients with preneoplastic lesions or with early CRC stages remains challenging and is important for reducing CRC incidence and increasing patient’s survival.
Methods We analysed 76 colorectal tissue samples originated from early CRC stages, normal or inflamed mucosa by label-free proteomics. The characterisation of three selected biomarker candidates was performed by immunohistochemistry on an independent set of precancerous and cancerous lesions harbouring increasing CRC stages. Results Out of 5258 proteins identified, we obtained 561 proteins with a significant differential distribution among groups of patients and controls. KNG1, OLFM4 and Sec24C distributions were validated in tissues and showed different expression levels especially in the two early CRC stages compared to normal and preneoplastic tissues. Conclusion We highlighted three proteins that require further investigations to better characterise their role in early CRC carcinogenesis and their potential as early CRC markers. Electronic supplementary material The online version of this article (doi:10.1186/s12014-017-9143-3) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Florence Quesada-Calvo
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Charlotte Massot
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Virginie Bertrand
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Rémi Longuespée
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Noëlla Blétard
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Joan Somja
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Gabriel Mazzucchelli
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Nicolas Smargiasso
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | | | - Marie-Claire De Pauw-Gillet
- Mammalian Cell Culture Laboratory, Department of Preclinical and Biomedical Sciences, GIGA-R, ULg, 4000 Liège, Belgium
| | - Philippe Delvenne
- Department of Anatomy and Pathology, GIGA-R, Liège University Hospital CHU, ULg, 4000 Liège, Belgium
| | - Michel Malaise
- Department of Clinical Sciences, Rheumatology, Liège University Hospital CHU, 4000 Liège, Belgium
| | | | - Marc Polus
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edwin De Pauw
- Laboratory of Mass Spectrometry, Chemistry Department, GIGA-R, CART, ULg, 4000 Liège, Belgium
| | - Marie-Alice Meuwis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
| | - Edouard Louis
- Gastroenterology Department, GIGA-R, Liège University Hospital CHU, ULg, GIGA CHU-B34 Avenue de l'Hôpital 11, 4000 Liège, Belgium
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Optimization of Urea Based Protein Extraction from Formalin-Fixed Paraffin-Embedded Tissue for Shotgun Proteomics. INTERNATIONAL JOURNAL OF PROTEOMICS 2016; 2016:4324987. [PMID: 27660725 PMCID: PMC5021876 DOI: 10.1155/2016/4324987] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/20/2016] [Accepted: 08/09/2016] [Indexed: 01/19/2023]
Abstract
Urea based protein extraction of formalin-fixed paraffin-embedded (FFPE) tissue provides the most efficient workflow for proteomics due to its compatibility with liquid chromatography electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS). This study optimizes the use of urea for proteomic analysis of clinical FFPE tissue. A series of protein extraction conditions manipulating temperature and buffer composition were compared to reduce carbamylation introduced by urea and increase protein detection. Each extraction was performed on a randomized pair of serial sections of homogenous FFPE tissue and analyzed with LC-ESI-MS/MS. Results were compared in terms of yield, missed cleavages, and peptide carbamylation. Lowering extraction temperature to 60°C decreased carbamylation at the cost of decreased protein detection and yield. Protein extraction for at least 20 minutes at 95°C followed by 60°C for 2 hours maximized total protein yield while maintaining protein detection and reducing carbamylation by 7.9%. When accounting for carbamylation during analysis, this modified extraction temperature provides equivalent peptide and protein detection relative to the commercially available Qproteome® FFPE Tissue Kit. No changes to buffer composition containing 7 M urea, 2 M thiourea, and 1 M ammonium bicarbonate resulted in improvements to control conditions. Optimized urea in-solution digestion provides an efficient workflow with maximized yields for proteomic analysis of clinically relevant FFPE tissue.
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15
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